update the script to support running in docker

fixed background image not showing at desktop application (electron)

.claude/.gitignore

@@ -0,0 +1 @@
+hans/

.claude/commands/gh-issue.md

@@ -0,0 +1,74 @@
+# GitHub Issue Fix Command
+
+Fetch a GitHub issue by number, verify it's a real issue, and fix it if valid.
+
+## Usage
+
+This command accepts a GitHub issue number as input (e.g., `123`).
+
+## Instructions
+
+1. **Get the issue number from the user**
+   - The issue number should be provided as an argument to this command
+   - If no number is provided, ask the user for it
+
+2. **Fetch the GitHub issue**
+   - Determine the current project path (check if there's a current project context)
+   - Verify the project has a GitHub remote:
+     ```bash
+     git remote get-url origin
+     ```
+   - Fetch the issue details using GitHub CLI:
+     ```bash
+     gh issue view <ISSUE_NUMBER> --json number,title,state,author,createdAt,labels,url,body,assignees
+     ```
+   - If the command fails, report the error and stop
+
+3. **Verify the issue is real and valid**
+   - Check that the issue exists (not 404)
+   - Check the issue state:
+     - If **closed**: Inform the user and ask if they still want to proceed
+     - If **open**: Proceed with validation
+   - Review the issue content:
+     - Read the title and body to understand what needs to be fixed
+     - Check labels for context (bug, enhancement, etc.)
+     - Note any assignees or linked PRs
+
+4. **Validate the issue**
+   - Determine if this is a legitimate issue that needs fixing:
+     - Is the description clear and actionable?
+     - Does it describe a real problem or feature request?
+     - Are there any obvious signs it's spam or invalid?
+   - If the issue seems invalid or unclear:
+     - Report findings to the user
+     - Ask if they want to proceed anyway
+     - Stop if user confirms it's not valid
+
+5. **If the issue is valid, proceed to fix it**
+   - Analyze what needs to be done based on the issue description
+   - Check the current codebase state:
+     - Run relevant tests to see current behavior
+     - Check if the issue is already fixed
+     - Look for related code that might need changes
+   - Implement the fix:
+     - Make necessary code changes
+     - Update or add tests as needed
+     - Ensure the fix addresses the issue description
+   - Verify the fix:
+     - Run tests to ensure nothing broke
+     - If possible, manually verify the fix addresses the issue
+
+6. **Report summary**
+   - Issue number and title
+   - Issue state (open/closed)
+   - Whether the issue was validated as real
+   - What was fixed (if anything)
+   - Any tests that were updated or added
+   - Next steps (if any)
+
+## Error Handling
+
+- If GitHub CLI (`gh`) is not installed or authenticated, report error and stop
+- If the project doesn't have a GitHub remote, report error and stop
+- If the issue number doesn't exist, report error and stop
+- If the issue is unclear or invalid, report findings and ask user before proceeding

.claude/commands/release.md

@@ -0,0 +1,77 @@
+# Release Command
+
+Bump the package.json version (major, minor, or patch) and build the Electron app with the new version.
+
+## Usage
+
+This command accepts a version bump type as input:
+
+- `patch` - Bump patch version (0.1.0 -> 0.1.1)
+- `minor` - Bump minor version (0.1.0 -> 0.2.0)
+- `major` - Bump major version (0.1.0 -> 1.0.0)
+
+## Instructions
+
+1. **Get the bump type from the user**
+   - The bump type should be provided as an argument (patch, minor, or major)
+   - If no type is provided, ask the user which type they want
+
+2. **Bump the version**
+   - Run the version bump script:
+     ```bash
+     node apps/ui/scripts/bump-version.mjs <type>
+     ```
+   - This updates both `apps/ui/package.json` and `apps/server/package.json` with the new version (keeps them in sync)
+   - Verify the version was updated correctly by checking the output
+
+3. **Build the Electron app**
+   - Run the electron build:
+     ```bash
+     npm run build:electron --workspace=apps/ui
+     ```
+   - The build process automatically:
+     - Uses the version from `package.json` for artifact names (e.g., `Automaker-1.2.3-x64.zip`)
+     - Injects the version into the app via Vite's `__APP_VERSION__` constant
+     - Displays the version below the logo in the sidebar
+
+4. **Commit the version bump**
+   - Stage the updated package.json files:
+     ```bash
+     git add apps/ui/package.json apps/server/package.json
+     ```
+   - Commit with a release message:
+     ```bash
+     git commit -m "chore: release v<version>"
+     ```
+
+5. **Create and push the git tag**
+   - Create an annotated tag for the release:
+     ```bash
+     git tag -a v<version> -m "Release v<version>"
+     ```
+   - Push the commit and tag to remote:
+     ```bash
+     git push && git push --tags
+     ```
+
+6. **Verify the release**
+   - Check that the build completed successfully
+   - Confirm the version appears correctly in the built artifacts
+   - The version will be displayed in the app UI below the logo
+   - Verify the tag is visible on the remote repository
+
+## Version Centralization
+
+The version is centralized and synchronized in both `apps/ui/package.json` and `apps/server/package.json`:
+
+- **Electron builds**: Automatically read from `apps/ui/package.json` via electron-builder's `${version}` variable in `artifactName`
+- **App display**: Injected at build time via Vite's `define` config as `__APP_VERSION__` constant (defined in `apps/ui/vite.config.mts`)
+- **Server API**: Read from `apps/server/package.json` via `apps/server/src/lib/version.ts` utility (used in health check endpoints)
+- **Type safety**: Defined in `apps/ui/src/vite-env.d.ts` as `declare const __APP_VERSION__: string`
+
+This ensures consistency across:
+
+- Build artifact names (e.g., `Automaker-1.2.3-x64.zip`)
+- App UI display (shown as `v1.2.3` below the logo in `apps/ui/src/components/layout/sidebar/components/automaker-logo.tsx`)
+- Server health endpoints (`/` and `/detailed`)
+- Package metadata (both UI and server packages stay in sync)

.claude/commands/validate-build.md

@@ -0,0 +1,49 @@
+# Project Build and Fix Command
+
+Run all builds and intelligently fix any failures based on what changed.
+
+## Instructions
+
+1. **Run the build**
+
+   ```bash
+   npm run build
+   ```
+
+   This builds all packages and the UI application.
+
+2. **If the build succeeds**, report success and stop.
+
+3. **If the build fails**, analyze the failures:
+   - Note which build step failed and the error messages
+   - Check for TypeScript compilation errors, missing dependencies, or configuration issues
+   - Run `git diff main` to see what code has changed
+
+4. **Determine the nature of the failure**:
+   - **If the failure is due to intentional changes** (new features, refactoring, dependency updates):
+     - Fix any TypeScript type errors introduced by the changes
+     - Update build configuration if needed (e.g., tsconfig.json, vite.config.mts)
+     - Ensure all new dependencies are properly installed
+     - Fix import paths or module resolution issues
+
+   - **If the failure appears to be a regression** (broken imports, missing files, configuration errors):
+     - Fix the source code to restore the build
+     - Check for accidentally deleted files or broken references
+     - Verify build configuration files are correct
+
+5. **Common build issues to check**:
+   - **TypeScript errors**: Fix type mismatches, missing types, or incorrect imports
+   - **Missing dependencies**: Run `npm install` if packages are missing
+   - **Import/export errors**: Fix incorrect import paths or missing exports
+   - **Build configuration**: Check tsconfig.json, vite.config.mts, or other build configs
+   - **Package build order**: Ensure `build:packages` completes before building apps
+
+6. **How to decide if it's intentional vs regression**:
+   - Look at the git diff and commit messages
+   - If the change was deliberate and introduced new code that needs fixing → fix the new code
+   - If the change broke existing functionality that should still build → fix the regression
+   - When in doubt, ask the user
+
+7. **After making fixes**, re-run the build to verify everything compiles successfully.
+
+8. **Report summary** of what was fixed (TypeScript errors, configuration issues, missing dependencies, etc.).

.claude/commands/validate-tests.md

@@ -0,0 +1,36 @@
+# Project Test and Fix Command
+
+Run all tests and intelligently fix any failures based on what changed.
+
+## Instructions
+
+1. **Run all tests**
+
+   ```bash
+   npm run test:all
+   ```
+
+2. **If all tests pass**, report success and stop.
+
+3. **If any tests fail**, analyze the failures:
+   - Note which tests failed and their error messages
+   - Run `git diff main` to see what code has changed
+
+4. **Determine the nature of the change**:
+   - **If the logic change is intentional** (new feature, refactor, behavior change):
+     - Update the failing tests to match the new expected behavior
+     - The tests should reflect what the code NOW does correctly
+
+   - **If the logic change appears to be a bug** (regression, unintended side effect):
+     - Fix the source code to restore the expected behavior
+     - Do NOT modify the tests - they are catching a real bug
+
+5. **How to decide if it's a bug vs intentional change**:
+   - Look at the git diff and commit messages
+   - If the change was deliberate and the test expectations are now outdated → update tests
+   - If the change broke existing functionality that should still work → fix the code
+   - When in doubt, ask the user
+
+6. **After making fixes**, re-run the tests to verify everything passes.
+
+7. **Report summary** of what was fixed (tests updated vs code fixed).

.claude_settings.json

@@ -1,24 +0,0 @@
-{
-  "sandbox": {
-    "enabled": true,
-    "autoAllowBashIfSandboxed": true
-  },
-  "permissions": {
-    "defaultMode": "acceptEdits",
-    "allow": [
-      "Read(./**)",
-      "Write(./**)",
-      "Edit(./**)",
-      "Glob(./**)",
-      "Grep(./**)",
-      "Bash(*)",
-      "mcp__puppeteer__puppeteer_navigate",
-      "mcp__puppeteer__puppeteer_screenshot",
-      "mcp__puppeteer__puppeteer_click",
-      "mcp__puppeteer__puppeteer_fill",
-      "mcp__puppeteer__puppeteer_select",
-      "mcp__puppeteer__puppeteer_hover",
-      "mcp__puppeteer__puppeteer_evaluate"
-    ]
-  }
-}

.dockerignore

@@ -0,0 +1 @@
+node_modules/

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,117 @@
+name: Bug Report
+description: File a bug report to help us improve Automaker
+title: '[Bug]: '
+labels: ['bug']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report a bug! Please fill out the form below with as much detail as possible.
+
+  - type: dropdown
+    id: operating-system
+    attributes:
+      label: Operating System
+      description: What operating system are you using?
+      options:
+        - macOS
+        - Windows
+        - Linux
+        - Other
+      default: 0
+    validations:
+      required: true
+
+  - type: dropdown
+    id: run-mode
+    attributes:
+      label: Run Mode
+      description: How are you running Automaker?
+      options:
+        - Electron (Desktop App)
+        - Web (Browser)
+        - Docker
+      default: 0
+    validations:
+      required: true
+
+  - type: input
+    id: app-version
+    attributes:
+      label: App Version
+      description: What version of Automaker are you using? (e.g., 0.1.0)
+      placeholder: '0.1.0'
+    validations:
+      required: true
+
+  - type: textarea
+    id: bug-description
+    attributes:
+      label: Bug Description
+      description: A clear and concise description of what the bug is.
+      placeholder: Describe the bug...
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: Steps to Reproduce
+      description: Steps to reproduce the behavior
+      placeholder: |
+        1. Go to '...'
+        2. Click on '...'
+        3. Scroll down to '...'
+        4. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: Expected Behavior
+      description: A clear and concise description of what you expected to happen.
+      placeholder: What should have happened?
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual-behavior
+    attributes:
+      label: Actual Behavior
+      description: A clear and concise description of what actually happened.
+      placeholder: What actually happened?
+    validations:
+      required: true
+
+  - type: textarea
+    id: screenshots
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots to help explain your problem.
+      placeholder: Drag and drop screenshots here or paste image URLs
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant Logs
+      description: If applicable, paste relevant logs or error messages.
+      placeholder: Paste logs here...
+      render: shell
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Add any other context about the problem here.
+      placeholder: Any additional information that might be helpful...
+
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Checklist
+      options:
+        - label: I have searched existing issues to ensure this bug hasn't been reported already
+          required: true
+        - label: I have provided all required information above
+          required: true

.gitignore

@@ -79,4 +79,8 @@ blob-report/
 # Misc
 *.pem
 
-docker-compose.override.yml
+docker-compose.override.yml
+.claude/docker-compose.override.yml
+
+pnpm-lock.yaml
+yarn.lock

.nvmrc

@@ -0,0 +1,2 @@
+22
+

CLAUDE.md

@@ -0,0 +1,172 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+Automaker is an autonomous AI development studio built as an npm workspace monorepo. It provides a Kanban-based workflow where AI agents (powered by Claude Agent SDK) implement features in isolated git worktrees.
+
+## Common Commands
+
+```bash
+# Development
+npm run dev                 # Interactive launcher (choose web or electron)
+npm run dev:web             # Web browser mode (localhost:3007)
+npm run dev:electron        # Desktop app mode
+npm run dev:electron:debug  # Desktop with DevTools open
+
+# Building
+npm run build               # Build web application
+npm run build:packages      # Build all shared packages (required before other builds)
+npm run build:electron      # Build desktop app for current platform
+npm run build:server        # Build server only
+
+# Testing
+npm run test                # E2E tests (Playwright, headless)
+npm run test:headed         # E2E tests with browser visible
+npm run test:server         # Server unit tests (Vitest)
+npm run test:packages       # All shared package tests
+npm run test:all            # All tests (packages + server)
+
+# Single test file
+npm run test:server -- tests/unit/specific.test.ts
+
+# Linting and formatting
+npm run lint                # ESLint
+npm run format              # Prettier write
+npm run format:check        # Prettier check
+```
+
+## Architecture
+
+### Monorepo Structure
+
+```
+automaker/
+├── apps/
+│   ├── ui/           # React + Vite + Electron frontend (port 3007)
+│   └── server/       # Express + WebSocket backend (port 3008)
+└── libs/             # Shared packages (@automaker/*)
+    ├── types/        # Core TypeScript definitions (no dependencies)
+    ├── utils/        # Logging, errors, image processing, context loading
+    ├── prompts/      # AI prompt templates
+    ├── platform/     # Path management, security, process spawning
+    ├── model-resolver/    # Claude model alias resolution
+    ├── dependency-resolver/  # Feature dependency ordering
+    └── git-utils/    # Git operations & worktree management
+```
+
+### Package Dependency Chain
+
+Packages can only depend on packages above them:
+
+```
+@automaker/types (no dependencies)
+    ↓
+@automaker/utils, @automaker/prompts, @automaker/platform, @automaker/model-resolver, @automaker/dependency-resolver
+    ↓
+@automaker/git-utils
+    ↓
+@automaker/server, @automaker/ui
+```
+
+### Key Technologies
+
+- **Frontend**: React 19, Vite 7, Electron 39, TanStack Router, Zustand 5, Tailwind CSS 4
+- **Backend**: Express 5, WebSocket (ws), Claude Agent SDK, node-pty
+- **Testing**: Playwright (E2E), Vitest (unit)
+
+### Server Architecture
+
+The server (`apps/server/src/`) follows a modular pattern:
+
+- `routes/` - Express route handlers organized by feature (agent, features, auto-mode, worktree, etc.)
+- `services/` - Business logic (AgentService, AutoModeService, FeatureLoader, TerminalService)
+- `providers/` - AI provider abstraction (currently Claude via Claude Agent SDK)
+- `lib/` - Utilities (events, auth, worktree metadata)
+
+### Frontend Architecture
+
+The UI (`apps/ui/src/`) uses:
+
+- `routes/` - TanStack Router file-based routing
+- `components/views/` - Main view components (board, settings, terminal, etc.)
+- `store/` - Zustand stores with persistence (app-store.ts, setup-store.ts)
+- `hooks/` - Custom React hooks
+- `lib/` - Utilities and API client
+
+## Data Storage
+
+### Per-Project Data (`.automaker/`)
+
+```
+.automaker/
+├── features/              # Feature JSON files and images
+│   └── {featureId}/
+│       ├── feature.json
+│       ├── agent-output.md
+│       └── images/
+├── context/               # Context files for AI agents (CLAUDE.md, etc.)
+├── settings.json          # Project-specific settings
+├── spec.md               # Project specification
+└── analysis.json         # Project structure analysis
+```
+
+### Global Data (`DATA_DIR`, default `./data`)
+
+```
+data/
+├── settings.json          # Global settings, profiles, shortcuts
+├── credentials.json       # API keys
+├── sessions-metadata.json # Chat session metadata
+└── agent-sessions/        # Conversation histories
+```
+
+## Import Conventions
+
+Always import from shared packages, never from old paths:
+
+```typescript
+// ✅ Correct
+import type { Feature, ExecuteOptions } from '@automaker/types';
+import { createLogger, classifyError } from '@automaker/utils';
+import { getEnhancementPrompt } from '@automaker/prompts';
+import { getFeatureDir, ensureAutomakerDir } from '@automaker/platform';
+import { resolveModelString } from '@automaker/model-resolver';
+import { resolveDependencies } from '@automaker/dependency-resolver';
+import { getGitRepositoryDiffs } from '@automaker/git-utils';
+
+// ❌ Never import from old paths
+import { Feature } from '../services/feature-loader'; // Wrong
+import { createLogger } from '../lib/logger'; // Wrong
+```
+
+## Key Patterns
+
+### Event-Driven Architecture
+
+All server operations emit events that stream to the frontend via WebSocket. Events are created using `createEventEmitter()` from `lib/events.ts`.
+
+### Git Worktree Isolation
+
+Each feature executes in an isolated git worktree, created via `@automaker/git-utils`. This protects the main branch during AI agent execution.
+
+### Context Files
+
+Project-specific rules are stored in `.automaker/context/` and automatically loaded into agent prompts via `loadContextFiles()` from `@automaker/utils`.
+
+### Model Resolution
+
+Use `resolveModelString()` from `@automaker/model-resolver` to convert model aliases:
+
+- `haiku` → `claude-haiku-4-5`
+- `sonnet` → `claude-sonnet-4-20250514`
+- `opus` → `claude-opus-4-5-20251101`
+
+## Environment Variables
+
+- `ANTHROPIC_API_KEY` - Anthropic API key (or use Claude Code CLI auth)
+- `PORT` - Server port (default: 3008)
+- `DATA_DIR` - Data storage directory (default: ./data)
+- `ALLOWED_ROOT_DIRECTORY` - Restrict file operations to specific directory
+- `AUTOMAKER_MOCK_AGENT=true` - Enable mock agent mode for CI testing

CONTRIBUTING.md

@@ -0,0 +1,685 @@
+# Contributing to Automaker
+
+Thank you for your interest in contributing to Automaker! We're excited to have you join our community of developers building the future of autonomous AI development.
+
+Automaker is an autonomous AI development studio that provides a Kanban-based workflow where AI agents implement features in isolated git worktrees. Whether you're fixing bugs, adding features, improving documentation, or suggesting ideas, your contributions help make this project better for everyone.
+
+This guide will help you get started with contributing to Automaker. Please take a moment to read through these guidelines to ensure a smooth contribution process.
+
+## Contribution License Agreement
+
+**Important:** By submitting, pushing, or contributing any code, documentation, pull requests, issues, or other materials to the Automaker project, you agree to assign all right, title, and interest in and to your contributions, including all copyrights, patents, and other intellectual property rights, to the Core Contributors of Automaker. This assignment is irrevocable and includes the right to use, modify, distribute, and monetize your contributions in any manner.
+
+**You understand and agree that you will have no right to receive any royalties, compensation, or other financial benefits from any revenue, income, or commercial use generated from your contributed code or any derivative works thereof.** All contributions are made without expectation of payment or financial return.
+
+For complete details on contribution terms and rights assignment, please review [Section 5 (CONTRIBUTIONS AND RIGHTS ASSIGNMENT) of the LICENSE](LICENSE#5-contributions-and-rights-assignment).
+
+## Table of Contents
+
+- [Contributing to Automaker](#contributing-to-automaker)
+  - [Table of Contents](#table-of-contents)
+  - [Getting Started](#getting-started)
+    - [Prerequisites](#prerequisites)
+    - [Fork and Clone](#fork-and-clone)
+    - [Development Setup](#development-setup)
+    - [Project Structure](#project-structure)
+  - [Pull Request Process](#pull-request-process)
+    - [Branch Naming Convention](#branch-naming-convention)
+    - [Commit Message Format](#commit-message-format)
+    - [Submitting a Pull Request](#submitting-a-pull-request)
+      - [1. Prepare Your Changes](#1-prepare-your-changes)
+      - [2. Run Pre-submission Checks](#2-run-pre-submission-checks)
+      - [3. Push Your Changes](#3-push-your-changes)
+      - [4. Open a Pull Request](#4-open-a-pull-request)
+      - [PR Requirements Checklist](#pr-requirements-checklist)
+    - [Review Process](#review-process)
+      - [What to Expect](#what-to-expect)
+      - [Review Focus Areas](#review-focus-areas)
+      - [Responding to Feedback](#responding-to-feedback)
+      - [Approval Criteria](#approval-criteria)
+      - [Getting Help](#getting-help)
+  - [Code Style Guidelines](#code-style-guidelines)
+  - [Testing Requirements](#testing-requirements)
+    - [Running Tests](#running-tests)
+    - [Test Frameworks](#test-frameworks)
+      - [End-to-End Tests (Playwright)](#end-to-end-tests-playwright)
+      - [Unit Tests (Vitest)](#unit-tests-vitest)
+    - [Writing Tests](#writing-tests)
+      - [When to Write Tests](#when-to-write-tests)
+    - [CI/CD Pipeline](#cicd-pipeline)
+      - [CI Checks](#ci-checks)
+      - [CI Testing Environment](#ci-testing-environment)
+      - [Viewing CI Results](#viewing-ci-results)
+      - [Common CI Failures](#common-ci-failures)
+    - [Coverage Requirements](#coverage-requirements)
+  - [Issue Reporting](#issue-reporting)
+    - [Bug Reports](#bug-reports)
+      - [Before Reporting](#before-reporting)
+      - [Bug Report Template](#bug-report-template)
+    - [Feature Requests](#feature-requests)
+      - [Before Requesting](#before-requesting)
+      - [Feature Request Template](#feature-request-template)
+    - [Security Issues](#security-issues)
+
+---
+
+## Getting Started
+
+### Prerequisites
+
+Before contributing to Automaker, ensure you have the following installed on your system:
+
+- **Node.js 18+** (tested with Node.js 22)
+  - Download from [nodejs.org](https://nodejs.org/)
+  - Verify installation: `node --version`
+- **npm** (comes with Node.js)
+  - Verify installation: `npm --version`
+- **Git** for version control
+  - Verify installation: `git --version`
+- **Claude Code CLI** or **Anthropic API Key** (for AI agent functionality)
+  - Required to run the AI development features
+
+**Optional but recommended:**
+
+- A code editor with TypeScript support (VS Code recommended)
+- GitHub CLI (`gh`) for easier PR management
+
+### Fork and Clone
+
+1. **Fork the repository** on GitHub
+   - Navigate to [https://github.com/AutoMaker-Org/automaker](https://github.com/AutoMaker-Org/automaker)
+   - Click the "Fork" button in the top-right corner
+   - This creates your own copy of the repository
+
+2. **Clone your fork locally**
+
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/automaker.git
+   cd automaker
+   ```
+
+3. **Add the upstream remote** to keep your fork in sync
+
+   ```bash
+   git remote add upstream https://github.com/AutoMaker-Org/automaker.git
+   ```
+
+4. **Verify remotes**
+   ```bash
+   git remote -v
+   # Should show:
+   # origin    https://github.com/YOUR_USERNAME/automaker.git (fetch)
+   # origin    https://github.com/YOUR_USERNAME/automaker.git (push)
+   # upstream  https://github.com/AutoMaker-Org/automaker.git (fetch)
+   # upstream  https://github.com/AutoMaker-Org/automaker.git (push)
+   ```
+
+### Development Setup
+
+1. **Install dependencies**
+
+   ```bash
+   npm install
+   ```
+
+2. **Build shared packages** (required before running the app)
+
+   ```bash
+   npm run build:packages
+   ```
+
+3. **Start the development server**
+   ```bash
+   npm run dev          # Interactive launcher - choose mode
+   npm run dev:web      # Browser mode (web interface)
+   npm run dev:electron # Desktop app mode
+   ```
+
+**Common development commands:**
+
+| Command                  | Description                      |
+| ------------------------ | -------------------------------- |
+| `npm run dev`            | Interactive development launcher |
+| `npm run dev:web`        | Start in browser mode            |
+| `npm run dev:electron`   | Start desktop app                |
+| `npm run build`          | Build all packages and apps      |
+| `npm run build:packages` | Build shared packages only       |
+| `npm run lint`           | Run ESLint checks                |
+| `npm run format`         | Format code with Prettier        |
+| `npm run format:check`   | Check formatting without changes |
+| `npm run test`           | Run E2E tests (Playwright)       |
+| `npm run test:server`    | Run server unit tests            |
+| `npm run test:packages`  | Run package tests                |
+| `npm run test:all`       | Run all tests                    |
+
+### Project Structure
+
+Automaker is organized as an npm workspace monorepo:
+
+```
+automaker/
+├── apps/
+│   ├── ui/              # React + Vite + Electron frontend
+│   └── server/          # Express + WebSocket backend
+├── libs/
+│   ├── @automaker/types/            # Shared TypeScript types
+│   ├── @automaker/utils/            # Utility functions
+│   ├── @automaker/prompts/          # AI prompt templates
+│   ├── @automaker/platform/         # Platform abstractions
+│   ├── @automaker/model-resolver/   # AI model resolution
+│   ├── @automaker/dependency-resolver/ # Dependency management
+│   └── @automaker/git-utils/        # Git operations
+├── docs/                # Documentation
+└── package.json         # Root package configuration
+```
+
+**Key conventions:**
+
+- Always import from `@automaker/*` shared packages, never use relative paths to `libs/`
+- Frontend code lives in `apps/ui/`
+- Backend code lives in `apps/server/`
+- Shared logic should be in the appropriate `libs/` package
+
+---
+
+## Pull Request Process
+
+This section covers everything you need to know about contributing changes through pull requests, from creating your branch to getting your code merged.
+
+### Branch Naming Convention
+
+We use a consistent branch naming pattern to keep our repository organized:
+
+```
+<type>/<description>
+```
+
+**Branch types:**
+
+| Type       | Purpose                  | Example                           |
+| ---------- | ------------------------ | --------------------------------- |
+| `feature`  | New functionality        | `feature/add-user-authentication` |
+| `fix`      | Bug fixes                | `fix/resolve-memory-leak`         |
+| `docs`     | Documentation changes    | `docs/update-contributing-guide`  |
+| `refactor` | Code restructuring       | `refactor/simplify-api-handlers`  |
+| `test`     | Adding or updating tests | `test/add-utils-unit-tests`       |
+| `chore`    | Maintenance tasks        | `chore/update-dependencies`       |
+
+**Guidelines:**
+
+- Use lowercase letters and hyphens (no underscores or spaces)
+- Keep descriptions short but descriptive
+- Include issue number when applicable: `feature/123-add-login`
+
+```bash
+# Create and checkout a new feature branch
+git checkout -b feature/add-dark-mode
+
+# Create a fix branch with issue reference
+git checkout -b fix/456-resolve-login-error
+```
+
+### Commit Message Format
+
+We follow the **Conventional Commits** style for clear, readable commit history:
+
+```
+<type>: <description>
+
+[optional body]
+```
+
+**Commit types:**
+
+| Type       | Purpose                     |
+| ---------- | --------------------------- |
+| `feat`     | New feature                 |
+| `fix`      | Bug fix                     |
+| `docs`     | Documentation only          |
+| `style`    | Formatting (no code change) |
+| `refactor` | Code restructuring          |
+| `test`     | Adding or updating tests    |
+| `chore`    | Maintenance tasks           |
+
+**Guidelines:**
+
+- Use **imperative mood** ("Add feature" not "Added feature")
+- Keep first line under **72 characters**
+- Capitalize the first letter after the type prefix
+- No period at the end of the subject line
+- Add a blank line before the body for detailed explanations
+
+**Examples:**
+
+```bash
+# Simple commit
+git commit -m "feat: Add user authentication flow"
+
+# Commit with body for more context
+git commit -m "fix: Resolve memory leak in WebSocket handler
+
+The connection cleanup was not being called when clients
+disconnected unexpectedly. Added proper cleanup in the
+error handler to prevent memory accumulation."
+
+# Documentation update
+git commit -m "docs: Update API documentation"
+
+# Refactoring
+git commit -m "refactor: Simplify state management logic"
+```
+
+### Submitting a Pull Request
+
+Follow these steps to submit your contribution:
+
+#### 1. Prepare Your Changes
+
+Ensure you've synced with the latest upstream changes:
+
+```bash
+# Fetch latest changes from upstream
+git fetch upstream
+
+# Rebase your branch on main (if needed)
+git rebase upstream/main
+```
+
+#### 2. Run Pre-submission Checks
+
+Before opening your PR, verify everything passes locally:
+
+```bash
+# Run all tests
+npm run test:all
+
+# Check formatting
+npm run format:check
+
+# Run linter
+npm run lint
+
+# Build to verify no compile errors
+npm run build
+```
+
+#### 3. Push Your Changes
+
+```bash
+# Push your branch to your fork
+git push origin feature/your-feature-name
+```
+
+#### 4. Open a Pull Request
+
+1. Go to your fork on GitHub
+2. Click "Compare & pull request" for your branch
+3. Ensure the base repository is `AutoMaker-Org/automaker` and base branch is `main`
+4. Fill out the PR template completely
+
+#### PR Requirements Checklist
+
+Your PR should include:
+
+- [ ] **Clear title** describing the change (use conventional commit format)
+- [ ] **Description** explaining what changed and why
+- [ ] **Link to related issue** (if applicable): `Closes #123` or `Fixes #456`
+- [ ] **All CI checks passing** (format, lint, build, tests)
+- [ ] **No merge conflicts** with main branch
+- [ ] **Tests included** for new functionality
+- [ ] **Documentation updated** if adding/changing public APIs
+
+**Example PR Description:**
+
+```markdown
+## Summary
+
+This PR adds dark mode support to the Automaker UI.
+
+- Implements theme toggle in settings panel
+- Adds CSS custom properties for theme colors
+- Persists theme preference to localStorage
+
+## Related Issue
+
+Closes #123
+
+## Testing
+
+- [x] Tested toggle functionality in Chrome and Firefox
+- [x] Verified theme persists across page reloads
+- [x] Checked accessibility contrast ratios
+
+## Screenshots
+
+[Include before/after screenshots for UI changes]
+```
+
+### Review Process
+
+All contributions go through code review to maintain quality:
+
+#### What to Expect
+
+1. **CI Checks Run First** - Automated checks (format, lint, build, tests) must pass before review
+2. **Maintainer Review** - The project maintainers will review your PR and decide whether to merge it
+3. **Feedback & Discussion** - The reviewer may ask questions or request changes
+4. **Iteration** - Make requested changes and push updates to the same branch
+5. **Approval & Merge** - Once approved and checks pass, your PR will be merged
+
+#### Review Focus Areas
+
+The reviewer checks for:
+
+- **Correctness** - Does the code work as intended?
+- **Clean Code** - Does it follow our [code style guidelines](#code-style-guidelines)?
+- **Test Coverage** - Are new features properly tested?
+- **Documentation** - Are public APIs documented?
+- **Breaking Changes** - Are any breaking changes discussed first?
+
+#### Responding to Feedback
+
+- Respond to **all** review comments, even if just to acknowledge
+- Ask questions if feedback is unclear
+- Push additional commits to address feedback (don't force-push during review)
+- Mark conversations as resolved once addressed
+
+#### Approval Criteria
+
+Your PR is ready to merge when:
+
+- ✅ All CI checks pass
+- ✅ The maintainer has approved the changes
+- ✅ All review comments are addressed
+- ✅ No unresolved merge conflicts
+
+#### Getting Help
+
+If your PR seems stuck:
+
+- Comment asking for status update (mention @webdevcody if needed)
+- Reach out on [Discord](https://discord.gg/jjem7aEDKU)
+- Make sure all checks are passing and you've responded to all feedback
+
+---
+
+## Code Style Guidelines
+
+Automaker uses automated tooling to enforce code style. Run `npm run format` to format code and `npm run lint` to check for issues. Pre-commit hooks automatically format staged files before committing.
+
+---
+
+## Testing Requirements
+
+Testing helps prevent regressions. Automaker uses **Playwright** for end-to-end testing and **Vitest** for unit tests.
+
+### Running Tests
+
+Use these commands to run tests locally:
+
+| Command                        | Description                           |
+| ------------------------------ | ------------------------------------- |
+| `npm run test`                 | Run E2E tests (Playwright)            |
+| `npm run test:server`          | Run server unit tests (Vitest)        |
+| `npm run test:packages`        | Run shared package tests              |
+| `npm run test:all`             | Run all tests                         |
+| `npm run test:server:coverage` | Run server tests with coverage report |
+
+**Before submitting a PR**, always run the full test suite:
+
+```bash
+npm run test:all
+```
+
+### Test Frameworks
+
+#### End-to-End Tests (Playwright)
+
+E2E tests verify the entire application works correctly from a user's perspective.
+
+- **Framework:** [Playwright](https://playwright.dev/)
+- **Location:** `e2e/` directory
+- **Test ports:** UI on port 3007, Server on port 3008
+
+**Running E2E tests:**
+
+```bash
+# Run all E2E tests
+npm run test
+
+# Run with headed browser (useful for debugging)
+npx playwright test --headed
+
+# Run a specific test file
+npm test --workspace=@automaker/ui -- tests/example.spec.ts
+```
+
+**E2E Test Guidelines:**
+
+- Write tests from a user's perspective
+- Use descriptive test names that explain the scenario
+- Clean up test data after each test
+- Use appropriate timeouts for async operations
+- Prefer `locator` over direct selectors for resilience
+
+#### Unit Tests (Vitest)
+
+Unit tests verify individual functions and modules work correctly in isolation.
+
+- **Framework:** [Vitest](https://vitest.dev/)
+- **Location:** In the `tests/` directory within each package (e.g., `apps/server/tests/`)
+
+**Running unit tests:**
+
+```bash
+# Run all server unit tests
+npm run test:server
+
+# Run with coverage report
+npm run test:server:coverage
+
+# Run package tests
+npm run test:packages
+
+# Run in watch mode during development
+npx vitest --watch
+```
+
+**Unit Test Guidelines:**
+
+- Keep tests small and focused on one behavior
+- Use descriptive test names: `it('should return null when user is not found')`
+- Follow the AAA pattern: Arrange, Act, Assert
+- Mock external dependencies to isolate the unit under test
+- Aim for meaningful coverage, not just line coverage
+
+### Writing Tests
+
+#### When to Write Tests
+
+- **New features:** All new features should include tests
+- **Bug fixes:** Add a test that reproduces the bug before fixing
+- **Refactoring:** Ensure existing tests pass after refactoring
+- **Public APIs:** All public APIs must have test coverage
+
+### CI/CD Pipeline
+
+Automaker uses **GitHub Actions** for continuous integration. Every pull request triggers automated checks.
+
+#### CI Checks
+
+The following checks must pass before your PR can be merged:
+
+| Check             | Description                                   |
+| ----------------- | --------------------------------------------- |
+| **Format**        | Verifies code is formatted with Prettier      |
+| **Build**         | Ensures the project compiles without errors   |
+| **Package Tests** | Runs tests for shared `@automaker/*` packages |
+| **Server Tests**  | Runs server unit tests with coverage          |
+
+#### CI Testing Environment
+
+For CI environments, Automaker supports a mock agent mode:
+
+```bash
+# Enable mock agent mode for CI testing
+AUTOMAKER_MOCK_AGENT=true npm run test
+```
+
+This allows tests to run without requiring a real Claude API connection.
+
+#### Viewing CI Results
+
+1. Go to your PR on GitHub
+2. Scroll to the "Checks" section at the bottom
+3. Click on any failed check to see detailed logs
+4. Fix issues locally and push updates
+
+#### Common CI Failures
+
+| Issue               | Solution                                      |
+| ------------------- | --------------------------------------------- |
+| Format check failed | Run `npm run format` locally                  |
+| Build failed        | Run `npm run build` and fix TypeScript errors |
+| Tests failed        | Run `npm run test:all` locally to reproduce   |
+| Coverage decreased  | Add tests for new code paths                  |
+
+### Coverage Requirements
+
+While we don't enforce strict coverage percentages, we expect:
+
+- **New features:** Should include comprehensive tests
+- **Bug fixes:** Should include a regression test
+- **Critical paths:** Must have test coverage (authentication, data persistence, etc.)
+
+To view coverage reports locally:
+
+```bash
+npm run test:server:coverage
+```
+
+This generates an HTML report you can open in your browser to see which lines are covered.
+
+---
+
+## Issue Reporting
+
+Found a bug or have an idea for a new feature? We'd love to hear from you! This section explains how to report issues effectively.
+
+### Bug Reports
+
+When reporting a bug, please provide as much information as possible to help us understand and reproduce the issue.
+
+#### Before Reporting
+
+1. **Search existing issues** - Check if the bug has already been reported
+2. **Try the latest version** - Make sure you're running the latest version of Automaker
+3. **Reproduce the issue** - Verify you can consistently reproduce the bug
+
+#### Bug Report Template
+
+When creating a bug report, include:
+
+- **Title:** A clear, descriptive title summarizing the issue
+- **Environment:**
+  - Operating System and version
+  - Node.js version (`node --version`)
+  - Automaker version or commit hash
+- **Steps to Reproduce:** Numbered list of steps to reproduce the bug
+- **Expected Behavior:** What you expected to happen
+- **Actual Behavior:** What actually happened
+- **Logs/Screenshots:** Any relevant error messages, console output, or screenshots
+
+**Example Bug Report:**
+
+```markdown
+## Bug: WebSocket connection drops after 5 minutes of inactivity
+
+### Environment
+
+- OS: Windows 11
+- Node.js: 22.11.0
+- Automaker: commit abc1234
+
+### Steps to Reproduce
+
+1. Start the application with `npm run dev:web`
+2. Open the Kanban board
+3. Leave the browser tab open for 5+ minutes without interaction
+4. Try to move a card
+
+### Expected Behavior
+
+The card should move to the new column.
+
+### Actual Behavior
+
+The UI shows "Connection lost" and the card doesn't move.
+
+### Logs
+
+[WebSocket] Connection closed: 1006
+```
+
+### Feature Requests
+
+We welcome ideas for improving Automaker! Here's how to submit a feature request:
+
+#### Before Requesting
+
+1. **Check existing issues** - Your idea may already be proposed or in development
+2. **Consider scope** - Think about whether the feature fits Automaker's mission as an autonomous AI development studio
+
+#### Feature Request Template
+
+A good feature request includes:
+
+- **Title:** A brief, descriptive title
+- **Problem Statement:** What problem does this feature solve?
+- **Proposed Solution:** How do you envision this working?
+- **Alternatives Considered:** What other approaches did you consider?
+- **Additional Context:** Mockups, examples, or references that help explain your idea
+
+**Example Feature Request:**
+
+```markdown
+## Feature: Dark Mode Support
+
+### Problem Statement
+
+Working late at night, the bright UI causes eye strain and doesn't match
+my system's dark theme preference.
+
+### Proposed Solution
+
+Add a theme toggle in the settings panel that allows switching between
+light and dark modes. Ideally, it should also detect system preference.
+
+### Alternatives Considered
+
+- Browser extension to force dark mode (doesn't work well with custom styling)
+- Custom CSS override (breaks with updates)
+
+### Additional Context
+
+Similar to how VS Code handles themes - a dropdown in settings with
+immediate preview.
+```
+
+### Security Issues
+
+**Important:** If you discover a security vulnerability, please do NOT open a public issue. Instead:
+
+1. Join our [Discord server](https://discord.gg/jjem7aEDKU) and send a direct message to the user `@webdevcody`
+2. Include detailed steps to reproduce
+3. Allow time for us to address the issue before public disclosure
+
+We take security seriously and appreciate responsible disclosure.
+
+---
+
+For license and contribution terms, see the [LICENSE](LICENSE) file in the repository root and the [README.md](README.md#license) for more details.
+
+---
+
+Thank you for contributing to Automaker!

Dockerfile

@@ -0,0 +1,154 @@
+# Automaker Multi-Stage Dockerfile
+# Single Dockerfile for both server and UI builds
+# Usage:
+#   docker build --target server -t automaker-server .
+#   docker build --target ui -t automaker-ui .
+# Or use docker-compose which selects targets automatically
+
+# =============================================================================
+# BASE STAGE - Common setup for all builds (DRY: defined once, used by all)
+# =============================================================================
+FROM node:22-alpine AS base
+
+# Install build dependencies for native modules (node-pty)
+RUN apk add --no-cache python3 make g++
+
+WORKDIR /app
+
+# Copy root package files
+COPY package*.json ./
+
+# Copy all libs package.json files (centralized - add new libs here)
+COPY libs/types/package*.json ./libs/types/
+COPY libs/utils/package*.json ./libs/utils/
+COPY libs/prompts/package*.json ./libs/prompts/
+COPY libs/platform/package*.json ./libs/platform/
+COPY libs/model-resolver/package*.json ./libs/model-resolver/
+COPY libs/dependency-resolver/package*.json ./libs/dependency-resolver/
+COPY libs/git-utils/package*.json ./libs/git-utils/
+
+# Copy scripts (needed by npm workspace)
+COPY scripts ./scripts
+
+# =============================================================================
+# SERVER BUILD STAGE
+# =============================================================================
+FROM base AS server-builder
+
+# Copy server-specific package.json
+COPY apps/server/package*.json ./apps/server/
+
+# Install dependencies (--ignore-scripts to skip husky/prepare, then rebuild native modules)
+RUN npm ci --ignore-scripts && npm rebuild node-pty
+
+# Copy all source files
+COPY libs ./libs
+COPY apps/server ./apps/server
+
+# Build packages in dependency order, then build server
+RUN npm run build:packages && npm run build --workspace=apps/server
+
+# =============================================================================
+# SERVER PRODUCTION STAGE
+# =============================================================================
+FROM node:22-alpine AS server
+
+# Install git, curl, bash (for terminal), and GitHub CLI (pinned version, multi-arch)
+RUN apk add --no-cache git curl bash && \
+    GH_VERSION="2.63.2" && \
+    ARCH=$(uname -m) && \
+    case "$ARCH" in \
+        x86_64) GH_ARCH="amd64" ;; \
+        aarch64|arm64) GH_ARCH="arm64" ;; \
+        *) echo "Unsupported architecture: $ARCH" && exit 1 ;; \
+    esac && \
+    curl -L "https://github.com/cli/cli/releases/download/v${GH_VERSION}/gh_${GH_VERSION}_linux_${GH_ARCH}.tar.gz" -o gh.tar.gz && \
+    tar -xzf gh.tar.gz && \
+    mv gh_${GH_VERSION}_linux_${GH_ARCH}/bin/gh /usr/local/bin/gh && \
+    rm -rf gh.tar.gz gh_${GH_VERSION}_linux_${GH_ARCH}
+
+# Install Claude CLI globally
+RUN npm install -g @anthropic-ai/claude-code
+
+WORKDIR /app
+
+# Create non-root user
+RUN addgroup -g 1001 -S automaker && \
+    adduser -S automaker -u 1001
+
+# Copy root package.json (needed for workspace resolution)
+COPY --from=server-builder /app/package*.json ./
+
+# Copy built libs (workspace packages are symlinked in node_modules)
+COPY --from=server-builder /app/libs ./libs
+
+# Copy built server
+COPY --from=server-builder /app/apps/server/dist ./apps/server/dist
+COPY --from=server-builder /app/apps/server/package*.json ./apps/server/
+
+# Copy node_modules (includes symlinks to libs)
+COPY --from=server-builder /app/node_modules ./node_modules
+
+# Create data and projects directories
+RUN mkdir -p /data /projects && chown automaker:automaker /data /projects
+
+# Configure git for mounted volumes and authentication
+# Use --system so it's not overwritten by mounted user .gitconfig
+RUN git config --system --add safe.directory '*' && \
+    # Use gh as credential helper (works with GH_TOKEN env var)
+    git config --system credential.helper '!gh auth git-credential'
+
+# Switch to non-root user
+USER automaker
+
+# Environment variables
+ENV PORT=3008
+ENV DATA_DIR=/data
+
+# Expose port
+EXPOSE 3008
+
+# Health check (using curl since it's already installed, more reliable than busybox wget)
+HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
+    CMD curl -f http://localhost:3008/api/health || exit 1
+
+# Start server
+CMD ["node", "apps/server/dist/index.js"]
+
+# =============================================================================
+# UI BUILD STAGE
+# =============================================================================
+FROM base AS ui-builder
+
+# Copy UI-specific package.json
+COPY apps/ui/package*.json ./apps/ui/
+
+# Install dependencies (--ignore-scripts to skip husky and build:packages in prepare script)
+RUN npm ci --ignore-scripts
+
+# Copy all source files
+COPY libs ./libs
+COPY apps/ui ./apps/ui
+
+# Build packages in dependency order, then build UI
+# VITE_SERVER_URL tells the UI where to find the API server
+# Use ARG to allow overriding at build time: --build-arg VITE_SERVER_URL=http://api.example.com
+ARG VITE_SERVER_URL=http://localhost:3008
+ENV VITE_SKIP_ELECTRON=true
+ENV VITE_SERVER_URL=${VITE_SERVER_URL}
+RUN npm run build:packages && npm run build --workspace=apps/ui
+
+# =============================================================================
+# UI PRODUCTION STAGE
+# =============================================================================
+FROM nginx:alpine AS ui
+
+# Copy built files
+COPY --from=ui-builder /app/apps/ui/dist /usr/share/nginx/html
+
+# Copy nginx config for SPA routing
+COPY apps/ui/nginx.conf /etc/nginx/conf.d/default.conf
+
+EXPOSE 80
+
+CMD ["nginx", "-g", "daemon off;"]

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="apps/ui/public/readme_logo.png" alt="Automaker Logo" height="80" />
+  <img src="apps/ui/public/readme_logo.svg" alt="Automaker Logo" height="80" />
 </p>
 
 > **[!TIP]**
@@ -19,7 +19,7 @@
 
 - [What Makes Automaker Different?](#what-makes-automaker-different)
   - [The Workflow](#the-workflow)
-  - [Powered by Claude Code](#powered-by-claude-code)
+  - [Powered by Claude Agent SDK](#powered-by-claude-agent-sdk)
   - [Why This Matters](#why-this-matters)
 - [Security Disclaimer](#security-disclaimer)
 - [Community & Support](#community--support)
@@ -28,22 +28,36 @@
   - [Quick Start](#quick-start)
 - [How to Run](#how-to-run)
   - [Development Mode](#development-mode)
-    - [Electron Desktop App (Recommended)](#electron-desktop-app-recommended)
-    - [Web Browser Mode](#web-browser-mode)
   - [Building for Production](#building-for-production)
-  - [Running Production Build](#running-production-build)
   - [Testing](#testing)
   - [Linting](#linting)
-  - [Authentication Options](#authentication-options)
-  - [Persistent Setup (Optional)](#persistent-setup-optional)
+  - [Environment Configuration](#environment-configuration)
+  - [Authentication Setup](#authentication-setup)
 - [Features](#features)
+  - [Core Workflow](#core-workflow)
+  - [AI & Planning](#ai--planning)
+  - [Project Management](#project-management)
+  - [Collaboration & Review](#collaboration--review)
+  - [Developer Tools](#developer-tools)
+  - [Advanced Features](#advanced-features)
 - [Tech Stack](#tech-stack)
+  - [Frontend](#frontend)
+  - [Backend](#backend)
+  - [Testing & Quality](#testing--quality)
+  - [Shared Libraries](#shared-libraries)
+- [Available Views](#available-views)
+- [Architecture](#architecture)
+  - [Monorepo Structure](#monorepo-structure)
+  - [How It Works](#how-it-works)
+  - [Key Architectural Patterns](#key-architectural-patterns)
+  - [Security & Isolation](#security--isolation)
+  - [Data Storage](#data-storage)
 - [Learn More](#learn-more)
 - [License](#license)
 
 </details>
 
-Automaker is an autonomous AI development studio that transforms how you build software. Instead of manually writing every line of code, you describe features on a Kanban board and watch as AI agents powered by Claude Code automatically implement them.
+Automaker is an autonomous AI development studio that transforms how you build software. Instead of manually writing every line of code, you describe features on a Kanban board and watch as AI agents powered by Claude Agent SDK automatically implement them. Built with React, Vite, Electron, and Express, Automaker provides a complete workflow for managing AI agents through a desktop application (or web browser), with features like real-time streaming, git worktree isolation, plan approval, and multi-agent task execution.
 
 ![Automaker UI](https://i.imgur.com/jdwKydM.png)
 
@@ -59,30 +73,14 @@ Traditional development tools help you write code. Automaker helps you **orchest
 4. **Review & Verify** - Review the changes, run tests, and approve when ready
 5. **Ship Faster** - Build entire applications in days, not weeks
 
-### Powered by Claude Code
+### Powered by Claude Agent SDK
 
-Automaker leverages the [Claude Agent SDK](https://platform.claude.com/docs/en/agent-sdk/overview) to give AI agents full access to your codebase. Agents can read files, write code, execute commands, run tests, and make git commits—all while working in isolated git worktrees to keep your main branch safe.
+Automaker leverages the [Claude Agent SDK](https://www.npmjs.com/package/@anthropic-ai/claude-agent-sdk) to give AI agents full access to your codebase. Agents can read files, write code, execute commands, run tests, and make git commits—all while working in isolated git worktrees to keep your main branch safe. The SDK provides autonomous AI agents that can use tools, make decisions, and complete complex multi-step tasks without constant human intervention.
 
 ### Why This Matters
 
 The future of software development is **agentic coding**—where developers become architects directing AI agents rather than manual coders. Automaker puts this future in your hands today, letting you experience what it's like to build software 10x faster with AI agents handling the implementation while you focus on architecture and business logic.
 
----
-
-> **[!CAUTION]**
->
-> ## Security Disclaimer
->
-> **This software uses AI-powered tooling that has access to your operating system and can read, modify, and delete files. Use at your own risk.**
->
-> We have reviewed this codebase for security vulnerabilities, but you assume all risk when running this software. You should review the code yourself before running it.
->
-> **We do not recommend running Automaker directly on your local computer** due to the risk of AI agents having access to your entire file system. Please sandbox this application using Docker or a virtual machine.
->
-> **[Read the full disclaimer](./DISCLAIMER.md)**
-
----
-
 ## Community & Support
 
 Join the **Agentic Jumpstart** to connect with other builders exploring **agentic coding** and autonomous development workflows.
@@ -95,8 +93,7 @@ In the Discord, you can:
 - 🚀 Show off projects built with AI agents
 - 🤝 Collaborate with other developers and contributors
 
-👉 **Join the Discord:**  
-https://discord.gg/jjem7aEDKU
+👉 **Join the Discord:** [Agentic Jumpstart Discord](https://discord.gg/jjem7aEDKU)
 
 ---
 
@@ -104,28 +101,49 @@ https://discord.gg/jjem7aEDKU
 
 ### Prerequisites
 
-- Node.js 18+
-- npm
-- [Claude Code CLI](https://code.claude.com/docs/en/overview) installed and authenticated
+- **Node.js 18+** (tested with Node.js 22)
+- **npm** (comes with Node.js)
+- **Authentication** (choose one):
+  - **[Claude Code CLI](https://code.claude.com/docs/en/overview)** (recommended) - Install and authenticate, credentials used automatically
+  - **Anthropic API Key** - Direct API key for Claude Agent SDK ([get one here](https://console.anthropic.com/))
 
 ### Quick Start
 
 ```bash
-# 1. Clone the repo
+# 1. Clone the repository
 git clone https://github.com/AutoMaker-Org/automaker.git
 cd automaker
 
 # 2. Install dependencies
 npm install
 
-# 3. Build local shared packages
+# 3. Build shared packages (Now can be skipped npm install / run dev does it automaticly)
 npm run build:packages
 
-# 4. Run Automaker (pick your mode)
+# 4. Set up authentication (skip if using Claude Code CLI)
+# If using Claude Code CLI: credentials are detected automatically
+# If using API key directly, choose one method:
+
+# Option A: Environment variable
+export ANTHROPIC_API_KEY="sk-ant-..."
+
+# Option B: Create .env file in project root
+echo "ANTHROPIC_API_KEY=sk-ant-..." > .env
+
+# 5. Start Automaker (interactive launcher)
 npm run dev
-# Then choose your run mode when prompted, or use specific commands below
+# Choose between:
+#   1. Web Application (browser at localhost:3007)
+#   2. Desktop Application (Electron - recommended)
 ```
 
+**Note:** The `npm run dev` command will:
+
+- Check for dependencies and install if needed
+- Install Playwright browsers for E2E tests
+- Kill any processes on ports 3007/3008
+- Present an interactive menu to choose your run mode
+
 ## How to Run
 
 ### Development Mode
@@ -163,31 +181,162 @@ npm run dev:web
 
 ### Building for Production
 
+#### Web Application
+
 ```bash
-# Build Next.js app
+# Build for web deployment (uses Vite)
 npm run build
 
-# Build Electron app for distribution
-npm run build:electron
-```
-
-### Running Production Build
-
-```bash
-# Start production Next.js server
+# Run production build
 npm run start
 ```
 
-### Testing
+#### Desktop Application
 
 ```bash
-# Run tests headless
-npm run test
+# Build for current platform (macOS/Windows/Linux)
+npm run build:electron
 
-# Run tests with browser visible
-npm run test:headed
+# Platform-specific builds
+npm run build:electron:mac     # macOS (DMG + ZIP, x64 + arm64)
+npm run build:electron:win     # Windows (NSIS installer, x64)
+npm run build:electron:linux   # Linux (AppImage + DEB, x64)
+
+# Output directory: apps/ui/release/
 ```
 
+#### Docker Deployment
+
+Docker provides the most secure way to run Automaker by isolating it from your host filesystem.
+
+```bash
+# Build and run with Docker Compose
+docker-compose up -d
+
+# Access UI at http://localhost:3007
+# API at http://localhost:3008
+
+# View logs
+docker-compose logs -f
+
+# Stop containers
+docker-compose down
+```
+
+##### Configuration
+
+Create a `.env` file in the project root if using API key authentication:
+
+```bash
+# Optional: Anthropic API key (not needed if using Claude CLI authentication)
+ANTHROPIC_API_KEY=sk-ant-...
+```
+
+**Note:** Most users authenticate via Claude CLI instead of API keys. See [Claude CLI Authentication](#claude-cli-authentication-optional) below.
+
+##### Working with Projects (Host Directory Access)
+
+By default, the container is isolated from your host filesystem. To work on projects from your host machine, create a `docker-compose.override.yml` file (gitignored):
+
+```yaml
+services:
+  server:
+    volumes:
+      # Mount your project directories
+      - /path/to/your/project:/projects/your-project
+```
+
+##### Claude CLI Authentication (Optional)
+
+To use Claude Code CLI authentication instead of an API key, mount your Claude CLI config directory:
+
+```yaml
+services:
+  server:
+    volumes:
+      # Linux/macOS
+      - ~/.claude:/home/automaker/.claude
+      # Windows
+      - C:/Users/YourName/.claude:/home/automaker/.claude
+```
+
+**Note:** The Claude CLI config must be writable (do not use `:ro` flag) as the CLI writes debug files.
+
+##### GitHub CLI Authentication (For Git Push/PR Operations)
+
+To enable git push and GitHub CLI operations inside the container:
+
+```yaml
+services:
+  server:
+    volumes:
+      # Mount GitHub CLI config
+      # Linux/macOS
+      - ~/.config/gh:/home/automaker/.config/gh
+      # Windows
+      - 'C:/Users/YourName/AppData/Roaming/GitHub CLI:/home/automaker/.config/gh'
+
+      # Mount git config for user identity (name, email)
+      - ~/.gitconfig:/home/automaker/.gitconfig:ro
+    environment:
+      # GitHub token (required on Windows where tokens are in Credential Manager)
+      # Get your token with: gh auth token
+      - GH_TOKEN=${GH_TOKEN}
+```
+
+Then add `GH_TOKEN` to your `.env` file:
+
+```bash
+GH_TOKEN=gho_your_github_token_here
+```
+
+##### Complete docker-compose.override.yml Example
+
+```yaml
+services:
+  server:
+    volumes:
+      # Your projects
+      - /path/to/project1:/projects/project1
+      - /path/to/project2:/projects/project2
+
+      # Authentication configs
+      - ~/.claude:/home/automaker/.claude
+      - ~/.config/gh:/home/automaker/.config/gh
+      - ~/.gitconfig:/home/automaker/.gitconfig:ro
+    environment:
+      - GH_TOKEN=${GH_TOKEN}
+```
+
+##### Architecture Support
+
+The Docker image supports both AMD64 and ARM64 architectures. The GitHub CLI and Claude CLI are automatically downloaded for the correct architecture during build.
+
+### Testing
+
+#### End-to-End Tests (Playwright)
+
+```bash
+npm run test            # Headless E2E tests
+npm run test:headed     # Browser visible E2E tests
+```
+
+#### Unit Tests (Vitest)
+
+```bash
+npm run test:server              # Server unit tests
+npm run test:server:coverage     # Server tests with coverage
+npm run test:packages            # All shared package tests
+npm run test:all                 # Packages + server tests
+```
+
+#### Test Configuration
+
+- E2E tests run on ports 3007 (UI) and 3008 (server)
+- Automatically starts test servers before running
+- Uses Chromium browser via Playwright
+- Mock agent mode available in CI with `AUTOMAKER_MOCK_AGENT=true`
+
 ### Linting
 
 ```bash
@@ -195,59 +344,300 @@ npm run test:headed
 npm run lint
 ```
 
-### Authentication Options
+### Environment Configuration
 
-Automaker supports multiple authentication methods (in order of priority):
+#### Authentication (if not using Claude Code CLI)
 
-| Method           | Environment Variable | Description                     |
-| ---------------- | -------------------- | ------------------------------- |
-| API Key (env)    | `ANTHROPIC_API_KEY`  | Anthropic API key               |
-| API Key (stored) | —                    | Anthropic API key stored in app |
+- `ANTHROPIC_API_KEY` - Your Anthropic API key for Claude Agent SDK (not needed if using Claude Code CLI)
 
-### Persistent Setup (Optional)
+#### Optional - Server
+
+- `PORT` - Server port (default: 3008)
+- `DATA_DIR` - Data storage directory (default: ./data)
+- `ENABLE_REQUEST_LOGGING` - HTTP request logging (default: true)
+
+#### Optional - Security
+
+- `AUTOMAKER_API_KEY` - Optional API authentication for the server
+- `ALLOWED_ROOT_DIRECTORY` - Restrict file operations to specific directory
+- `CORS_ORIGIN` - CORS policy (default: \*)
+
+#### Optional - Development
+
+- `VITE_SKIP_ELECTRON` - Skip Electron in dev mode
+- `OPEN_DEVTOOLS` - Auto-open DevTools in Electron
+
+### Authentication Setup
+
+#### Option 1: Claude Code CLI (Recommended)
+
+Install and authenticate the Claude Code CLI following the [official quickstart guide](https://code.claude.com/docs/en/quickstart).
+
+Once authenticated, Automaker will automatically detect and use your CLI credentials. No additional configuration needed!
+
+#### Option 2: Direct API Key
+
+If you prefer not to use the CLI, you can provide an Anthropic API key directly using one of these methods:
+
+##### 2a. Shell Configuration
 
 Add to your `~/.bashrc` or `~/.zshrc`:
 
 ```bash
-export ANTHROPIC_API_KEY="YOUR_API_KEY_HERE"
+export ANTHROPIC_API_KEY="sk-ant-..."
 ```
 
-Then restart your terminal or run `source ~/.bashrc`.
+Then restart your terminal or run `source ~/.bashrc` (or `source ~/.zshrc`).
+
+##### 2b. .env File
+
+Create a `.env` file in the project root (gitignored):
+
+```bash
+ANTHROPIC_API_KEY=sk-ant-...
+PORT=3008
+DATA_DIR=./data
+```
+
+##### 2c. In-App Storage
+
+The application can store your API key securely in the settings UI. The key is persisted in the `DATA_DIR` directory.
 
 ## Features
 
+### Core Workflow
+
 - 📋 **Kanban Board** - Visual drag-and-drop board to manage features through backlog, in progress, waiting approval, and verified stages
 - 🤖 **AI Agent Integration** - Automatic AI agent assignment to implement features when moved to "In Progress"
-- 🧠 **Multi-Model Support** - Choose from multiple AI models including Claude Opus, Sonnet, and more
-- 💭 **Extended Thinking** - Enable extended thinking modes for complex problem-solving
-- 📡 **Real-time Agent Output** - View live agent output, logs, and file diffs as features are being implemented
-- 🔍 **Project Analysis** - AI-powered project structure analysis to understand your codebase
-- 📁 **Context Management** - Add context files to help AI agents understand your project better
-- 💡 **Feature Suggestions** - AI-generated feature suggestions based on your project
-- 🖼️ **Image Support** - Attach images and screenshots to feature descriptions
-- ⚡ **Concurrent Processing** - Configure concurrency to process multiple features simultaneously
-- 🧪 **Test Integration** - Automatic test running and verification for implemented features
-- 🔀 **Git Integration** - View git diffs and track changes made by AI agents
-- 👤 **AI Profiles** - Create and manage different AI agent profiles for various tasks
-- 💬 **Chat History** - Keep track of conversations and interactions with AI agents
-- ⌨️ **Keyboard Shortcuts** - Efficient navigation and actions via keyboard shortcuts
-- 🎨 **Dark/Light Theme** - Beautiful UI with theme support
-- 🖥️ **Cross-Platform** - Desktop application built with Electron for Windows, macOS, and Linux
+- 🔀 **Git Worktree Isolation** - Each feature executes in isolated git worktrees to protect your main branch
+- 📡 **Real-time Streaming** - Watch AI agents work in real-time with live tool usage, progress updates, and task completion
+- 🔄 **Follow-up Instructions** - Send additional instructions to running agents without stopping them
+
+### AI & Planning
+
+- 🧠 **Multi-Model Support** - Choose from Claude Opus, Sonnet, and Haiku per feature
+- 💭 **Extended Thinking** - Enable thinking modes (none, medium, deep, ultra) for complex problem-solving
+- 📝 **Planning Modes** - Four planning levels: skip (direct implementation), lite (quick plan), spec (task breakdown), full (phased execution)
+- ✅ **Plan Approval** - Review and approve AI-generated plans before implementation begins
+- 📊 **Multi-Agent Task Execution** - Spec mode spawns dedicated agents per task for focused implementation
+
+### Project Management
+
+- 🔍 **Project Analysis** - AI-powered codebase analysis to understand your project structure
+- 💡 **Feature Suggestions** - AI-generated feature suggestions based on project analysis
+- 📁 **Context Management** - Add markdown, images, and documentation files that agents automatically reference
+- 🔗 **Dependency Blocking** - Features can depend on other features, enforcing execution order
+- 🌳 **Graph View** - Visualize feature dependencies with interactive graph visualization
+- 📋 **GitHub Integration** - Import issues, validate feasibility, and convert to tasks automatically
+
+### Collaboration & Review
+
+- 🧪 **Verification Workflow** - Features move to "Waiting Approval" for review and testing
+- 💬 **Agent Chat** - Interactive chat sessions with AI agents for exploratory work
+- 👤 **AI Profiles** - Create custom agent configurations with different prompts, models, and settings
+- 📜 **Session History** - Persistent chat sessions across restarts with full conversation history
+- 🔍 **Git Diff Viewer** - Review changes made by agents before approving
+
+### Developer Tools
+
+- 🖥️ **Integrated Terminal** - Full terminal access with tabs, splits, and persistent sessions
+- 🖼️ **Image Support** - Attach screenshots and diagrams to feature descriptions for visual context
+- ⚡ **Concurrent Execution** - Configure how many features can run simultaneously (default: 3)
+- ⌨️ **Keyboard Shortcuts** - Fully customizable shortcuts for navigation and actions
+- 🎨 **Theme System** - 25+ themes including Dark, Light, Dracula, Nord, Catppuccin, and more
+- 🖥️ **Cross-Platform** - Desktop app for macOS (x64, arm64), Windows (x64), and Linux (x64)
+- 🌐 **Web Mode** - Run in browser or as Electron desktop app
+
+### Advanced Features
+
+- 🔐 **Docker Isolation** - Security-focused Docker deployment with no host filesystem access
+- 🎯 **Worktree Management** - Create, switch, commit, and create PRs from worktrees
+- 📊 **Usage Tracking** - Monitor Claude API usage with detailed metrics
+- 🔊 **Audio Notifications** - Optional completion sounds (mutable in settings)
+- 💾 **Auto-save** - All work automatically persisted to `.automaker/` directory
 
 ## Tech Stack
 
-- [Next.js](https://nextjs.org) - React framework
-- [Electron](https://www.electronjs.org/) - Desktop application framework
-- [Tailwind CSS](https://tailwindcss.com/) - Styling
-- [Zustand](https://zustand-demo.pmnd.rs/) - State management
-- [dnd-kit](https://dndkit.com/) - Drag and drop functionality
+### Frontend
+
+- **React 19** - UI framework
+- **Vite 7** - Build tool and development server
+- **Electron 39** - Desktop application framework
+- **TypeScript 5.9** - Type safety
+- **TanStack Router** - File-based routing
+- **Zustand 5** - State management with persistence
+- **Tailwind CSS 4** - Utility-first styling with 25+ themes
+- **Radix UI** - Accessible component primitives
+- **dnd-kit** - Drag and drop for Kanban board
+- **@xyflow/react** - Graph visualization for dependencies
+- **xterm.js** - Integrated terminal emulator
+- **CodeMirror 6** - Code editor for XML/syntax highlighting
+- **Lucide Icons** - Icon library
+
+### Backend
+
+- **Node.js** - JavaScript runtime with ES modules
+- **Express 5** - HTTP server framework
+- **TypeScript 5.9** - Type safety
+- **Claude Agent SDK** - AI agent integration (@anthropic-ai/claude-agent-sdk)
+- **WebSocket (ws)** - Real-time event streaming
+- **node-pty** - PTY terminal sessions
+
+### Testing & Quality
+
+- **Playwright** - End-to-end testing
+- **Vitest** - Unit testing framework
+- **ESLint 9** - Code linting
+- **Prettier 3** - Code formatting
+- **Husky** - Git hooks for pre-commit formatting
+
+### Shared Libraries
+
+- **@automaker/types** - Shared TypeScript definitions
+- **@automaker/utils** - Logging, error handling, image processing
+- **@automaker/prompts** - AI prompt templates
+- **@automaker/platform** - Path management and security
+- **@automaker/model-resolver** - Claude model alias resolution
+- **@automaker/dependency-resolver** - Feature dependency ordering
+- **@automaker/git-utils** - Git operations and worktree management
+
+## Available Views
+
+Automaker provides several specialized views accessible via the sidebar or keyboard shortcuts:
+
+| View               | Shortcut | Description                                                                                      |
+| ------------------ | -------- | ------------------------------------------------------------------------------------------------ |
+| **Board**          | `K`      | Kanban board for managing feature workflow (Backlog → In Progress → Waiting Approval → Verified) |
+| **Agent**          | `A`      | Interactive chat sessions with AI agents for exploratory work and questions                      |
+| **Spec**           | `D`      | Project specification editor with AI-powered generation and feature suggestions                  |
+| **Context**        | `C`      | Manage context files (markdown, images) that AI agents automatically reference                   |
+| **Profiles**       | `M`      | Create and manage AI agent profiles with custom prompts and configurations                       |
+| **Settings**       | `S`      | Configure themes, shortcuts, defaults, authentication, and more                                  |
+| **Terminal**       | `T`      | Integrated terminal with tabs, splits, and persistent sessions                                   |
+| **GitHub Issues**  | -        | Import and validate GitHub issues, convert to tasks                                              |
+| **Running Agents** | -        | View all active agents across projects with status and progress                                  |
+
+### Keyboard Navigation
+
+All shortcuts are customizable in Settings. Default shortcuts:
+
+- **Navigation:** `K` (Board), `A` (Agent), `D` (Spec), `C` (Context), `S` (Settings), `M` (Profiles), `T` (Terminal)
+- **UI:** `` ` `` (Toggle sidebar)
+- **Actions:** `N` (New item in current view), `G` (Start next features), `O` (Open project), `P` (Project picker)
+- **Projects:** `Q`/`E` (Cycle previous/next project)
+
+## Architecture
+
+### Monorepo Structure
+
+Automaker is built as an npm workspace monorepo with two main applications and seven shared packages:
+
+```text
+automaker/
+├── apps/
+│   ├── ui/          # React + Vite + Electron frontend
+│   └── server/      # Express + WebSocket backend
+└── libs/            # Shared packages
+    ├── types/                  # Core TypeScript definitions
+    ├── utils/                  # Logging, errors, utilities
+    ├── prompts/                # AI prompt templates
+    ├── platform/               # Path management, security
+    ├── model-resolver/         # Claude model aliasing
+    ├── dependency-resolver/    # Feature dependency ordering
+    └── git-utils/              # Git operations & worktree management
+```
+
+### How It Works
+
+1. **Feature Definition** - Users create feature cards on the Kanban board with descriptions, images, and configuration
+2. **Git Worktree Creation** - When a feature starts, a git worktree is created for isolated development
+3. **Agent Execution** - Claude Agent SDK executes in the worktree with full file system and command access
+4. **Real-time Streaming** - Agent output streams via WebSocket to the frontend for live monitoring
+5. **Plan Approval** (optional) - For spec/full planning modes, agents generate plans that require user approval
+6. **Multi-Agent Tasks** (spec mode) - Each task in the spec gets a dedicated agent for focused implementation
+7. **Verification** - Features move to "Waiting Approval" where changes can be reviewed via git diff
+8. **Integration** - After approval, changes can be committed and PRs created from the worktree
+
+### Key Architectural Patterns
+
+- **Event-Driven Architecture** - All server operations emit events that stream to the frontend
+- **Provider Pattern** - Extensible AI provider system (currently Claude, designed for future providers)
+- **Service-Oriented Backend** - Modular services for agent management, features, terminals, settings
+- **State Management** - Zustand with persistence for frontend state across restarts
+- **File-Based Storage** - No database; features stored as JSON files in `.automaker/` directory
+
+### Security & Isolation
+
+- **Git Worktrees** - Each feature executes in an isolated git worktree, protecting your main branch
+- **Path Sandboxing** - Optional `ALLOWED_ROOT_DIRECTORY` restricts file access
+- **Docker Isolation** - Recommended deployment uses Docker with no host filesystem access
+- **Plan Approval** - Optional plan review before implementation prevents unwanted changes
+
+### Data Storage
+
+Automaker uses a file-based storage system (no database required):
+
+#### Per-Project Data
+
+Stored in `{projectPath}/.automaker/`:
+
+```text
+.automaker/
+├── features/              # Feature JSON files and images
+│   └── {featureId}/
+│       ├── feature.json   # Feature metadata
+│       ├── agent-output.md # AI agent output log
+│       └── images/        # Attached images
+├── context/               # Context files for AI agents
+├── settings.json          # Project-specific settings
+├── spec.md               # Project specification
+├── analysis.json         # Project structure analysis
+└── feature-suggestions.json # AI-generated suggestions
+```
+
+#### Global Data
+
+Stored in `DATA_DIR` (default `./data`):
+
+```text
+data/
+├── settings.json          # Global settings, profiles, shortcuts
+├── credentials.json       # API keys (encrypted)
+├── sessions-metadata.json # Chat session metadata
+└── agent-sessions/        # Conversation histories
+    └── {sessionId}.json
+```
+
+---
+
+> **[!CAUTION]**
+>
+> ## Security Disclaimer
+>
+> **This software uses AI-powered tooling that has access to your operating system and can read, modify, and delete files. Use at your own risk.**
+>
+> We have reviewed this codebase for security vulnerabilities, but you assume all risk when running this software. You should review the code yourself before running it.
+>
+> **We do not recommend running Automaker directly on your local computer** due to the risk of AI agents having access to your entire file system. Please sandbox this application using Docker or a virtual machine.
+>
+> **[Read the full disclaimer](./DISCLAIMER.md)**
+
+---
 
 ## Learn More
 
-To learn more about Next.js, take a look at the following resources:
+### Documentation
 
-- [Next.js Documentation](https://nextjs.org/docs) - learn about Next.js features and API.
-- [Learn Next.js](https://nextjs.org/learn) - an interactive Next.js tutorial.
+- [Contributing Guide](./CONTRIBUTING.md) - How to contribute to Automaker
+- [Project Documentation](./docs/) - Architecture guides, patterns, and developer docs
+- [Docker Isolation Guide](./docs/docker-isolation.md) - Security-focused Docker deployment
+- [Shared Packages Guide](./docs/llm-shared-packages.md) - Using monorepo packages
+
+### Community
+
+Join the **Agentic Jumpstart** Discord to connect with other builders exploring **agentic coding**:
+
+👉 [Agentic Jumpstart Discord](https://discord.gg/jjem7aEDKU)
 
 ## License
 

apps/app/server-bundle/package.json

@@ -1,15 +0,0 @@
-{
-  "name": "@automaker/server-bundle",
-  "version": "0.1.0",
-  "type": "module",
-  "main": "dist/index.js",
-  "dependencies": {
-    "@anthropic-ai/claude-agent-sdk": "^0.1.61",
-    "cors": "^2.8.5",
-    "dotenv": "^17.2.3",
-    "express": "^5.1.0",
-    "morgan": "^1.10.1",
-    "node-pty": "1.1.0-beta41",
-    "ws": "^8.18.0"
-  }
-}

apps/server/.env.example

@@ -24,7 +24,7 @@ ALLOWED_ROOT_DIRECTORY=
 
 # CORS origin - which domains can access the API
 # Use "*" for development, set specific origin for production
-CORS_ORIGIN=*
+CORS_ORIGIN=http://localhost:3007
 
 # ============================================
 # OPTIONAL - Server

apps/server/Dockerfile

@@ -1,67 +0,0 @@
-# Automaker Backend Server
-# Multi-stage build for minimal production image
-
-# Build stage
-FROM node:20-alpine AS builder
-
-# Install build dependencies for native modules (node-pty)
-RUN apk add --no-cache python3 make g++
-
-WORKDIR /app
-
-# Copy package files and scripts needed for postinstall
-COPY package*.json ./
-COPY apps/server/package*.json ./apps/server/
-COPY scripts ./scripts
-
-# Install dependencies
-RUN npm ci --workspace=apps/server
-
-# Copy source
-COPY apps/server ./apps/server
-
-# Build TypeScript
-RUN npm run build --workspace=apps/server
-
-# Production stage
-FROM node:20-alpine
-
-# Install git, curl, and GitHub CLI (pinned version for reproducible builds)
-RUN apk add --no-cache git curl && \
-    GH_VERSION="2.63.2" && \
-    curl -L "https://github.com/cli/cli/releases/download/v${GH_VERSION}/gh_${GH_VERSION}_linux_amd64.tar.gz" -o gh.tar.gz && \
-    tar -xzf gh.tar.gz && \
-    mv "gh_${GH_VERSION}_linux_amd64/bin/gh" /usr/local/bin/gh && \
-    rm -rf gh.tar.gz "gh_${GH_VERSION}_linux_amd64"
-
-WORKDIR /app
-
-# Create non-root user
-RUN addgroup -g 1001 -S automaker && \
-    adduser -S automaker -u 1001
-
-# Copy built files and production dependencies
-COPY --from=builder /app/apps/server/dist ./dist
-COPY --from=builder /app/apps/server/package*.json ./
-COPY --from=builder /app/node_modules ./node_modules
-
-# Create data directory
-RUN mkdir -p /data && chown automaker:automaker /data
-
-# Switch to non-root user
-USER automaker
-
-# Environment variables
-ENV NODE_ENV=production
-ENV PORT=3008
-ENV DATA_DIR=/data
-
-# Expose port
-EXPOSE 3008
-
-# Health check
-HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
-    CMD wget --no-verbose --tries=1 --spider http://localhost:3008/api/health || exit 1
-
-# Start server
-CMD ["node", "dist/index.js"]

apps/server/package.json

@@ -1,14 +1,18 @@
 {
   "name": "@automaker/server",
-  "version": "0.1.0",
+  "version": "0.7.3",
   "description": "Backend server for Automaker - provides API for both web and Electron modes",
   "author": "AutoMaker Team",
   "license": "SEE LICENSE IN LICENSE",
   "private": true,
+  "engines": {
+    "node": ">=22.0.0 <23.0.0"
+  },
   "type": "module",
   "main": "dist/index.js",
   "scripts": {
     "dev": "tsx watch src/index.ts",
+    "dev:test": "tsx src/index.ts",
     "build": "tsc",
     "start": "node dist/index.js",
     "lint": "eslint src/",
@@ -20,31 +24,35 @@
     "test:unit": "vitest run tests/unit"
   },
   "dependencies": {
-    "@anthropic-ai/claude-agent-sdk": "^0.1.72",
-    "@automaker/dependency-resolver": "^1.0.0",
-    "@automaker/git-utils": "^1.0.0",
-    "@automaker/model-resolver": "^1.0.0",
-    "@automaker/platform": "^1.0.0",
-    "@automaker/prompts": "^1.0.0",
-    "@automaker/types": "^1.0.0",
-    "@automaker/utils": "^1.0.0",
-    "cors": "^2.8.5",
-    "dotenv": "^17.2.3",
-    "express": "^5.2.1",
-    "morgan": "^1.10.1",
+    "@anthropic-ai/claude-agent-sdk": "0.1.76",
+    "@automaker/dependency-resolver": "1.0.0",
+    "@automaker/git-utils": "1.0.0",
+    "@automaker/model-resolver": "1.0.0",
+    "@automaker/platform": "1.0.0",
+    "@automaker/prompts": "1.0.0",
+    "@automaker/types": "1.0.0",
+    "@automaker/utils": "1.0.0",
+    "@modelcontextprotocol/sdk": "1.25.1",
+    "cookie-parser": "1.4.7",
+    "cors": "2.8.5",
+    "dotenv": "17.2.3",
+    "express": "5.2.1",
+    "morgan": "1.10.1",
     "node-pty": "1.1.0-beta41",
-    "ws": "^8.18.3"
+    "ws": "8.18.3"
   },
   "devDependencies": {
-    "@types/cors": "^2.8.19",
-    "@types/express": "^5.0.6",
-    "@types/morgan": "^1.9.10",
-    "@types/node": "^22",
-    "@types/ws": "^8.18.1",
-    "@vitest/coverage-v8": "^4.0.16",
-    "@vitest/ui": "^4.0.16",
-    "tsx": "^4.21.0",
-    "typescript": "^5",
-    "vitest": "^4.0.16"
+    "@types/cookie": "0.6.0",
+    "@types/cookie-parser": "1.4.10",
+    "@types/cors": "2.8.19",
+    "@types/express": "5.0.6",
+    "@types/morgan": "1.9.10",
+    "@types/node": "22.19.3",
+    "@types/ws": "8.18.1",
+    "@vitest/coverage-v8": "4.0.16",
+    "@vitest/ui": "4.0.16",
+    "tsx": "4.21.0",
+    "typescript": "5.9.3",
+    "vitest": "4.0.16"
   }
 }

apps/server/src/index.ts

@@ -9,15 +9,19 @@
 import express from 'express';
 import cors from 'cors';
 import morgan from 'morgan';
+import cookieParser from 'cookie-parser';
+import cookie from 'cookie';
 import { WebSocketServer, WebSocket } from 'ws';
 import { createServer } from 'http';
 import dotenv from 'dotenv';
 
 import { createEventEmitter, type EventEmitter } from './lib/events.js';
 import { initAllowedPaths } from '@automaker/platform';
-import { authMiddleware, getAuthStatus } from './lib/auth.js';
+import { authMiddleware, validateWsConnectionToken, checkRawAuthentication } from './lib/auth.js';
+import { requireJsonContentType } from './middleware/require-json-content-type.js';
+import { createAuthRoutes } from './routes/auth/index.js';
 import { createFsRoutes } from './routes/fs/index.js';
-import { createHealthRoutes } from './routes/health/index.js';
+import { createHealthRoutes, createDetailedHandler } from './routes/health/index.js';
 import { createAgentRoutes } from './routes/agent/index.js';
 import { createSessionsRoutes } from './routes/sessions/index.js';
 import { createFeaturesRoutes } from './routes/features/index.js';
@@ -48,6 +52,12 @@ import { createClaudeRoutes } from './routes/claude/index.js';
 import { ClaudeUsageService } from './services/claude-usage-service.js';
 import { createGitHubRoutes } from './routes/github/index.js';
 import { createContextRoutes } from './routes/context/index.js';
+import { createBacklogPlanRoutes } from './routes/backlog-plan/index.js';
+import { cleanupStaleValidations } from './routes/github/routes/validation-common.js';
+import { createMCPRoutes } from './routes/mcp/index.js';
+import { MCPTestService } from './services/mcp-test-service.js';
+import { createPipelineRoutes } from './routes/pipeline/index.js';
+import { pipelineService } from './services/pipeline-service.js';
 
 // Load environment variables
 dotenv.config();
@@ -85,7 +95,7 @@ const app = express();
 // Middleware
 // Custom colored logger showing only endpoint and status code (configurable via ENABLE_REQUEST_LOGGING env var)
 if (ENABLE_REQUEST_LOGGING) {
-  morgan.token('status-colored', (req, res) => {
+  morgan.token('status-colored', (_req, res) => {
     const status = res.statusCode;
     if (status >= 500) return `\x1b[31m${status}\x1b[0m`; // Red for server errors
     if (status >= 400) return `\x1b[33m${status}\x1b[0m`; // Yellow for client errors
@@ -99,23 +109,59 @@ if (ENABLE_REQUEST_LOGGING) {
     })
   );
 }
+// CORS configuration
+// When using credentials (cookies), origin cannot be '*'
+// We dynamically allow the requesting origin for local development
 app.use(
   cors({
-    origin: process.env.CORS_ORIGIN || '*',
+    origin: (origin, callback) => {
+      // Allow requests with no origin (like mobile apps, curl, Electron)
+      if (!origin) {
+        callback(null, true);
+        return;
+      }
+
+      // If CORS_ORIGIN is set, use it (can be comma-separated list)
+      const allowedOrigins = process.env.CORS_ORIGIN?.split(',').map((o) => o.trim());
+      if (allowedOrigins && allowedOrigins.length > 0 && allowedOrigins[0] !== '*') {
+        if (allowedOrigins.includes(origin)) {
+          callback(null, origin);
+        } else {
+          callback(new Error('Not allowed by CORS'));
+        }
+        return;
+      }
+
+      // For local development, allow localhost origins
+      if (
+        origin.startsWith('http://localhost:') ||
+        origin.startsWith('http://127.0.0.1:') ||
+        origin.startsWith('http://[::1]:')
+      ) {
+        callback(null, origin);
+        return;
+      }
+
+      // Reject other origins by default for security
+      callback(new Error('Not allowed by CORS'));
+    },
     credentials: true,
   })
 );
 app.use(express.json({ limit: '50mb' }));
+app.use(cookieParser());
 
 // Create shared event emitter for streaming
 const events: EventEmitter = createEventEmitter();
 
 // Create services
-const agentService = new AgentService(DATA_DIR, events);
-const featureLoader = new FeatureLoader();
-const autoModeService = new AutoModeService(events);
+// Note: settingsService is created first so it can be injected into other services
 const settingsService = new SettingsService(DATA_DIR);
+const agentService = new AgentService(DATA_DIR, events, settingsService);
+const featureLoader = new FeatureLoader();
+const autoModeService = new AutoModeService(events, settingsService);
 const claudeUsageService = new ClaudeUsageService();
+const mcpTestService = new MCPTestService(settingsService);
 
 // Initialize services
 (async () => {
@@ -123,32 +169,52 @@ const claudeUsageService = new ClaudeUsageService();
   console.log('[Server] Agent service initialized');
 })();
 
-// Mount API routes - health is unauthenticated for monitoring
+// Run stale validation cleanup every hour to prevent memory leaks from crashed validations
+const VALIDATION_CLEANUP_INTERVAL_MS = 60 * 60 * 1000; // 1 hour
+setInterval(() => {
+  const cleaned = cleanupStaleValidations();
+  if (cleaned > 0) {
+    console.log(`[Server] Cleaned up ${cleaned} stale validation entries`);
+  }
+}, VALIDATION_CLEANUP_INTERVAL_MS);
+
+// Require Content-Type: application/json for all API POST/PUT/PATCH requests
+// This helps prevent CSRF and content-type confusion attacks
+app.use('/api', requireJsonContentType);
+
+// Mount API routes - health and auth are unauthenticated
 app.use('/api/health', createHealthRoutes());
+app.use('/api/auth', createAuthRoutes());
 
 // Apply authentication to all other routes
 app.use('/api', authMiddleware);
 
+// Protected health endpoint with detailed info
+app.get('/api/health/detailed', createDetailedHandler());
+
 app.use('/api/fs', createFsRoutes(events));
 app.use('/api/agent', createAgentRoutes(agentService, events));
 app.use('/api/sessions', createSessionsRoutes(agentService));
 app.use('/api/features', createFeaturesRoutes(featureLoader));
 app.use('/api/auto-mode', createAutoModeRoutes(autoModeService));
-app.use('/api/enhance-prompt', createEnhancePromptRoutes());
+app.use('/api/enhance-prompt', createEnhancePromptRoutes(settingsService));
 app.use('/api/worktree', createWorktreeRoutes());
 app.use('/api/git', createGitRoutes());
 app.use('/api/setup', createSetupRoutes());
-app.use('/api/suggestions', createSuggestionsRoutes(events));
+app.use('/api/suggestions', createSuggestionsRoutes(events, settingsService));
 app.use('/api/models', createModelsRoutes());
-app.use('/api/spec-regeneration', createSpecRegenerationRoutes(events));
+app.use('/api/spec-regeneration', createSpecRegenerationRoutes(events, settingsService));
 app.use('/api/running-agents', createRunningAgentsRoutes(autoModeService));
 app.use('/api/workspace', createWorkspaceRoutes());
 app.use('/api/templates', createTemplatesRoutes());
 app.use('/api/terminal', createTerminalRoutes());
 app.use('/api/settings', createSettingsRoutes(settingsService));
 app.use('/api/claude', createClaudeRoutes(claudeUsageService));
-app.use('/api/github', createGitHubRoutes());
-app.use('/api/context', createContextRoutes());
+app.use('/api/github', createGitHubRoutes(events, settingsService));
+app.use('/api/context', createContextRoutes(settingsService));
+app.use('/api/backlog-plan', createBacklogPlanRoutes(events, settingsService));
+app.use('/api/mcp', createMCPRoutes(mcpTestService));
+app.use('/api/pipeline', createPipelineRoutes(pipelineService));
 
 // Create HTTP server
 const server = createServer(app);
@@ -158,10 +224,55 @@ const wss = new WebSocketServer({ noServer: true });
 const terminalWss = new WebSocketServer({ noServer: true });
 const terminalService = getTerminalService();
 
+/**
+ * Authenticate WebSocket upgrade requests
+ * Checks for API key in header/query, session token in header/query, OR valid session cookie
+ */
+function authenticateWebSocket(request: import('http').IncomingMessage): boolean {
+  const url = new URL(request.url || '', `http://${request.headers.host}`);
+
+  // Convert URL search params to query object
+  const query: Record<string, string | undefined> = {};
+  url.searchParams.forEach((value, key) => {
+    query[key] = value;
+  });
+
+  // Parse cookies from header
+  const cookieHeader = request.headers.cookie;
+  const cookies = cookieHeader ? cookie.parse(cookieHeader) : {};
+
+  // Use shared authentication logic for standard auth methods
+  if (
+    checkRawAuthentication(
+      request.headers as Record<string, string | string[] | undefined>,
+      query,
+      cookies
+    )
+  ) {
+    return true;
+  }
+
+  // Additionally check for short-lived WebSocket connection token (WebSocket-specific)
+  const wsToken = url.searchParams.get('wsToken');
+  if (wsToken && validateWsConnectionToken(wsToken)) {
+    return true;
+  }
+
+  return false;
+}
+
 // Handle HTTP upgrade requests manually to route to correct WebSocket server
 server.on('upgrade', (request, socket, head) => {
   const { pathname } = new URL(request.url || '', `http://${request.headers.host}`);
 
+  // Authenticate all WebSocket connections
+  if (!authenticateWebSocket(request)) {
+    console.log('[WebSocket] Authentication failed, rejecting connection');
+    socket.write('HTTP/1.1 401 Unauthorized\r\n\r\n');
+    socket.destroy();
+    return;
+  }
+
   if (pathname === '/api/events') {
     wss.handleUpgrade(request, socket, head, (ws) => {
       wss.emit('connection', ws, request);
@@ -177,12 +288,31 @@ server.on('upgrade', (request, socket, head) => {
 
 // Events WebSocket connection handler
 wss.on('connection', (ws: WebSocket) => {
-  console.log('[WebSocket] Client connected');
+  console.log('[WebSocket] Client connected, ready state:', ws.readyState);
 
   // Subscribe to all events and forward to this client
   const unsubscribe = events.subscribe((type, payload) => {
+    console.log('[WebSocket] Event received:', {
+      type,
+      hasPayload: !!payload,
+      payloadKeys: payload ? Object.keys(payload) : [],
+      wsReadyState: ws.readyState,
+      wsOpen: ws.readyState === WebSocket.OPEN,
+    });
+
     if (ws.readyState === WebSocket.OPEN) {
-      ws.send(JSON.stringify({ type, payload }));
+      const message = JSON.stringify({ type, payload });
+      console.log('[WebSocket] Sending event to client:', {
+        type,
+        messageLength: message.length,
+        sessionId: (payload as any)?.sessionId,
+      });
+      ws.send(message);
+    } else {
+      console.log(
+        '[WebSocket] WARNING: Cannot send event, WebSocket not open. ReadyState:',
+        ws.readyState
+      );
     }
   });
 
@@ -192,7 +322,7 @@ wss.on('connection', (ws: WebSocket) => {
   });
 
   ws.on('error', (error) => {
-    console.error('[WebSocket] Error:', error);
+    console.error('[WebSocket] ERROR:', error);
     unsubscribe();
   });
 });

apps/server/src/lib/auth.ts

@@ -1,54 +1,378 @@
 /**
  * Authentication middleware for API security
  *
- * Supports API key authentication via header or environment variable.
+ * Supports two authentication methods:
+ * 1. Header-based (X-API-Key) - Used by Electron mode
+ * 2. Cookie-based (HTTP-only session cookie) - Used by web mode
+ *
+ * Auto-generates an API key on first run if none is configured.
  */
 
 import type { Request, Response, NextFunction } from 'express';
+import crypto from 'crypto';
+import path from 'path';
+import * as secureFs from './secure-fs.js';
 
-// API key from environment (optional - if not set, auth is disabled)
-const API_KEY = process.env.AUTOMAKER_API_KEY;
+const DATA_DIR = process.env.DATA_DIR || './data';
+const API_KEY_FILE = path.join(DATA_DIR, '.api-key');
+const SESSIONS_FILE = path.join(DATA_DIR, '.sessions');
+const SESSION_COOKIE_NAME = 'automaker_session';
+const SESSION_MAX_AGE_MS = 30 * 24 * 60 * 60 * 1000; // 30 days
+const WS_TOKEN_MAX_AGE_MS = 5 * 60 * 1000; // 5 minutes for WebSocket connection tokens
+
+// Session store - persisted to file for survival across server restarts
+const validSessions = new Map<string, { createdAt: number; expiresAt: number }>();
+
+// Short-lived WebSocket connection tokens (in-memory only, not persisted)
+const wsConnectionTokens = new Map<string, { createdAt: number; expiresAt: number }>();
+
+// Clean up expired WebSocket tokens periodically
+setInterval(() => {
+  const now = Date.now();
+  wsConnectionTokens.forEach((data, token) => {
+    if (data.expiresAt <= now) {
+      wsConnectionTokens.delete(token);
+    }
+  });
+}, 60 * 1000); // Clean up every minute
+
+/**
+ * Load sessions from file on startup
+ */
+function loadSessions(): void {
+  try {
+    if (secureFs.existsSync(SESSIONS_FILE)) {
+      const data = secureFs.readFileSync(SESSIONS_FILE, 'utf-8') as string;
+      const sessions = JSON.parse(data) as Array<
+        [string, { createdAt: number; expiresAt: number }]
+      >;
+      const now = Date.now();
+      let loadedCount = 0;
+      let expiredCount = 0;
+
+      for (const [token, session] of sessions) {
+        // Only load non-expired sessions
+        if (session.expiresAt > now) {
+          validSessions.set(token, session);
+          loadedCount++;
+        } else {
+          expiredCount++;
+        }
+      }
+
+      if (loadedCount > 0 || expiredCount > 0) {
+        console.log(`[Auth] Loaded ${loadedCount} sessions (${expiredCount} expired)`);
+      }
+    }
+  } catch (error) {
+    console.warn('[Auth] Error loading sessions:', error);
+  }
+}
+
+/**
+ * Save sessions to file (async)
+ */
+async function saveSessions(): Promise<void> {
+  try {
+    await secureFs.mkdir(path.dirname(SESSIONS_FILE), { recursive: true });
+    const sessions = Array.from(validSessions.entries());
+    await secureFs.writeFile(SESSIONS_FILE, JSON.stringify(sessions), {
+      encoding: 'utf-8',
+      mode: 0o600,
+    });
+  } catch (error) {
+    console.error('[Auth] Failed to save sessions:', error);
+  }
+}
+
+// Load existing sessions on startup
+loadSessions();
+
+/**
+ * Ensure an API key exists - either from env var, file, or generate new one.
+ * This provides CSRF protection by requiring a secret key for all API requests.
+ */
+function ensureApiKey(): string {
+  // First check environment variable (Electron passes it this way)
+  if (process.env.AUTOMAKER_API_KEY) {
+    console.log('[Auth] Using API key from environment variable');
+    return process.env.AUTOMAKER_API_KEY;
+  }
+
+  // Try to read from file
+  try {
+    if (secureFs.existsSync(API_KEY_FILE)) {
+      const key = (secureFs.readFileSync(API_KEY_FILE, 'utf-8') as string).trim();
+      if (key) {
+        console.log('[Auth] Loaded API key from file');
+        return key;
+      }
+    }
+  } catch (error) {
+    console.warn('[Auth] Error reading API key file:', error);
+  }
+
+  // Generate new key
+  const newKey = crypto.randomUUID();
+  try {
+    secureFs.mkdirSync(path.dirname(API_KEY_FILE), { recursive: true });
+    secureFs.writeFileSync(API_KEY_FILE, newKey, { encoding: 'utf-8', mode: 0o600 });
+    console.log('[Auth] Generated new API key');
+  } catch (error) {
+    console.error('[Auth] Failed to save API key:', error);
+  }
+  return newKey;
+}
+
+// API key - always generated/loaded on startup for CSRF protection
+const API_KEY = ensureApiKey();
+
+// Print API key to console for web mode users (unless suppressed for production logging)
+if (process.env.AUTOMAKER_HIDE_API_KEY !== 'true') {
+  console.log(`
+╔═══════════════════════════════════════════════════════════════════════╗
+║  🔐 API Key for Web Mode Authentication                               ║
+╠═══════════════════════════════════════════════════════════════════════╣
+║                                                                       ║
+║  When accessing via browser, you'll be prompted to enter this key:    ║
+║                                                                       ║
+║    ${API_KEY}
+║                                                                       ║
+║  In Electron mode, authentication is handled automatically.          ║
+╚═══════════════════════════════════════════════════════════════════════╝
+`);
+} else {
+  console.log('[Auth] API key banner hidden (AUTOMAKER_HIDE_API_KEY=true)');
+}
+
+/**
+ * Generate a cryptographically secure session token
+ */
+function generateSessionToken(): string {
+  return crypto.randomBytes(32).toString('hex');
+}
+
+/**
+ * Create a new session and return the token
+ */
+export async function createSession(): Promise<string> {
+  const token = generateSessionToken();
+  const now = Date.now();
+  validSessions.set(token, {
+    createdAt: now,
+    expiresAt: now + SESSION_MAX_AGE_MS,
+  });
+  await saveSessions(); // Persist to file
+  return token;
+}
+
+/**
+ * Validate a session token
+ * Note: This returns synchronously but triggers async persistence if session expired
+ */
+export function validateSession(token: string): boolean {
+  const session = validSessions.get(token);
+  if (!session) return false;
+
+  if (Date.now() > session.expiresAt) {
+    validSessions.delete(token);
+    // Fire-and-forget: persist removal asynchronously
+    saveSessions().catch((err) => console.error('[Auth] Error saving sessions:', err));
+    return false;
+  }
+
+  return true;
+}
+
+/**
+ * Invalidate a session token
+ */
+export async function invalidateSession(token: string): Promise<void> {
+  validSessions.delete(token);
+  await saveSessions(); // Persist removal
+}
+
+/**
+ * Create a short-lived WebSocket connection token
+ * Used for initial WebSocket handshake authentication
+ */
+export function createWsConnectionToken(): string {
+  const token = generateSessionToken();
+  const now = Date.now();
+  wsConnectionTokens.set(token, {
+    createdAt: now,
+    expiresAt: now + WS_TOKEN_MAX_AGE_MS,
+  });
+  return token;
+}
+
+/**
+ * Validate a WebSocket connection token
+ * These tokens are single-use and short-lived (5 minutes)
+ * Token is invalidated immediately after first successful use
+ */
+export function validateWsConnectionToken(token: string): boolean {
+  const tokenData = wsConnectionTokens.get(token);
+  if (!tokenData) return false;
+
+  // Always delete the token (single-use)
+  wsConnectionTokens.delete(token);
+
+  // Check if expired
+  if (Date.now() > tokenData.expiresAt) {
+    return false;
+  }
+
+  return true;
+}
+
+/**
+ * Validate the API key using timing-safe comparison
+ * Prevents timing attacks that could leak information about the key
+ */
+export function validateApiKey(key: string): boolean {
+  if (!key || typeof key !== 'string') return false;
+
+  // Both buffers must be the same length for timingSafeEqual
+  const keyBuffer = Buffer.from(key);
+  const apiKeyBuffer = Buffer.from(API_KEY);
+
+  // If lengths differ, compare against a dummy to maintain constant time
+  if (keyBuffer.length !== apiKeyBuffer.length) {
+    crypto.timingSafeEqual(apiKeyBuffer, apiKeyBuffer);
+    return false;
+  }
+
+  return crypto.timingSafeEqual(keyBuffer, apiKeyBuffer);
+}
+
+/**
+ * Get session cookie options
+ */
+export function getSessionCookieOptions(): {
+  httpOnly: boolean;
+  secure: boolean;
+  sameSite: 'strict' | 'lax' | 'none';
+  maxAge: number;
+  path: string;
+} {
+  return {
+    httpOnly: true, // JavaScript cannot access this cookie
+    secure: process.env.NODE_ENV === 'production', // HTTPS only in production
+    sameSite: 'strict', // Only sent for same-site requests (CSRF protection)
+    maxAge: SESSION_MAX_AGE_MS,
+    path: '/',
+  };
+}
+
+/**
+ * Get the session cookie name
+ */
+export function getSessionCookieName(): string {
+  return SESSION_COOKIE_NAME;
+}
+
+/**
+ * Authentication result type
+ */
+type AuthResult =
+  | { authenticated: true }
+  | { authenticated: false; errorType: 'invalid_api_key' | 'invalid_session' | 'no_auth' };
+
+/**
+ * Core authentication check - shared between middleware and status check
+ * Extracts auth credentials from various sources and validates them
+ */
+function checkAuthentication(
+  headers: Record<string, string | string[] | undefined>,
+  query: Record<string, string | undefined>,
+  cookies: Record<string, string | undefined>
+): AuthResult {
+  // Check for API key in header (Electron mode)
+  const headerKey = headers['x-api-key'] as string | undefined;
+  if (headerKey) {
+    if (validateApiKey(headerKey)) {
+      return { authenticated: true };
+    }
+    return { authenticated: false, errorType: 'invalid_api_key' };
+  }
+
+  // Check for session token in header (web mode with explicit token)
+  const sessionTokenHeader = headers['x-session-token'] as string | undefined;
+  if (sessionTokenHeader) {
+    if (validateSession(sessionTokenHeader)) {
+      return { authenticated: true };
+    }
+    return { authenticated: false, errorType: 'invalid_session' };
+  }
+
+  // Check for API key in query parameter (fallback)
+  const queryKey = query.apiKey;
+  if (queryKey) {
+    if (validateApiKey(queryKey)) {
+      return { authenticated: true };
+    }
+    return { authenticated: false, errorType: 'invalid_api_key' };
+  }
+
+  // Check for session cookie (web mode)
+  const sessionToken = cookies[SESSION_COOKIE_NAME];
+  if (sessionToken && validateSession(sessionToken)) {
+    return { authenticated: true };
+  }
+
+  return { authenticated: false, errorType: 'no_auth' };
+}
 
 /**
  * Authentication middleware
  *
- * If AUTOMAKER_API_KEY is set, requires matching key in X-API-Key header.
- * If not set, allows all requests (development mode).
+ * Accepts either:
+ * 1. X-API-Key header (for Electron mode)
+ * 2. X-Session-Token header (for web mode with explicit token)
+ * 3. apiKey query parameter (fallback for cases where headers can't be set)
+ * 4. Session cookie (for web mode)
  */
 export function authMiddleware(req: Request, res: Response, next: NextFunction): void {
-  // If no API key is configured, allow all requests
-  if (!API_KEY) {
+  const result = checkAuthentication(
+    req.headers as Record<string, string | string[] | undefined>,
+    req.query as Record<string, string | undefined>,
+    (req.cookies || {}) as Record<string, string | undefined>
+  );
+
+  if (result.authenticated) {
     next();
     return;
   }
 
-  // Check for API key in header
-  const providedKey = req.headers['x-api-key'] as string | undefined;
-
-  if (!providedKey) {
-    res.status(401).json({
-      success: false,
-      error: 'Authentication required. Provide X-API-Key header.',
-    });
-    return;
+  // Return appropriate error based on what failed
+  switch (result.errorType) {
+    case 'invalid_api_key':
+      res.status(403).json({
+        success: false,
+        error: 'Invalid API key.',
+      });
+      break;
+    case 'invalid_session':
+      res.status(403).json({
+        success: false,
+        error: 'Invalid or expired session token.',
+      });
+      break;
+    case 'no_auth':
+    default:
+      res.status(401).json({
+        success: false,
+        error: 'Authentication required.',
+      });
   }
-
-  if (providedKey !== API_KEY) {
-    res.status(403).json({
-      success: false,
-      error: 'Invalid API key.',
-    });
-    return;
-  }
-
-  next();
 }
 
 /**
- * Check if authentication is enabled
+ * Check if authentication is enabled (always true now)
  */
 export function isAuthEnabled(): boolean {
-  return !!API_KEY;
+  return true;
 }
 
 /**
@@ -56,7 +380,31 @@ export function isAuthEnabled(): boolean {
  */
 export function getAuthStatus(): { enabled: boolean; method: string } {
   return {
-    enabled: !!API_KEY,
-    method: API_KEY ? 'api_key' : 'none',
+    enabled: true,
+    method: 'api_key_or_session',
   };
 }
+
+/**
+ * Check if a request is authenticated (for status endpoint)
+ */
+export function isRequestAuthenticated(req: Request): boolean {
+  const result = checkAuthentication(
+    req.headers as Record<string, string | string[] | undefined>,
+    req.query as Record<string, string | undefined>,
+    (req.cookies || {}) as Record<string, string | undefined>
+  );
+  return result.authenticated;
+}
+
+/**
+ * Check if raw credentials are authenticated
+ * Used for WebSocket authentication where we don't have Express request objects
+ */
+export function checkRawAuthentication(
+  headers: Record<string, string | string[] | undefined>,
+  query: Record<string, string | undefined>,
+  cookies: Record<string, string | undefined>
+): boolean {
+  return checkAuthentication(headers, query, cookies).authenticated;
+}

apps/server/src/lib/sdk-options.ts

@@ -16,9 +16,10 @@
  */
 
 import type { Options } from '@anthropic-ai/claude-agent-sdk';
+import os from 'os';
 import path from 'path';
 import { resolveModelString } from '@automaker/model-resolver';
-import { DEFAULT_MODELS, CLAUDE_MODEL_MAP } from '@automaker/types';
+import { DEFAULT_MODELS, CLAUDE_MODEL_MAP, type McpServerConfig } from '@automaker/types';
 import { isPathAllowed, PathNotAllowedError, getAllowedRootDirectory } from '@automaker/platform';
 
 /**
@@ -47,6 +48,128 @@ export function validateWorkingDirectory(cwd: string): void {
   }
 }
 
+/**
+ * Known cloud storage path patterns where sandbox mode is incompatible.
+ *
+ * The Claude CLI sandbox feature uses filesystem isolation that conflicts with
+ * cloud storage providers' virtual filesystem implementations. This causes the
+ * Claude process to exit with code 1 when sandbox is enabled for these paths.
+ *
+ * Affected providers (macOS paths):
+ * - Dropbox: ~/Library/CloudStorage/Dropbox-*
+ * - Google Drive: ~/Library/CloudStorage/GoogleDrive-*
+ * - OneDrive: ~/Library/CloudStorage/OneDrive-*
+ * - iCloud Drive: ~/Library/Mobile Documents/
+ * - Box: ~/Library/CloudStorage/Box-*
+ *
+ * @see https://github.com/anthropics/claude-code/issues/XXX (TODO: file upstream issue)
+ */
+
+/**
+ * macOS-specific cloud storage patterns that appear under ~/Library/
+ * These are specific enough to use with includes() safely.
+ */
+const MACOS_CLOUD_STORAGE_PATTERNS = [
+  '/Library/CloudStorage/', // Dropbox, Google Drive, OneDrive, Box on macOS
+  '/Library/Mobile Documents/', // iCloud Drive on macOS
+] as const;
+
+/**
+ * Generic cloud storage folder names that need to be anchored to the home directory
+ * to avoid false positives (e.g., /home/user/my-project-about-dropbox/).
+ */
+const HOME_ANCHORED_CLOUD_FOLDERS = [
+  'Google Drive', // Google Drive on some systems
+  'Dropbox', // Dropbox on Linux/alternative installs
+  'OneDrive', // OneDrive on Linux/alternative installs
+] as const;
+
+/**
+ * Check if a path is within a cloud storage location.
+ *
+ * Cloud storage providers use virtual filesystem implementations that are
+ * incompatible with the Claude CLI sandbox feature, causing process crashes.
+ *
+ * Uses two detection strategies:
+ * 1. macOS-specific patterns (under ~/Library/) - checked via includes()
+ * 2. Generic folder names - anchored to home directory to avoid false positives
+ *
+ * @param cwd - The working directory path to check
+ * @returns true if the path is in a cloud storage location
+ */
+export function isCloudStoragePath(cwd: string): boolean {
+  const resolvedPath = path.resolve(cwd);
+
+  // Check macOS-specific patterns (these are specific enough to use includes)
+  if (MACOS_CLOUD_STORAGE_PATTERNS.some((pattern) => resolvedPath.includes(pattern))) {
+    return true;
+  }
+
+  // Check home-anchored patterns to avoid false positives
+  // e.g., /home/user/my-project-about-dropbox/ should NOT match
+  const home = os.homedir();
+  for (const folder of HOME_ANCHORED_CLOUD_FOLDERS) {
+    const cloudPath = path.join(home, folder);
+    // Check if resolved path starts with the cloud storage path followed by a separator
+    // This ensures we match ~/Dropbox/project but not ~/Dropbox-archive or ~/my-dropbox-tool
+    if (resolvedPath === cloudPath || resolvedPath.startsWith(cloudPath + path.sep)) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
+/**
+ * Result of sandbox compatibility check
+ */
+export interface SandboxCheckResult {
+  /** Whether sandbox should be enabled */
+  enabled: boolean;
+  /** If disabled, the reason why */
+  disabledReason?: 'cloud_storage' | 'user_setting';
+  /** Human-readable message for logging/UI */
+  message?: string;
+}
+
+/**
+ * Determine if sandbox mode should be enabled for a given configuration.
+ *
+ * Sandbox mode is automatically disabled for cloud storage paths because the
+ * Claude CLI sandbox feature is incompatible with virtual filesystem
+ * implementations used by cloud storage providers (Dropbox, Google Drive, etc.).
+ *
+ * @param cwd - The working directory
+ * @param enableSandboxMode - User's sandbox mode setting
+ * @returns SandboxCheckResult with enabled status and reason if disabled
+ */
+export function checkSandboxCompatibility(
+  cwd: string,
+  enableSandboxMode?: boolean
+): SandboxCheckResult {
+  // User has explicitly disabled sandbox mode
+  if (enableSandboxMode === false) {
+    return {
+      enabled: false,
+      disabledReason: 'user_setting',
+    };
+  }
+
+  // Check for cloud storage incompatibility (applies when enabled or undefined)
+  if (isCloudStoragePath(cwd)) {
+    return {
+      enabled: false,
+      disabledReason: 'cloud_storage',
+      message: `Sandbox mode auto-disabled: Project is in a cloud storage location (${cwd}). The Claude CLI sandbox feature is incompatible with cloud storage filesystems. To use sandbox mode, move your project to a local directory.`,
+    };
+  }
+
+  // Sandbox is compatible and enabled (true or undefined defaults to enabled)
+  return {
+    enabled: true,
+  };
+}
+
 /**
  * Tool presets for different use cases
  */
@@ -136,6 +259,106 @@ function getBaseOptions(): Partial<Options> {
   };
 }
 
+/**
+ * MCP permission options result
+ */
+interface McpPermissionOptions {
+  /** Whether tools should be restricted to a preset */
+  shouldRestrictTools: boolean;
+  /** Options to spread when MCP bypass is enabled */
+  bypassOptions: Partial<Options>;
+  /** Options to spread for MCP servers */
+  mcpServerOptions: Partial<Options>;
+}
+
+/**
+ * Build MCP-related options based on configuration.
+ * Centralizes the logic for determining permission modes and tool restrictions
+ * when MCP servers are configured.
+ *
+ * @param config - The SDK options config
+ * @returns Object with MCP permission settings to spread into final options
+ */
+function buildMcpOptions(config: CreateSdkOptionsConfig): McpPermissionOptions {
+  const hasMcpServers = config.mcpServers && Object.keys(config.mcpServers).length > 0;
+  // Default to true for autonomous workflow. Security is enforced when adding servers
+  // via the security warning dialog that explains the risks.
+  const mcpAutoApprove = config.mcpAutoApproveTools ?? true;
+  const mcpUnrestricted = config.mcpUnrestrictedTools ?? true;
+
+  // Determine if we should bypass permissions based on settings
+  const shouldBypassPermissions = hasMcpServers && mcpAutoApprove;
+  // Determine if we should restrict tools (only when no MCP or unrestricted is disabled)
+  const shouldRestrictTools = !hasMcpServers || !mcpUnrestricted;
+
+  return {
+    shouldRestrictTools,
+    // Only include bypass options when MCP is configured and auto-approve is enabled
+    bypassOptions: shouldBypassPermissions
+      ? {
+          permissionMode: 'bypassPermissions' as const,
+          // Required flag when using bypassPermissions mode
+          allowDangerouslySkipPermissions: true,
+        }
+      : {},
+    // Include MCP servers if configured
+    mcpServerOptions: config.mcpServers ? { mcpServers: config.mcpServers } : {},
+  };
+}
+
+/**
+ * Build system prompt configuration based on autoLoadClaudeMd setting.
+ * When autoLoadClaudeMd is true:
+ * - Uses preset mode with 'claude_code' to enable CLAUDE.md auto-loading
+ * - If there's a custom systemPrompt, appends it to the preset
+ * - Sets settingSources to ['project'] for SDK to load CLAUDE.md files
+ *
+ * @param config - The SDK options config
+ * @returns Object with systemPrompt and settingSources for SDK options
+ */
+function buildClaudeMdOptions(config: CreateSdkOptionsConfig): {
+  systemPrompt?: string | SystemPromptConfig;
+  settingSources?: Array<'user' | 'project' | 'local'>;
+} {
+  if (!config.autoLoadClaudeMd) {
+    // Standard mode - just pass through the system prompt as-is
+    return config.systemPrompt ? { systemPrompt: config.systemPrompt } : {};
+  }
+
+  // Auto-load CLAUDE.md mode - use preset with settingSources
+  const result: {
+    systemPrompt: SystemPromptConfig;
+    settingSources: Array<'user' | 'project' | 'local'>;
+  } = {
+    systemPrompt: {
+      type: 'preset',
+      preset: 'claude_code',
+    },
+    // Load both user (~/.claude/CLAUDE.md) and project (.claude/CLAUDE.md) settings
+    settingSources: ['user', 'project'],
+  };
+
+  // If there's a custom system prompt, append it to the preset
+  if (config.systemPrompt) {
+    result.systemPrompt.append = config.systemPrompt;
+  }
+
+  return result;
+}
+
+/**
+ * System prompt configuration for SDK options
+ * When using preset mode with claude_code, CLAUDE.md files are automatically loaded
+ */
+export interface SystemPromptConfig {
+  /** Use preset mode with claude_code to enable CLAUDE.md auto-loading */
+  type: 'preset';
+  /** The preset to use - 'claude_code' enables CLAUDE.md loading */
+  preset: 'claude_code';
+  /** Optional additional prompt to append to the preset */
+  append?: string;
+}
+
 /**
  * Options configuration for creating SDK options
  */
@@ -160,8 +383,31 @@ export interface CreateSdkOptionsConfig {
     type: 'json_schema';
     schema: Record<string, unknown>;
   };
+
+  /** Enable auto-loading of CLAUDE.md files via SDK's settingSources */
+  autoLoadClaudeMd?: boolean;
+
+  /** Enable sandbox mode for bash command isolation */
+  enableSandboxMode?: boolean;
+
+  /** MCP servers to make available to the agent */
+  mcpServers?: Record<string, McpServerConfig>;
+
+  /** Auto-approve MCP tool calls without permission prompts */
+  mcpAutoApproveTools?: boolean;
+
+  /** Allow unrestricted tools when MCP servers are enabled */
+  mcpUnrestrictedTools?: boolean;
 }
 
+// Re-export MCP types from @automaker/types for convenience
+export type {
+  McpServerConfig,
+  McpStdioServerConfig,
+  McpSSEServerConfig,
+  McpHttpServerConfig,
+} from '@automaker/types';
+
 /**
  * Create SDK options for spec generation
  *
@@ -169,11 +415,15 @@ export interface CreateSdkOptionsConfig {
  * - Uses read-only tools for codebase analysis
  * - Extended turns for thorough exploration
  * - Opus model by default (can be overridden)
+ * - When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createSpecGenerationOptions(config: CreateSdkOptionsConfig): Options {
   // Validate working directory before creating options
   validateWorkingDirectory(config.cwd);
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
   return {
     ...getBaseOptions(),
     // Override permissionMode - spec generation only needs read-only tools
@@ -184,7 +434,7 @@ export function createSpecGenerationOptions(config: CreateSdkOptionsConfig): Opt
     maxTurns: MAX_TURNS.maximum,
     cwd: config.cwd,
     allowedTools: [...TOOL_PRESETS.specGeneration],
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
     ...(config.outputFormat && { outputFormat: config.outputFormat }),
   };
@@ -197,11 +447,15 @@ export function createSpecGenerationOptions(config: CreateSdkOptionsConfig): Opt
  * - Uses read-only tools (just needs to read the spec)
  * - Quick turns since it's mostly JSON generation
  * - Sonnet model by default for speed
+ * - When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createFeatureGenerationOptions(config: CreateSdkOptionsConfig): Options {
   // Validate working directory before creating options
   validateWorkingDirectory(config.cwd);
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
   return {
     ...getBaseOptions(),
     // Override permissionMode - feature generation only needs read-only tools
@@ -210,7 +464,7 @@ export function createFeatureGenerationOptions(config: CreateSdkOptionsConfig):
     maxTurns: MAX_TURNS.quick,
     cwd: config.cwd,
     allowedTools: [...TOOL_PRESETS.readOnly],
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
   };
 }
@@ -222,18 +476,22 @@ export function createFeatureGenerationOptions(config: CreateSdkOptionsConfig):
  * - Uses read-only tools for analysis
  * - Standard turns to allow thorough codebase exploration and structured output generation
  * - Opus model by default for thorough analysis
+ * - When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createSuggestionsOptions(config: CreateSdkOptionsConfig): Options {
   // Validate working directory before creating options
   validateWorkingDirectory(config.cwd);
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
   return {
     ...getBaseOptions(),
     model: getModelForUseCase('suggestions', config.model),
     maxTurns: MAX_TURNS.extended,
     cwd: config.cwd,
     allowedTools: [...TOOL_PRESETS.readOnly],
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
     ...(config.outputFormat && { outputFormat: config.outputFormat }),
   };
@@ -246,7 +504,8 @@ export function createSuggestionsOptions(config: CreateSdkOptionsConfig): Option
  * - Full tool access for code modification
  * - Standard turns for interactive sessions
  * - Model priority: explicit model > session model > chat default
- * - Sandbox enabled for bash safety
+ * - Sandbox mode controlled by enableSandboxMode setting (auto-disabled for cloud storage)
+ * - When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createChatOptions(config: CreateSdkOptionsConfig): Options {
   // Validate working directory before creating options
@@ -255,18 +514,33 @@ export function createChatOptions(config: CreateSdkOptionsConfig): Options {
   // Model priority: explicit model > session model > chat default
   const effectiveModel = config.model || config.sessionModel;
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
+  // Build MCP-related options
+  const mcpOptions = buildMcpOptions(config);
+
+  // Check sandbox compatibility (auto-disables for cloud storage paths)
+  const sandboxCheck = checkSandboxCompatibility(config.cwd, config.enableSandboxMode);
+
   return {
     ...getBaseOptions(),
     model: getModelForUseCase('chat', effectiveModel),
     maxTurns: MAX_TURNS.standard,
     cwd: config.cwd,
-    allowedTools: [...TOOL_PRESETS.chat],
-    sandbox: {
-      enabled: true,
-      autoAllowBashIfSandboxed: true,
-    },
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    // Only restrict tools if no MCP servers configured or unrestricted is disabled
+    ...(mcpOptions.shouldRestrictTools && { allowedTools: [...TOOL_PRESETS.chat] }),
+    // Apply MCP bypass options if configured
+    ...mcpOptions.bypassOptions,
+    ...(sandboxCheck.enabled && {
+      sandbox: {
+        enabled: true,
+        autoAllowBashIfSandboxed: true,
+      },
+    }),
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
+    ...mcpOptions.mcpServerOptions,
   };
 }
 
@@ -277,24 +551,40 @@ export function createChatOptions(config: CreateSdkOptionsConfig): Options {
  * - Full tool access for code modification and implementation
  * - Extended turns for thorough feature implementation
  * - Uses default model (can be overridden)
- * - Sandbox enabled for bash safety
+ * - Sandbox mode controlled by enableSandboxMode setting (auto-disabled for cloud storage)
+ * - When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createAutoModeOptions(config: CreateSdkOptionsConfig): Options {
   // Validate working directory before creating options
   validateWorkingDirectory(config.cwd);
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
+  // Build MCP-related options
+  const mcpOptions = buildMcpOptions(config);
+
+  // Check sandbox compatibility (auto-disables for cloud storage paths)
+  const sandboxCheck = checkSandboxCompatibility(config.cwd, config.enableSandboxMode);
+
   return {
     ...getBaseOptions(),
     model: getModelForUseCase('auto', config.model),
     maxTurns: MAX_TURNS.maximum,
     cwd: config.cwd,
-    allowedTools: [...TOOL_PRESETS.fullAccess],
-    sandbox: {
-      enabled: true,
-      autoAllowBashIfSandboxed: true,
-    },
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    // Only restrict tools if no MCP servers configured or unrestricted is disabled
+    ...(mcpOptions.shouldRestrictTools && { allowedTools: [...TOOL_PRESETS.fullAccess] }),
+    // Apply MCP bypass options if configured
+    ...mcpOptions.bypassOptions,
+    ...(sandboxCheck.enabled && {
+      sandbox: {
+        enabled: true,
+        autoAllowBashIfSandboxed: true,
+      },
+    }),
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
+    ...mcpOptions.mcpServerOptions,
   };
 }
 
@@ -302,6 +592,7 @@ export function createAutoModeOptions(config: CreateSdkOptionsConfig): Options {
  * Create custom SDK options with explicit configuration
  *
  * Use this when the preset options don't fit your use case.
+ * When autoLoadClaudeMd is true, uses preset mode and settingSources for CLAUDE.md loading
  */
 export function createCustomOptions(
   config: CreateSdkOptionsConfig & {
@@ -313,14 +604,30 @@ export function createCustomOptions(
   // Validate working directory before creating options
   validateWorkingDirectory(config.cwd);
 
+  // Build CLAUDE.md auto-loading options if enabled
+  const claudeMdOptions = buildClaudeMdOptions(config);
+
+  // Build MCP-related options
+  const mcpOptions = buildMcpOptions(config);
+
+  // For custom options: use explicit allowedTools if provided, otherwise use preset based on MCP settings
+  const effectiveAllowedTools = config.allowedTools
+    ? [...config.allowedTools]
+    : mcpOptions.shouldRestrictTools
+      ? [...TOOL_PRESETS.readOnly]
+      : undefined;
+
   return {
     ...getBaseOptions(),
     model: getModelForUseCase('default', config.model),
     maxTurns: config.maxTurns ?? MAX_TURNS.maximum,
     cwd: config.cwd,
-    allowedTools: config.allowedTools ? [...config.allowedTools] : [...TOOL_PRESETS.readOnly],
+    ...(effectiveAllowedTools && { allowedTools: effectiveAllowedTools }),
     ...(config.sandbox && { sandbox: config.sandbox }),
-    ...(config.systemPrompt && { systemPrompt: config.systemPrompt }),
+    // Apply MCP bypass options if configured
+    ...mcpOptions.bypassOptions,
+    ...claudeMdOptions,
     ...(config.abortController && { abortController: config.abortController }),
+    ...mcpOptions.mcpServerOptions,
   };
 }

apps/server/src/lib/secure-fs.ts

@@ -6,6 +6,7 @@
 import { secureFs } from '@automaker/platform';
 
 export const {
+  // Async methods
   access,
   readFile,
   writeFile,
@@ -20,4 +21,19 @@ export const {
   lstat,
   joinPath,
   resolvePath,
+  // Sync methods
+  existsSync,
+  readFileSync,
+  writeFileSync,
+  mkdirSync,
+  readdirSync,
+  statSync,
+  accessSync,
+  unlinkSync,
+  rmSync,
+  // Throttling configuration and monitoring
+  configureThrottling,
+  getThrottlingConfig,
+  getPendingOperations,
+  getActiveOperations,
 } = secureFs;

apps/server/src/lib/settings-helpers.ts

@@ -0,0 +1,306 @@
+/**
+ * Helper utilities for loading settings and context file handling across different parts of the server
+ */
+
+import type { SettingsService } from '../services/settings-service.js';
+import type { ContextFilesResult, ContextFileInfo } from '@automaker/utils';
+import { createLogger } from '@automaker/utils';
+import type { MCPServerConfig, McpServerConfig, PromptCustomization } from '@automaker/types';
+import {
+  mergeAutoModePrompts,
+  mergeAgentPrompts,
+  mergeBacklogPlanPrompts,
+  mergeEnhancementPrompts,
+} from '@automaker/prompts';
+
+const logger = createLogger('SettingsHelper');
+
+/**
+ * Get the autoLoadClaudeMd setting, with project settings taking precedence over global.
+ * Returns false if settings service is not available.
+ *
+ * @param projectPath - Path to the project
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages (e.g., '[DescribeImage]')
+ * @returns Promise resolving to the autoLoadClaudeMd setting value
+ */
+export async function getAutoLoadClaudeMdSetting(
+  projectPath: string,
+  settingsService?: SettingsService | null,
+  logPrefix = '[SettingsHelper]'
+): Promise<boolean> {
+  if (!settingsService) {
+    logger.info(`${logPrefix} SettingsService not available, autoLoadClaudeMd disabled`);
+    return false;
+  }
+
+  try {
+    // Check project settings first (takes precedence)
+    const projectSettings = await settingsService.getProjectSettings(projectPath);
+    if (projectSettings.autoLoadClaudeMd !== undefined) {
+      logger.info(
+        `${logPrefix} autoLoadClaudeMd from project settings: ${projectSettings.autoLoadClaudeMd}`
+      );
+      return projectSettings.autoLoadClaudeMd;
+    }
+
+    // Fall back to global settings
+    const globalSettings = await settingsService.getGlobalSettings();
+    const result = globalSettings.autoLoadClaudeMd ?? false;
+    logger.info(`${logPrefix} autoLoadClaudeMd from global settings: ${result}`);
+    return result;
+  } catch (error) {
+    logger.error(`${logPrefix} Failed to load autoLoadClaudeMd setting:`, error);
+    throw error;
+  }
+}
+
+/**
+ * Get the enableSandboxMode setting from global settings.
+ * Returns false if settings service is not available.
+ *
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages (e.g., '[AgentService]')
+ * @returns Promise resolving to the enableSandboxMode setting value
+ */
+export async function getEnableSandboxModeSetting(
+  settingsService?: SettingsService | null,
+  logPrefix = '[SettingsHelper]'
+): Promise<boolean> {
+  if (!settingsService) {
+    logger.info(`${logPrefix} SettingsService not available, sandbox mode disabled`);
+    return false;
+  }
+
+  try {
+    const globalSettings = await settingsService.getGlobalSettings();
+    const result = globalSettings.enableSandboxMode ?? false;
+    logger.info(`${logPrefix} enableSandboxMode from global settings: ${result}`);
+    return result;
+  } catch (error) {
+    logger.error(`${logPrefix} Failed to load enableSandboxMode setting:`, error);
+    throw error;
+  }
+}
+
+/**
+ * Filters out CLAUDE.md from context files when autoLoadClaudeMd is enabled
+ * and rebuilds the formatted prompt without it.
+ *
+ * When autoLoadClaudeMd is true, the SDK handles CLAUDE.md loading via settingSources,
+ * so we need to exclude it from the manual context loading to avoid duplication.
+ * Other context files (CODE_QUALITY.md, CONVENTIONS.md, etc.) are preserved.
+ *
+ * @param contextResult - Result from loadContextFiles
+ * @param autoLoadClaudeMd - Whether SDK auto-loading is enabled
+ * @returns Filtered context prompt (empty string if no non-CLAUDE.md files)
+ */
+export function filterClaudeMdFromContext(
+  contextResult: ContextFilesResult,
+  autoLoadClaudeMd: boolean
+): string {
+  // If autoLoadClaudeMd is disabled, return the original prompt unchanged
+  if (!autoLoadClaudeMd || contextResult.files.length === 0) {
+    return contextResult.formattedPrompt;
+  }
+
+  // Filter out CLAUDE.md (case-insensitive)
+  const nonClaudeFiles = contextResult.files.filter((f) => f.name.toLowerCase() !== 'claude.md');
+
+  // If all files were CLAUDE.md, return empty string
+  if (nonClaudeFiles.length === 0) {
+    return '';
+  }
+
+  // Rebuild prompt without CLAUDE.md using the same format as loadContextFiles
+  const formattedFiles = nonClaudeFiles.map((file) => formatContextFileEntry(file));
+
+  return `# Project Context Files
+
+The following context files provide project-specific rules, conventions, and guidelines.
+Each file serves a specific purpose - use the description to understand when to reference it.
+If you need more details about a context file, you can read the full file at the path provided.
+
+**IMPORTANT**: You MUST follow the rules and conventions specified in these files.
+- Follow ALL commands exactly as shown (e.g., if the project uses \`pnpm\`, NEVER use \`npm\` or \`npx\`)
+- Follow ALL coding conventions, commit message formats, and architectural patterns specified
+- Reference these rules before running ANY shell commands or making commits
+
+---
+
+${formattedFiles.join('\n\n---\n\n')}
+
+---
+
+**REMINDER**: Before taking any action, verify you are following the conventions specified above.
+`;
+}
+
+/**
+ * Format a single context file entry for the prompt
+ * (Matches the format used in @automaker/utils/context-loader.ts)
+ */
+function formatContextFileEntry(file: ContextFileInfo): string {
+  const header = `## ${file.name}`;
+  const pathInfo = `**Path:** \`${file.path}\``;
+  const descriptionInfo = file.description ? `\n**Purpose:** ${file.description}` : '';
+  return `${header}\n${pathInfo}${descriptionInfo}\n\n${file.content}`;
+}
+
+/**
+ * Get enabled MCP servers from global settings, converted to SDK format.
+ * Returns an empty object if settings service is not available or no servers are configured.
+ *
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages (e.g., '[AgentService]')
+ * @returns Promise resolving to MCP servers in SDK format (keyed by name)
+ */
+export async function getMCPServersFromSettings(
+  settingsService?: SettingsService | null,
+  logPrefix = '[SettingsHelper]'
+): Promise<Record<string, McpServerConfig>> {
+  if (!settingsService) {
+    return {};
+  }
+
+  try {
+    const globalSettings = await settingsService.getGlobalSettings();
+    const mcpServers = globalSettings.mcpServers || [];
+
+    // Filter to only enabled servers and convert to SDK format
+    const enabledServers = mcpServers.filter((s) => s.enabled !== false);
+
+    if (enabledServers.length === 0) {
+      return {};
+    }
+
+    // Convert settings format to SDK format (keyed by name)
+    const sdkServers: Record<string, McpServerConfig> = {};
+    for (const server of enabledServers) {
+      sdkServers[server.name] = convertToSdkFormat(server);
+    }
+
+    logger.info(
+      `${logPrefix} Loaded ${enabledServers.length} MCP server(s): ${enabledServers.map((s) => s.name).join(', ')}`
+    );
+
+    return sdkServers;
+  } catch (error) {
+    logger.error(`${logPrefix} Failed to load MCP servers setting:`, error);
+    return {};
+  }
+}
+
+/**
+ * Get MCP permission settings from global settings.
+ *
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages (e.g., '[AgentService]')
+ * @returns Promise resolving to MCP permission settings
+ */
+export async function getMCPPermissionSettings(
+  settingsService?: SettingsService | null,
+  logPrefix = '[SettingsHelper]'
+): Promise<{ mcpAutoApproveTools: boolean; mcpUnrestrictedTools: boolean }> {
+  // Default to true for autonomous workflow. Security is enforced when adding servers
+  // via the security warning dialog that explains the risks.
+  const defaults = { mcpAutoApproveTools: true, mcpUnrestrictedTools: true };
+
+  if (!settingsService) {
+    return defaults;
+  }
+
+  try {
+    const globalSettings = await settingsService.getGlobalSettings();
+    const result = {
+      mcpAutoApproveTools: globalSettings.mcpAutoApproveTools ?? true,
+      mcpUnrestrictedTools: globalSettings.mcpUnrestrictedTools ?? true,
+    };
+    logger.info(
+      `${logPrefix} MCP permission settings: autoApprove=${result.mcpAutoApproveTools}, unrestricted=${result.mcpUnrestrictedTools}`
+    );
+    return result;
+  } catch (error) {
+    logger.error(`${logPrefix} Failed to load MCP permission settings:`, error);
+    return defaults;
+  }
+}
+
+/**
+ * Convert a settings MCPServerConfig to SDK McpServerConfig format.
+ * Validates required fields and throws informative errors if missing.
+ */
+function convertToSdkFormat(server: MCPServerConfig): McpServerConfig {
+  if (server.type === 'sse') {
+    if (!server.url) {
+      throw new Error(`SSE MCP server "${server.name}" is missing a URL.`);
+    }
+    return {
+      type: 'sse',
+      url: server.url,
+      headers: server.headers,
+    };
+  }
+
+  if (server.type === 'http') {
+    if (!server.url) {
+      throw new Error(`HTTP MCP server "${server.name}" is missing a URL.`);
+    }
+    return {
+      type: 'http',
+      url: server.url,
+      headers: server.headers,
+    };
+  }
+
+  // Default to stdio
+  if (!server.command) {
+    throw new Error(`Stdio MCP server "${server.name}" is missing a command.`);
+  }
+  return {
+    type: 'stdio',
+    command: server.command,
+    args: server.args,
+    env: server.env,
+  };
+}
+
+/**
+ * Get prompt customization from global settings and merge with defaults.
+ * Returns prompts merged with built-in defaults - custom prompts override defaults.
+ *
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages
+ * @returns Promise resolving to merged prompts for all categories
+ */
+export async function getPromptCustomization(
+  settingsService?: SettingsService | null,
+  logPrefix = '[PromptHelper]'
+): Promise<{
+  autoMode: ReturnType<typeof mergeAutoModePrompts>;
+  agent: ReturnType<typeof mergeAgentPrompts>;
+  backlogPlan: ReturnType<typeof mergeBacklogPlanPrompts>;
+  enhancement: ReturnType<typeof mergeEnhancementPrompts>;
+}> {
+  let customization: PromptCustomization = {};
+
+  if (settingsService) {
+    try {
+      const globalSettings = await settingsService.getGlobalSettings();
+      customization = globalSettings.promptCustomization || {};
+      logger.info(`${logPrefix} Loaded prompt customization from settings`);
+    } catch (error) {
+      logger.error(`${logPrefix} Failed to load prompt customization:`, error);
+      // Fall through to use empty customization (all defaults)
+    }
+  } else {
+    logger.info(`${logPrefix} SettingsService not available, using default prompts`);
+  }
+
+  return {
+    autoMode: mergeAutoModePrompts(customization.autoMode),
+    agent: mergeAgentPrompts(customization.agent),
+    backlogPlan: mergeBacklogPlanPrompts(customization.backlogPlan),
+    enhancement: mergeEnhancementPrompts(customization.enhancement),
+  };
+}

apps/server/src/lib/validation-storage.ts

@@ -0,0 +1,181 @@
+/**
+ * Validation Storage - CRUD operations for GitHub issue validation results
+ *
+ * Stores validation results in .automaker/validations/{issueNumber}/validation.json
+ * Results include the validation verdict, metadata, and timestamp for cache invalidation.
+ */
+
+import * as secureFs from './secure-fs.js';
+import { getValidationsDir, getValidationDir, getValidationPath } from '@automaker/platform';
+import type { StoredValidation } from '@automaker/types';
+
+// Re-export StoredValidation for convenience
+export type { StoredValidation };
+
+/** Number of hours before a validation is considered stale */
+const VALIDATION_CACHE_TTL_HOURS = 24;
+
+/**
+ * Write validation result to storage
+ *
+ * Creates the validation directory if needed and stores the result as JSON.
+ *
+ * @param projectPath - Absolute path to project directory
+ * @param issueNumber - GitHub issue number
+ * @param data - Validation data to store
+ */
+export async function writeValidation(
+  projectPath: string,
+  issueNumber: number,
+  data: StoredValidation
+): Promise<void> {
+  const validationDir = getValidationDir(projectPath, issueNumber);
+  const validationPath = getValidationPath(projectPath, issueNumber);
+
+  // Ensure directory exists
+  await secureFs.mkdir(validationDir, { recursive: true });
+
+  // Write validation result
+  await secureFs.writeFile(validationPath, JSON.stringify(data, null, 2), 'utf-8');
+}
+
+/**
+ * Read validation result from storage
+ *
+ * @param projectPath - Absolute path to project directory
+ * @param issueNumber - GitHub issue number
+ * @returns Stored validation or null if not found
+ */
+export async function readValidation(
+  projectPath: string,
+  issueNumber: number
+): Promise<StoredValidation | null> {
+  try {
+    const validationPath = getValidationPath(projectPath, issueNumber);
+    const content = (await secureFs.readFile(validationPath, 'utf-8')) as string;
+    return JSON.parse(content) as StoredValidation;
+  } catch {
+    // File doesn't exist or can't be read
+    return null;
+  }
+}
+
+/**
+ * Get all stored validations for a project
+ *
+ * @param projectPath - Absolute path to project directory
+ * @returns Array of stored validations
+ */
+export async function getAllValidations(projectPath: string): Promise<StoredValidation[]> {
+  const validationsDir = getValidationsDir(projectPath);
+
+  try {
+    const dirs = await secureFs.readdir(validationsDir, { withFileTypes: true });
+
+    // Read all validation files in parallel for better performance
+    const promises = dirs
+      .filter((dir) => dir.isDirectory())
+      .map((dir) => {
+        const issueNumber = parseInt(dir.name, 10);
+        if (!isNaN(issueNumber)) {
+          return readValidation(projectPath, issueNumber);
+        }
+        return Promise.resolve(null);
+      });
+
+    const results = await Promise.all(promises);
+    const validations = results.filter((v): v is StoredValidation => v !== null);
+
+    // Sort by issue number
+    validations.sort((a, b) => a.issueNumber - b.issueNumber);
+
+    return validations;
+  } catch {
+    // Directory doesn't exist
+    return [];
+  }
+}
+
+/**
+ * Delete a validation from storage
+ *
+ * @param projectPath - Absolute path to project directory
+ * @param issueNumber - GitHub issue number
+ * @returns true if validation was deleted, false if not found
+ */
+export async function deleteValidation(projectPath: string, issueNumber: number): Promise<boolean> {
+  try {
+    const validationDir = getValidationDir(projectPath, issueNumber);
+    await secureFs.rm(validationDir, { recursive: true, force: true });
+    return true;
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Check if a validation is stale (older than TTL)
+ *
+ * @param validation - Stored validation to check
+ * @returns true if validation is older than 24 hours
+ */
+export function isValidationStale(validation: StoredValidation): boolean {
+  const validatedAt = new Date(validation.validatedAt);
+  const now = new Date();
+  const hoursDiff = (now.getTime() - validatedAt.getTime()) / (1000 * 60 * 60);
+  return hoursDiff > VALIDATION_CACHE_TTL_HOURS;
+}
+
+/**
+ * Get validation with freshness info
+ *
+ * @param projectPath - Absolute path to project directory
+ * @param issueNumber - GitHub issue number
+ * @returns Object with validation and isStale flag, or null if not found
+ */
+export async function getValidationWithFreshness(
+  projectPath: string,
+  issueNumber: number
+): Promise<{ validation: StoredValidation; isStale: boolean } | null> {
+  const validation = await readValidation(projectPath, issueNumber);
+  if (!validation) {
+    return null;
+  }
+
+  return {
+    validation,
+    isStale: isValidationStale(validation),
+  };
+}
+
+/**
+ * Mark a validation as viewed by the user
+ *
+ * @param projectPath - Absolute path to project directory
+ * @param issueNumber - GitHub issue number
+ * @returns true if validation was marked as viewed, false if not found
+ */
+export async function markValidationViewed(
+  projectPath: string,
+  issueNumber: number
+): Promise<boolean> {
+  const validation = await readValidation(projectPath, issueNumber);
+  if (!validation) {
+    return false;
+  }
+
+  validation.viewedAt = new Date().toISOString();
+  await writeValidation(projectPath, issueNumber, validation);
+  return true;
+}
+
+/**
+ * Get count of unviewed, non-stale validations for a project
+ *
+ * @param projectPath - Absolute path to project directory
+ * @returns Number of unviewed validations
+ */
+export async function getUnviewedValidationsCount(projectPath: string): Promise<number> {
+  const validations = await getAllValidations(projectPath);
+  return validations.filter((v) => !v.viewedAt && !isValidationStale(v)).length;
+}

apps/server/src/lib/version.ts

@@ -0,0 +1,33 @@
+/**
+ * Version utility - Reads version from package.json
+ */
+
+import { readFileSync } from 'fs';
+import { fileURLToPath } from 'url';
+import { dirname, join } from 'path';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+let cachedVersion: string | null = null;
+
+/**
+ * Get the version from package.json
+ * Caches the result for performance
+ */
+export function getVersion(): string {
+  if (cachedVersion) {
+    return cachedVersion;
+  }
+
+  try {
+    const packageJsonPath = join(__dirname, '..', '..', 'package.json');
+    const packageJson = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));
+    const version = packageJson.version || '0.0.0';
+    cachedVersion = version;
+    return version;
+  } catch (error) {
+    console.warn('Failed to read version from package.json:', error);
+    return '0.0.0';
+  }
+}

apps/server/src/middleware/require-json-content-type.ts

@@ -0,0 +1,50 @@
+/**
+ * Middleware to enforce Content-Type: application/json for request bodies
+ *
+ * This security middleware prevents malicious requests by requiring proper
+ * Content-Type headers for all POST, PUT, and PATCH requests.
+ *
+ * Rejecting requests without proper Content-Type helps prevent:
+ * - CSRF attacks via form submissions (which use application/x-www-form-urlencoded)
+ * - Content-type confusion attacks
+ * - Malformed request exploitation
+ */
+
+import type { Request, Response, NextFunction } from 'express';
+
+// HTTP methods that typically include request bodies
+const METHODS_REQUIRING_JSON = ['POST', 'PUT', 'PATCH'];
+
+/**
+ * Middleware that requires Content-Type: application/json for POST/PUT/PATCH requests
+ *
+ * Returns 415 Unsupported Media Type if:
+ * - The request method is POST, PUT, or PATCH
+ * - AND the Content-Type header is missing or not application/json
+ *
+ * Allows requests to pass through if:
+ * - The request method is GET, DELETE, OPTIONS, HEAD, etc.
+ * - OR the Content-Type is properly set to application/json (with optional charset)
+ */
+export function requireJsonContentType(req: Request, res: Response, next: NextFunction): void {
+  // Skip validation for methods that don't require a body
+  if (!METHODS_REQUIRING_JSON.includes(req.method)) {
+    next();
+    return;
+  }
+
+  const contentType = req.headers['content-type'];
+
+  // Check if Content-Type header exists and contains application/json
+  // Allows for charset parameter: "application/json; charset=utf-8"
+  if (!contentType || !contentType.toLowerCase().includes('application/json')) {
+    res.status(415).json({
+      success: false,
+      error: 'Unsupported Media Type',
+      message: 'Content-Type header must be application/json',
+    });
+    return;
+  }
+
+  next();
+}

apps/server/src/providers/claude-provider.ts

@@ -7,6 +7,7 @@
 
 import { query, type Options } from '@anthropic-ai/claude-agent-sdk';
 import { BaseProvider } from './base-provider.js';
+import { classifyError, getUserFriendlyErrorMessage } from '@automaker/utils';
 import type {
   ExecuteOptions,
   ProviderMessage,
@@ -14,6 +15,32 @@ import type {
   ModelDefinition,
 } from './types.js';
 
+// Explicit allowlist of environment variables to pass to the SDK.
+// Only these vars are passed - nothing else from process.env leaks through.
+const ALLOWED_ENV_VARS = [
+  'ANTHROPIC_API_KEY',
+  'PATH',
+  'HOME',
+  'SHELL',
+  'TERM',
+  'USER',
+  'LANG',
+  'LC_ALL',
+];
+
+/**
+ * Build environment for the SDK with only explicitly allowed variables
+ */
+function buildEnv(): Record<string, string | undefined> {
+  const env: Record<string, string | undefined> = {};
+  for (const key of ALLOWED_ENV_VARS) {
+    if (process.env[key]) {
+      env[key] = process.env[key];
+    }
+  }
+  return env;
+}
+
 export class ClaudeProvider extends BaseProvider {
   getName(): string {
     return 'claude';
@@ -36,25 +63,46 @@ export class ClaudeProvider extends BaseProvider {
     } = options;
 
     // Build Claude SDK options
+    // MCP permission logic - determines how to handle tool permissions when MCP servers are configured.
+    // This logic mirrors buildMcpOptions() in sdk-options.ts but is applied here since
+    // the provider is the final point where SDK options are constructed.
+    const hasMcpServers = options.mcpServers && Object.keys(options.mcpServers).length > 0;
+    // Default to true for autonomous workflow. Security is enforced when adding servers
+    // via the security warning dialog that explains the risks.
+    const mcpAutoApprove = options.mcpAutoApproveTools ?? true;
+    const mcpUnrestricted = options.mcpUnrestrictedTools ?? true;
     const defaultTools = ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'];
-    const toolsToUse = allowedTools || defaultTools;
+
+    // Determine permission mode based on settings
+    const shouldBypassPermissions = hasMcpServers && mcpAutoApprove;
+    // Determine if we should restrict tools (only when no MCP or unrestricted is disabled)
+    const shouldRestrictTools = !hasMcpServers || !mcpUnrestricted;
 
     const sdkOptions: Options = {
       model,
       systemPrompt,
       maxTurns,
       cwd,
-      allowedTools: toolsToUse,
-      permissionMode: 'acceptEdits',
-      sandbox: {
-        enabled: true,
-        autoAllowBashIfSandboxed: true,
-      },
+      // Pass only explicitly allowed environment variables to SDK
+      env: buildEnv(),
+      // Only restrict tools if explicitly set OR (no MCP / unrestricted disabled)
+      ...(allowedTools && shouldRestrictTools && { allowedTools }),
+      ...(!allowedTools && shouldRestrictTools && { allowedTools: defaultTools }),
+      // When MCP servers are configured and auto-approve is enabled, use bypassPermissions
+      permissionMode: shouldBypassPermissions ? 'bypassPermissions' : 'default',
+      // Required when using bypassPermissions mode
+      ...(shouldBypassPermissions && { allowDangerouslySkipPermissions: true }),
       abortController,
       // Resume existing SDK session if we have a session ID
       ...(sdkSessionId && conversationHistory && conversationHistory.length > 0
         ? { resume: sdkSessionId }
         : {}),
+      // Forward settingSources for CLAUDE.md file loading
+      ...(options.settingSources && { settingSources: options.settingSources }),
+      // Forward sandbox configuration
+      ...(options.sandbox && { sandbox: options.sandbox }),
+      // Forward MCP servers configuration
+      ...(options.mcpServers && { mcpServers: options.mcpServers }),
     };
 
     // Build prompt payload
@@ -88,8 +136,32 @@ export class ClaudeProvider extends BaseProvider {
         yield msg as ProviderMessage;
       }
     } catch (error) {
-      console.error('[ClaudeProvider] executeQuery() error during execution:', error);
-      throw error;
+      // Enhance error with user-friendly message and classification
+      const errorInfo = classifyError(error);
+      const userMessage = getUserFriendlyErrorMessage(error);
+
+      console.error('[ClaudeProvider] executeQuery() error during execution:', {
+        type: errorInfo.type,
+        message: errorInfo.message,
+        isRateLimit: errorInfo.isRateLimit,
+        retryAfter: errorInfo.retryAfter,
+        stack: (error as Error).stack,
+      });
+
+      // Build enhanced error message with additional guidance for rate limits
+      const message = errorInfo.isRateLimit
+        ? `${userMessage}\n\nTip: If you're running multiple features in auto-mode, consider reducing concurrency (maxConcurrency setting) to avoid hitting rate limits.`
+        : userMessage;
+
+      const enhancedError = new Error(message);
+      (enhancedError as any).originalError = error;
+      (enhancedError as any).type = errorInfo.type;
+
+      if (errorInfo.isRateLimit) {
+        (enhancedError as any).retryAfter = errorInfo.retryAfter;
+      }
+
+      throw enhancedError;
     }
   }
 

apps/server/src/providers/types.ts

@@ -1,39 +1,19 @@
 /**
  * Shared types for AI model providers
+ *
+ * Re-exports types from @automaker/types for consistency across the codebase.
  */
 
-/**
- * Configuration for a provider instance
- */
-export interface ProviderConfig {
-  apiKey?: string;
-  cliPath?: string;
-  env?: Record<string, string>;
-}
-
-/**
- * Message in conversation history
- */
-export interface ConversationMessage {
-  role: 'user' | 'assistant';
-  content: string | Array<{ type: string; text?: string; source?: object }>;
-}
-
-/**
- * Options for executing a query via a provider
- */
-export interface ExecuteOptions {
-  prompt: string | Array<{ type: string; text?: string; source?: object }>;
-  model: string;
-  cwd: string;
-  systemPrompt?: string;
-  maxTurns?: number;
-  allowedTools?: string[];
-  mcpServers?: Record<string, unknown>;
-  abortController?: AbortController;
-  conversationHistory?: ConversationMessage[]; // Previous messages for context
-  sdkSessionId?: string; // Claude SDK session ID for resuming conversations
-}
+// Re-export all provider types from @automaker/types
+export type {
+  ProviderConfig,
+  ConversationMessage,
+  ExecuteOptions,
+  McpServerConfig,
+  McpStdioServerConfig,
+  McpSSEServerConfig,
+  McpHttpServerConfig,
+} from '@automaker/types';
 
 /**
  * Content block in a provider message (matches Claude SDK format)

apps/server/src/routes/agent/index.ts

@@ -12,6 +12,10 @@ import { createHistoryHandler } from './routes/history.js';
 import { createStopHandler } from './routes/stop.js';
 import { createClearHandler } from './routes/clear.js';
 import { createModelHandler } from './routes/model.js';
+import { createQueueAddHandler } from './routes/queue-add.js';
+import { createQueueListHandler } from './routes/queue-list.js';
+import { createQueueRemoveHandler } from './routes/queue-remove.js';
+import { createQueueClearHandler } from './routes/queue-clear.js';
 
 export function createAgentRoutes(agentService: AgentService, _events: EventEmitter): Router {
   const router = Router();
@@ -27,5 +31,15 @@ export function createAgentRoutes(agentService: AgentService, _events: EventEmit
   router.post('/clear', createClearHandler(agentService));
   router.post('/model', createModelHandler(agentService));
 
+  // Queue routes
+  router.post(
+    '/queue/add',
+    validatePathParams('imagePaths[]'),
+    createQueueAddHandler(agentService)
+  );
+  router.post('/queue/list', createQueueListHandler(agentService));
+  router.post('/queue/remove', createQueueRemoveHandler(agentService));
+  router.post('/queue/clear', createQueueClearHandler(agentService));
+
   return router;
 }

apps/server/src/routes/agent/routes/queue-add.ts

@@ -0,0 +1,34 @@
+/**
+ * POST /queue/add endpoint - Add a prompt to the queue
+ */
+
+import type { Request, Response } from 'express';
+import { AgentService } from '../../../services/agent-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createQueueAddHandler(agentService: AgentService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { sessionId, message, imagePaths, model } = req.body as {
+        sessionId: string;
+        message: string;
+        imagePaths?: string[];
+        model?: string;
+      };
+
+      if (!sessionId || !message) {
+        res.status(400).json({
+          success: false,
+          error: 'sessionId and message are required',
+        });
+        return;
+      }
+
+      const result = await agentService.addToQueue(sessionId, { message, imagePaths, model });
+      res.json(result);
+    } catch (error) {
+      logError(error, 'Add to queue failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/agent/routes/queue-clear.ts

@@ -0,0 +1,29 @@
+/**
+ * POST /queue/clear endpoint - Clear all prompts from the queue
+ */
+
+import type { Request, Response } from 'express';
+import { AgentService } from '../../../services/agent-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createQueueClearHandler(agentService: AgentService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { sessionId } = req.body as { sessionId: string };
+
+      if (!sessionId) {
+        res.status(400).json({
+          success: false,
+          error: 'sessionId is required',
+        });
+        return;
+      }
+
+      const result = await agentService.clearQueue(sessionId);
+      res.json(result);
+    } catch (error) {
+      logError(error, 'Clear queue failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/agent/routes/queue-list.ts

@@ -0,0 +1,29 @@
+/**
+ * POST /queue/list endpoint - List queued prompts
+ */
+
+import type { Request, Response } from 'express';
+import { AgentService } from '../../../services/agent-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createQueueListHandler(agentService: AgentService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { sessionId } = req.body as { sessionId: string };
+
+      if (!sessionId) {
+        res.status(400).json({
+          success: false,
+          error: 'sessionId is required',
+        });
+        return;
+      }
+
+      const result = agentService.getQueue(sessionId);
+      res.json(result);
+    } catch (error) {
+      logError(error, 'List queue failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/agent/routes/queue-remove.ts

@@ -0,0 +1,32 @@
+/**
+ * POST /queue/remove endpoint - Remove a prompt from the queue
+ */
+
+import type { Request, Response } from 'express';
+import { AgentService } from '../../../services/agent-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createQueueRemoveHandler(agentService: AgentService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { sessionId, promptId } = req.body as {
+        sessionId: string;
+        promptId: string;
+      };
+
+      if (!sessionId || !promptId) {
+        res.status(400).json({
+          success: false,
+          error: 'sessionId and promptId are required',
+        });
+        return;
+      }
+
+      const result = await agentService.removeFromQueue(sessionId, promptId);
+      res.json(result);
+    } catch (error) {
+      logError(error, 'Remove from queue failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/agent/routes/send.ts

@@ -19,7 +19,16 @@ export function createSendHandler(agentService: AgentService) {
         model?: string;
       };
 
+      console.log('[Send Handler] Received request:', {
+        sessionId,
+        messageLength: message?.length,
+        workingDirectory,
+        imageCount: imagePaths?.length || 0,
+        model,
+      });
+
       if (!sessionId || !message) {
+        console.log('[Send Handler] ERROR: Validation failed - missing sessionId or message');
         res.status(400).json({
           success: false,
           error: 'sessionId and message are required',
@@ -27,6 +36,8 @@ export function createSendHandler(agentService: AgentService) {
         return;
       }
 
+      console.log('[Send Handler] Validation passed, calling agentService.sendMessage()');
+
       // Start the message processing (don't await - it streams via WebSocket)
       agentService
         .sendMessage({
@@ -37,12 +48,16 @@ export function createSendHandler(agentService: AgentService) {
           model,
         })
         .catch((error) => {
+          console.error('[Send Handler] ERROR: Background error in sendMessage():', error);
           logError(error, 'Send message failed (background)');
         });
 
+      console.log('[Send Handler] Returning immediate response to client');
+
       // Return immediately - responses come via WebSocket
       res.json({ success: true, message: 'Message sent' });
     } catch (error) {
+      console.error('[Send Handler] ERROR: Synchronous error:', error);
       logError(error, 'Send message failed');
       res.status(500).json({ success: false, error: getErrorMessage(error) });
     }

apps/server/src/routes/app-spec/generate-features-from-spec.ts

@@ -10,6 +10,8 @@ import { createFeatureGenerationOptions } from '../../lib/sdk-options.js';
 import { logAuthStatus } from './common.js';
 import { parseAndCreateFeatures } from './parse-and-create-features.js';
 import { getAppSpecPath } from '@automaker/platform';
+import type { SettingsService } from '../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
 
 const logger = createLogger('SpecRegeneration');
 
@@ -19,7 +21,8 @@ export async function generateFeaturesFromSpec(
   projectPath: string,
   events: EventEmitter,
   abortController: AbortController,
-  maxFeatures?: number
+  maxFeatures?: number,
+  settingsService?: SettingsService
 ): Promise<void> {
   const featureCount = maxFeatures ?? DEFAULT_MAX_FEATURES;
   logger.debug('========== generateFeaturesFromSpec() started ==========');
@@ -91,9 +94,17 @@ IMPORTANT: Do not ask for clarification. The specification is provided above. Ge
     projectPath: projectPath,
   });
 
+  // Load autoLoadClaudeMd setting
+  const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+    projectPath,
+    settingsService,
+    '[FeatureGeneration]'
+  );
+
   const options = createFeatureGenerationOptions({
     cwd: projectPath,
     abortController,
+    autoLoadClaudeMd,
   });
 
   logger.debug('SDK Options:', JSON.stringify(options, null, 2));

apps/server/src/routes/app-spec/generate-spec.ts

@@ -17,6 +17,8 @@ import { createSpecGenerationOptions } from '../../lib/sdk-options.js';
 import { logAuthStatus } from './common.js';
 import { generateFeaturesFromSpec } from './generate-features-from-spec.js';
 import { ensureAutomakerDir, getAppSpecPath } from '@automaker/platform';
+import type { SettingsService } from '../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
 
 const logger = createLogger('SpecRegeneration');
 
@@ -27,7 +29,8 @@ export async function generateSpec(
   abortController: AbortController,
   generateFeatures?: boolean,
   analyzeProject?: boolean,
-  maxFeatures?: number
+  maxFeatures?: number,
+  settingsService?: SettingsService
 ): Promise<void> {
   logger.info('========== generateSpec() started ==========');
   logger.info('projectPath:', projectPath);
@@ -83,9 +86,17 @@ ${getStructuredSpecPromptInstruction()}`;
     content: 'Starting spec generation...\n',
   });
 
+  // Load autoLoadClaudeMd setting
+  const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+    projectPath,
+    settingsService,
+    '[SpecRegeneration]'
+  );
+
   const options = createSpecGenerationOptions({
     cwd: projectPath,
     abortController,
+    autoLoadClaudeMd,
     outputFormat: {
       type: 'json_schema',
       schema: specOutputSchema,
@@ -269,7 +280,13 @@ ${getStructuredSpecPromptInstruction()}`;
     // Create a new abort controller for feature generation
     const featureAbortController = new AbortController();
     try {
-      await generateFeaturesFromSpec(projectPath, events, featureAbortController, maxFeatures);
+      await generateFeaturesFromSpec(
+        projectPath,
+        events,
+        featureAbortController,
+        maxFeatures,
+        settingsService
+      );
       // Final completion will be emitted by generateFeaturesFromSpec -> parseAndCreateFeatures
     } catch (featureError) {
       logger.error('Feature generation failed:', featureError);

apps/server/src/routes/app-spec/index.ts

@@ -9,13 +9,17 @@ import { createGenerateHandler } from './routes/generate.js';
 import { createGenerateFeaturesHandler } from './routes/generate-features.js';
 import { createStopHandler } from './routes/stop.js';
 import { createStatusHandler } from './routes/status.js';
+import type { SettingsService } from '../../services/settings-service.js';
 
-export function createSpecRegenerationRoutes(events: EventEmitter): Router {
+export function createSpecRegenerationRoutes(
+  events: EventEmitter,
+  settingsService?: SettingsService
+): Router {
   const router = Router();
 
   router.post('/create', createCreateHandler(events));
-  router.post('/generate', createGenerateHandler(events));
-  router.post('/generate-features', createGenerateFeaturesHandler(events));
+  router.post('/generate', createGenerateHandler(events, settingsService));
+  router.post('/generate-features', createGenerateFeaturesHandler(events, settingsService));
   router.post('/stop', createStopHandler());
   router.get('/status', createStatusHandler());
 

apps/server/src/routes/app-spec/routes/generate-features.ts

@@ -13,10 +13,14 @@ import {
   getErrorMessage,
 } from '../common.js';
 import { generateFeaturesFromSpec } from '../generate-features-from-spec.js';
+import type { SettingsService } from '../../../services/settings-service.js';
 
 const logger = createLogger('SpecRegeneration');
 
-export function createGenerateFeaturesHandler(events: EventEmitter) {
+export function createGenerateFeaturesHandler(
+  events: EventEmitter,
+  settingsService?: SettingsService
+) {
   return async (req: Request, res: Response): Promise<void> => {
     logger.info('========== /generate-features endpoint called ==========');
     logger.debug('Request body:', JSON.stringify(req.body, null, 2));
@@ -49,7 +53,7 @@ export function createGenerateFeaturesHandler(events: EventEmitter) {
       setRunningState(true, abortController);
       logger.info('Starting background feature generation task...');
 
-      generateFeaturesFromSpec(projectPath, events, abortController, maxFeatures)
+      generateFeaturesFromSpec(projectPath, events, abortController, maxFeatures, settingsService)
         .catch((error) => {
           logError(error, 'Feature generation failed with error');
           events.emit('spec-regeneration:event', {

apps/server/src/routes/app-spec/routes/generate.ts

@@ -13,10 +13,11 @@ import {
   getErrorMessage,
 } from '../common.js';
 import { generateSpec } from '../generate-spec.js';
+import type { SettingsService } from '../../../services/settings-service.js';
 
 const logger = createLogger('SpecRegeneration');
 
-export function createGenerateHandler(events: EventEmitter) {
+export function createGenerateHandler(events: EventEmitter, settingsService?: SettingsService) {
   return async (req: Request, res: Response): Promise<void> => {
     logger.info('========== /generate endpoint called ==========');
     logger.debug('Request body:', JSON.stringify(req.body, null, 2));
@@ -67,7 +68,8 @@ export function createGenerateHandler(events: EventEmitter) {
         abortController,
         generateFeatures,
         analyzeProject,
-        maxFeatures
+        maxFeatures,
+        settingsService
       )
         .catch((error) => {
           logError(error, 'Generation failed with error');

apps/server/src/routes/auth/index.ts

@@ -0,0 +1,247 @@
+/**
+ * Auth routes - Login, logout, and status endpoints
+ *
+ * Security model:
+ * - Web mode: User enters API key (shown on server console) to get HTTP-only session cookie
+ * - Electron mode: Uses X-API-Key header (handled automatically via IPC)
+ *
+ * The session cookie is:
+ * - HTTP-only: JavaScript cannot read it (protects against XSS)
+ * - SameSite=Strict: Only sent for same-site requests (protects against CSRF)
+ *
+ * Mounted at /api/auth in the main server (BEFORE auth middleware).
+ */
+
+import { Router } from 'express';
+import type { Request } from 'express';
+import {
+  validateApiKey,
+  createSession,
+  invalidateSession,
+  getSessionCookieOptions,
+  getSessionCookieName,
+  isRequestAuthenticated,
+  createWsConnectionToken,
+} from '../../lib/auth.js';
+
+// Rate limiting configuration
+const RATE_LIMIT_WINDOW_MS = 60 * 1000; // 1 minute window
+const RATE_LIMIT_MAX_ATTEMPTS = 5; // Max 5 attempts per window
+
+// Check if we're in test mode - disable rate limiting for E2E tests
+const isTestMode = process.env.AUTOMAKER_MOCK_AGENT === 'true';
+
+// In-memory rate limit tracking (resets on server restart)
+const loginAttempts = new Map<string, { count: number; windowStart: number }>();
+
+// Clean up old rate limit entries periodically (every 5 minutes)
+setInterval(
+  () => {
+    const now = Date.now();
+    loginAttempts.forEach((data, ip) => {
+      if (now - data.windowStart > RATE_LIMIT_WINDOW_MS * 2) {
+        loginAttempts.delete(ip);
+      }
+    });
+  },
+  5 * 60 * 1000
+);
+
+/**
+ * Get client IP address from request
+ * Handles X-Forwarded-For header for reverse proxy setups
+ */
+function getClientIp(req: Request): string {
+  const forwarded = req.headers['x-forwarded-for'];
+  if (forwarded) {
+    // X-Forwarded-For can be a comma-separated list; take the first (original client)
+    const forwardedIp = Array.isArray(forwarded) ? forwarded[0] : forwarded.split(',')[0];
+    return forwardedIp.trim();
+  }
+  return req.ip || req.socket.remoteAddress || 'unknown';
+}
+
+/**
+ * Check if an IP is rate limited
+ * Returns { limited: boolean, retryAfter?: number }
+ */
+function checkRateLimit(ip: string): { limited: boolean; retryAfter?: number } {
+  const now = Date.now();
+  const attempt = loginAttempts.get(ip);
+
+  if (!attempt) {
+    return { limited: false };
+  }
+
+  // Check if window has expired
+  if (now - attempt.windowStart > RATE_LIMIT_WINDOW_MS) {
+    loginAttempts.delete(ip);
+    return { limited: false };
+  }
+
+  // Check if over limit
+  if (attempt.count >= RATE_LIMIT_MAX_ATTEMPTS) {
+    const retryAfter = Math.ceil((RATE_LIMIT_WINDOW_MS - (now - attempt.windowStart)) / 1000);
+    return { limited: true, retryAfter };
+  }
+
+  return { limited: false };
+}
+
+/**
+ * Record a login attempt for rate limiting
+ */
+function recordLoginAttempt(ip: string): void {
+  const now = Date.now();
+  const attempt = loginAttempts.get(ip);
+
+  if (!attempt || now - attempt.windowStart > RATE_LIMIT_WINDOW_MS) {
+    // Start new window
+    loginAttempts.set(ip, { count: 1, windowStart: now });
+  } else {
+    // Increment existing window
+    attempt.count++;
+  }
+}
+
+/**
+ * Create auth routes
+ *
+ * @returns Express Router with auth endpoints
+ */
+export function createAuthRoutes(): Router {
+  const router = Router();
+
+  /**
+   * GET /api/auth/status
+   *
+   * Returns whether the current request is authenticated.
+   * Used by the UI to determine if login is needed.
+   */
+  router.get('/status', (req, res) => {
+    const authenticated = isRequestAuthenticated(req);
+    res.json({
+      success: true,
+      authenticated,
+      required: true,
+    });
+  });
+
+  /**
+   * POST /api/auth/login
+   *
+   * Validates the API key and sets a session cookie.
+   * Body: { apiKey: string }
+   *
+   * Rate limited to 5 attempts per minute per IP to prevent brute force attacks.
+   */
+  router.post('/login', async (req, res) => {
+    const clientIp = getClientIp(req);
+
+    // Skip rate limiting in test mode to allow parallel E2E tests
+    if (!isTestMode) {
+      // Check rate limit before processing
+      const rateLimit = checkRateLimit(clientIp);
+      if (rateLimit.limited) {
+        res.status(429).json({
+          success: false,
+          error: 'Too many login attempts. Please try again later.',
+          retryAfter: rateLimit.retryAfter,
+        });
+        return;
+      }
+    }
+
+    const { apiKey } = req.body as { apiKey?: string };
+
+    if (!apiKey) {
+      res.status(400).json({
+        success: false,
+        error: 'API key is required.',
+      });
+      return;
+    }
+
+    // Record this attempt (only for actual API key validation attempts, skip in test mode)
+    if (!isTestMode) {
+      recordLoginAttempt(clientIp);
+    }
+
+    if (!validateApiKey(apiKey)) {
+      res.status(401).json({
+        success: false,
+        error: 'Invalid API key.',
+      });
+      return;
+    }
+
+    // Create session and set cookie
+    const sessionToken = await createSession();
+    const cookieOptions = getSessionCookieOptions();
+    const cookieName = getSessionCookieName();
+
+    res.cookie(cookieName, sessionToken, cookieOptions);
+    res.json({
+      success: true,
+      message: 'Logged in successfully.',
+      // Return token for explicit header-based auth (works around cross-origin cookie issues)
+      token: sessionToken,
+    });
+  });
+
+  /**
+   * GET /api/auth/token
+   *
+   * Generates a short-lived WebSocket connection token if the user has a valid session.
+   * This token is used for initial WebSocket handshake authentication and expires in 5 minutes.
+   * The token is NOT the session cookie value - it's a separate, short-lived token.
+   */
+  router.get('/token', (req, res) => {
+    // Validate the session is still valid (via cookie, API key, or session token header)
+    if (!isRequestAuthenticated(req)) {
+      res.status(401).json({
+        success: false,
+        error: 'Authentication required.',
+      });
+      return;
+    }
+
+    // Generate a new short-lived WebSocket connection token
+    const wsToken = createWsConnectionToken();
+
+    res.json({
+      success: true,
+      token: wsToken,
+      expiresIn: 300, // 5 minutes in seconds
+    });
+  });
+
+  /**
+   * POST /api/auth/logout
+   *
+   * Clears the session cookie and invalidates the session.
+   */
+  router.post('/logout', async (req, res) => {
+    const cookieName = getSessionCookieName();
+    const sessionToken = req.cookies?.[cookieName] as string | undefined;
+
+    if (sessionToken) {
+      await invalidateSession(sessionToken);
+    }
+
+    // Clear the cookie
+    res.clearCookie(cookieName, {
+      httpOnly: true,
+      secure: process.env.NODE_ENV === 'production',
+      sameSite: 'strict',
+      path: '/',
+    });
+
+    res.json({
+      success: true,
+      message: 'Logged out successfully.',
+    });
+  });
+
+  return router;
+}

apps/server/src/routes/backlog-plan/common.ts

@@ -0,0 +1,39 @@
+/**
+ * Common utilities for backlog plan routes
+ */
+
+import { createLogger } from '@automaker/utils';
+
+const logger = createLogger('BacklogPlan');
+
+// State for tracking running generation
+let isRunning = false;
+let currentAbortController: AbortController | null = null;
+
+export function getBacklogPlanStatus(): { isRunning: boolean } {
+  return { isRunning };
+}
+
+export function setRunningState(running: boolean, abortController?: AbortController | null): void {
+  isRunning = running;
+  if (abortController !== undefined) {
+    currentAbortController = abortController;
+  }
+}
+
+export function getAbortController(): AbortController | null {
+  return currentAbortController;
+}
+
+export function getErrorMessage(error: unknown): string {
+  if (error instanceof Error) {
+    return error.message;
+  }
+  return String(error);
+}
+
+export function logError(error: unknown, context: string): void {
+  logger.error(`[BacklogPlan] ${context}:`, getErrorMessage(error));
+}
+
+export { logger };

apps/server/src/routes/backlog-plan/generate-plan.ts

@@ -0,0 +1,162 @@
+/**
+ * Generate backlog plan using Claude AI
+ */
+
+import type { EventEmitter } from '../../lib/events.js';
+import type { Feature, BacklogPlanResult, BacklogChange, DependencyUpdate } from '@automaker/types';
+import { FeatureLoader } from '../../services/feature-loader.js';
+import { ProviderFactory } from '../../providers/provider-factory.js';
+import { logger, setRunningState, getErrorMessage } from './common.js';
+import type { SettingsService } from '../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting, getPromptCustomization } from '../../lib/settings-helpers.js';
+
+const featureLoader = new FeatureLoader();
+
+/**
+ * Format features for the AI prompt
+ */
+function formatFeaturesForPrompt(features: Feature[]): string {
+  if (features.length === 0) {
+    return 'No features in backlog yet.';
+  }
+
+  return features
+    .map((f) => {
+      const deps = f.dependencies?.length ? `Dependencies: [${f.dependencies.join(', ')}]` : '';
+      const priority = f.priority !== undefined ? `Priority: ${f.priority}` : '';
+      return `- ID: ${f.id}
+  Title: ${f.title || 'Untitled'}
+  Description: ${f.description}
+  Category: ${f.category}
+  Status: ${f.status || 'backlog'}
+  ${priority}
+  ${deps}`.trim();
+    })
+    .join('\n\n');
+}
+
+/**
+ * Parse the AI response into a BacklogPlanResult
+ */
+function parsePlanResponse(response: string): BacklogPlanResult {
+  try {
+    // Try to extract JSON from the response
+    const jsonMatch = response.match(/```json\n?([\s\S]*?)\n?```/);
+    if (jsonMatch) {
+      return JSON.parse(jsonMatch[1]);
+    }
+
+    // Try to parse the whole response as JSON
+    return JSON.parse(response);
+  } catch {
+    // If parsing fails, return an empty result
+    logger.warn('[BacklogPlan] Failed to parse AI response as JSON');
+    return {
+      changes: [],
+      summary: 'Failed to parse AI response',
+      dependencyUpdates: [],
+    };
+  }
+}
+
+/**
+ * Generate a backlog modification plan based on user prompt
+ */
+export async function generateBacklogPlan(
+  projectPath: string,
+  prompt: string,
+  events: EventEmitter,
+  abortController: AbortController,
+  settingsService?: SettingsService,
+  model?: string
+): Promise<BacklogPlanResult> {
+  try {
+    // Load current features
+    const features = await featureLoader.getAll(projectPath);
+
+    events.emit('backlog-plan:event', {
+      type: 'backlog_plan_progress',
+      content: `Loaded ${features.length} features from backlog`,
+    });
+
+    // Load prompts from settings
+    const prompts = await getPromptCustomization(settingsService, '[BacklogPlan]');
+
+    // Build the system prompt
+    const systemPrompt = prompts.backlogPlan.systemPrompt;
+
+    // Build the user prompt from template
+    const currentFeatures = formatFeaturesForPrompt(features);
+    const userPrompt = prompts.backlogPlan.userPromptTemplate
+      .replace('{{currentFeatures}}', currentFeatures)
+      .replace('{{userRequest}}', prompt);
+
+    events.emit('backlog-plan:event', {
+      type: 'backlog_plan_progress',
+      content: 'Generating plan with AI...',
+    });
+
+    // Get the model to use
+    const effectiveModel = model || 'sonnet';
+    const provider = ProviderFactory.getProviderForModel(effectiveModel);
+
+    // Get autoLoadClaudeMd setting
+    const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+      projectPath,
+      settingsService,
+      '[BacklogPlan]'
+    );
+
+    // Execute the query
+    const stream = provider.executeQuery({
+      prompt: userPrompt,
+      model: effectiveModel,
+      cwd: projectPath,
+      systemPrompt,
+      maxTurns: 1,
+      allowedTools: [], // No tools needed for this
+      abortController,
+      settingSources: autoLoadClaudeMd ? ['user', 'project'] : undefined,
+    });
+
+    let responseText = '';
+
+    for await (const msg of stream) {
+      if (abortController.signal.aborted) {
+        throw new Error('Generation aborted');
+      }
+
+      if (msg.type === 'assistant') {
+        if (msg.message?.content) {
+          for (const block of msg.message.content) {
+            if (block.type === 'text') {
+              responseText += block.text;
+            }
+          }
+        }
+      }
+    }
+
+    // Parse the response
+    const result = parsePlanResponse(responseText);
+
+    events.emit('backlog-plan:event', {
+      type: 'backlog_plan_complete',
+      result,
+    });
+
+    return result;
+  } catch (error) {
+    const errorMessage = getErrorMessage(error);
+    logger.error('[BacklogPlan] Generation failed:', errorMessage);
+
+    events.emit('backlog-plan:event', {
+      type: 'backlog_plan_error',
+      error: errorMessage,
+    });
+
+    throw error;
+  } finally {
+    setRunningState(false, null);
+  }
+}

apps/server/src/routes/backlog-plan/index.ts

@@ -0,0 +1,30 @@
+/**
+ * Backlog Plan routes - HTTP API for AI-assisted backlog modification
+ */
+
+import { Router } from 'express';
+import type { EventEmitter } from '../../lib/events.js';
+import { validatePathParams } from '../../middleware/validate-paths.js';
+import { createGenerateHandler } from './routes/generate.js';
+import { createStopHandler } from './routes/stop.js';
+import { createStatusHandler } from './routes/status.js';
+import { createApplyHandler } from './routes/apply.js';
+import type { SettingsService } from '../../services/settings-service.js';
+
+export function createBacklogPlanRoutes(
+  events: EventEmitter,
+  settingsService?: SettingsService
+): Router {
+  const router = Router();
+
+  router.post(
+    '/generate',
+    validatePathParams('projectPath'),
+    createGenerateHandler(events, settingsService)
+  );
+  router.post('/stop', createStopHandler());
+  router.get('/status', createStatusHandler());
+  router.post('/apply', validatePathParams('projectPath'), createApplyHandler());
+
+  return router;
+}

apps/server/src/routes/backlog-plan/routes/apply.ts

@@ -0,0 +1,147 @@
+/**
+ * POST /apply endpoint - Apply a backlog plan
+ */
+
+import type { Request, Response } from 'express';
+import type { BacklogPlanResult, BacklogChange, Feature } from '@automaker/types';
+import { FeatureLoader } from '../../../services/feature-loader.js';
+import { getErrorMessage, logError, logger } from '../common.js';
+
+const featureLoader = new FeatureLoader();
+
+export function createApplyHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, plan } = req.body as {
+        projectPath: string;
+        plan: BacklogPlanResult;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath required' });
+        return;
+      }
+
+      if (!plan || !plan.changes) {
+        res.status(400).json({ success: false, error: 'plan with changes required' });
+        return;
+      }
+
+      const appliedChanges: string[] = [];
+
+      // Load current features for dependency validation
+      const allFeatures = await featureLoader.getAll(projectPath);
+      const featureMap = new Map(allFeatures.map((f) => [f.id, f]));
+
+      // Process changes in order: deletes first, then adds, then updates
+      // This ensures we can remove dependencies before they cause issues
+
+      // 1. First pass: Handle deletes
+      const deletions = plan.changes.filter((c) => c.type === 'delete');
+      for (const change of deletions) {
+        if (!change.featureId) continue;
+
+        try {
+          // Before deleting, update any features that depend on this one
+          for (const feature of allFeatures) {
+            if (feature.dependencies?.includes(change.featureId)) {
+              const newDeps = feature.dependencies.filter((d) => d !== change.featureId);
+              await featureLoader.update(projectPath, feature.id, { dependencies: newDeps });
+              logger.info(
+                `[BacklogPlan] Removed dependency ${change.featureId} from ${feature.id}`
+              );
+            }
+          }
+
+          // Now delete the feature
+          const deleted = await featureLoader.delete(projectPath, change.featureId);
+          if (deleted) {
+            appliedChanges.push(`deleted:${change.featureId}`);
+            featureMap.delete(change.featureId);
+            logger.info(`[BacklogPlan] Deleted feature ${change.featureId}`);
+          }
+        } catch (error) {
+          logger.error(
+            `[BacklogPlan] Failed to delete ${change.featureId}:`,
+            getErrorMessage(error)
+          );
+        }
+      }
+
+      // 2. Second pass: Handle adds
+      const additions = plan.changes.filter((c) => c.type === 'add');
+      for (const change of additions) {
+        if (!change.feature) continue;
+
+        try {
+          // Create the new feature
+          const newFeature = await featureLoader.create(projectPath, {
+            title: change.feature.title,
+            description: change.feature.description || '',
+            category: change.feature.category || 'Uncategorized',
+            dependencies: change.feature.dependencies,
+            priority: change.feature.priority,
+            status: 'backlog',
+          });
+
+          appliedChanges.push(`added:${newFeature.id}`);
+          featureMap.set(newFeature.id, newFeature);
+          logger.info(`[BacklogPlan] Created feature ${newFeature.id}: ${newFeature.title}`);
+        } catch (error) {
+          logger.error(`[BacklogPlan] Failed to add feature:`, getErrorMessage(error));
+        }
+      }
+
+      // 3. Third pass: Handle updates
+      const updates = plan.changes.filter((c) => c.type === 'update');
+      for (const change of updates) {
+        if (!change.featureId || !change.feature) continue;
+
+        try {
+          const updated = await featureLoader.update(projectPath, change.featureId, change.feature);
+          appliedChanges.push(`updated:${change.featureId}`);
+          featureMap.set(change.featureId, updated);
+          logger.info(`[BacklogPlan] Updated feature ${change.featureId}`);
+        } catch (error) {
+          logger.error(
+            `[BacklogPlan] Failed to update ${change.featureId}:`,
+            getErrorMessage(error)
+          );
+        }
+      }
+
+      // 4. Apply dependency updates from the plan
+      if (plan.dependencyUpdates) {
+        for (const depUpdate of plan.dependencyUpdates) {
+          try {
+            const feature = featureMap.get(depUpdate.featureId);
+            if (feature) {
+              const currentDeps = feature.dependencies || [];
+              const newDeps = currentDeps
+                .filter((d) => !depUpdate.removedDependencies.includes(d))
+                .concat(depUpdate.addedDependencies.filter((d) => !currentDeps.includes(d)));
+
+              await featureLoader.update(projectPath, depUpdate.featureId, {
+                dependencies: newDeps,
+              });
+              logger.info(`[BacklogPlan] Updated dependencies for ${depUpdate.featureId}`);
+            }
+          } catch (error) {
+            logger.error(
+              `[BacklogPlan] Failed to update dependencies for ${depUpdate.featureId}:`,
+              getErrorMessage(error)
+            );
+          }
+        }
+      }
+
+      res.json({
+        success: true,
+        appliedChanges,
+      });
+    } catch (error) {
+      logError(error, 'Apply backlog plan failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/backlog-plan/routes/generate.ts

@@ -0,0 +1,62 @@
+/**
+ * POST /generate endpoint - Generate a backlog plan
+ */
+
+import type { Request, Response } from 'express';
+import type { EventEmitter } from '../../../lib/events.js';
+import { getBacklogPlanStatus, setRunningState, getErrorMessage, logError } from '../common.js';
+import { generateBacklogPlan } from '../generate-plan.js';
+import type { SettingsService } from '../../../services/settings-service.js';
+
+export function createGenerateHandler(events: EventEmitter, settingsService?: SettingsService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, prompt, model } = req.body as {
+        projectPath: string;
+        prompt: string;
+        model?: string;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath required' });
+        return;
+      }
+
+      if (!prompt) {
+        res.status(400).json({ success: false, error: 'prompt required' });
+        return;
+      }
+
+      const { isRunning } = getBacklogPlanStatus();
+      if (isRunning) {
+        res.json({
+          success: false,
+          error: 'Backlog plan generation is already running',
+        });
+        return;
+      }
+
+      setRunningState(true);
+      const abortController = new AbortController();
+      setRunningState(true, abortController);
+
+      // Start generation in background
+      generateBacklogPlan(projectPath, prompt, events, abortController, settingsService, model)
+        .catch((error) => {
+          logError(error, 'Generate backlog plan failed (background)');
+          events.emit('backlog-plan:event', {
+            type: 'backlog_plan_error',
+            error: getErrorMessage(error),
+          });
+        })
+        .finally(() => {
+          setRunningState(false, null);
+        });
+
+      res.json({ success: true });
+    } catch (error) {
+      logError(error, 'Generate backlog plan failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/backlog-plan/routes/status.ts

@@ -0,0 +1,18 @@
+/**
+ * GET /status endpoint - Get backlog plan generation status
+ */
+
+import type { Request, Response } from 'express';
+import { getBacklogPlanStatus, getErrorMessage, logError } from '../common.js';
+
+export function createStatusHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      const status = getBacklogPlanStatus();
+      res.json({ success: true, ...status });
+    } catch (error) {
+      logError(error, 'Get backlog plan status failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/backlog-plan/routes/stop.ts

@@ -0,0 +1,22 @@
+/**
+ * POST /stop endpoint - Stop the current backlog plan generation
+ */
+
+import type { Request, Response } from 'express';
+import { getAbortController, setRunningState, getErrorMessage, logError } from '../common.js';
+
+export function createStopHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      const abortController = getAbortController();
+      if (abortController) {
+        abortController.abort();
+        setRunningState(false, null);
+      }
+      res.json({ success: true });
+    } catch (error) {
+      logError(error, 'Stop backlog plan failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/context/index.ts

@@ -8,17 +8,19 @@
 import { Router } from 'express';
 import { createDescribeImageHandler } from './routes/describe-image.js';
 import { createDescribeFileHandler } from './routes/describe-file.js';
+import type { SettingsService } from '../../services/settings-service.js';
 
 /**
  * Create the context router
  *
+ * @param settingsService - Optional settings service for loading autoLoadClaudeMd setting
  * @returns Express router with context endpoints
  */
-export function createContextRoutes(): Router {
+export function createContextRoutes(settingsService?: SettingsService): Router {
   const router = Router();
 
-  router.post('/describe-image', createDescribeImageHandler());
-  router.post('/describe-file', createDescribeFileHandler());
+  router.post('/describe-image', createDescribeImageHandler(settingsService));
+  router.post('/describe-file', createDescribeFileHandler(settingsService));
 
   return router;
 }

apps/server/src/routes/context/routes/describe-file.ts

@@ -17,6 +17,8 @@ import { PathNotAllowedError } from '@automaker/platform';
 import { createCustomOptions } from '../../../lib/sdk-options.js';
 import * as secureFs from '../../../lib/secure-fs.js';
 import * as path from 'path';
+import type { SettingsService } from '../../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('DescribeFile');
 
@@ -72,9 +74,12 @@ async function extractTextFromStream(
 /**
  * Create the describe-file request handler
  *
+ * @param settingsService - Optional settings service for loading autoLoadClaudeMd setting
  * @returns Express request handler for file description
  */
-export function createDescribeFileHandler(): (req: Request, res: Response) => Promise<void> {
+export function createDescribeFileHandler(
+  settingsService?: SettingsService
+): (req: Request, res: Response) => Promise<void> {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { filePath } = req.body as DescribeFileRequestBody;
@@ -165,6 +170,13 @@ File: ${fileName}${truncated ? ' (truncated)' : ''}`;
       // Use the file's directory as the working directory
       const cwd = path.dirname(resolvedPath);
 
+      // Load autoLoadClaudeMd setting
+      const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+        cwd,
+        settingsService,
+        '[DescribeFile]'
+      );
+
       // Use centralized SDK options with proper cwd validation
       // No tools needed since we're passing file content directly
       const sdkOptions = createCustomOptions({
@@ -172,6 +184,7 @@ File: ${fileName}${truncated ? ' (truncated)' : ''}`;
         model: CLAUDE_MODEL_MAP.haiku,
         maxTurns: 1,
         allowedTools: [],
+        autoLoadClaudeMd,
         sandbox: { enabled: true, autoAllowBashIfSandboxed: true },
       });
 

apps/server/src/routes/context/routes/describe-image.ts

@@ -15,8 +15,10 @@ import { query } from '@anthropic-ai/claude-agent-sdk';
 import { createLogger, readImageAsBase64 } from '@automaker/utils';
 import { CLAUDE_MODEL_MAP } from '@automaker/types';
 import { createCustomOptions } from '../../../lib/sdk-options.js';
-import * as fs from 'fs';
+import * as secureFs from '../../../lib/secure-fs.js';
 import * as path from 'path';
+import type { SettingsService } from '../../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('DescribeImage');
 
@@ -55,13 +57,13 @@ function filterSafeHeaders(headers: Record<string, unknown>): Record<string, unk
  */
 function findActualFilePath(requestedPath: string): string | null {
   // First, try the exact path
-  if (fs.existsSync(requestedPath)) {
+  if (secureFs.existsSync(requestedPath)) {
     return requestedPath;
   }
 
   // Try with Unicode normalization
   const normalizedPath = requestedPath.normalize('NFC');
-  if (fs.existsSync(normalizedPath)) {
+  if (secureFs.existsSync(normalizedPath)) {
     return normalizedPath;
   }
 
@@ -70,12 +72,12 @@ function findActualFilePath(requestedPath: string): string | null {
   const dir = path.dirname(requestedPath);
   const baseName = path.basename(requestedPath);
 
-  if (!fs.existsSync(dir)) {
+  if (!secureFs.existsSync(dir)) {
     return null;
   }
 
   try {
-    const files = fs.readdirSync(dir);
+    const files = secureFs.readdirSync(dir);
 
     // Normalize the requested basename for comparison
     // Replace various space-like characters with regular space for comparison
@@ -226,9 +228,12 @@ async function extractTextFromStream(
  * Uses Claude SDK query with multi-part content blocks to include the image (base64),
  * matching the agent runner behavior.
  *
+ * @param settingsService - Optional settings service for loading autoLoadClaudeMd setting
  * @returns Express request handler for image description
  */
-export function createDescribeImageHandler(): (req: Request, res: Response) => Promise<void> {
+export function createDescribeImageHandler(
+  settingsService?: SettingsService
+): (req: Request, res: Response) => Promise<void> {
   return async (req: Request, res: Response): Promise<void> => {
     const requestId = `describe-image-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
     const startedAt = Date.now();
@@ -276,9 +281,9 @@ export function createDescribeImageHandler(): (req: Request, res: Response) => P
       }
 
       // Log path + stats (this is often where issues start: missing file, perms, size)
-      let stat: fs.Stats | null = null;
+      let stat: ReturnType<typeof secureFs.statSync> | null = null;
       try {
-        stat = fs.statSync(actualPath);
+        stat = secureFs.statSync(actualPath);
         logger.info(
           `[${requestId}] fileStats size=${stat.size} bytes mtime=${stat.mtime.toISOString()}`
         );
@@ -325,12 +330,20 @@ export function createDescribeImageHandler(): (req: Request, res: Response) => P
       const cwd = path.dirname(actualPath);
       logger.info(`[${requestId}] Using cwd=${cwd}`);
 
+      // Load autoLoadClaudeMd setting
+      const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+        cwd,
+        settingsService,
+        '[DescribeImage]'
+      );
+
       // Use the same centralized option builder used across the server (validates cwd)
       const sdkOptions = createCustomOptions({
         cwd,
         model: CLAUDE_MODEL_MAP.haiku,
         maxTurns: 1,
         allowedTools: [],
+        autoLoadClaudeMd,
         sandbox: { enabled: true, autoAllowBashIfSandboxed: true },
       });
 

apps/server/src/routes/enhance-prompt/index.ts

@@ -6,17 +6,19 @@
  */
 
 import { Router } from 'express';
+import type { SettingsService } from '../../services/settings-service.js';
 import { createEnhanceHandler } from './routes/enhance.js';
 
 /**
  * Create the enhance-prompt router
  *
+ * @param settingsService - Settings service for loading custom prompts
  * @returns Express router with enhance-prompt endpoints
  */
-export function createEnhancePromptRoutes(): Router {
+export function createEnhancePromptRoutes(settingsService?: SettingsService): Router {
   const router = Router();
 
-  router.post('/', createEnhanceHandler());
+  router.post('/', createEnhanceHandler(settingsService));
 
   return router;
 }

apps/server/src/routes/enhance-prompt/routes/enhance.ts

@@ -10,8 +10,9 @@ import { query } from '@anthropic-ai/claude-agent-sdk';
 import { createLogger } from '@automaker/utils';
 import { resolveModelString } from '@automaker/model-resolver';
 import { CLAUDE_MODEL_MAP } from '@automaker/types';
+import type { SettingsService } from '../../../services/settings-service.js';
+import { getPromptCustomization } from '../../../lib/settings-helpers.js';
 import {
-  getSystemPrompt,
   buildUserPrompt,
   isValidEnhancementMode,
   type EnhancementMode,
@@ -83,9 +84,12 @@ async function extractTextFromStream(
 /**
  * Create the enhance request handler
  *
+ * @param settingsService - Optional settings service for loading custom prompts
  * @returns Express request handler for text enhancement
  */
-export function createEnhanceHandler(): (req: Request, res: Response) => Promise<void> {
+export function createEnhanceHandler(
+  settingsService?: SettingsService
+): (req: Request, res: Response) => Promise<void> {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { originalText, enhancementMode, model } = req.body as EnhanceRequestBody;
@@ -128,8 +132,19 @@ export function createEnhanceHandler(): (req: Request, res: Response) => Promise
 
       logger.info(`Enhancing text with mode: ${validMode}, length: ${trimmedText.length} chars`);
 
-      // Get the system prompt for this mode
-      const systemPrompt = getSystemPrompt(validMode);
+      // Load enhancement prompts from settings (merges custom + defaults)
+      const prompts = await getPromptCustomization(settingsService, '[EnhancePrompt]');
+
+      // Get the system prompt for this mode from merged prompts
+      const systemPromptMap: Record<EnhancementMode, string> = {
+        improve: prompts.enhancement.improveSystemPrompt,
+        technical: prompts.enhancement.technicalSystemPrompt,
+        simplify: prompts.enhancement.simplifySystemPrompt,
+        acceptance: prompts.enhancement.acceptanceSystemPrompt,
+      };
+      const systemPrompt = systemPromptMap[validMode];
+
+      logger.debug(`Using ${validMode} system prompt (length: ${systemPrompt.length} chars)`);
 
       // Build the user prompt with few-shot examples
       // This helps the model understand this is text transformation, not a coding task

apps/server/src/routes/fs/routes/browse.ts

@@ -6,7 +6,7 @@ import type { Request, Response } from 'express';
 import * as secureFs from '../../../lib/secure-fs.js';
 import os from 'os';
 import path from 'path';
-import { getAllowedRootDirectory, PathNotAllowedError } from '@automaker/platform';
+import { getAllowedRootDirectory, PathNotAllowedError, isPathAllowed } from '@automaker/platform';
 import { getErrorMessage, logError } from '../common.js';
 
 export function createBrowseHandler() {
@@ -40,9 +40,16 @@ export function createBrowseHandler() {
         return drives;
       };
 
-      // Get parent directory
+      // Get parent directory - only if it's within the allowed root
       const parentPath = path.dirname(targetPath);
-      const hasParent = parentPath !== targetPath;
+
+      // Determine if parent navigation should be allowed:
+      // 1. Must have a different parent (not at filesystem root)
+      // 2. If ALLOWED_ROOT_DIRECTORY is set, parent must be within it
+      const hasParent = parentPath !== targetPath && isPathAllowed(parentPath);
+
+      // Security: Don't expose parent path outside allowed root
+      const safeParentPath = hasParent ? parentPath : null;
 
       // Get available drives
       const drives = await detectDrives();
@@ -70,7 +77,7 @@ export function createBrowseHandler() {
         res.json({
           success: true,
           currentPath: targetPath,
-          parentPath: hasParent ? parentPath : null,
+          parentPath: safeParentPath,
           directories,
           drives,
         });
@@ -84,7 +91,7 @@ export function createBrowseHandler() {
           res.json({
             success: true,
             currentPath: targetPath,
-            parentPath: hasParent ? parentPath : null,
+            parentPath: safeParentPath,
             directories: [],
             drives,
             warning:

apps/server/src/routes/fs/routes/validate-path.ts

@@ -5,7 +5,7 @@
 import type { Request, Response } from 'express';
 import * as secureFs from '../../../lib/secure-fs.js';
 import path from 'path';
-import { isPathAllowed } from '@automaker/platform';
+import { isPathAllowed, PathNotAllowedError, getAllowedRootDirectory } from '@automaker/platform';
 import { getErrorMessage, logError } from '../common.js';
 
 export function createValidatePathHandler() {
@@ -20,6 +20,20 @@ export function createValidatePathHandler() {
 
       const resolvedPath = path.resolve(filePath);
 
+      // Validate path against ALLOWED_ROOT_DIRECTORY before checking if it exists
+      if (!isPathAllowed(resolvedPath)) {
+        const allowedRoot = getAllowedRootDirectory();
+        const errorMessage = allowedRoot
+          ? `Path not allowed: ${filePath}. Must be within ALLOWED_ROOT_DIRECTORY: ${allowedRoot}`
+          : `Path not allowed: ${filePath}`;
+        res.status(403).json({
+          success: false,
+          error: errorMessage,
+          isAllowed: false,
+        });
+        return;
+      }
+
       // Check if path exists
       try {
         const stats = await secureFs.stat(resolvedPath);
@@ -32,7 +46,7 @@ export function createValidatePathHandler() {
         res.json({
           success: true,
           path: resolvedPath,
-          isAllowed: isPathAllowed(resolvedPath),
+          isAllowed: true,
         });
       } catch {
         res.status(400).json({ success: false, error: 'Path does not exist' });

apps/server/src/routes/github/index.ts

@@ -3,16 +3,56 @@
  */
 
 import { Router } from 'express';
+import type { EventEmitter } from '../../lib/events.js';
+import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createCheckGitHubRemoteHandler } from './routes/check-github-remote.js';
 import { createListIssuesHandler } from './routes/list-issues.js';
 import { createListPRsHandler } from './routes/list-prs.js';
+import { createListCommentsHandler } from './routes/list-comments.js';
+import { createValidateIssueHandler } from './routes/validate-issue.js';
+import {
+  createValidationStatusHandler,
+  createValidationStopHandler,
+  createGetValidationsHandler,
+  createDeleteValidationHandler,
+  createMarkViewedHandler,
+} from './routes/validation-endpoints.js';
+import type { SettingsService } from '../../services/settings-service.js';
 
-export function createGitHubRoutes(): Router {
+export function createGitHubRoutes(
+  events: EventEmitter,
+  settingsService?: SettingsService
+): Router {
   const router = Router();
 
-  router.post('/check-remote', createCheckGitHubRemoteHandler());
-  router.post('/issues', createListIssuesHandler());
-  router.post('/prs', createListPRsHandler());
+  router.post('/check-remote', validatePathParams('projectPath'), createCheckGitHubRemoteHandler());
+  router.post('/issues', validatePathParams('projectPath'), createListIssuesHandler());
+  router.post('/prs', validatePathParams('projectPath'), createListPRsHandler());
+  router.post('/issue-comments', validatePathParams('projectPath'), createListCommentsHandler());
+  router.post(
+    '/validate-issue',
+    validatePathParams('projectPath'),
+    createValidateIssueHandler(events, settingsService)
+  );
+
+  // Validation management endpoints
+  router.post(
+    '/validation-status',
+    validatePathParams('projectPath'),
+    createValidationStatusHandler()
+  );
+  router.post('/validation-stop', validatePathParams('projectPath'), createValidationStopHandler());
+  router.post('/validations', validatePathParams('projectPath'), createGetValidationsHandler());
+  router.post(
+    '/validation-delete',
+    validatePathParams('projectPath'),
+    createDeleteValidationHandler()
+  );
+  router.post(
+    '/validation-mark-viewed',
+    validatePathParams('projectPath'),
+    createMarkViewedHandler(events)
+  );
 
   return router;
 }

apps/server/src/routes/github/routes/list-comments.ts

@@ -0,0 +1,212 @@
+/**
+ * POST /issue-comments endpoint - Fetch comments for a GitHub issue
+ */
+
+import { spawn } from 'child_process';
+import type { Request, Response } from 'express';
+import type { GitHubComment, IssueCommentsResult } from '@automaker/types';
+import { execEnv, getErrorMessage, logError } from './common.js';
+import { checkGitHubRemote } from './check-github-remote.js';
+
+interface ListCommentsRequest {
+  projectPath: string;
+  issueNumber: number;
+  cursor?: string;
+}
+
+interface GraphQLComment {
+  id: string;
+  author: {
+    login: string;
+    avatarUrl?: string;
+  } | null;
+  body: string;
+  createdAt: string;
+  updatedAt: string;
+}
+
+interface GraphQLResponse {
+  data?: {
+    repository?: {
+      issue?: {
+        comments: {
+          totalCount: number;
+          pageInfo: {
+            hasNextPage: boolean;
+            endCursor: string | null;
+          };
+          nodes: GraphQLComment[];
+        };
+      };
+    };
+  };
+  errors?: Array<{ message: string }>;
+}
+
+/** Timeout for GitHub API requests in milliseconds */
+const GITHUB_API_TIMEOUT_MS = 30000;
+
+/**
+ * Validate cursor format (GraphQL cursors are typically base64 strings)
+ */
+function isValidCursor(cursor: string): boolean {
+  return /^[A-Za-z0-9+/=]+$/.test(cursor);
+}
+
+/**
+ * Fetch comments for a specific issue using GitHub GraphQL API
+ */
+async function fetchIssueComments(
+  projectPath: string,
+  owner: string,
+  repo: string,
+  issueNumber: number,
+  cursor?: string
+): Promise<IssueCommentsResult> {
+  // Validate cursor format to prevent potential injection
+  if (cursor && !isValidCursor(cursor)) {
+    throw new Error('Invalid cursor format');
+  }
+
+  // Use GraphQL variables instead of string interpolation for safety
+  const query = `
+    query GetIssueComments($owner: String!, $repo: String!, $issueNumber: Int!, $cursor: String) {
+      repository(owner: $owner, name: $repo) {
+        issue(number: $issueNumber) {
+          comments(first: 50, after: $cursor) {
+            totalCount
+            pageInfo {
+              hasNextPage
+              endCursor
+            }
+            nodes {
+              id
+              author {
+                login
+                avatarUrl
+              }
+              body
+              createdAt
+              updatedAt
+            }
+          }
+        }
+      }
+    }`;
+
+  const variables = {
+    owner,
+    repo,
+    issueNumber,
+    cursor: cursor || null,
+  };
+
+  const requestBody = JSON.stringify({ query, variables });
+
+  const response = await new Promise<GraphQLResponse>((resolve, reject) => {
+    const gh = spawn('gh', ['api', 'graphql', '--input', '-'], {
+      cwd: projectPath,
+      env: execEnv,
+    });
+
+    // Add timeout to prevent hanging indefinitely
+    const timeoutId = setTimeout(() => {
+      gh.kill();
+      reject(new Error('GitHub API request timed out'));
+    }, GITHUB_API_TIMEOUT_MS);
+
+    let stdout = '';
+    let stderr = '';
+    gh.stdout.on('data', (data: Buffer) => (stdout += data.toString()));
+    gh.stderr.on('data', (data: Buffer) => (stderr += data.toString()));
+
+    gh.on('close', (code) => {
+      clearTimeout(timeoutId);
+      if (code !== 0) {
+        return reject(new Error(`gh process exited with code ${code}: ${stderr}`));
+      }
+      try {
+        resolve(JSON.parse(stdout));
+      } catch (e) {
+        reject(e);
+      }
+    });
+
+    gh.stdin.write(requestBody);
+    gh.stdin.end();
+  });
+
+  if (response.errors && response.errors.length > 0) {
+    throw new Error(response.errors[0].message);
+  }
+
+  const commentsData = response.data?.repository?.issue?.comments;
+
+  if (!commentsData) {
+    throw new Error('Issue not found or no comments data available');
+  }
+
+  const comments: GitHubComment[] = commentsData.nodes.map((node) => ({
+    id: node.id,
+    author: {
+      login: node.author?.login || 'ghost',
+      avatarUrl: node.author?.avatarUrl,
+    },
+    body: node.body,
+    createdAt: node.createdAt,
+    updatedAt: node.updatedAt,
+  }));
+
+  return {
+    comments,
+    totalCount: commentsData.totalCount,
+    hasNextPage: commentsData.pageInfo.hasNextPage,
+    endCursor: commentsData.pageInfo.endCursor || undefined,
+  };
+}
+
+export function createListCommentsHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber, cursor } = req.body as ListCommentsRequest;
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!issueNumber || typeof issueNumber !== 'number') {
+        res
+          .status(400)
+          .json({ success: false, error: 'issueNumber is required and must be a number' });
+        return;
+      }
+
+      // First check if this is a GitHub repo and get owner/repo
+      const remoteStatus = await checkGitHubRemote(projectPath);
+      if (!remoteStatus.hasGitHubRemote || !remoteStatus.owner || !remoteStatus.repo) {
+        res.status(400).json({
+          success: false,
+          error: 'Project does not have a GitHub remote',
+        });
+        return;
+      }
+
+      const result = await fetchIssueComments(
+        projectPath,
+        remoteStatus.owner,
+        remoteStatus.repo,
+        issueNumber,
+        cursor
+      );
+
+      res.json({
+        success: true,
+        ...result,
+      });
+    } catch (error) {
+      logError(error, `Fetch comments for issue failed`);
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/github/routes/list-issues.ts

@@ -2,6 +2,7 @@
  * POST /list-issues endpoint - List GitHub issues for a project
  */
 
+import { spawn } from 'child_process';
 import type { Request, Response } from 'express';
 import { execAsync, execEnv, getErrorMessage, logError } from './common.js';
 import { checkGitHubRemote } from './check-github-remote.js';
@@ -13,6 +14,19 @@ export interface GitHubLabel {
 
 export interface GitHubAuthor {
   login: string;
+  avatarUrl?: string;
+}
+
+export interface GitHubAssignee {
+  login: string;
+  avatarUrl?: string;
+}
+
+export interface LinkedPullRequest {
+  number: number;
+  title: string;
+  state: string;
+  url: string;
 }
 
 export interface GitHubIssue {
@@ -24,6 +38,8 @@ export interface GitHubIssue {
   labels: GitHubLabel[];
   url: string;
   body: string;
+  assignees: GitHubAssignee[];
+  linkedPRs?: LinkedPullRequest[];
 }
 
 export interface ListIssuesResult {
@@ -33,6 +49,146 @@ export interface ListIssuesResult {
   error?: string;
 }
 
+/**
+ * Fetch linked PRs for a list of issues using GitHub GraphQL API
+ */
+async function fetchLinkedPRs(
+  projectPath: string,
+  owner: string,
+  repo: string,
+  issueNumbers: number[]
+): Promise<Map<number, LinkedPullRequest[]>> {
+  const linkedPRsMap = new Map<number, LinkedPullRequest[]>();
+
+  if (issueNumbers.length === 0) {
+    return linkedPRsMap;
+  }
+
+  // Build GraphQL query for batch fetching linked PRs
+  // We fetch up to 20 issues at a time to avoid query limits
+  const batchSize = 20;
+  for (let i = 0; i < issueNumbers.length; i += batchSize) {
+    const batch = issueNumbers.slice(i, i + batchSize);
+
+    const issueQueries = batch
+      .map(
+        (num, idx) => `
+        issue${idx}: issue(number: ${num}) {
+          number
+          timelineItems(first: 10, itemTypes: [CROSS_REFERENCED_EVENT, CONNECTED_EVENT]) {
+            nodes {
+              ... on CrossReferencedEvent {
+                source {
+                  ... on PullRequest {
+                    number
+                    title
+                    state
+                    url
+                  }
+                }
+              }
+              ... on ConnectedEvent {
+                subject {
+                  ... on PullRequest {
+                    number
+                    title
+                    state
+                    url
+                  }
+                }
+              }
+            }
+          }
+        }`
+      )
+      .join('\n');
+
+    const query = `{
+      repository(owner: "${owner}", name: "${repo}") {
+        ${issueQueries}
+      }
+    }`;
+
+    try {
+      // Use spawn with stdin to avoid shell injection vulnerabilities
+      // --input - reads the JSON request body from stdin
+      const requestBody = JSON.stringify({ query });
+      const response = await new Promise<Record<string, unknown>>((resolve, reject) => {
+        const gh = spawn('gh', ['api', 'graphql', '--input', '-'], {
+          cwd: projectPath,
+          env: execEnv,
+        });
+
+        let stdout = '';
+        let stderr = '';
+        gh.stdout.on('data', (data: Buffer) => (stdout += data.toString()));
+        gh.stderr.on('data', (data: Buffer) => (stderr += data.toString()));
+
+        gh.on('close', (code) => {
+          if (code !== 0) {
+            return reject(new Error(`gh process exited with code ${code}: ${stderr}`));
+          }
+          try {
+            resolve(JSON.parse(stdout));
+          } catch (e) {
+            reject(e);
+          }
+        });
+
+        gh.stdin.write(requestBody);
+        gh.stdin.end();
+      });
+
+      const repoData = (response?.data as Record<string, unknown>)?.repository as Record<
+        string,
+        unknown
+      > | null;
+
+      if (repoData) {
+        batch.forEach((issueNum, idx) => {
+          const issueData = repoData[`issue${idx}`] as {
+            timelineItems?: {
+              nodes?: Array<{
+                source?: { number?: number; title?: string; state?: string; url?: string };
+                subject?: { number?: number; title?: string; state?: string; url?: string };
+              }>;
+            };
+          } | null;
+          if (issueData?.timelineItems?.nodes) {
+            const linkedPRs: LinkedPullRequest[] = [];
+            const seenPRs = new Set<number>();
+
+            for (const node of issueData.timelineItems.nodes) {
+              const pr = node?.source || node?.subject;
+              if (pr?.number && !seenPRs.has(pr.number)) {
+                seenPRs.add(pr.number);
+                linkedPRs.push({
+                  number: pr.number,
+                  title: pr.title || '',
+                  state: (pr.state || '').toLowerCase(),
+                  url: pr.url || '',
+                });
+              }
+            }
+
+            if (linkedPRs.length > 0) {
+              linkedPRsMap.set(issueNum, linkedPRs);
+            }
+          }
+        });
+      }
+    } catch (error) {
+      // If GraphQL fails, continue without linked PRs
+      console.warn(
+        'Failed to fetch linked PRs via GraphQL:',
+        error instanceof Error ? error.message : error
+      );
+    }
+  }
+
+  return linkedPRsMap;
+}
+
 export function createListIssuesHandler() {
   return async (req: Request, res: Response): Promise<void> => {
     try {
@@ -53,17 +209,17 @@ export function createListIssuesHandler() {
         return;
       }
 
-      // Fetch open and closed issues in parallel
+      // Fetch open and closed issues in parallel (now including assignees)
       const [openResult, closedResult] = await Promise.all([
         execAsync(
-          'gh issue list --state open --json number,title,state,author,createdAt,labels,url,body --limit 100',
+          'gh issue list --state open --json number,title,state,author,createdAt,labels,url,body,assignees --limit 100',
           {
             cwd: projectPath,
             env: execEnv,
           }
         ),
         execAsync(
-          'gh issue list --state closed --json number,title,state,author,createdAt,labels,url,body --limit 50',
+          'gh issue list --state closed --json number,title,state,author,createdAt,labels,url,body,assignees --limit 50',
           {
             cwd: projectPath,
             env: execEnv,
@@ -77,6 +233,24 @@ export function createListIssuesHandler() {
       const openIssues: GitHubIssue[] = JSON.parse(openStdout || '[]');
       const closedIssues: GitHubIssue[] = JSON.parse(closedStdout || '[]');
 
+      // Fetch linked PRs for open issues (more relevant for active work)
+      if (remoteStatus.owner && remoteStatus.repo && openIssues.length > 0) {
+        const linkedPRsMap = await fetchLinkedPRs(
+          projectPath,
+          remoteStatus.owner,
+          remoteStatus.repo,
+          openIssues.map((i) => i.number)
+        );
+
+        // Attach linked PRs to issues
+        for (const issue of openIssues) {
+          const linkedPRs = linkedPRsMap.get(issue.number);
+          if (linkedPRs) {
+            issue.linkedPRs = linkedPRs;
+          }
+        }
+      }
+
       res.json({
         success: true,
         openIssues,

apps/server/src/routes/github/routes/validate-issue.ts

@@ -0,0 +1,340 @@
+/**
+ * POST /validate-issue endpoint - Validate a GitHub issue using Claude SDK (async)
+ *
+ * Scans the codebase to determine if an issue is valid, invalid, or needs clarification.
+ * Runs asynchronously and emits events for progress and completion.
+ */
+
+import type { Request, Response } from 'express';
+import { query } from '@anthropic-ai/claude-agent-sdk';
+import type { EventEmitter } from '../../../lib/events.js';
+import type {
+  IssueValidationResult,
+  IssueValidationEvent,
+  AgentModel,
+  GitHubComment,
+  LinkedPRInfo,
+} from '@automaker/types';
+import { createSuggestionsOptions } from '../../../lib/sdk-options.js';
+import { writeValidation } from '../../../lib/validation-storage.js';
+import {
+  issueValidationSchema,
+  ISSUE_VALIDATION_SYSTEM_PROMPT,
+  buildValidationPrompt,
+  ValidationComment,
+  ValidationLinkedPR,
+} from './validation-schema.js';
+import {
+  trySetValidationRunning,
+  clearValidationStatus,
+  getErrorMessage,
+  logError,
+  logger,
+} from './validation-common.js';
+import type { SettingsService } from '../../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
+
+/** Valid model values for validation */
+const VALID_MODELS: readonly AgentModel[] = ['opus', 'sonnet', 'haiku'] as const;
+
+/**
+ * Request body for issue validation
+ */
+interface ValidateIssueRequestBody {
+  projectPath: string;
+  issueNumber: number;
+  issueTitle: string;
+  issueBody: string;
+  issueLabels?: string[];
+  /** Model to use for validation (opus, sonnet, haiku) */
+  model?: AgentModel;
+  /** Comments to include in validation analysis */
+  comments?: GitHubComment[];
+  /** Linked pull requests for this issue */
+  linkedPRs?: LinkedPRInfo[];
+}
+
+/**
+ * Run the validation asynchronously
+ *
+ * Emits events for start, progress, complete, and error.
+ * Stores result on completion.
+ */
+async function runValidation(
+  projectPath: string,
+  issueNumber: number,
+  issueTitle: string,
+  issueBody: string,
+  issueLabels: string[] | undefined,
+  model: AgentModel,
+  events: EventEmitter,
+  abortController: AbortController,
+  settingsService?: SettingsService,
+  comments?: ValidationComment[],
+  linkedPRs?: ValidationLinkedPR[]
+): Promise<void> {
+  // Emit start event
+  const startEvent: IssueValidationEvent = {
+    type: 'issue_validation_start',
+    issueNumber,
+    issueTitle,
+    projectPath,
+  };
+  events.emit('issue-validation:event', startEvent);
+
+  // Set up timeout (6 minutes)
+  const VALIDATION_TIMEOUT_MS = 360000;
+  const timeoutId = setTimeout(() => {
+    logger.warn(`Validation timeout reached after ${VALIDATION_TIMEOUT_MS}ms`);
+    abortController.abort();
+  }, VALIDATION_TIMEOUT_MS);
+
+  try {
+    // Build the prompt (include comments and linked PRs if provided)
+    const prompt = buildValidationPrompt(
+      issueNumber,
+      issueTitle,
+      issueBody,
+      issueLabels,
+      comments,
+      linkedPRs
+    );
+
+    // Load autoLoadClaudeMd setting
+    const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+      projectPath,
+      settingsService,
+      '[ValidateIssue]'
+    );
+
+    // Create SDK options with structured output and abort controller
+    const options = createSuggestionsOptions({
+      cwd: projectPath,
+      model,
+      systemPrompt: ISSUE_VALIDATION_SYSTEM_PROMPT,
+      abortController,
+      autoLoadClaudeMd,
+      outputFormat: {
+        type: 'json_schema',
+        schema: issueValidationSchema as Record<string, unknown>,
+      },
+    });
+
+    // Execute the query
+    const stream = query({ prompt, options });
+    let validationResult: IssueValidationResult | null = null;
+
+    for await (const msg of stream) {
+      // Emit progress events for assistant text
+      if (msg.type === 'assistant' && msg.message?.content) {
+        for (const block of msg.message.content) {
+          if (block.type === 'text') {
+            const progressEvent: IssueValidationEvent = {
+              type: 'issue_validation_progress',
+              issueNumber,
+              content: block.text,
+              projectPath,
+            };
+            events.emit('issue-validation:event', progressEvent);
+          }
+        }
+      }
+
+      // Extract structured output on success
+      if (msg.type === 'result' && msg.subtype === 'success') {
+        const resultMsg = msg as { structured_output?: IssueValidationResult };
+        if (resultMsg.structured_output) {
+          validationResult = resultMsg.structured_output;
+        }
+      }
+
+      // Handle errors
+      if (msg.type === 'result') {
+        const resultMsg = msg as { subtype?: string };
+        if (resultMsg.subtype === 'error_max_structured_output_retries') {
+          logger.error('Failed to produce valid structured output after retries');
+          throw new Error('Could not produce valid validation output');
+        }
+      }
+    }
+
+    // Clear timeout
+    clearTimeout(timeoutId);
+
+    // Require structured output
+    if (!validationResult) {
+      logger.error('No structured output received from Claude SDK');
+      throw new Error('Validation failed: no structured output received');
+    }
+
+    logger.info(`Issue #${issueNumber} validation complete: ${validationResult.verdict}`);
+
+    // Store the result
+    await writeValidation(projectPath, issueNumber, {
+      issueNumber,
+      issueTitle,
+      validatedAt: new Date().toISOString(),
+      model,
+      result: validationResult,
+    });
+
+    // Emit completion event
+    const completeEvent: IssueValidationEvent = {
+      type: 'issue_validation_complete',
+      issueNumber,
+      issueTitle,
+      result: validationResult,
+      projectPath,
+      model,
+    };
+    events.emit('issue-validation:event', completeEvent);
+  } catch (error) {
+    clearTimeout(timeoutId);
+
+    const errorMessage = getErrorMessage(error);
+    logError(error, `Issue #${issueNumber} validation failed`);
+
+    // Emit error event
+    const errorEvent: IssueValidationEvent = {
+      type: 'issue_validation_error',
+      issueNumber,
+      error: errorMessage,
+      projectPath,
+    };
+    events.emit('issue-validation:event', errorEvent);
+
+    throw error;
+  }
+}
+
+/**
+ * Creates the handler for validating GitHub issues against the codebase.
+ *
+ * Uses Claude SDK with:
+ * - Read-only tools (Read, Glob, Grep) for codebase analysis
+ * - JSON schema structured output for reliable parsing
+ * - System prompt guiding the validation process
+ * - Async execution with event emission
+ */
+export function createValidateIssueHandler(
+  events: EventEmitter,
+  settingsService?: SettingsService
+) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const {
+        projectPath,
+        issueNumber,
+        issueTitle,
+        issueBody,
+        issueLabels,
+        model = 'opus',
+        comments: rawComments,
+        linkedPRs: rawLinkedPRs,
+      } = req.body as ValidateIssueRequestBody;
+
+      // Transform GitHubComment[] to ValidationComment[] if provided
+      const validationComments: ValidationComment[] | undefined = rawComments?.map((c) => ({
+        author: c.author?.login || 'ghost',
+        createdAt: c.createdAt,
+        body: c.body,
+      }));
+
+      // Transform LinkedPRInfo[] to ValidationLinkedPR[] if provided
+      const validationLinkedPRs: ValidationLinkedPR[] | undefined = rawLinkedPRs?.map((pr) => ({
+        number: pr.number,
+        title: pr.title,
+        state: pr.state,
+      }));
+
+      logger.info(
+        `[ValidateIssue] Received validation request for issue #${issueNumber}` +
+          (rawComments?.length ? ` with ${rawComments.length} comments` : ' (no comments)') +
+          (rawLinkedPRs?.length ? ` and ${rawLinkedPRs.length} linked PRs` : '')
+      );
+
+      // Validate required fields
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!issueNumber || typeof issueNumber !== 'number') {
+        res
+          .status(400)
+          .json({ success: false, error: 'issueNumber is required and must be a number' });
+        return;
+      }
+
+      if (!issueTitle || typeof issueTitle !== 'string') {
+        res.status(400).json({ success: false, error: 'issueTitle is required' });
+        return;
+      }
+
+      if (typeof issueBody !== 'string') {
+        res.status(400).json({ success: false, error: 'issueBody must be a string' });
+        return;
+      }
+
+      // Validate model parameter at runtime
+      if (!VALID_MODELS.includes(model)) {
+        res.status(400).json({
+          success: false,
+          error: `Invalid model. Must be one of: ${VALID_MODELS.join(', ')}`,
+        });
+        return;
+      }
+
+      logger.info(`Starting async validation for issue #${issueNumber}: ${issueTitle}`);
+
+      // Create abort controller and atomically try to claim validation slot
+      // This prevents TOCTOU race conditions
+      const abortController = new AbortController();
+      if (!trySetValidationRunning(projectPath, issueNumber, abortController)) {
+        res.json({
+          success: false,
+          error: `Validation is already running for issue #${issueNumber}`,
+        });
+        return;
+      }
+
+      // Start validation in background (fire-and-forget)
+      runValidation(
+        projectPath,
+        issueNumber,
+        issueTitle,
+        issueBody,
+        issueLabels,
+        model,
+        events,
+        abortController,
+        settingsService,
+        validationComments,
+        validationLinkedPRs
+      )
+        .catch(() => {
+          // Error is already handled inside runValidation (event emitted)
+        })
+        .finally(() => {
+          clearValidationStatus(projectPath, issueNumber);
+        });
+
+      // Return immediately
+      res.json({
+        success: true,
+        message: `Validation started for issue #${issueNumber}`,
+        issueNumber,
+      });
+    } catch (error) {
+      logError(error, `Issue validation failed`);
+      logger.error('Issue validation error:', error);
+
+      if (!res.headersSent) {
+        res.status(500).json({
+          success: false,
+          error: getErrorMessage(error),
+        });
+      }
+    }
+  };
+}

apps/server/src/routes/github/routes/validation-common.ts

@@ -0,0 +1,174 @@
+/**
+ * Common utilities and state for issue validation routes
+ *
+ * Tracks running validation status per issue to support:
+ * - Checking if a validation is in progress
+ * - Cancelling a running validation
+ * - Preventing duplicate validations for the same issue
+ */
+
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage as getErrorMessageShared, createLogError } from '../../common.js';
+
+const logger = createLogger('IssueValidation');
+
+/**
+ * Status of a validation in progress
+ */
+interface ValidationStatus {
+  isRunning: boolean;
+  abortController: AbortController;
+  startedAt: Date;
+}
+
+/**
+ * Map of issue number to validation status
+ * Key format: `${projectPath}||${issueNumber}` to support multiple projects
+ * Note: Using `||` as delimiter since `:` appears in Windows paths (e.g., C:\)
+ */
+const validationStatusMap = new Map<string, ValidationStatus>();
+
+/** Maximum age for stale validation entries before cleanup (1 hour) */
+const MAX_VALIDATION_AGE_MS = 60 * 60 * 1000;
+
+/**
+ * Create a unique key for a validation
+ * Uses `||` as delimiter since `:` appears in Windows paths
+ */
+function getValidationKey(projectPath: string, issueNumber: number): string {
+  return `${projectPath}||${issueNumber}`;
+}
+
+/**
+ * Check if a validation is currently running for an issue
+ */
+export function isValidationRunning(projectPath: string, issueNumber: number): boolean {
+  const key = getValidationKey(projectPath, issueNumber);
+  const status = validationStatusMap.get(key);
+  return status?.isRunning ?? false;
+}
+
+/**
+ * Get validation status for an issue
+ */
+export function getValidationStatus(
+  projectPath: string,
+  issueNumber: number
+): { isRunning: boolean; startedAt?: Date } | null {
+  const key = getValidationKey(projectPath, issueNumber);
+  const status = validationStatusMap.get(key);
+  if (!status) {
+    return null;
+  }
+  return {
+    isRunning: status.isRunning,
+    startedAt: status.startedAt,
+  };
+}
+
+/**
+ * Get all running validations for a project
+ */
+export function getRunningValidations(projectPath: string): number[] {
+  const runningIssues: number[] = [];
+  const prefix = `${projectPath}||`;
+  for (const [key, status] of validationStatusMap.entries()) {
+    if (status.isRunning && key.startsWith(prefix)) {
+      const issueNumber = parseInt(key.slice(prefix.length), 10);
+      if (!isNaN(issueNumber)) {
+        runningIssues.push(issueNumber);
+      }
+    }
+  }
+  return runningIssues;
+}
+
+/**
+ * Set a validation as running
+ */
+export function setValidationRunning(
+  projectPath: string,
+  issueNumber: number,
+  abortController: AbortController
+): void {
+  const key = getValidationKey(projectPath, issueNumber);
+  validationStatusMap.set(key, {
+    isRunning: true,
+    abortController,
+    startedAt: new Date(),
+  });
+}
+
+/**
+ * Atomically try to set a validation as running (check-and-set)
+ * Prevents TOCTOU race conditions when starting validations
+ *
+ * @returns true if successfully claimed, false if already running
+ */
+export function trySetValidationRunning(
+  projectPath: string,
+  issueNumber: number,
+  abortController: AbortController
+): boolean {
+  const key = getValidationKey(projectPath, issueNumber);
+  if (validationStatusMap.has(key)) {
+    return false; // Already running
+  }
+  validationStatusMap.set(key, {
+    isRunning: true,
+    abortController,
+    startedAt: new Date(),
+  });
+  return true; // Successfully claimed
+}
+
+/**
+ * Cleanup stale validation entries (e.g., from crashed validations)
+ * Should be called periodically to prevent memory leaks
+ */
+export function cleanupStaleValidations(): number {
+  const now = Date.now();
+  let cleanedCount = 0;
+  for (const [key, status] of validationStatusMap.entries()) {
+    if (now - status.startedAt.getTime() > MAX_VALIDATION_AGE_MS) {
+      status.abortController.abort();
+      validationStatusMap.delete(key);
+      cleanedCount++;
+    }
+  }
+  if (cleanedCount > 0) {
+    logger.info(`Cleaned up ${cleanedCount} stale validation entries`);
+  }
+  return cleanedCount;
+}
+
+/**
+ * Clear validation status (call when validation completes or errors)
+ */
+export function clearValidationStatus(projectPath: string, issueNumber: number): void {
+  const key = getValidationKey(projectPath, issueNumber);
+  validationStatusMap.delete(key);
+}
+
+/**
+ * Abort a running validation
+ *
+ * @returns true if validation was aborted, false if not running
+ */
+export function abortValidation(projectPath: string, issueNumber: number): boolean {
+  const key = getValidationKey(projectPath, issueNumber);
+  const status = validationStatusMap.get(key);
+
+  if (!status || !status.isRunning) {
+    return false;
+  }
+
+  status.abortController.abort();
+  validationStatusMap.delete(key);
+  return true;
+}
+
+// Re-export shared utilities
+export { getErrorMessageShared as getErrorMessage };
+export const logError = createLogError(logger);
+export { logger };

apps/server/src/routes/github/routes/validation-endpoints.ts

@@ -0,0 +1,236 @@
+/**
+ * Additional validation endpoints for status, stop, and retrieving stored validations
+ */
+
+import type { Request, Response } from 'express';
+import type { EventEmitter } from '../../../lib/events.js';
+import type { IssueValidationEvent } from '@automaker/types';
+import {
+  isValidationRunning,
+  getValidationStatus,
+  getRunningValidations,
+  abortValidation,
+  getErrorMessage,
+  logError,
+  logger,
+} from './validation-common.js';
+import {
+  readValidation,
+  getAllValidations,
+  getValidationWithFreshness,
+  deleteValidation,
+  markValidationViewed,
+} from '../../../lib/validation-storage.js';
+
+/**
+ * POST /validation-status - Check if validation is running for an issue
+ */
+export function createValidationStatusHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber } = req.body as {
+        projectPath: string;
+        issueNumber?: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      // If issueNumber provided, check specific issue
+      if (issueNumber !== undefined) {
+        const status = getValidationStatus(projectPath, issueNumber);
+        res.json({
+          success: true,
+          isRunning: status?.isRunning ?? false,
+          startedAt: status?.startedAt?.toISOString(),
+        });
+        return;
+      }
+
+      // Otherwise, return all running validations for the project
+      const runningIssues = getRunningValidations(projectPath);
+      res.json({
+        success: true,
+        runningIssues,
+      });
+    } catch (error) {
+      logError(error, 'Validation status check failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * POST /validation-stop - Cancel a running validation
+ */
+export function createValidationStopHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber } = req.body as {
+        projectPath: string;
+        issueNumber: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!issueNumber || typeof issueNumber !== 'number') {
+        res
+          .status(400)
+          .json({ success: false, error: 'issueNumber is required and must be a number' });
+        return;
+      }
+
+      const wasAborted = abortValidation(projectPath, issueNumber);
+
+      if (wasAborted) {
+        logger.info(`Validation for issue #${issueNumber} was stopped`);
+        res.json({
+          success: true,
+          message: `Validation for issue #${issueNumber} has been stopped`,
+        });
+      } else {
+        res.json({
+          success: false,
+          error: `No validation is running for issue #${issueNumber}`,
+        });
+      }
+    } catch (error) {
+      logError(error, 'Validation stop failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * POST /validations - Get stored validations for a project
+ */
+export function createGetValidationsHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber } = req.body as {
+        projectPath: string;
+        issueNumber?: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      // If issueNumber provided, get specific validation with freshness info
+      if (issueNumber !== undefined) {
+        const result = await getValidationWithFreshness(projectPath, issueNumber);
+
+        if (!result) {
+          res.json({
+            success: true,
+            validation: null,
+          });
+          return;
+        }
+
+        res.json({
+          success: true,
+          validation: result.validation,
+          isStale: result.isStale,
+        });
+        return;
+      }
+
+      // Otherwise, get all validations for the project
+      const validations = await getAllValidations(projectPath);
+
+      res.json({
+        success: true,
+        validations,
+      });
+    } catch (error) {
+      logError(error, 'Get validations failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * POST /validation-delete - Delete a stored validation
+ */
+export function createDeleteValidationHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber } = req.body as {
+        projectPath: string;
+        issueNumber: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!issueNumber || typeof issueNumber !== 'number') {
+        res
+          .status(400)
+          .json({ success: false, error: 'issueNumber is required and must be a number' });
+        return;
+      }
+
+      const deleted = await deleteValidation(projectPath, issueNumber);
+
+      res.json({
+        success: true,
+        deleted,
+      });
+    } catch (error) {
+      logError(error, 'Delete validation failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * POST /validation-mark-viewed - Mark a validation as viewed by the user
+ */
+export function createMarkViewedHandler(events: EventEmitter) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, issueNumber } = req.body as {
+        projectPath: string;
+        issueNumber: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!issueNumber || typeof issueNumber !== 'number') {
+        res
+          .status(400)
+          .json({ success: false, error: 'issueNumber is required and must be a number' });
+        return;
+      }
+
+      const success = await markValidationViewed(projectPath, issueNumber);
+
+      if (success) {
+        // Emit event so UI can update the unviewed count
+        const viewedEvent: IssueValidationEvent = {
+          type: 'issue_validation_viewed',
+          issueNumber,
+          projectPath,
+        };
+        events.emit('issue-validation:event', viewedEvent);
+      }
+
+      res.json({ success });
+    } catch (error) {
+      logError(error, 'Mark validation viewed failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/github/routes/validation-schema.ts

@@ -0,0 +1,239 @@
+/**
+ * Issue Validation Schema and System Prompt
+ *
+ * Defines the JSON schema for Claude's structured output and
+ * the system prompt that guides the validation process.
+ */
+
+/**
+ * JSON Schema for issue validation structured output.
+ * Used with Claude SDK's outputFormat option to ensure reliable parsing.
+ */
+export const issueValidationSchema = {
+  type: 'object',
+  properties: {
+    verdict: {
+      type: 'string',
+      enum: ['valid', 'invalid', 'needs_clarification'],
+      description: 'The validation verdict for the issue',
+    },
+    confidence: {
+      type: 'string',
+      enum: ['high', 'medium', 'low'],
+      description: 'How confident the AI is in its assessment',
+    },
+    reasoning: {
+      type: 'string',
+      description: 'Detailed explanation of the verdict',
+    },
+    bugConfirmed: {
+      type: 'boolean',
+      description: 'For bug reports: whether the bug was confirmed in the codebase',
+    },
+    relatedFiles: {
+      type: 'array',
+      items: { type: 'string' },
+      description: 'Files related to the issue found during analysis',
+    },
+    suggestedFix: {
+      type: 'string',
+      description: 'Suggested approach to fix or implement the issue',
+    },
+    missingInfo: {
+      type: 'array',
+      items: { type: 'string' },
+      description: 'Information needed when verdict is needs_clarification',
+    },
+    estimatedComplexity: {
+      type: 'string',
+      enum: ['trivial', 'simple', 'moderate', 'complex', 'very_complex'],
+      description: 'Estimated effort to address the issue',
+    },
+    prAnalysis: {
+      type: 'object',
+      properties: {
+        hasOpenPR: {
+          type: 'boolean',
+          description: 'Whether there is an open PR linked to this issue',
+        },
+        prFixesIssue: {
+          type: 'boolean',
+          description: 'Whether the PR appears to fix the issue based on the diff',
+        },
+        prNumber: {
+          type: 'number',
+          description: 'The PR number that was analyzed',
+        },
+        prSummary: {
+          type: 'string',
+          description: 'Brief summary of what the PR changes',
+        },
+        recommendation: {
+          type: 'string',
+          enum: ['wait_for_merge', 'pr_needs_work', 'no_pr'],
+          description:
+            'Recommendation: wait for PR to merge, PR needs more work, or no relevant PR',
+        },
+      },
+      description: 'Analysis of linked pull requests if any exist',
+    },
+  },
+  required: ['verdict', 'confidence', 'reasoning'],
+  additionalProperties: false,
+} as const;
+
+/**
+ * System prompt that guides Claude in validating GitHub issues.
+ * Instructs the model to use read-only tools to analyze the codebase.
+ */
+export const ISSUE_VALIDATION_SYSTEM_PROMPT = `You are an expert code analyst validating GitHub issues against a codebase.
+
+Your task is to analyze a GitHub issue and determine if it's valid by scanning the codebase.
+
+## Validation Process
+
+1. **Read the issue carefully** - Understand what is being reported or requested
+2. **Search the codebase** - Use Glob to find relevant files by pattern, Grep to search for keywords
+3. **Examine the code** - Use Read to look at the actual implementation in relevant files
+4. **Check linked PRs** - If there are linked pull requests, use \`gh pr diff <PR_NUMBER>\` to review the changes
+5. **Form your verdict** - Based on your analysis, determine if the issue is valid
+
+## Verdicts
+
+- **valid**: The issue describes a real problem that exists in the codebase, or a clear feature request that can be implemented. The referenced files/components exist and the issue is actionable.
+
+- **invalid**: The issue describes behavior that doesn't exist, references non-existent files or components, is based on a misunderstanding of the code, or the described "bug" is actually expected behavior.
+
+- **needs_clarification**: The issue lacks sufficient detail to verify. Specify what additional information is needed in the missingInfo field.
+
+## For Bug Reports, Check:
+- Do the referenced files/components exist?
+- Does the code match what the issue describes?
+- Is the described behavior actually a bug or expected?
+- Can you locate the code that would cause the reported issue?
+
+## For Feature Requests, Check:
+- Does the feature already exist?
+- Is the implementation location clear?
+- Is the request technically feasible given the codebase structure?
+
+## Analyzing Linked Pull Requests
+
+When an issue has linked PRs (especially open ones), you MUST analyze them:
+
+1. **Run \`gh pr diff <PR_NUMBER>\`** to see what changes the PR makes
+2. **Run \`gh pr view <PR_NUMBER>\`** to see PR description and status
+3. **Evaluate if the PR fixes the issue** - Does the diff address the reported problem?
+4. **Provide a recommendation**:
+   - \`wait_for_merge\`: The PR appears to fix the issue correctly. No additional work needed - just wait for it to be merged.
+   - \`pr_needs_work\`: The PR attempts to fix the issue but is incomplete or has problems.
+   - \`no_pr\`: No relevant PR exists for this issue.
+
+5. **Include prAnalysis in your response** with:
+   - hasOpenPR: true/false
+   - prFixesIssue: true/false (based on diff analysis)
+   - prNumber: the PR number you analyzed
+   - prSummary: brief description of what the PR changes
+   - recommendation: one of the above values
+
+## Response Guidelines
+
+- **Always include relatedFiles** when you find relevant code
+- **Set bugConfirmed to true** only if you can definitively confirm a bug exists in the code
+- **Provide a suggestedFix** when you have a clear idea of how to address the issue
+- **Use missingInfo** when the verdict is needs_clarification to list what's needed
+- **Include prAnalysis** when there are linked PRs - this is critical for avoiding duplicate work
+- **Set estimatedComplexity** to help prioritize:
+  - trivial: Simple text changes, one-line fixes
+  - simple: Small changes to one file
+  - moderate: Changes to multiple files or moderate logic changes
+  - complex: Significant refactoring or new feature implementation
+  - very_complex: Major architectural changes or cross-cutting concerns
+
+Be thorough in your analysis but focus on files that are directly relevant to the issue.`;
+
+/**
+ * Comment data structure for validation prompt
+ */
+export interface ValidationComment {
+  author: string;
+  createdAt: string;
+  body: string;
+}
+
+/**
+ * Linked PR data structure for validation prompt
+ */
+export interface ValidationLinkedPR {
+  number: number;
+  title: string;
+  state: string;
+}
+
+/**
+ * Build the user prompt for issue validation.
+ *
+ * Creates a structured prompt that includes the issue details for Claude
+ * to analyze against the codebase.
+ *
+ * @param issueNumber - The GitHub issue number
+ * @param issueTitle - The issue title
+ * @param issueBody - The issue body/description
+ * @param issueLabels - Optional array of label names
+ * @param comments - Optional array of comments to include in analysis
+ * @param linkedPRs - Optional array of linked pull requests
+ * @returns Formatted prompt string for the validation request
+ */
+export function buildValidationPrompt(
+  issueNumber: number,
+  issueTitle: string,
+  issueBody: string,
+  issueLabels?: string[],
+  comments?: ValidationComment[],
+  linkedPRs?: ValidationLinkedPR[]
+): string {
+  const labelsSection = issueLabels?.length ? `\n\n**Labels:** ${issueLabels.join(', ')}` : '';
+
+  let linkedPRsSection = '';
+  if (linkedPRs && linkedPRs.length > 0) {
+    const prsText = linkedPRs
+      .map((pr) => `- PR #${pr.number} (${pr.state}): ${pr.title}`)
+      .join('\n');
+    linkedPRsSection = `\n\n### Linked Pull Requests\n\n${prsText}`;
+  }
+
+  let commentsSection = '';
+  if (comments && comments.length > 0) {
+    // Limit to most recent 10 comments to control prompt size
+    const recentComments = comments.slice(-10);
+    const commentsText = recentComments
+      .map(
+        (c) => `**${c.author}** (${new Date(c.createdAt).toISOString().slice(0, 10)}):\n${c.body}`
+      )
+      .join('\n\n---\n\n');
+
+    commentsSection = `\n\n### Comments (${comments.length} total${comments.length > 10 ? ', showing last 10' : ''})\n\n${commentsText}`;
+  }
+
+  const hasWorkInProgress =
+    linkedPRs && linkedPRs.some((pr) => pr.state === 'open' || pr.state === 'OPEN');
+  const workInProgressNote = hasWorkInProgress
+    ? '\n\n**Note:** This issue has an open pull request linked. Consider that someone may already be working on a fix.'
+    : '';
+
+  return `Please validate the following GitHub issue by analyzing the codebase:
+
+## Issue #${issueNumber}: ${issueTitle}
+${labelsSection}
+${linkedPRsSection}
+
+### Description
+
+${issueBody || '(No description provided)'}
+${commentsSection}
+${workInProgressNote}
+
+---
+
+Scan the codebase to verify this issue. Look for the files, components, or functionality mentioned. Determine if this issue is valid, invalid, or needs clarification.${comments && comments.length > 0 ? ' Consider the context provided in the comments as well.' : ''}${hasWorkInProgress ? ' Also note in your analysis if there is already work in progress on this issue.' : ''}`;
+}

apps/server/src/routes/health/index.ts

@@ -1,16 +1,30 @@
 /**
  * Health check routes
+ *
+ * NOTE: Only the basic health check (/) and environment check are unauthenticated.
+ * The /detailed endpoint requires authentication.
  */
 
 import { Router } from 'express';
 import { createIndexHandler } from './routes/index.js';
-import { createDetailedHandler } from './routes/detailed.js';
+import { createEnvironmentHandler } from './routes/environment.js';
 
+/**
+ * Create unauthenticated health routes (basic check only)
+ * Used by load balancers and container orchestration
+ */
 export function createHealthRoutes(): Router {
   const router = Router();
 
+  // Basic health check - no sensitive info
   router.get('/', createIndexHandler());
-  router.get('/detailed', createDetailedHandler());
+
+  // Environment info including containerization status
+  // This is unauthenticated so the UI can check on startup
+  router.get('/environment', createEnvironmentHandler());
 
   return router;
 }
+
+// Re-export detailed handler for use in authenticated routes
+export { createDetailedHandler } from './routes/detailed.js';

apps/server/src/routes/health/routes/detailed.ts

@@ -4,13 +4,14 @@
 
 import type { Request, Response } from 'express';
 import { getAuthStatus } from '../../../lib/auth.js';
+import { getVersion } from '../../../lib/version.js';
 
 export function createDetailedHandler() {
   return (_req: Request, res: Response): void => {
     res.json({
       status: 'ok',
       timestamp: new Date().toISOString(),
-      version: process.env.npm_package_version || '0.1.0',
+      version: getVersion(),
       uptime: process.uptime(),
       memory: process.memoryUsage(),
       dataDir: process.env.DATA_DIR || './data',

apps/server/src/routes/health/routes/environment.ts

@@ -0,0 +1,20 @@
+/**
+ * GET /environment endpoint - Environment information including containerization status
+ *
+ * This endpoint is unauthenticated so the UI can check it on startup
+ * before login to determine if sandbox risk warnings should be shown.
+ */
+
+import type { Request, Response } from 'express';
+
+export interface EnvironmentResponse {
+  isContainerized: boolean;
+}
+
+export function createEnvironmentHandler() {
+  return (_req: Request, res: Response): void => {
+    res.json({
+      isContainerized: process.env.IS_CONTAINERIZED === 'true',
+    } satisfies EnvironmentResponse);
+  };
+}

apps/server/src/routes/health/routes/index.ts

@@ -3,13 +3,14 @@
  */
 
 import type { Request, Response } from 'express';
+import { getVersion } from '../../../lib/version.js';
 
 export function createIndexHandler() {
   return (_req: Request, res: Response): void => {
     res.json({
       status: 'ok',
       timestamp: new Date().toISOString(),
-      version: process.env.npm_package_version || '0.1.0',
+      version: getVersion(),
     });
   };
 }

apps/server/src/routes/mcp/common.ts

@@ -0,0 +1,20 @@
+/**
+ * Common utilities for MCP routes
+ */
+
+/**
+ * Extract error message from unknown error
+ */
+export function getErrorMessage(error: unknown): string {
+  if (error instanceof Error) {
+    return error.message;
+  }
+  return String(error);
+}
+
+/**
+ * Log error with prefix
+ */
+export function logError(error: unknown, message: string): void {
+  console.error(`[MCP] ${message}:`, error);
+}

apps/server/src/routes/mcp/index.ts

@@ -0,0 +1,36 @@
+/**
+ * MCP routes - HTTP API for testing MCP servers
+ *
+ * Provides endpoints for:
+ * - Testing MCP server connections
+ * - Listing available tools from MCP servers
+ *
+ * Mounted at /api/mcp in the main server.
+ */
+
+import { Router } from 'express';
+import type { MCPTestService } from '../../services/mcp-test-service.js';
+import { createTestServerHandler } from './routes/test-server.js';
+import { createListToolsHandler } from './routes/list-tools.js';
+
+/**
+ * Create MCP router with all endpoints
+ *
+ * Endpoints:
+ * - POST /test - Test MCP server connection
+ * - POST /tools - List tools from MCP server
+ *
+ * @param mcpTestService - Instance of MCPTestService for testing connections
+ * @returns Express Router configured with all MCP endpoints
+ */
+export function createMCPRoutes(mcpTestService: MCPTestService): Router {
+  const router = Router();
+
+  // Test MCP server connection
+  router.post('/test', createTestServerHandler(mcpTestService));
+
+  // List tools from MCP server
+  router.post('/tools', createListToolsHandler(mcpTestService));
+
+  return router;
+}

apps/server/src/routes/mcp/routes/list-tools.ts

@@ -0,0 +1,57 @@
+/**
+ * POST /api/mcp/tools - List tools for an MCP server
+ *
+ * Lists available tools for an MCP server.
+ * Similar to test but focused on tool discovery.
+ *
+ * SECURITY: Only accepts serverId to look up saved configs. Does NOT accept
+ * arbitrary serverConfig to prevent drive-by command execution attacks.
+ * Users must explicitly save a server config through the UI before testing.
+ *
+ * Request body:
+ *   { serverId: string } - Get tools by server ID from settings
+ *
+ * Response: { success: boolean, tools?: MCPToolInfo[], error?: string }
+ */
+
+import type { Request, Response } from 'express';
+import type { MCPTestService } from '../../../services/mcp-test-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+interface ListToolsRequest {
+  serverId: string;
+}
+
+/**
+ * Create handler factory for POST /api/mcp/tools
+ */
+export function createListToolsHandler(mcpTestService: MCPTestService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const body = req.body as ListToolsRequest;
+
+      if (!body.serverId || typeof body.serverId !== 'string') {
+        res.status(400).json({
+          success: false,
+          error: 'serverId is required',
+        });
+        return;
+      }
+
+      const result = await mcpTestService.testServerById(body.serverId);
+
+      // Return only tool-related information
+      res.json({
+        success: result.success,
+        tools: result.tools,
+        error: result.error,
+      });
+    } catch (error) {
+      logError(error, 'List tools failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}

apps/server/src/routes/mcp/routes/test-server.ts

@@ -0,0 +1,50 @@
+/**
+ * POST /api/mcp/test - Test MCP server connection and list tools
+ *
+ * Tests connection to an MCP server and returns available tools.
+ *
+ * SECURITY: Only accepts serverId to look up saved configs. Does NOT accept
+ * arbitrary serverConfig to prevent drive-by command execution attacks.
+ * Users must explicitly save a server config through the UI before testing.
+ *
+ * Request body:
+ *   { serverId: string } - Test server by ID from settings
+ *
+ * Response: { success: boolean, tools?: MCPToolInfo[], error?: string, connectionTime?: number }
+ */
+
+import type { Request, Response } from 'express';
+import type { MCPTestService } from '../../../services/mcp-test-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+interface TestServerRequest {
+  serverId: string;
+}
+
+/**
+ * Create handler factory for POST /api/mcp/test
+ */
+export function createTestServerHandler(mcpTestService: MCPTestService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const body = req.body as TestServerRequest;
+
+      if (!body.serverId || typeof body.serverId !== 'string') {
+        res.status(400).json({
+          success: false,
+          error: 'serverId is required',
+        });
+        return;
+      }
+
+      const result = await mcpTestService.testServerById(body.serverId);
+      res.json(result);
+    } catch (error) {
+      logError(error, 'Test server failed');
+      res.status(500).json({
+        success: false,
+        error: getErrorMessage(error),
+      });
+    }
+  };
+}

apps/server/src/routes/pipeline/common.ts

@@ -0,0 +1,21 @@
+/**
+ * Common utilities for pipeline routes
+ *
+ * Provides logger and error handling utilities shared across all pipeline endpoints.
+ */
+
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
+
+/** Logger instance for pipeline-related operations */
+export const logger = createLogger('Pipeline');
+
+/**
+ * Extract user-friendly error message from error objects
+ */
+export { getErrorMessageShared as getErrorMessage };
+
+/**
+ * Log error with automatic logger binding
+ */
+export const logError = createLogError(logger);

apps/server/src/routes/pipeline/index.ts

@@ -0,0 +1,77 @@
+/**
+ * Pipeline routes - HTTP API for pipeline configuration management
+ *
+ * Provides endpoints for:
+ * - Getting pipeline configuration
+ * - Saving pipeline configuration
+ * - Adding, updating, deleting, and reordering pipeline steps
+ *
+ * All endpoints use handler factories that receive the PipelineService instance.
+ * Mounted at /api/pipeline in the main server.
+ */
+
+import { Router } from 'express';
+import type { PipelineService } from '../../services/pipeline-service.js';
+import { validatePathParams } from '../../middleware/validate-paths.js';
+import { createGetConfigHandler } from './routes/get-config.js';
+import { createSaveConfigHandler } from './routes/save-config.js';
+import { createAddStepHandler } from './routes/add-step.js';
+import { createUpdateStepHandler } from './routes/update-step.js';
+import { createDeleteStepHandler } from './routes/delete-step.js';
+import { createReorderStepsHandler } from './routes/reorder-steps.js';
+
+/**
+ * Create pipeline router with all endpoints
+ *
+ * Endpoints:
+ * - POST /config - Get pipeline configuration
+ * - POST /config/save - Save entire pipeline configuration
+ * - POST /steps/add - Add a new pipeline step
+ * - POST /steps/update - Update an existing pipeline step
+ * - POST /steps/delete - Delete a pipeline step
+ * - POST /steps/reorder - Reorder pipeline steps
+ *
+ * @param pipelineService - Instance of PipelineService for file I/O
+ * @returns Express Router configured with all pipeline endpoints
+ */
+export function createPipelineRoutes(pipelineService: PipelineService): Router {
+  const router = Router();
+
+  // Get pipeline configuration
+  router.post(
+    '/config',
+    validatePathParams('projectPath'),
+    createGetConfigHandler(pipelineService)
+  );
+
+  // Save entire pipeline configuration
+  router.post(
+    '/config/save',
+    validatePathParams('projectPath'),
+    createSaveConfigHandler(pipelineService)
+  );
+
+  // Pipeline step operations
+  router.post(
+    '/steps/add',
+    validatePathParams('projectPath'),
+    createAddStepHandler(pipelineService)
+  );
+  router.post(
+    '/steps/update',
+    validatePathParams('projectPath'),
+    createUpdateStepHandler(pipelineService)
+  );
+  router.post(
+    '/steps/delete',
+    validatePathParams('projectPath'),
+    createDeleteStepHandler(pipelineService)
+  );
+  router.post(
+    '/steps/reorder',
+    validatePathParams('projectPath'),
+    createReorderStepsHandler(pipelineService)
+  );
+
+  return router;
+}

apps/server/src/routes/pipeline/routes/add-step.ts

@@ -0,0 +1,54 @@
+/**
+ * POST /api/pipeline/steps/add - Add a new pipeline step
+ *
+ * Adds a new step to the pipeline configuration.
+ *
+ * Request body: { projectPath: string, step: { name, order, instructions, colorClass } }
+ * Response: { success: true, step: PipelineStep }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import type { PipelineStep } from '@automaker/types';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createAddStepHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, step } = req.body as {
+        projectPath: string;
+        step: Omit<PipelineStep, 'id' | 'createdAt' | 'updatedAt'>;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!step) {
+        res.status(400).json({ success: false, error: 'step is required' });
+        return;
+      }
+
+      if (!step.name) {
+        res.status(400).json({ success: false, error: 'step.name is required' });
+        return;
+      }
+
+      if (step.instructions === undefined) {
+        res.status(400).json({ success: false, error: 'step.instructions is required' });
+        return;
+      }
+
+      const newStep = await pipelineService.addStep(projectPath, step);
+
+      res.json({
+        success: true,
+        step: newStep,
+      });
+    } catch (error) {
+      logError(error, 'Add pipeline step failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/pipeline/routes/delete-step.ts

@@ -0,0 +1,42 @@
+/**
+ * POST /api/pipeline/steps/delete - Delete a pipeline step
+ *
+ * Removes a step from the pipeline configuration.
+ *
+ * Request body: { projectPath: string, stepId: string }
+ * Response: { success: true }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createDeleteStepHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, stepId } = req.body as {
+        projectPath: string;
+        stepId: string;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!stepId) {
+        res.status(400).json({ success: false, error: 'stepId is required' });
+        return;
+      }
+
+      await pipelineService.deleteStep(projectPath, stepId);
+
+      res.json({
+        success: true,
+      });
+    } catch (error) {
+      logError(error, 'Delete pipeline step failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/pipeline/routes/get-config.ts

@@ -0,0 +1,35 @@
+/**
+ * POST /api/pipeline/config - Get pipeline configuration
+ *
+ * Returns the pipeline configuration for a project.
+ *
+ * Request body: { projectPath: string }
+ * Response: { success: true, config: PipelineConfig }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createGetConfigHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body;
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      const config = await pipelineService.getPipelineConfig(projectPath);
+
+      res.json({
+        success: true,
+        config,
+      });
+    } catch (error) {
+      logError(error, 'Get pipeline config failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/pipeline/routes/reorder-steps.ts

@@ -0,0 +1,42 @@
+/**
+ * POST /api/pipeline/steps/reorder - Reorder pipeline steps
+ *
+ * Reorders the steps in the pipeline configuration.
+ *
+ * Request body: { projectPath: string, stepIds: string[] }
+ * Response: { success: true }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createReorderStepsHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, stepIds } = req.body as {
+        projectPath: string;
+        stepIds: string[];
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!stepIds || !Array.isArray(stepIds)) {
+        res.status(400).json({ success: false, error: 'stepIds array is required' });
+        return;
+      }
+
+      await pipelineService.reorderSteps(projectPath, stepIds);
+
+      res.json({
+        success: true,
+      });
+    } catch (error) {
+      logError(error, 'Reorder pipeline steps failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/pipeline/routes/save-config.ts

@@ -0,0 +1,43 @@
+/**
+ * POST /api/pipeline/config/save - Save entire pipeline configuration
+ *
+ * Saves the complete pipeline configuration for a project.
+ *
+ * Request body: { projectPath: string, config: PipelineConfig }
+ * Response: { success: true }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import type { PipelineConfig } from '@automaker/types';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createSaveConfigHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, config } = req.body as {
+        projectPath: string;
+        config: PipelineConfig;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!config) {
+        res.status(400).json({ success: false, error: 'config is required' });
+        return;
+      }
+
+      await pipelineService.savePipelineConfig(projectPath, config);
+
+      res.json({
+        success: true,
+      });
+    } catch (error) {
+      logError(error, 'Save pipeline config failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/pipeline/routes/update-step.ts

@@ -0,0 +1,50 @@
+/**
+ * POST /api/pipeline/steps/update - Update an existing pipeline step
+ *
+ * Updates a step in the pipeline configuration.
+ *
+ * Request body: { projectPath: string, stepId: string, updates: Partial<PipelineStep> }
+ * Response: { success: true, step: PipelineStep }
+ */
+
+import type { Request, Response } from 'express';
+import type { PipelineService } from '../../../services/pipeline-service.js';
+import type { PipelineStep } from '@automaker/types';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createUpdateStepHandler(pipelineService: PipelineService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, stepId, updates } = req.body as {
+        projectPath: string;
+        stepId: string;
+        updates: Partial<Omit<PipelineStep, 'id' | 'createdAt'>>;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!stepId) {
+        res.status(400).json({ success: false, error: 'stepId is required' });
+        return;
+      }
+
+      if (!updates || Object.keys(updates).length === 0) {
+        res.status(400).json({ success: false, error: 'updates is required' });
+        return;
+      }
+
+      const updatedStep = await pipelineService.updateStep(projectPath, stepId, updates);
+
+      res.json({
+        success: true,
+        step: updatedStep,
+      });
+    } catch (error) {
+      logError(error, 'Update pipeline step failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/running-agents/routes/index.ts

@@ -9,8 +9,7 @@ import { getErrorMessage, logError } from '../common.js';
 export function createIndexHandler(autoModeService: AutoModeService) {
   return async (_req: Request, res: Response): Promise<void> => {
     try {
-      const runningAgents = autoModeService.getRunningAgents();
-      const status = autoModeService.getStatus();
+      const runningAgents = await autoModeService.getRunningAgents();
 
       res.json({
         success: true,

apps/server/src/routes/setup/common.ts

@@ -4,7 +4,7 @@
 
 import { createLogger } from '@automaker/utils';
 import path from 'path';
-import fs from 'fs/promises';
+import { secureFs } from '@automaker/platform';
 import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
 
 const logger = createLogger('Setup');
@@ -35,36 +35,13 @@ export function getAllApiKeys(): Record<string, string> {
 
 /**
  * Helper to persist API keys to .env file
+ * Uses centralized secureFs.writeEnvKey for path validation
  */
 export async function persistApiKeyToEnv(key: string, value: string): Promise<void> {
   const envPath = path.join(process.cwd(), '.env');
 
   try {
-    let envContent = '';
-    try {
-      envContent = await fs.readFile(envPath, 'utf-8');
-    } catch {
-      // .env file doesn't exist, we'll create it
-    }
-
-    // Parse existing env content
-    const lines = envContent.split('\n');
-    const keyRegex = new RegExp(`^${key}=`);
-    let found = false;
-    const newLines = lines.map((line) => {
-      if (keyRegex.test(line)) {
-        found = true;
-        return `${key}=${value}`;
-      }
-      return line;
-    });
-
-    if (!found) {
-      // Add the key at the end
-      newLines.push(`${key}=${value}`);
-    }
-
-    await fs.writeFile(envPath, newLines.join('\n'));
+    await secureFs.writeEnvKey(envPath, key, value);
     logger.info(`[Setup] Persisted ${key} to .env file`);
   } catch (error) {
     logger.error(`[Setup] Failed to persist ${key} to .env:`, error);

apps/server/src/routes/setup/get-claude-status.ts

@@ -4,9 +4,7 @@
 
 import { exec } from 'child_process';
 import { promisify } from 'util';
-import os from 'os';
-import path from 'path';
-import fs from 'fs/promises';
+import { getClaudeCliPaths, getClaudeAuthIndicators, systemPathAccess } from '@automaker/platform';
 import { getApiKey } from './common.js';
 
 const execAsync = promisify(exec);
@@ -37,42 +35,25 @@ export async function getClaudeStatus() {
       // Version command might not be available
     }
   } catch {
-    // Not in PATH, try common locations based on platform
-    const commonPaths = isWindows
-      ? (() => {
-          const appData = process.env.APPDATA || path.join(os.homedir(), 'AppData', 'Roaming');
-          return [
-            // Windows-specific paths
-            path.join(os.homedir(), '.local', 'bin', 'claude.exe'),
-            path.join(appData, 'npm', 'claude.cmd'),
-            path.join(appData, 'npm', 'claude'),
-            path.join(appData, '.npm-global', 'bin', 'claude.cmd'),
-            path.join(appData, '.npm-global', 'bin', 'claude'),
-          ];
-        })()
-      : [
-          // Unix (Linux/macOS) paths
-          path.join(os.homedir(), '.local', 'bin', 'claude'),
-          path.join(os.homedir(), '.claude', 'local', 'claude'),
-          '/usr/local/bin/claude',
-          path.join(os.homedir(), '.npm-global', 'bin', 'claude'),
-        ];
+    // Not in PATH, try common locations from centralized system paths
+    const commonPaths = getClaudeCliPaths();
 
     for (const p of commonPaths) {
       try {
-        await fs.access(p);
-        cliPath = p;
-        installed = true;
-        method = 'local';
+        if (await systemPathAccess(p)) {
+          cliPath = p;
+          installed = true;
+          method = 'local';
 
-        // Get version from this path
-        try {
-          const { stdout: versionOut } = await execAsync(`"${p}" --version`);
-          version = versionOut.trim();
-        } catch {
-          // Version command might not be available
+          // Get version from this path
+          try {
+            const { stdout: versionOut } = await execAsync(`"${p}" --version`);
+            version = versionOut.trim();
+          } catch {
+            // Version command might not be available
+          }
+          break;
         }
-        break;
       } catch {
         // Not found at this path
       }
@@ -82,7 +63,7 @@ export async function getClaudeStatus() {
   // Check authentication - detect all possible auth methods
   // Note: apiKeys.anthropic_oauth_token stores OAuth tokens from subscription auth
   //       apiKeys.anthropic stores direct API keys for pay-per-use
-  let auth = {
+  const auth = {
     authenticated: false,
     method: 'none' as string,
     hasCredentialsFile: false,
@@ -97,76 +78,36 @@ export async function getClaudeStatus() {
     hasRecentActivity: false,
   };
 
-  const claudeDir = path.join(os.homedir(), '.claude');
+  // Use centralized system paths to check Claude authentication indicators
+  const indicators = await getClaudeAuthIndicators();
 
-  // Check for recent Claude CLI activity - indicates working authentication
-  // The stats-cache.json file is only populated when the CLI is working properly
-  const statsCachePath = path.join(claudeDir, 'stats-cache.json');
-  try {
-    const statsContent = await fs.readFile(statsCachePath, 'utf-8');
-    const stats = JSON.parse(statsContent);
+  // Check for recent activity (indicates working authentication)
+  if (indicators.hasStatsCacheWithActivity) {
+    auth.hasRecentActivity = true;
+    auth.hasCliAuth = true;
+    auth.authenticated = true;
+    auth.method = 'cli_authenticated';
+  }
 
-    // Check if there's any activity (which means the CLI is authenticated and working)
-    if (stats.dailyActivity && stats.dailyActivity.length > 0) {
-      auth.hasRecentActivity = true;
-      auth.hasCliAuth = true;
+  // Check for settings + sessions (indicates CLI is set up)
+  if (!auth.hasCliAuth && indicators.hasSettingsFile && indicators.hasProjectsSessions) {
+    auth.hasCliAuth = true;
+    auth.authenticated = true;
+    auth.method = 'cli_authenticated';
+  }
+
+  // Check credentials file
+  if (indicators.hasCredentialsFile && indicators.credentials) {
+    auth.hasCredentialsFile = true;
+    if (indicators.credentials.hasOAuthToken) {
+      auth.hasStoredOAuthToken = true;
+      auth.oauthTokenValid = true;
       auth.authenticated = true;
-      auth.method = 'cli_authenticated';
-    }
-  } catch {
-    // Stats file doesn't exist or is invalid
-  }
-
-  // Check for settings.json - indicates CLI has been set up
-  const settingsPath = path.join(claudeDir, 'settings.json');
-  try {
-    await fs.access(settingsPath);
-    // If settings exist but no activity, CLI might be set up but not authenticated
-    if (!auth.hasCliAuth) {
-      // Try to check for other indicators of auth
-      const sessionsDir = path.join(claudeDir, 'projects');
-      try {
-        const sessions = await fs.readdir(sessionsDir);
-        if (sessions.length > 0) {
-          auth.hasCliAuth = true;
-          auth.authenticated = true;
-          auth.method = 'cli_authenticated';
-        }
-      } catch {
-        // Sessions directory doesn't exist
-      }
-    }
-  } catch {
-    // Settings file doesn't exist
-  }
-
-  // Check for credentials file (OAuth tokens from claude login)
-  // Note: Claude CLI may use ".credentials.json" (hidden) or "credentials.json" depending on version/platform
-  const credentialsPaths = [
-    path.join(claudeDir, '.credentials.json'),
-    path.join(claudeDir, 'credentials.json'),
-  ];
-
-  for (const credentialsPath of credentialsPaths) {
-    try {
-      const credentialsContent = await fs.readFile(credentialsPath, 'utf-8');
-      const credentials = JSON.parse(credentialsContent);
-      auth.hasCredentialsFile = true;
-
-      // Check what type of token is in credentials
-      if (credentials.oauth_token || credentials.access_token) {
-        auth.hasStoredOAuthToken = true;
-        auth.oauthTokenValid = true;
-        auth.authenticated = true;
-        auth.method = 'oauth_token'; // Stored OAuth token from credentials file
-      } else if (credentials.api_key) {
-        auth.apiKeyValid = true;
-        auth.authenticated = true;
-        auth.method = 'api_key'; // Stored API key in credentials file
-      }
-      break; // Found and processed credentials file
-    } catch {
-      // No credentials file at this path or invalid format
+      auth.method = 'oauth_token';
+    } else if (indicators.credentials.hasApiKey) {
+      auth.apiKeyValid = true;
+      auth.authenticated = true;
+      auth.method = 'api_key';
     }
   }
 
@@ -174,21 +115,21 @@ export async function getClaudeStatus() {
   if (auth.hasEnvApiKey) {
     auth.authenticated = true;
     auth.apiKeyValid = true;
-    auth.method = 'api_key_env'; // API key from ANTHROPIC_API_KEY env var
+    auth.method = 'api_key_env';
   }
 
   // In-memory stored OAuth token (from setup wizard - subscription auth)
   if (!auth.authenticated && getApiKey('anthropic_oauth_token')) {
     auth.authenticated = true;
     auth.oauthTokenValid = true;
-    auth.method = 'oauth_token'; // Stored OAuth token from setup wizard
+    auth.method = 'oauth_token';
   }
 
   // In-memory stored API key (from settings UI - pay-per-use)
   if (!auth.authenticated && getApiKey('anthropic')) {
     auth.authenticated = true;
     auth.apiKeyValid = true;
-    auth.method = 'api_key'; // Manually stored API key
+    auth.method = 'api_key';
   }
 
   return {

apps/server/src/routes/setup/routes/delete-api-key.ts

@@ -5,40 +5,22 @@
 import type { Request, Response } from 'express';
 import { createLogger } from '@automaker/utils';
 import path from 'path';
-import fs from 'fs/promises';
+import { secureFs } from '@automaker/platform';
 
 const logger = createLogger('Setup');
 
 // In-memory storage reference (imported from common.ts pattern)
-// We need to modify common.ts to export a deleteApiKey function
 import { setApiKey } from '../common.js';
 
 /**
  * Remove an API key from the .env file
+ * Uses centralized secureFs.removeEnvKey for path validation
  */
 async function removeApiKeyFromEnv(key: string): Promise<void> {
   const envPath = path.join(process.cwd(), '.env');
 
   try {
-    let envContent = '';
-    try {
-      envContent = await fs.readFile(envPath, 'utf-8');
-    } catch {
-      // .env file doesn't exist, nothing to delete
-      return;
-    }
-
-    // Parse existing env content and remove the key
-    const lines = envContent.split('\n');
-    const keyRegex = new RegExp(`^${key}=`);
-    const newLines = lines.filter((line) => !keyRegex.test(line));
-
-    // Remove empty lines at the end
-    while (newLines.length > 0 && newLines[newLines.length - 1].trim() === '') {
-      newLines.pop();
-    }
-
-    await fs.writeFile(envPath, newLines.join('\n') + (newLines.length > 0 ? '\n' : ''));
+    await secureFs.removeEnvKey(envPath, key);
     logger.info(`[Setup] Removed ${key} from .env file`);
   } catch (error) {
     logger.error(`[Setup] Failed to remove ${key} from .env:`, error);

apps/server/src/routes/setup/routes/gh-status.ts

@@ -5,27 +5,14 @@
 import type { Request, Response } from 'express';
 import { exec } from 'child_process';
 import { promisify } from 'util';
-import os from 'os';
-import path from 'path';
-import fs from 'fs/promises';
+import { getGitHubCliPaths, getExtendedPath, systemPathAccess } from '@automaker/platform';
 import { getErrorMessage, logError } from '../common.js';
 
 const execAsync = promisify(exec);
 
-// Extended PATH to include common tool installation locations
-const extendedPath = [
-  process.env.PATH,
-  '/opt/homebrew/bin',
-  '/usr/local/bin',
-  '/home/linuxbrew/.linuxbrew/bin',
-  `${process.env.HOME}/.local/bin`,
-]
-  .filter(Boolean)
-  .join(':');
-
 const execEnv = {
   ...process.env,
-  PATH: extendedPath,
+  PATH: getExtendedPath(),
 };
 
 export interface GhStatus {
@@ -55,25 +42,16 @@ async function getGhStatus(): Promise<GhStatus> {
     status.path = stdout.trim().split(/\r?\n/)[0];
     status.installed = true;
   } catch {
-    // gh not in PATH, try common locations
-    const commonPaths = isWindows
-      ? [
-          path.join(process.env.LOCALAPPDATA || '', 'Programs', 'gh', 'bin', 'gh.exe'),
-          path.join(process.env.ProgramFiles || '', 'GitHub CLI', 'gh.exe'),
-        ]
-      : [
-          '/opt/homebrew/bin/gh',
-          '/usr/local/bin/gh',
-          path.join(os.homedir(), '.local', 'bin', 'gh'),
-          '/home/linuxbrew/.linuxbrew/bin/gh',
-        ];
+    // gh not in PATH, try common locations from centralized system paths
+    const commonPaths = getGitHubCliPaths();
 
     for (const p of commonPaths) {
       try {
-        await fs.access(p);
-        status.path = p;
-        status.installed = true;
-        break;
+        if (await systemPathAccess(p)) {
+          status.path = p;
+          status.installed = true;
+          break;
+        }
       } catch {
         // Not found at this path
       }
@@ -94,23 +72,37 @@ async function getGhStatus(): Promise<GhStatus> {
     // Version command failed
   }
 
-  // Check authentication status
+  // Check authentication status by actually making an API call
+  // gh auth status can return non-zero even when GH_TOKEN is valid
+  let apiCallSucceeded = false;
   try {
-    const { stdout } = await execAsync('gh auth status', { env: execEnv });
-    // If this succeeds without error, we're authenticated
-    status.authenticated = true;
-
-    // Try to extract username from output
-    const userMatch =
-      stdout.match(/Logged in to [^\s]+ account ([^\s]+)/i) ||
-      stdout.match(/Logged in to [^\s]+ as ([^\s]+)/i);
-    if (userMatch) {
-      status.user = userMatch[1];
+    const { stdout } = await execAsync('gh api user --jq ".login"', { env: execEnv });
+    const user = stdout.trim();
+    if (user) {
+      status.authenticated = true;
+      status.user = user;
+      apiCallSucceeded = true;
     }
-  } catch (error: unknown) {
-    // Auth status returns non-zero if not authenticated
-    const err = error as { stderr?: string };
-    if (err.stderr?.includes('not logged in')) {
+    // If stdout is empty, fall through to gh auth status fallback
+  } catch {
+    // API call failed - fall through to gh auth status fallback
+  }
+
+  // Fallback: try gh auth status if API call didn't succeed
+  if (!apiCallSucceeded) {
+    try {
+      const { stdout } = await execAsync('gh auth status', { env: execEnv });
+      status.authenticated = true;
+
+      // Try to extract username from output
+      const userMatch =
+        stdout.match(/Logged in to [^\s]+ account ([^\s]+)/i) ||
+        stdout.match(/Logged in to [^\s]+ as ([^\s]+)/i);
+      if (userMatch) {
+        status.user = userMatch[1];
+      }
+    } catch {
+      // Auth status returns non-zero if not authenticated
       status.authenticated = false;
     }
   }

apps/server/src/routes/suggestions/generate-suggestions.ts

@@ -6,9 +6,94 @@ import { query } from '@anthropic-ai/claude-agent-sdk';
 import type { EventEmitter } from '../../lib/events.js';
 import { createLogger } from '@automaker/utils';
 import { createSuggestionsOptions } from '../../lib/sdk-options.js';
+import { FeatureLoader } from '../../services/feature-loader.js';
+import { getAppSpecPath } from '@automaker/platform';
+import * as secureFs from '../../lib/secure-fs.js';
+import type { SettingsService } from '../../services/settings-service.js';
+import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
 
 const logger = createLogger('Suggestions');
 
+/**
+ * Extract implemented features from app_spec.txt XML content
+ *
+ * Note: This uses regex-based parsing which is sufficient for our controlled
+ * XML structure. If more complex XML parsing is needed in the future, consider
+ * using a library like 'fast-xml-parser' or 'xml2js'.
+ */
+function extractImplementedFeatures(specContent: string): string[] {
+  const features: string[] = [];
+
+  // Match <implemented_features>...</implemented_features> section
+  const implementedMatch = specContent.match(
+    /<implemented_features>([\s\S]*?)<\/implemented_features>/
+  );
+
+  if (implementedMatch) {
+    const implementedSection = implementedMatch[1];
+
+    // Extract feature names from <name>...</name> tags using matchAll
+    const nameRegex = /<name>(.*?)<\/name>/g;
+    const matches = implementedSection.matchAll(nameRegex);
+
+    for (const match of matches) {
+      features.push(match[1].trim());
+    }
+  }
+
+  return features;
+}
+
+/**
+ * Load existing context (app spec and backlog features) to avoid duplicates
+ */
+async function loadExistingContext(projectPath: string): Promise<string> {
+  let context = '';
+
+  // 1. Read app_spec.txt for implemented features
+  try {
+    const appSpecPath = getAppSpecPath(projectPath);
+    const specContent = (await secureFs.readFile(appSpecPath, 'utf-8')) as string;
+
+    if (specContent && specContent.trim().length > 0) {
+      const implementedFeatures = extractImplementedFeatures(specContent);
+
+      if (implementedFeatures.length > 0) {
+        context += '\n\n=== ALREADY IMPLEMENTED FEATURES ===\n';
+        context += 'These features are already implemented in the codebase:\n';
+        context += implementedFeatures.map((feature) => `- ${feature}`).join('\n') + '\n';
+      }
+    }
+  } catch (error) {
+    // app_spec.txt doesn't exist or can't be read - that's okay
+    logger.debug('No app_spec.txt found or error reading it:', error);
+  }
+
+  // 2. Load existing features from backlog
+  try {
+    const featureLoader = new FeatureLoader();
+    const features = await featureLoader.getAll(projectPath);
+
+    if (features.length > 0) {
+      context += '\n\n=== EXISTING FEATURES IN BACKLOG ===\n';
+      context += 'These features are already planned or in progress:\n';
+      context +=
+        features
+          .map((feature) => {
+            const status = feature.status || 'pending';
+            const title = feature.title || feature.description?.substring(0, 50) || 'Untitled';
+            return `- ${title} (${status})`;
+          })
+          .join('\n') + '\n';
+    }
+  } catch (error) {
+    // Features directory doesn't exist or can't be read - that's okay
+    logger.debug('No features found or error loading them:', error);
+  }
+
+  return context;
+}
+
 /**
  * JSON Schema for suggestions output
  */
@@ -42,7 +127,8 @@ export async function generateSuggestions(
   projectPath: string,
   suggestionType: string,
   events: EventEmitter,
-  abortController: AbortController
+  abortController: AbortController,
+  settingsService?: SettingsService
 ): Promise<void> {
   const typePrompts: Record<string, string> = {
     features: 'Analyze this project and suggest new features that would add value.',
@@ -51,8 +137,13 @@ export async function generateSuggestions(
     performance: 'Analyze this project for performance issues and suggest optimizations.',
   };
 
-  const prompt = `${typePrompts[suggestionType] || typePrompts.features}
+  // Load existing context to avoid duplicates
+  const existingContext = await loadExistingContext(projectPath);
 
+  const prompt = `${typePrompts[suggestionType] || typePrompts.features}
+${existingContext}
+
+${existingContext ? '\nIMPORTANT: Do NOT suggest features that are already implemented or already in the backlog above. Focus on NEW ideas that complement what already exists.\n' : ''}
 Look at the codebase and provide 3-5 concrete suggestions.
 
 For each suggestion, provide:
@@ -63,14 +154,20 @@ For each suggestion, provide:
 
 The response will be automatically formatted as structured JSON.`;
 
-  events.emit('suggestions:event', {
-    type: 'suggestions_progress',
-    content: `Starting ${suggestionType} analysis...\n`,
-  });
+  // Don't send initial message - let the agent output speak for itself
+  // The first agent message will be captured as an info entry
+
+  // Load autoLoadClaudeMd setting
+  const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+    projectPath,
+    settingsService,
+    '[Suggestions]'
+  );
 
   const options = createSuggestionsOptions({
     cwd: projectPath,
     abortController,
+    autoLoadClaudeMd,
     outputFormat: {
       type: 'json_schema',
       schema: suggestionsSchema,

apps/server/src/routes/suggestions/index.ts

@@ -8,11 +8,19 @@ import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createGenerateHandler } from './routes/generate.js';
 import { createStopHandler } from './routes/stop.js';
 import { createStatusHandler } from './routes/status.js';
+import type { SettingsService } from '../../services/settings-service.js';
 
-export function createSuggestionsRoutes(events: EventEmitter): Router {
+export function createSuggestionsRoutes(
+  events: EventEmitter,
+  settingsService?: SettingsService
+): Router {
   const router = Router();
 
-  router.post('/generate', validatePathParams('projectPath'), createGenerateHandler(events));
+  router.post(
+    '/generate',
+    validatePathParams('projectPath'),
+    createGenerateHandler(events, settingsService)
+  );
   router.post('/stop', createStopHandler());
   router.get('/status', createStatusHandler());
 

apps/server/src/routes/suggestions/routes/generate.ts

@@ -7,10 +7,11 @@ import type { EventEmitter } from '../../../lib/events.js';
 import { createLogger } from '@automaker/utils';
 import { getSuggestionsStatus, setRunningState, getErrorMessage, logError } from '../common.js';
 import { generateSuggestions } from '../generate-suggestions.js';
+import type { SettingsService } from '../../../services/settings-service.js';
 
 const logger = createLogger('Suggestions');
 
-export function createGenerateHandler(events: EventEmitter) {
+export function createGenerateHandler(events: EventEmitter, settingsService?: SettingsService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { projectPath, suggestionType = 'features' } = req.body as {
@@ -37,7 +38,7 @@ export function createGenerateHandler(events: EventEmitter) {
       setRunningState(true, abortController);
 
       // Start generation in background
-      generateSuggestions(projectPath, suggestionType, events, abortController)
+      generateSuggestions(projectPath, suggestionType, events, abortController, settingsService)
         .catch((error) => {
           logError(error, 'Generate suggestions failed (background)');
           events.emit('suggestions:event', {

apps/server/src/routes/terminal/routes/sessions.ts

@@ -22,12 +22,12 @@ export function createSessionsListHandler() {
 }
 
 export function createSessionsCreateHandler() {
-  return (req: Request, res: Response): void => {
+  return async (req: Request, res: Response): Promise<void> => {
     try {
       const terminalService = getTerminalService();
       const { cwd, cols, rows, shell } = req.body;
 
-      const session = terminalService.createSession({
+      const session = await terminalService.createSession({
         cwd,
         cols: cols || 80,
         rows: rows || 24,

apps/server/src/routes/worktree/common.ts

@@ -158,8 +158,13 @@ export const logError = createLogError(logger);
 /**
  * Ensure the repository has at least one commit so git commands that rely on HEAD work.
  * Returns true if an empty commit was created, false if the repo already had commits.
+ * @param repoPath - Path to the git repository
+ * @param env - Optional environment variables to pass to git (e.g., GIT_AUTHOR_NAME, GIT_AUTHOR_EMAIL)
  */
-export async function ensureInitialCommit(repoPath: string): Promise<boolean> {
+export async function ensureInitialCommit(
+  repoPath: string,
+  env?: Record<string, string>
+): Promise<boolean> {
   try {
     await execAsync('git rev-parse --verify HEAD', { cwd: repoPath });
     return false;
@@ -167,6 +172,7 @@ export async function ensureInitialCommit(repoPath: string): Promise<boolean> {
     try {
       await execAsync(`git commit --allow-empty -m "${AUTOMAKER_INITIAL_COMMIT_MESSAGE}"`, {
         cwd: repoPath,
+        env: { ...process.env, ...env },
       });
       logger.info(`[Worktree] Created initial empty commit to enable worktrees in ${repoPath}`);
       return true;

apps/server/src/routes/worktree/routes/create-pr.ts

@@ -56,32 +56,56 @@ export function createCreatePRHandler() {
       }
 
       // Check for uncommitted changes
+      console.log(`[CreatePR] Checking for uncommitted changes in: ${worktreePath}`);
       const { stdout: status } = await execAsync('git status --porcelain', {
         cwd: worktreePath,
         env: execEnv,
       });
       const hasChanges = status.trim().length > 0;
+      console.log(`[CreatePR] Has uncommitted changes: ${hasChanges}`);
+      if (hasChanges) {
+        console.log(`[CreatePR] Changed files:\n${status}`);
+      }
 
       // If there are changes, commit them
       let commitHash: string | null = null;
+      let commitError: string | null = null;
       if (hasChanges) {
         const message = commitMessage || `Changes from ${branchName}`;
+        console.log(`[CreatePR] Committing changes with message: ${message}`);
 
-        // Stage all changes
-        await execAsync('git add -A', { cwd: worktreePath, env: execEnv });
+        try {
+          // Stage all changes
+          console.log(`[CreatePR] Running: git add -A`);
+          await execAsync('git add -A', { cwd: worktreePath, env: execEnv });
 
-        // Create commit
-        await execAsync(`git commit -m "${message.replace(/"/g, '\\"')}"`, {
-          cwd: worktreePath,
-          env: execEnv,
-        });
+          // Create commit
+          console.log(`[CreatePR] Running: git commit`);
+          await execAsync(`git commit -m "${message.replace(/"/g, '\\"')}"`, {
+            cwd: worktreePath,
+            env: execEnv,
+          });
 
-        // Get commit hash
-        const { stdout: hashOutput } = await execAsync('git rev-parse HEAD', {
-          cwd: worktreePath,
-          env: execEnv,
-        });
-        commitHash = hashOutput.trim().substring(0, 8);
+          // Get commit hash
+          const { stdout: hashOutput } = await execAsync('git rev-parse HEAD', {
+            cwd: worktreePath,
+            env: execEnv,
+          });
+          commitHash = hashOutput.trim().substring(0, 8);
+          console.log(`[CreatePR] Commit successful: ${commitHash}`);
+        } catch (commitErr: unknown) {
+          const err = commitErr as { stderr?: string; message?: string };
+          commitError = err.stderr || err.message || 'Commit failed';
+          console.error(`[CreatePR] Commit failed: ${commitError}`);
+
+          // Return error immediately - don't proceed with push/PR if commit fails
+          res.status(500).json({
+            success: false,
+            error: `Failed to commit changes: ${commitError}`,
+            commitError,
+          });
+          return;
+        }
       }
 
       // Push the branch to remote
@@ -360,8 +384,9 @@ export function createCreatePRHandler() {
         success: true,
         result: {
           branch: branchName,
-          committed: hasChanges,
+          committed: hasChanges && !commitError,
           commitHash,
+          commitError: commitError || undefined,
           pushed: true,
           prUrl,
           prNumber,

apps/server/src/routes/worktree/routes/create.ts

@@ -100,7 +100,14 @@ export function createCreateHandler() {
       }
 
       // Ensure the repository has at least one commit so worktree commands referencing HEAD succeed
-      await ensureInitialCommit(projectPath);
+      // Pass git identity env vars so commits work without global git config
+      const gitEnv = {
+        GIT_AUTHOR_NAME: 'Automaker',
+        GIT_AUTHOR_EMAIL: 'automaker@localhost',
+        GIT_COMMITTER_NAME: 'Automaker',
+        GIT_COMMITTER_EMAIL: 'automaker@localhost',
+      };
+      await ensureInitialCommit(projectPath, gitEnv);
 
       // First, check if git already has a worktree for this branch (anywhere)
       const existingWorktree = await findExistingWorktreeForBranch(projectPath, branchName);

apps/server/src/services/agent-service.ts

@@ -12,10 +12,20 @@ import {
   buildPromptWithImages,
   isAbortError,
   loadContextFiles,
+  createLogger,
 } from '@automaker/utils';
 import { ProviderFactory } from '../providers/provider-factory.js';
 import { createChatOptions, validateWorkingDirectory } from '../lib/sdk-options.js';
 import { PathNotAllowedError } from '@automaker/platform';
+import type { SettingsService } from './settings-service.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getEnableSandboxModeSetting,
+  filterClaudeMdFromContext,
+  getMCPServersFromSettings,
+  getMCPPermissionSettings,
+  getPromptCustomization,
+} from '../lib/settings-helpers.js';
 
 interface Message {
   id: string;
@@ -30,6 +40,14 @@ interface Message {
   isError?: boolean;
 }
 
+interface QueuedPrompt {
+  id: string;
+  message: string;
+  imagePaths?: string[];
+  model?: string;
+  addedAt: string;
+}
+
 interface Session {
   messages: Message[];
   isRunning: boolean;
@@ -37,6 +55,7 @@ interface Session {
   workingDirectory: string;
   model?: string;
   sdkSessionId?: string; // Claude SDK session ID for conversation continuity
+  promptQueue: QueuedPrompt[]; // Queue of prompts to auto-run after current task
 }
 
 interface SessionMetadata {
@@ -57,11 +76,14 @@ export class AgentService {
   private stateDir: string;
   private metadataFile: string;
   private events: EventEmitter;
+  private settingsService: SettingsService | null = null;
+  private logger = createLogger('AgentService');
 
-  constructor(dataDir: string, events: EventEmitter) {
+  constructor(dataDir: string, events: EventEmitter, settingsService?: SettingsService) {
     this.stateDir = path.join(dataDir, 'agent-sessions');
     this.metadataFile = path.join(dataDir, 'sessions-metadata.json');
     this.events = events;
+    this.settingsService = settingsService ?? null;
   }
 
   async initialize(): Promise<void> {
@@ -90,12 +112,16 @@ export class AgentService {
       // Validate that the working directory is allowed using centralized validation
       validateWorkingDirectory(resolvedWorkingDirectory);
 
+      // Load persisted queue
+      const promptQueue = await this.loadQueueState(sessionId);
+
       this.sessions.set(sessionId, {
         messages,
         isRunning: false,
         abortController: null,
         workingDirectory: resolvedWorkingDirectory,
         sdkSessionId: sessionMetadata?.sdkSessionId, // Load persisted SDK session ID
+        promptQueue,
       });
     }
 
@@ -125,10 +151,12 @@ export class AgentService {
   }) {
     const session = this.sessions.get(sessionId);
     if (!session) {
+      this.logger.error('ERROR: Session not found:', sessionId);
       throw new Error(`Session ${sessionId} not found`);
     }
 
     if (session.isRunning) {
+      this.logger.error('ERROR: Agent already running for session:', sessionId);
       throw new Error('Agent is already processing a message');
     }
 
@@ -150,7 +178,7 @@ export class AgentService {
             filename: imageData.filename,
           });
         } catch (error) {
-          console.error(`[AgentService] Failed to load image ${imagePath}:`, error);
+          this.logger.error(`Failed to load image ${imagePath}:`, error);
         }
       }
     }
@@ -174,6 +202,11 @@ export class AgentService {
     session.isRunning = true;
     session.abortController = new AbortController();
 
+    // Emit started event so UI can show thinking indicator
+    this.emitAgentEvent(sessionId, {
+      type: 'started',
+    });
+
     // Emit user message event
     this.emitAgentEvent(sessionId, {
       type: 'message',
@@ -186,14 +219,37 @@ export class AgentService {
       // Determine the effective working directory for context loading
       const effectiveWorkDir = workingDirectory || session.workingDirectory;
 
+      // Load autoLoadClaudeMd setting (project setting takes precedence over global)
+      const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+        effectiveWorkDir,
+        this.settingsService,
+        '[AgentService]'
+      );
+
+      // Load enableSandboxMode setting (global setting only)
+      const enableSandboxMode = await getEnableSandboxModeSetting(
+        this.settingsService,
+        '[AgentService]'
+      );
+
+      // Load MCP servers from settings (global setting only)
+      const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AgentService]');
+
+      // Load MCP permission settings (global setting only)
+      const mcpPermissions = await getMCPPermissionSettings(this.settingsService, '[AgentService]');
+
       // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.)
-      const { formattedPrompt: contextFilesPrompt } = await loadContextFiles({
+      const contextResult = await loadContextFiles({
         projectPath: effectiveWorkDir,
         fsModule: secureFs as Parameters<typeof loadContextFiles>[0]['fsModule'],
       });
 
+      // When autoLoadClaudeMd is enabled, filter out CLAUDE.md to avoid duplication
+      // (SDK handles CLAUDE.md via settingSources), but keep other context files like CODE_QUALITY.md
+      const contextFilesPrompt = filterClaudeMdFromContext(contextResult, autoLoadClaudeMd);
+
       // Build combined system prompt with base prompt and context files
-      const baseSystemPrompt = this.getSystemPrompt();
+      const baseSystemPrompt = await this.getSystemPrompt();
       const combinedSystemPrompt = contextFilesPrompt
         ? `${contextFilesPrompt}\n\n${baseSystemPrompt}`
         : baseSystemPrompt;
@@ -205,6 +261,11 @@ export class AgentService {
         sessionModel: session.model,
         systemPrompt: combinedSystemPrompt,
         abortController: session.abortController!,
+        autoLoadClaudeMd,
+        enableSandboxMode,
+        mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
+        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
+        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
       });
 
       // Extract model, maxTurns, and allowedTools from SDK options
@@ -215,21 +276,22 @@ export class AgentService {
       // Get provider for this model
       const provider = ProviderFactory.getProviderForModel(effectiveModel);
 
-      console.log(
-        `[AgentService] Using provider "${provider.getName()}" for model "${effectiveModel}"`
-      );
-
       // Build options for provider
       const options: ExecuteOptions = {
         prompt: '', // Will be set below based on images
         model: effectiveModel,
         cwd: effectiveWorkDir,
-        systemPrompt: combinedSystemPrompt,
+        systemPrompt: sdkOptions.systemPrompt,
         maxTurns: maxTurns,
         allowedTools: allowedTools,
         abortController: session.abortController!,
         conversationHistory: conversationHistory.length > 0 ? conversationHistory : undefined,
+        settingSources: sdkOptions.settingSources,
+        sandbox: sdkOptions.sandbox, // Pass sandbox configuration
         sdkSessionId: session.sdkSessionId, // Pass SDK session ID for resuming
+        mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined, // Pass MCP servers configuration
+        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools, // Pass MCP auto-approve setting
+        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools, // Pass MCP unrestricted tools setting
       };
 
       // Build prompt content with images
@@ -254,7 +316,6 @@ export class AgentService {
         // Capture SDK session ID from any message and persist it
         if (msg.session_id && !session.sdkSessionId) {
           session.sdkSessionId = msg.session_id;
-          console.log(`[AgentService] Captured SDK session ID: ${msg.session_id}`);
           // Persist the SDK session ID to ensure conversation continuity across server restarts
           await this.updateSession(sessionId, { sdkSessionId: msg.session_id });
         }
@@ -319,6 +380,9 @@ export class AgentService {
       session.isRunning = false;
       session.abortController = null;
 
+      // Process next item in queue after completion
+      setImmediate(() => this.processNextInQueue(sessionId));
+
       return {
         success: true,
         message: currentAssistantMessage,
@@ -330,7 +394,7 @@ export class AgentService {
         return { success: false, aborted: true };
       }
 
-      console.error('[AgentService] Error:', error);
+      this.logger.error('Error:', error);
 
       session.isRunning = false;
       session.abortController = null;
@@ -424,7 +488,7 @@ export class AgentService {
       await secureFs.writeFile(sessionFile, JSON.stringify(messages, null, 2), 'utf-8');
       await this.updateSessionTimestamp(sessionId);
     } catch (error) {
-      console.error('[AgentService] Failed to save session:', error);
+      this.logger.error('Failed to save session:', error);
     }
   }
 
@@ -557,42 +621,173 @@ export class AgentService {
     return true;
   }
 
+  // Queue management methods
+
+  /**
+   * Add a prompt to the queue for later execution
+   */
+  async addToQueue(
+    sessionId: string,
+    prompt: { message: string; imagePaths?: string[]; model?: string }
+  ): Promise<{ success: boolean; queuedPrompt?: QueuedPrompt; error?: string }> {
+    const session = this.sessions.get(sessionId);
+    if (!session) {
+      return { success: false, error: 'Session not found' };
+    }
+
+    const queuedPrompt: QueuedPrompt = {
+      id: this.generateId(),
+      message: prompt.message,
+      imagePaths: prompt.imagePaths,
+      model: prompt.model,
+      addedAt: new Date().toISOString(),
+    };
+
+    session.promptQueue.push(queuedPrompt);
+    await this.saveQueueState(sessionId, session.promptQueue);
+
+    // Emit queue update event
+    this.emitAgentEvent(sessionId, {
+      type: 'queue_updated',
+      queue: session.promptQueue,
+    });
+
+    return { success: true, queuedPrompt };
+  }
+
+  /**
+   * Get the current queue for a session
+   */
+  getQueue(sessionId: string): { success: boolean; queue?: QueuedPrompt[]; error?: string } {
+    const session = this.sessions.get(sessionId);
+    if (!session) {
+      return { success: false, error: 'Session not found' };
+    }
+    return { success: true, queue: session.promptQueue };
+  }
+
+  /**
+   * Remove a specific prompt from the queue
+   */
+  async removeFromQueue(
+    sessionId: string,
+    promptId: string
+  ): Promise<{ success: boolean; error?: string }> {
+    const session = this.sessions.get(sessionId);
+    if (!session) {
+      return { success: false, error: 'Session not found' };
+    }
+
+    const index = session.promptQueue.findIndex((p) => p.id === promptId);
+    if (index === -1) {
+      return { success: false, error: 'Prompt not found in queue' };
+    }
+
+    session.promptQueue.splice(index, 1);
+    await this.saveQueueState(sessionId, session.promptQueue);
+
+    this.emitAgentEvent(sessionId, {
+      type: 'queue_updated',
+      queue: session.promptQueue,
+    });
+
+    return { success: true };
+  }
+
+  /**
+   * Clear all prompts from the queue
+   */
+  async clearQueue(sessionId: string): Promise<{ success: boolean; error?: string }> {
+    const session = this.sessions.get(sessionId);
+    if (!session) {
+      return { success: false, error: 'Session not found' };
+    }
+
+    session.promptQueue = [];
+    await this.saveQueueState(sessionId, []);
+
+    this.emitAgentEvent(sessionId, {
+      type: 'queue_updated',
+      queue: [],
+    });
+
+    return { success: true };
+  }
+
+  /**
+   * Save queue state to disk for persistence
+   */
+  private async saveQueueState(sessionId: string, queue: QueuedPrompt[]): Promise<void> {
+    const queueFile = path.join(this.stateDir, `${sessionId}-queue.json`);
+    try {
+      await secureFs.writeFile(queueFile, JSON.stringify(queue, null, 2), 'utf-8');
+    } catch (error) {
+      this.logger.error('Failed to save queue state:', error);
+    }
+  }
+
+  /**
+   * Load queue state from disk
+   */
+  private async loadQueueState(sessionId: string): Promise<QueuedPrompt[]> {
+    const queueFile = path.join(this.stateDir, `${sessionId}-queue.json`);
+    try {
+      const data = (await secureFs.readFile(queueFile, 'utf-8')) as string;
+      return JSON.parse(data);
+    } catch {
+      return [];
+    }
+  }
+
+  /**
+   * Process the next item in the queue (called after task completion)
+   */
+  private async processNextInQueue(sessionId: string): Promise<void> {
+    const session = this.sessions.get(sessionId);
+    if (!session || session.promptQueue.length === 0) {
+      return;
+    }
+
+    // Don't process if already running
+    if (session.isRunning) {
+      return;
+    }
+
+    const nextPrompt = session.promptQueue.shift();
+    if (!nextPrompt) return;
+
+    await this.saveQueueState(sessionId, session.promptQueue);
+
+    this.emitAgentEvent(sessionId, {
+      type: 'queue_updated',
+      queue: session.promptQueue,
+    });
+
+    try {
+      await this.sendMessage({
+        sessionId,
+        message: nextPrompt.message,
+        imagePaths: nextPrompt.imagePaths,
+        model: nextPrompt.model,
+      });
+    } catch (error) {
+      this.logger.error('Failed to process queued prompt:', error);
+      this.emitAgentEvent(sessionId, {
+        type: 'queue_error',
+        error: (error as Error).message,
+        promptId: nextPrompt.id,
+      });
+    }
+  }
+
   private emitAgentEvent(sessionId: string, data: Record<string, unknown>): void {
     this.events.emit('agent:stream', { sessionId, ...data });
   }
 
-  private getSystemPrompt(): string {
-    return `You are an AI assistant helping users build software. You are part of the Automaker application,
-which is designed to help developers plan, design, and implement software projects autonomously.
-
-**Feature Storage:**
-Features are stored in .automaker/features/{id}/feature.json - each feature has its own folder.
-Use the UpdateFeatureStatus tool to manage features, not direct file edits.
-
-Your role is to:
-- Help users define their project requirements and specifications
-- Ask clarifying questions to better understand their needs
-- Suggest technical approaches and architectures
-- Guide them through the development process
-- Be conversational and helpful
-- Write, edit, and modify code files as requested
-- Execute commands and tests
-- Search and analyze the codebase
-
-When discussing projects, help users think through:
-- Core functionality and features
-- Technical stack choices
-- Data models and architecture
-- User experience considerations
-- Testing strategies
-
-You have full access to the codebase and can:
-- Read files to understand existing code
-- Write new files
-- Edit existing files
-- Run bash commands
-- Search for code patterns
-- Execute tests and builds`;
+  private async getSystemPrompt(): Promise<string> {
+    // Load from settings (no caching - allows hot reload of custom prompts)
+    const prompts = await getPromptCustomization(this.settingsService, '[AgentService]');
+    return prompts.agent.systemPrompt;
   }
 
   private generateId(): string {

apps/server/src/services/auto-mode-service.ts

@@ -10,7 +10,7 @@
  */
 
 import { ProviderFactory } from '../providers/provider-factory.js';
-import type { ExecuteOptions, Feature } from '@automaker/types';
+import type { ExecuteOptions, Feature, PipelineConfig, PipelineStep } from '@automaker/types';
 import {
   buildPromptWithImages,
   isAbortError,
@@ -25,8 +25,22 @@ import { promisify } from 'util';
 import path from 'path';
 import * as secureFs from '../lib/secure-fs.js';
 import type { EventEmitter } from '../lib/events.js';
-import { createAutoModeOptions, validateWorkingDirectory } from '../lib/sdk-options.js';
+import {
+  createAutoModeOptions,
+  createCustomOptions,
+  validateWorkingDirectory,
+} from '../lib/sdk-options.js';
 import { FeatureLoader } from './feature-loader.js';
+import type { SettingsService } from './settings-service.js';
+import { pipelineService, PipelineService } from './pipeline-service.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getEnableSandboxModeSetting,
+  filterClaudeMdFromContext,
+  getMCPServersFromSettings,
+  getMCPPermissionSettings,
+  getPromptCustomization,
+} from '../lib/settings-helpers.js';
 
 const execAsync = promisify(exec);
 
@@ -54,162 +68,6 @@ interface PlanSpec {
   tasks?: ParsedTask[];
 }
 
-const PLANNING_PROMPTS = {
-  lite: `## Planning Phase (Lite Mode)
-
-IMPORTANT: Do NOT output exploration text, tool usage, or thinking before the plan. Start DIRECTLY with the planning outline format below. Silently analyze the codebase first, then output ONLY the structured plan.
-
-Create a brief planning outline:
-
-1. **Goal**: What are we accomplishing? (1 sentence)
-2. **Approach**: How will we do it? (2-3 sentences)
-3. **Files to Touch**: List files and what changes
-4. **Tasks**: Numbered task list (3-7 items)
-5. **Risks**: Any gotchas to watch for
-
-After generating the outline, output:
-"[PLAN_GENERATED] Planning outline complete."
-
-Then proceed with implementation.`,
-
-  lite_with_approval: `## Planning Phase (Lite Mode)
-
-IMPORTANT: Do NOT output exploration text, tool usage, or thinking before the plan. Start DIRECTLY with the planning outline format below. Silently analyze the codebase first, then output ONLY the structured plan.
-
-Create a brief planning outline:
-
-1. **Goal**: What are we accomplishing? (1 sentence)
-2. **Approach**: How will we do it? (2-3 sentences)
-3. **Files to Touch**: List files and what changes
-4. **Tasks**: Numbered task list (3-7 items)
-5. **Risks**: Any gotchas to watch for
-
-After generating the outline, output:
-"[SPEC_GENERATED] Please review the planning outline above. Reply with 'approved' to proceed or provide feedback for revisions."
-
-DO NOT proceed with implementation until you receive explicit approval.`,
-
-  spec: `## Specification Phase (Spec Mode)
-
-IMPORTANT: Do NOT output exploration text, tool usage, or thinking before the spec. Start DIRECTLY with the specification format below. Silently analyze the codebase first, then output ONLY the structured specification.
-
-Generate a specification with an actionable task breakdown. WAIT for approval before implementing.
-
-### Specification Format
-
-1. **Problem**: What problem are we solving? (user perspective)
-
-2. **Solution**: Brief approach (1-2 sentences)
-
-3. **Acceptance Criteria**: 3-5 items in GIVEN-WHEN-THEN format
-   - GIVEN [context], WHEN [action], THEN [outcome]
-
-4. **Files to Modify**:
-   | File | Purpose | Action |
-   |------|---------|--------|
-   | path/to/file | description | create/modify/delete |
-
-5. **Implementation Tasks**:
-   Use this EXACT format for each task (the system will parse these):
-   \`\`\`tasks
-   - [ ] T001: [Description] | File: [path/to/file]
-   - [ ] T002: [Description] | File: [path/to/file]
-   - [ ] T003: [Description] | File: [path/to/file]
-   \`\`\`
-
-   Task ID rules:
-   - Sequential: T001, T002, T003, etc.
-   - Description: Clear action (e.g., "Create user model", "Add API endpoint")
-   - File: Primary file affected (helps with context)
-   - Order by dependencies (foundational tasks first)
-
-6. **Verification**: How to confirm feature works
-
-After generating the spec, output on its own line:
-"[SPEC_GENERATED] Please review the specification above. Reply with 'approved' to proceed or provide feedback for revisions."
-
-DO NOT proceed with implementation until you receive explicit approval.
-
-When approved, execute tasks SEQUENTIALLY in order. For each task:
-1. BEFORE starting, output: "[TASK_START] T###: Description"
-2. Implement the task
-3. AFTER completing, output: "[TASK_COMPLETE] T###: Brief summary"
-
-This allows real-time progress tracking during implementation.`,
-
-  full: `## Full Specification Phase (Full SDD Mode)
-
-IMPORTANT: Do NOT output exploration text, tool usage, or thinking before the spec. Start DIRECTLY with the specification format below. Silently analyze the codebase first, then output ONLY the structured specification.
-
-Generate a comprehensive specification with phased task breakdown. WAIT for approval before implementing.
-
-### Specification Format
-
-1. **Problem Statement**: 2-3 sentences from user perspective
-
-2. **User Story**: As a [user], I want [goal], so that [benefit]
-
-3. **Acceptance Criteria**: Multiple scenarios with GIVEN-WHEN-THEN
-   - **Happy Path**: GIVEN [context], WHEN [action], THEN [expected outcome]
-   - **Edge Cases**: GIVEN [edge condition], WHEN [action], THEN [handling]
-   - **Error Handling**: GIVEN [error condition], WHEN [action], THEN [error response]
-
-4. **Technical Context**:
-   | Aspect | Value |
-   |--------|-------|
-   | Affected Files | list of files |
-   | Dependencies | external libs if any |
-   | Constraints | technical limitations |
-   | Patterns to Follow | existing patterns in codebase |
-
-5. **Non-Goals**: What this feature explicitly does NOT include
-
-6. **Implementation Tasks**:
-   Use this EXACT format for each task (the system will parse these):
-   \`\`\`tasks
-   ## Phase 1: Foundation
-   - [ ] T001: [Description] | File: [path/to/file]
-   - [ ] T002: [Description] | File: [path/to/file]
-
-   ## Phase 2: Core Implementation
-   - [ ] T003: [Description] | File: [path/to/file]
-   - [ ] T004: [Description] | File: [path/to/file]
-
-   ## Phase 3: Integration & Testing
-   - [ ] T005: [Description] | File: [path/to/file]
-   - [ ] T006: [Description] | File: [path/to/file]
-   \`\`\`
-
-   Task ID rules:
-   - Sequential across all phases: T001, T002, T003, etc.
-   - Description: Clear action verb + target
-   - File: Primary file affected
-   - Order by dependencies within each phase
-   - Phase structure helps organize complex work
-
-7. **Success Metrics**: How we know it's done (measurable criteria)
-
-8. **Risks & Mitigations**:
-   | Risk | Mitigation |
-   |------|------------|
-   | description | approach |
-
-After generating the spec, output on its own line:
-"[SPEC_GENERATED] Please review the comprehensive specification above. Reply with 'approved' to proceed or provide feedback for revisions."
-
-DO NOT proceed with implementation until you receive explicit approval.
-
-When approved, execute tasks SEQUENTIALLY by phase. For each task:
-1. BEFORE starting, output: "[TASK_START] T###: Description"
-2. Implement the task
-3. AFTER completing, output: "[TASK_COMPLETE] T###: Brief summary"
-
-After completing all tasks in a phase, output:
-"[PHASE_COMPLETE] Phase N complete"
-
-This allows real-time progress tracking during implementation.`,
-};
-
 /**
  * Parse tasks from generated spec content
  * Looks for the ```tasks code block and extracts task lines
@@ -332,6 +190,10 @@ interface AutoModeConfig {
   projectPath: string;
 }
 
+// Constants for consecutive failure tracking
+const CONSECUTIVE_FAILURE_THRESHOLD = 3; // Pause after 3 consecutive failures
+const FAILURE_WINDOW_MS = 60000; // Failures within 1 minute count as consecutive
+
 export class AutoModeService {
   private events: EventEmitter;
   private runningFeatures = new Map<string, RunningFeature>();
@@ -341,9 +203,88 @@ export class AutoModeService {
   private autoLoopAbortController: AbortController | null = null;
   private config: AutoModeConfig | null = null;
   private pendingApprovals = new Map<string, PendingApproval>();
+  private settingsService: SettingsService | null = null;
+  // Track consecutive failures to detect quota/API issues
+  private consecutiveFailures: { timestamp: number; error: string }[] = [];
+  private pausedDueToFailures = false;
 
-  constructor(events: EventEmitter) {
+  constructor(events: EventEmitter, settingsService?: SettingsService) {
     this.events = events;
+    this.settingsService = settingsService ?? null;
+  }
+
+  /**
+   * Track a failure and check if we should pause due to consecutive failures.
+   * This handles cases where the SDK doesn't return useful error messages.
+   */
+  private trackFailureAndCheckPause(errorInfo: { type: string; message: string }): boolean {
+    const now = Date.now();
+
+    // Add this failure
+    this.consecutiveFailures.push({ timestamp: now, error: errorInfo.message });
+
+    // Remove old failures outside the window
+    this.consecutiveFailures = this.consecutiveFailures.filter(
+      (f) => now - f.timestamp < FAILURE_WINDOW_MS
+    );
+
+    // Check if we've hit the threshold
+    if (this.consecutiveFailures.length >= CONSECUTIVE_FAILURE_THRESHOLD) {
+      return true; // Should pause
+    }
+
+    // Also immediately pause for known quota/rate limit errors
+    if (errorInfo.type === 'quota_exhausted' || errorInfo.type === 'rate_limit') {
+      return true;
+    }
+
+    return false;
+  }
+
+  /**
+   * Signal that we should pause due to repeated failures or quota exhaustion.
+   * This will pause the auto loop to prevent repeated failures.
+   */
+  private signalShouldPause(errorInfo: { type: string; message: string }): void {
+    if (this.pausedDueToFailures) {
+      return; // Already paused
+    }
+
+    this.pausedDueToFailures = true;
+    const failureCount = this.consecutiveFailures.length;
+    console.log(
+      `[AutoMode] Pausing auto loop after ${failureCount} consecutive failures. Last error: ${errorInfo.type}`
+    );
+
+    // Emit event to notify UI
+    this.emitAutoModeEvent('auto_mode_paused_failures', {
+      message:
+        failureCount >= CONSECUTIVE_FAILURE_THRESHOLD
+          ? `Auto Mode paused: ${failureCount} consecutive failures detected. This may indicate a quota limit or API issue. Please check your usage and try again.`
+          : 'Auto Mode paused: Usage limit or API error detected. Please wait for your quota to reset or check your API configuration.',
+      errorType: errorInfo.type,
+      originalError: errorInfo.message,
+      failureCount,
+      projectPath: this.config?.projectPath,
+    });
+
+    // Stop the auto loop
+    this.stopAutoLoop();
+  }
+
+  /**
+   * Reset failure tracking (called when user manually restarts auto mode)
+   */
+  private resetFailureTracking(): void {
+    this.consecutiveFailures = [];
+    this.pausedDueToFailures = false;
+  }
+
+  /**
+   * Record a successful feature completion to reset consecutive failure count
+   */
+  private recordSuccess(): void {
+    this.consecutiveFailures = [];
   }
 
   /**
@@ -354,6 +295,9 @@ export class AutoModeService {
       throw new Error('Auto mode is already running');
     }
 
+    // Reset failure tracking when user manually starts auto mode
+    this.resetFailureTracking();
+
     this.autoLoopRunning = true;
     this.autoLoopAbortController = new AbortController();
     this.config = {
@@ -551,14 +495,25 @@ export class AutoModeService {
       // Update feature status to in_progress
       await this.updateFeatureStatus(projectPath, featureId, 'in_progress');
 
+      // Load autoLoadClaudeMd setting to determine context loading strategy
+      const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+        projectPath,
+        this.settingsService,
+        '[AutoMode]'
+      );
+
       // Build the prompt - use continuation prompt if provided (for recovery after plan approval)
       let prompt: string;
       // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.) - passed as system prompt
-      const { formattedPrompt: contextFilesPrompt } = await loadContextFiles({
+      const contextResult = await loadContextFiles({
         projectPath,
         fsModule: secureFs as Parameters<typeof loadContextFiles>[0]['fsModule'],
       });
 
+      // When autoLoadClaudeMd is enabled, filter out CLAUDE.md to avoid duplication
+      // (SDK handles CLAUDE.md via settingSources), but keep other context files like CODE_QUALITY.md
+      const contextFilesPrompt = filterClaudeMdFromContext(contextResult, autoLoadClaudeMd);
+
       if (options?.continuationPrompt) {
         // Continuation prompt is used when recovering from a plan approval
         // The plan was already approved, so skip the planning phase
@@ -567,7 +522,7 @@ export class AutoModeService {
       } else {
         // Normal flow: build prompt with planning phase
         const featurePrompt = this.buildFeaturePrompt(feature);
-        const planningPrefix = this.getPlanningPromptPrefix(feature);
+        const planningPrefix = await this.getPlanningPromptPrefix(feature);
         prompt = planningPrefix + featurePrompt;
 
         // Emit planning mode info
@@ -604,15 +559,36 @@ export class AutoModeService {
           planningMode: feature.planningMode,
           requirePlanApproval: feature.requirePlanApproval,
           systemPrompt: contextFilesPrompt || undefined,
+          autoLoadClaudeMd,
         }
       );
 
+      // Check for pipeline steps and execute them
+      const pipelineConfig = await pipelineService.getPipelineConfig(projectPath);
+      const sortedSteps = [...(pipelineConfig?.steps || [])].sort((a, b) => a.order - b.order);
+
+      if (sortedSteps.length > 0) {
+        // Execute pipeline steps sequentially
+        await this.executePipelineSteps(
+          projectPath,
+          featureId,
+          feature,
+          sortedSteps,
+          workDir,
+          abortController,
+          autoLoadClaudeMd
+        );
+      }
+
       // Determine final status based on testing mode:
       // - skipTests=false (automated testing): go directly to 'verified' (no manual verify needed)
       // - skipTests=true (manual verification): go to 'waiting_approval' for manual review
       const finalStatus = feature.skipTests ? 'waiting_approval' : 'verified';
       await this.updateFeatureStatus(projectPath, featureId, finalStatus);
 
+      // Record success to reset consecutive failure tracking
+      this.recordSuccess();
+
       this.emitAutoModeEvent('auto_mode_feature_complete', {
         featureId,
         passes: true,
@@ -640,6 +616,21 @@ export class AutoModeService {
           errorType: errorInfo.type,
           projectPath,
         });
+
+        // Track this failure and check if we should pause auto mode
+        // This handles both specific quota/rate limit errors AND generic failures
+        // that may indicate quota exhaustion (SDK doesn't always return useful errors)
+        const shouldPause = this.trackFailureAndCheckPause({
+          type: errorInfo.type,
+          message: errorInfo.message,
+        });
+
+        if (shouldPause) {
+          this.signalShouldPause({
+            type: errorInfo.type,
+            message: errorInfo.message,
+          });
+        }
       }
     } finally {
       console.log(`[AutoMode] Feature ${featureId} execution ended, cleaning up runningFeatures`);
@@ -650,6 +641,143 @@ export class AutoModeService {
     }
   }
 
+  /**
+   * Execute pipeline steps sequentially after initial feature implementation
+   */
+  private async executePipelineSteps(
+    projectPath: string,
+    featureId: string,
+    feature: Feature,
+    steps: PipelineStep[],
+    workDir: string,
+    abortController: AbortController,
+    autoLoadClaudeMd: boolean
+  ): Promise<void> {
+    console.log(`[AutoMode] Executing ${steps.length} pipeline step(s) for feature ${featureId}`);
+
+    // Load context files once
+    const contextResult = await loadContextFiles({
+      projectPath,
+      fsModule: secureFs as Parameters<typeof loadContextFiles>[0]['fsModule'],
+    });
+    const contextFilesPrompt = filterClaudeMdFromContext(contextResult, autoLoadClaudeMd);
+
+    // Load previous agent output for context continuity
+    const featureDir = getFeatureDir(projectPath, featureId);
+    const contextPath = path.join(featureDir, 'agent-output.md');
+    let previousContext = '';
+    try {
+      previousContext = (await secureFs.readFile(contextPath, 'utf-8')) as string;
+    } catch {
+      // No previous context
+    }
+
+    for (let i = 0; i < steps.length; i++) {
+      const step = steps[i];
+      const pipelineStatus = `pipeline_${step.id}`;
+
+      // Update feature status to current pipeline step
+      await this.updateFeatureStatus(projectPath, featureId, pipelineStatus);
+
+      this.emitAutoModeEvent('auto_mode_progress', {
+        featureId,
+        content: `Starting pipeline step ${i + 1}/${steps.length}: ${step.name}`,
+        projectPath,
+      });
+
+      this.emitAutoModeEvent('pipeline_step_started', {
+        featureId,
+        stepId: step.id,
+        stepName: step.name,
+        stepIndex: i,
+        totalSteps: steps.length,
+        projectPath,
+      });
+
+      // Build prompt for this pipeline step
+      const prompt = this.buildPipelineStepPrompt(step, feature, previousContext);
+
+      // Get model from feature
+      const model = resolveModelString(feature.model, DEFAULT_MODELS.claude);
+
+      // Run the agent for this pipeline step
+      await this.runAgent(
+        workDir,
+        featureId,
+        prompt,
+        abortController,
+        projectPath,
+        undefined, // no images for pipeline steps
+        model,
+        {
+          projectPath,
+          planningMode: 'skip', // Pipeline steps don't need planning
+          requirePlanApproval: false,
+          previousContent: previousContext,
+          systemPrompt: contextFilesPrompt || undefined,
+          autoLoadClaudeMd,
+        }
+      );
+
+      // Load updated context for next step
+      try {
+        previousContext = (await secureFs.readFile(contextPath, 'utf-8')) as string;
+      } catch {
+        // No context update
+      }
+
+      this.emitAutoModeEvent('pipeline_step_complete', {
+        featureId,
+        stepId: step.id,
+        stepName: step.name,
+        stepIndex: i,
+        totalSteps: steps.length,
+        projectPath,
+      });
+
+      console.log(
+        `[AutoMode] Pipeline step ${i + 1}/${steps.length} (${step.name}) completed for feature ${featureId}`
+      );
+    }
+
+    console.log(`[AutoMode] All pipeline steps completed for feature ${featureId}`);
+  }
+
+  /**
+   * Build the prompt for a pipeline step
+   */
+  private buildPipelineStepPrompt(
+    step: PipelineStep,
+    feature: Feature,
+    previousContext: string
+  ): string {
+    let prompt = `## Pipeline Step: ${step.name}
+
+This is an automated pipeline step following the initial feature implementation.
+
+### Feature Context
+${this.buildFeaturePrompt(feature)}
+
+`;
+
+    if (previousContext) {
+      prompt += `### Previous Work
+The following is the output from the previous work on this feature:
+
+${previousContext}
+
+`;
+    }
+
+    prompt += `### Pipeline Step Instructions
+${step.instructions}
+
+### Task
+Complete the pipeline step instructions above. Review the previous work and apply the required changes or actions.`;
+
+    return prompt;
+  }
+
   /**
    * Stop a specific feature
    */
@@ -663,6 +791,11 @@ export class AutoModeService {
     this.cancelPlanApproval(featureId);
 
     running.abortController.abort();
+
+    // Remove from running features immediately to allow resume
+    // The abort signal will still propagate to stop any ongoing execution
+    this.runningFeatures.delete(featureId);
+
     return true;
   }
 
@@ -746,12 +879,23 @@ export class AutoModeService {
       // No previous context
     }
 
+    // Load autoLoadClaudeMd setting to determine context loading strategy
+    const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+      projectPath,
+      this.settingsService,
+      '[AutoMode]'
+    );
+
     // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.) - passed as system prompt
-    const { formattedPrompt: contextFilesPrompt } = await loadContextFiles({
+    const contextResult = await loadContextFiles({
       projectPath,
       fsModule: secureFs as Parameters<typeof loadContextFiles>[0]['fsModule'],
     });
 
+    // When autoLoadClaudeMd is enabled, filter out CLAUDE.md to avoid duplication
+    // (SDK handles CLAUDE.md via settingSources), but keep other context files like CODE_QUALITY.md
+    const contextFilesPrompt = filterClaudeMdFromContext(contextResult, autoLoadClaudeMd);
+
     // Build complete prompt with feature info, previous context, and follow-up instructions
     let fullPrompt = `## Follow-up on Feature Implementation
 
@@ -879,6 +1023,7 @@ Address the follow-up instructions above. Review the previous work and make the
           planningMode: 'skip', // Follow-ups don't require approval
           previousContent: previousContext || undefined,
           systemPrompt: contextFilesPrompt || undefined,
+          autoLoadClaudeMd,
         }
       );
 
@@ -888,6 +1033,9 @@ Address the follow-up instructions above. Review the previous work and make the
       const finalStatus = feature?.skipTests ? 'waiting_approval' : 'verified';
       await this.updateFeatureStatus(projectPath, featureId, finalStatus);
 
+      // Record success to reset consecutive failure tracking
+      this.recordSuccess();
+
       this.emitAutoModeEvent('auto_mode_feature_complete', {
         featureId,
         passes: true,
@@ -903,6 +1051,19 @@ Address the follow-up instructions above. Review the previous work and make the
           errorType: errorInfo.type,
           projectPath,
         });
+
+        // Track this failure and check if we should pause auto mode
+        const shouldPause = this.trackFailureAndCheckPause({
+          type: errorInfo.type,
+          message: errorInfo.message,
+        });
+
+        if (shouldPause) {
+          this.signalShouldPause({
+            type: errorInfo.type,
+            message: errorInfo.message,
+          });
+        }
       }
     } finally {
       this.runningFeatures.delete(featureId);
@@ -1065,11 +1226,6 @@ Address the follow-up instructions above. Review the previous work and make the
    * Analyze project to gather context
    */
   async analyzeProject(projectPath: string): Promise<void> {
-    // Validate project path before proceeding
-    // This is called here because analyzeProject builds ExecuteOptions directly
-    // without using a factory function from sdk-options.ts
-    validateWorkingDirectory(projectPath);
-
     const abortController = new AbortController();
 
     const analysisFeatureId = `analysis-${Date.now()}`;
@@ -1097,13 +1253,32 @@ Format your response as a structured markdown document.`;
       const analysisModel = resolveModelString(undefined, DEFAULT_MODELS.claude);
       const provider = ProviderFactory.getProviderForModel(analysisModel);
 
-      const options: ExecuteOptions = {
-        prompt,
+      // Load autoLoadClaudeMd setting
+      const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+        projectPath,
+        this.settingsService,
+        '[AutoMode]'
+      );
+
+      // Use createCustomOptions for centralized SDK configuration with CLAUDE.md support
+      const sdkOptions = createCustomOptions({
+        cwd: projectPath,
         model: analysisModel,
         maxTurns: 5,
-        cwd: projectPath,
         allowedTools: ['Read', 'Glob', 'Grep'],
         abortController,
+        autoLoadClaudeMd,
+      });
+
+      const options: ExecuteOptions = {
+        prompt,
+        model: sdkOptions.model ?? analysisModel,
+        cwd: sdkOptions.cwd ?? projectPath,
+        maxTurns: sdkOptions.maxTurns,
+        allowedTools: sdkOptions.allowedTools as string[],
+        abortController,
+        settingSources: sdkOptions.settingSources,
+        sandbox: sdkOptions.sandbox, // Pass sandbox configuration
       };
 
       const stream = provider.executeQuery(options);
@@ -1167,18 +1342,43 @@ Format your response as a structured markdown document.`;
   /**
    * Get detailed info about all running agents
    */
-  getRunningAgents(): Array<{
-    featureId: string;
-    projectPath: string;
-    projectName: string;
-    isAutoMode: boolean;
-  }> {
-    return Array.from(this.runningFeatures.values()).map((rf) => ({
-      featureId: rf.featureId,
-      projectPath: rf.projectPath,
-      projectName: path.basename(rf.projectPath),
-      isAutoMode: rf.isAutoMode,
-    }));
+  async getRunningAgents(): Promise<
+    Array<{
+      featureId: string;
+      projectPath: string;
+      projectName: string;
+      isAutoMode: boolean;
+      title?: string;
+      description?: string;
+    }>
+  > {
+    const agents = await Promise.all(
+      Array.from(this.runningFeatures.values()).map(async (rf) => {
+        // Try to fetch feature data to get title and description
+        let title: string | undefined;
+        let description: string | undefined;
+
+        try {
+          const feature = await this.featureLoader.get(rf.projectPath, rf.featureId);
+          if (feature) {
+            title = feature.title;
+            description = feature.description;
+          }
+        } catch (error) {
+          // Silently ignore errors - title/description are optional
+        }
+
+        return {
+          featureId: rf.featureId,
+          projectPath: rf.projectPath,
+          projectName: path.basename(rf.projectPath),
+          isAutoMode: rf.isAutoMode,
+          title,
+          description,
+        };
+      })
+    );
+    return agents;
   }
 
   /**
@@ -1552,20 +1752,29 @@ Format your response as a structured markdown document.`;
   /**
    * Get the planning prompt prefix based on feature's planning mode
    */
-  private getPlanningPromptPrefix(feature: Feature): string {
+  private async getPlanningPromptPrefix(feature: Feature): Promise<string> {
     const mode = feature.planningMode || 'skip';
 
     if (mode === 'skip') {
       return ''; // No planning phase
     }
 
+    // Load prompts from settings (no caching - allows hot reload of custom prompts)
+    const prompts = await getPromptCustomization(this.settingsService, '[AutoMode]');
+    const planningPrompts: Record<string, string> = {
+      lite: prompts.autoMode.planningLite,
+      lite_with_approval: prompts.autoMode.planningLiteWithApproval,
+      spec: prompts.autoMode.planningSpec,
+      full: prompts.autoMode.planningFull,
+    };
+
     // For lite mode, use the approval variant if requirePlanApproval is true
     let promptKey: string = mode;
     if (mode === 'lite' && feature.requirePlanApproval === true) {
       promptKey = 'lite_with_approval';
     }
 
-    const planningPrompt = PLANNING_PROMPTS[promptKey as keyof typeof PLANNING_PROMPTS];
+    const planningPrompt = planningPrompts[promptKey];
     if (!planningPrompt) {
       return '';
     }
@@ -1708,6 +1917,7 @@ This helps parse your summary correctly in the output logs.`;
       requirePlanApproval?: boolean;
       previousContent?: string;
       systemPrompt?: string;
+      autoLoadClaudeMd?: boolean;
     }
   ): Promise<void> {
     const finalProjectPath = options?.projectPath || projectPath;
@@ -1780,11 +1990,32 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
       return;
     }
 
+    // Load autoLoadClaudeMd setting (project setting takes precedence over global)
+    // Use provided value if available, otherwise load from settings
+    const autoLoadClaudeMd =
+      options?.autoLoadClaudeMd !== undefined
+        ? options.autoLoadClaudeMd
+        : await getAutoLoadClaudeMdSetting(finalProjectPath, this.settingsService, '[AutoMode]');
+
+    // Load enableSandboxMode setting (global setting only)
+    const enableSandboxMode = await getEnableSandboxModeSetting(this.settingsService, '[AutoMode]');
+
+    // Load MCP servers from settings (global setting only)
+    const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AutoMode]');
+
+    // Load MCP permission settings (global setting only)
+    const mcpPermissions = await getMCPPermissionSettings(this.settingsService, '[AutoMode]');
+
     // Build SDK options using centralized configuration for feature implementation
     const sdkOptions = createAutoModeOptions({
       cwd: workDir,
       model: model,
       abortController,
+      autoLoadClaudeMd,
+      enableSandboxMode,
+      mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
+      mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
+      mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
     });
 
     // Extract model, maxTurns, and allowedTools from SDK options
@@ -1823,11 +2054,18 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
       cwd: workDir,
       allowedTools: allowedTools,
       abortController,
-      systemPrompt: options?.systemPrompt,
+      systemPrompt: sdkOptions.systemPrompt,
+      settingSources: sdkOptions.settingSources,
+      sandbox: sdkOptions.sandbox, // Pass sandbox configuration
+      mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined, // Pass MCP servers configuration
+      mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools, // Pass MCP auto-approve setting
+      mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools, // Pass MCP unrestricted tools setting
     };
 
     // Execute via provider
+    console.log(`[AutoMode] Starting stream for feature ${featureId}...`);
     const stream = provider.executeQuery(executeOptions);
+    console.log(`[AutoMode] Stream created, starting to iterate...`);
     // Initialize with previous content if this is a follow-up, with a separator
     let responseText = previousContent
       ? `${previousContent}\n\n---\n\n## Follow-up Session\n\n`
@@ -1865,6 +2103,7 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
     };
 
     streamLoop: for await (const msg of stream) {
+      console.log(`[AutoMode] Stream message received:`, msg.type, msg.subtype || '');
       if (msg.type === 'assistant' && msg.message?.content) {
         for (const block of msg.message.content) {
           if (block.type === 'text') {
@@ -2051,6 +2290,9 @@ After generating the revised spec, output:
                         cwd: workDir,
                         allowedTools: allowedTools,
                         abortController,
+                        mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
+                        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
+                        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                       });
 
                       let revisionText = '';
@@ -2188,6 +2430,9 @@ After generating the revised spec, output:
                     cwd: workDir,
                     allowedTools: allowedTools,
                     abortController,
+                    mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
+                    mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
+                    mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                   });
 
                   let taskOutput = '';
@@ -2277,6 +2522,9 @@ Implement all the changes described in the plan above.`;
                   cwd: workDir,
                   allowedTools: allowedTools,
                   abortController,
+                  mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
+                  mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
+                  mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                 });
 
                 for await (const msg of continuationStream) {
@@ -2311,6 +2559,9 @@ Implement all the changes described in the plan above.`;
 
             // Only emit progress for non-marker text (marker was already handled above)
             if (!specDetected) {
+              console.log(
+                `[AutoMode] Emitting progress event for ${featureId}, content length: ${block.text?.length || 0}`
+              );
               this.emitAutoModeEvent('auto_mode_progress', {
                 featureId,
                 content: block.text,

apps/server/src/services/claude-usage-service.ts

@@ -12,12 +12,13 @@ import { ClaudeUsage } from '../routes/claude/types.js';
  *
  * Platform-specific implementations:
  * - macOS: Uses 'expect' command for PTY
- * - Windows: Uses node-pty for PTY
+ * - Windows/Linux: Uses node-pty for PTY
  */
 export class ClaudeUsageService {
   private claudeBinary = 'claude';
   private timeout = 30000; // 30 second timeout
   private isWindows = os.platform() === 'win32';
+  private isLinux = os.platform() === 'linux';
 
   /**
    * Check if Claude CLI is available on the system
@@ -48,8 +49,8 @@ export class ClaudeUsageService {
    * Uses platform-specific PTY implementation
    */
   private executeClaudeUsageCommand(): Promise<string> {
-    if (this.isWindows) {
-      return this.executeClaudeUsageCommandWindows();
+    if (this.isWindows || this.isLinux) {
+      return this.executeClaudeUsageCommandPty();
     }
     return this.executeClaudeUsageCommandMac();
   }
@@ -147,17 +148,23 @@ export class ClaudeUsageService {
   }
 
   /**
-   * Windows implementation using node-pty
+   * Windows/Linux implementation using node-pty
    */
-  private executeClaudeUsageCommandWindows(): Promise<string> {
+  private executeClaudeUsageCommandPty(): Promise<string> {
     return new Promise((resolve, reject) => {
       let output = '';
       let settled = false;
       let hasSeenUsageData = false;
 
-      const workingDirectory = process.env.USERPROFILE || os.homedir() || 'C:\\';
+      const workingDirectory = this.isWindows
+        ? process.env.USERPROFILE || os.homedir() || 'C:\\'
+        : process.env.HOME || os.homedir() || '/tmp';
 
-      const ptyProcess = pty.spawn('cmd.exe', ['/c', 'claude', '/usage'], {
+      // Use platform-appropriate shell and command
+      const shell = this.isWindows ? 'cmd.exe' : '/bin/sh';
+      const args = this.isWindows ? ['/c', 'claude', '/usage'] : ['-c', 'claude /usage'];
+
+      const ptyProcess = pty.spawn(shell, args, {
         name: 'xterm-256color',
         cols: 120,
         rows: 30,
@@ -172,7 +179,12 @@ export class ClaudeUsageService {
         if (!settled) {
           settled = true;
           ptyProcess.kill();
-          reject(new Error('Command timed out'));
+          // Don't fail if we have data - return it instead
+          if (output.includes('Current session')) {
+            resolve(output);
+          } else {
+            reject(new Error('Command timed out'));
+          }
         }
       }, this.timeout);
 
@@ -186,6 +198,13 @@ export class ClaudeUsageService {
           setTimeout(() => {
             if (!settled) {
               ptyProcess.write('\x1b'); // Send escape key
+
+              // Fallback: if ESC doesn't exit (Linux), use SIGTERM after 2s
+              setTimeout(() => {
+                if (!settled) {
+                  ptyProcess.kill('SIGTERM');
+                }
+              }, 2000);
             }
           }, 2000);
         }

apps/server/src/services/feature-loader.ts

@@ -185,9 +185,8 @@ export class FeatureLoader {
       })) as any[];
       const featureDirs = entries.filter((entry) => entry.isDirectory());
 
-      // Load each feature
-      const features: Feature[] = [];
-      for (const dir of featureDirs) {
+      // Load all features concurrently (secureFs has built-in concurrency limiting)
+      const featurePromises = featureDirs.map(async (dir) => {
         const featureId = dir.name;
         const featureJsonPath = this.getFeatureJsonPath(projectPath, featureId);
 
@@ -199,13 +198,13 @@ export class FeatureLoader {
             logger.warn(
               `[FeatureLoader] Feature ${featureId} missing required 'id' field, skipping`
             );
-            continue;
+            return null;
           }
 
-          features.push(feature);
+          return feature as Feature;
         } catch (error) {
           if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
-            continue;
+            return null;
           } else if (error instanceof SyntaxError) {
             logger.warn(
               `[FeatureLoader] Failed to parse feature.json for ${featureId}: ${error.message}`
@@ -216,8 +215,12 @@ export class FeatureLoader {
               (error as Error).message
             );
           }
+          return null;
         }
-      }
+      });
+
+      const results = await Promise.all(featurePromises);
+      const features = results.filter((f): f is Feature => f !== null);
 
       // Sort by creation order (feature IDs contain timestamp)
       features.sort((a, b) => {

apps/server/src/services/mcp-test-service.ts

@@ -0,0 +1,251 @@
+/**
+ * MCP Test Service
+ *
+ * Provides functionality to test MCP server connections and list available tools.
+ * Supports stdio, SSE, and HTTP transport types.
+ */
+
+import { Client } from '@modelcontextprotocol/sdk/client/index.js';
+import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js';
+import { SSEClientTransport } from '@modelcontextprotocol/sdk/client/sse.js';
+import { StreamableHTTPClientTransport } from '@modelcontextprotocol/sdk/client/streamableHttp.js';
+import { exec } from 'child_process';
+import { promisify } from 'util';
+import type { MCPServerConfig, MCPToolInfo } from '@automaker/types';
+import type { SettingsService } from './settings-service.js';
+
+const execAsync = promisify(exec);
+const DEFAULT_TIMEOUT = 10000; // 10 seconds
+const IS_WINDOWS = process.platform === 'win32';
+
+export interface MCPTestResult {
+  success: boolean;
+  tools?: MCPToolInfo[];
+  error?: string;
+  connectionTime?: number;
+  serverInfo?: {
+    name?: string;
+    version?: string;
+  };
+}
+
+/**
+ * MCP Test Service for testing server connections and listing tools
+ */
+export class MCPTestService {
+  private settingsService: SettingsService;
+
+  constructor(settingsService: SettingsService) {
+    this.settingsService = settingsService;
+  }
+
+  /**
+   * Test connection to an MCP server and list its tools
+   */
+  async testServer(serverConfig: MCPServerConfig): Promise<MCPTestResult> {
+    const startTime = Date.now();
+    let client: Client | null = null;
+    let transport:
+      | StdioClientTransport
+      | SSEClientTransport
+      | StreamableHTTPClientTransport
+      | null = null;
+
+    try {
+      client = new Client({
+        name: 'automaker-mcp-test',
+        version: '1.0.0',
+      });
+
+      // Create transport based on server type
+      transport = await this.createTransport(serverConfig);
+
+      // Connect with timeout
+      await Promise.race([
+        client.connect(transport),
+        this.timeout(DEFAULT_TIMEOUT, 'Connection timeout'),
+      ]);
+
+      // List tools with timeout
+      const toolsResult = await Promise.race([
+        client.listTools(),
+        this.timeout<{
+          tools: Array<{
+            name: string;
+            description?: string;
+            inputSchema?: Record<string, unknown>;
+          }>;
+        }>(DEFAULT_TIMEOUT, 'List tools timeout'),
+      ]);
+
+      const connectionTime = Date.now() - startTime;
+
+      // Convert tools to MCPToolInfo format
+      const tools: MCPToolInfo[] = (toolsResult.tools || []).map(
+        (tool: { name: string; description?: string; inputSchema?: Record<string, unknown> }) => ({
+          name: tool.name,
+          description: tool.description,
+          inputSchema: tool.inputSchema,
+          enabled: true,
+        })
+      );
+
+      return {
+        success: true,
+        tools,
+        connectionTime,
+        serverInfo: {
+          name: serverConfig.name,
+          version: undefined, // Could be extracted from server info if available
+        },
+      };
+    } catch (error) {
+      const connectionTime = Date.now() - startTime;
+      return {
+        success: false,
+        error: this.getErrorMessage(error),
+        connectionTime,
+      };
+    } finally {
+      // Clean up client connection and ensure process termination
+      await this.cleanupConnection(client, transport);
+    }
+  }
+
+  /**
+   * Clean up MCP client connection and terminate spawned processes
+   *
+   * On Windows, child processes spawned via 'cmd /c' don't get terminated when the
+   * parent process is killed. We use taskkill with /t flag to kill the entire process tree.
+   * This prevents orphaned MCP server processes that would spam logs with ping warnings.
+   *
+   * IMPORTANT: We must run taskkill BEFORE client.close() because:
+   * - client.close() kills only the parent cmd.exe process
+   * - This orphans the child node.exe processes before we can kill them
+   * - taskkill /t needs the parent PID to exist to traverse the process tree
+   */
+  private async cleanupConnection(
+    client: Client | null,
+    transport: StdioClientTransport | SSEClientTransport | StreamableHTTPClientTransport | null
+  ): Promise<void> {
+    // Get the PID before any cleanup (only available for stdio transports)
+    const pid = transport instanceof StdioClientTransport ? transport.pid : null;
+
+    // On Windows with stdio transport, kill the entire process tree FIRST
+    // This must happen before client.close() which would orphan child processes
+    if (IS_WINDOWS && pid) {
+      try {
+        // taskkill /f = force, /t = kill process tree, /pid = process ID
+        await execAsync(`taskkill /f /t /pid ${pid}`);
+      } catch {
+        // Process may have already exited, which is fine
+      }
+    }
+
+    // Now do the standard close (may be a no-op if taskkill already killed everything)
+    if (client) {
+      try {
+        await client.close();
+      } catch {
+        // Expected if taskkill already terminated the process
+      }
+    }
+  }
+
+  /**
+   * Test server by ID (looks up config from settings)
+   */
+  async testServerById(serverId: string): Promise<MCPTestResult> {
+    try {
+      const globalSettings = await this.settingsService.getGlobalSettings();
+      const serverConfig = globalSettings.mcpServers?.find((s) => s.id === serverId);
+
+      if (!serverConfig) {
+        return {
+          success: false,
+          error: `Server with ID "${serverId}" not found`,
+        };
+      }
+
+      return this.testServer(serverConfig);
+    } catch (error) {
+      return {
+        success: false,
+        error: this.getErrorMessage(error),
+      };
+    }
+  }
+
+  /**
+   * Create appropriate transport based on server type
+   */
+  private async createTransport(
+    config: MCPServerConfig
+  ): Promise<StdioClientTransport | SSEClientTransport | StreamableHTTPClientTransport> {
+    if (config.type === 'sse') {
+      if (!config.url) {
+        throw new Error('URL is required for SSE transport');
+      }
+      // Use eventSourceInit workaround for SSE headers (SDK bug workaround)
+      // See: https://github.com/modelcontextprotocol/typescript-sdk/issues/436
+      const headers = config.headers;
+      return new SSEClientTransport(new URL(config.url), {
+        requestInit: headers ? { headers } : undefined,
+        eventSourceInit: headers
+          ? {
+              fetch: (url: string | URL | Request, init?: RequestInit) => {
+                const fetchHeaders = new Headers(init?.headers || {});
+                for (const [key, value] of Object.entries(headers)) {
+                  fetchHeaders.set(key, value);
+                }
+                return fetch(url, { ...init, headers: fetchHeaders });
+              },
+            }
+          : undefined,
+      });
+    }
+
+    if (config.type === 'http') {
+      if (!config.url) {
+        throw new Error('URL is required for HTTP transport');
+      }
+      return new StreamableHTTPClientTransport(new URL(config.url), {
+        requestInit: config.headers
+          ? {
+              headers: config.headers,
+            }
+          : undefined,
+      });
+    }
+
+    // Default to stdio
+    if (!config.command) {
+      throw new Error('Command is required for stdio transport');
+    }
+
+    return new StdioClientTransport({
+      command: config.command,
+      args: config.args,
+      env: config.env,
+    });
+  }
+
+  /**
+   * Create a timeout promise
+   */
+  private timeout<T>(ms: number, message: string): Promise<T> {
+    return new Promise((_, reject) => {
+      setTimeout(() => reject(new Error(message)), ms);
+    });
+  }
+
+  /**
+   * Extract error message from unknown error
+   */
+  private getErrorMessage(error: unknown): string {
+    if (error instanceof Error) {
+      return error.message;
+    }
+    return String(error);
+  }
+}

apps/server/src/services/pipeline-service.ts

@@ -0,0 +1,320 @@
+/**
+ * Pipeline Service - Handles reading/writing pipeline configuration
+ *
+ * Provides persistent storage for:
+ * - Pipeline configuration ({projectPath}/.automaker/pipeline.json)
+ */
+
+import path from 'path';
+import { createLogger } from '@automaker/utils';
+import * as secureFs from '../lib/secure-fs.js';
+import { ensureAutomakerDir } from '@automaker/platform';
+import type { PipelineConfig, PipelineStep, FeatureStatusWithPipeline } from '@automaker/types';
+
+const logger = createLogger('PipelineService');
+
+// Default empty pipeline config
+const DEFAULT_PIPELINE_CONFIG: PipelineConfig = {
+  version: 1,
+  steps: [],
+};
+
+/**
+ * Atomic file write - write to temp file then rename
+ */
+async function atomicWriteJson(filePath: string, data: unknown): Promise<void> {
+  const tempPath = `${filePath}.tmp.${Date.now()}`;
+  const content = JSON.stringify(data, null, 2);
+
+  try {
+    await secureFs.writeFile(tempPath, content, 'utf-8');
+    await secureFs.rename(tempPath, filePath);
+  } catch (error) {
+    // Clean up temp file if it exists
+    try {
+      await secureFs.unlink(tempPath);
+    } catch {
+      // Ignore cleanup errors
+    }
+    throw error;
+  }
+}
+
+/**
+ * Safely read JSON file with fallback to default
+ */
+async function readJsonFile<T>(filePath: string, defaultValue: T): Promise<T> {
+  try {
+    const content = (await secureFs.readFile(filePath, 'utf-8')) as string;
+    return JSON.parse(content) as T;
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+      return defaultValue;
+    }
+    logger.error(`Error reading ${filePath}:`, error);
+    return defaultValue;
+  }
+}
+
+/**
+ * Generate a unique ID for pipeline steps
+ */
+function generateStepId(): string {
+  return `step_${Date.now().toString(36)}_${Math.random().toString(36).substring(2, 8)}`;
+}
+
+/**
+ * Get the pipeline config file path for a project
+ */
+function getPipelineConfigPath(projectPath: string): string {
+  return path.join(projectPath, '.automaker', 'pipeline.json');
+}
+
+/**
+ * PipelineService - Manages pipeline configuration for workflow automation
+ *
+ * Handles reading and writing pipeline config to JSON files with atomic operations.
+ * Pipeline steps define custom columns that appear between "in_progress" and
+ * "waiting_approval/verified" columns in the kanban board.
+ */
+export class PipelineService {
+  /**
+   * Get pipeline configuration for a project
+   *
+   * @param projectPath - Absolute path to the project
+   * @returns Promise resolving to PipelineConfig (empty steps array if no config exists)
+   */
+  async getPipelineConfig(projectPath: string): Promise<PipelineConfig> {
+    const configPath = getPipelineConfigPath(projectPath);
+    const config = await readJsonFile<PipelineConfig>(configPath, DEFAULT_PIPELINE_CONFIG);
+
+    // Ensure version is set
+    return {
+      ...DEFAULT_PIPELINE_CONFIG,
+      ...config,
+    };
+  }
+
+  /**
+   * Save entire pipeline configuration
+   *
+   * @param projectPath - Absolute path to the project
+   * @param config - Complete PipelineConfig to save
+   */
+  async savePipelineConfig(projectPath: string, config: PipelineConfig): Promise<void> {
+    await ensureAutomakerDir(projectPath);
+    const configPath = getPipelineConfigPath(projectPath);
+    await atomicWriteJson(configPath, config);
+    logger.info(`Pipeline config saved for project: ${projectPath}`);
+  }
+
+  /**
+   * Add a new pipeline step
+   *
+   * @param projectPath - Absolute path to the project
+   * @param step - Step data (without id, createdAt, updatedAt)
+   * @returns Promise resolving to the created PipelineStep
+   */
+  async addStep(
+    projectPath: string,
+    step: Omit<PipelineStep, 'id' | 'createdAt' | 'updatedAt'>
+  ): Promise<PipelineStep> {
+    const config = await this.getPipelineConfig(projectPath);
+    const now = new Date().toISOString();
+
+    const newStep: PipelineStep = {
+      ...step,
+      id: generateStepId(),
+      createdAt: now,
+      updatedAt: now,
+    };
+
+    config.steps.push(newStep);
+
+    // Normalize order values
+    config.steps.sort((a, b) => a.order - b.order);
+    config.steps.forEach((s, index) => {
+      s.order = index;
+    });
+
+    await this.savePipelineConfig(projectPath, config);
+    logger.info(`Pipeline step added: ${newStep.name} (${newStep.id})`);
+
+    return newStep;
+  }
+
+  /**
+   * Update an existing pipeline step
+   *
+   * @param projectPath - Absolute path to the project
+   * @param stepId - ID of the step to update
+   * @param updates - Partial step data to merge
+   */
+  async updateStep(
+    projectPath: string,
+    stepId: string,
+    updates: Partial<Omit<PipelineStep, 'id' | 'createdAt'>>
+  ): Promise<PipelineStep> {
+    const config = await this.getPipelineConfig(projectPath);
+    const stepIndex = config.steps.findIndex((s) => s.id === stepId);
+
+    if (stepIndex === -1) {
+      throw new Error(`Pipeline step not found: ${stepId}`);
+    }
+
+    config.steps[stepIndex] = {
+      ...config.steps[stepIndex],
+      ...updates,
+      updatedAt: new Date().toISOString(),
+    };
+
+    await this.savePipelineConfig(projectPath, config);
+    logger.info(`Pipeline step updated: ${stepId}`);
+
+    return config.steps[stepIndex];
+  }
+
+  /**
+   * Delete a pipeline step
+   *
+   * @param projectPath - Absolute path to the project
+   * @param stepId - ID of the step to delete
+   */
+  async deleteStep(projectPath: string, stepId: string): Promise<void> {
+    const config = await this.getPipelineConfig(projectPath);
+    const stepIndex = config.steps.findIndex((s) => s.id === stepId);
+
+    if (stepIndex === -1) {
+      throw new Error(`Pipeline step not found: ${stepId}`);
+    }
+
+    config.steps.splice(stepIndex, 1);
+
+    // Normalize order values after deletion
+    config.steps.forEach((s, index) => {
+      s.order = index;
+    });
+
+    await this.savePipelineConfig(projectPath, config);
+    logger.info(`Pipeline step deleted: ${stepId}`);
+  }
+
+  /**
+   * Reorder pipeline steps
+   *
+   * @param projectPath - Absolute path to the project
+   * @param stepIds - Array of step IDs in the desired order
+   */
+  async reorderSteps(projectPath: string, stepIds: string[]): Promise<void> {
+    const config = await this.getPipelineConfig(projectPath);
+
+    // Validate all step IDs exist
+    const existingIds = new Set(config.steps.map((s) => s.id));
+    for (const id of stepIds) {
+      if (!existingIds.has(id)) {
+        throw new Error(`Pipeline step not found: ${id}`);
+      }
+    }
+
+    // Create a map for quick lookup
+    const stepMap = new Map(config.steps.map((s) => [s.id, s]));
+
+    // Reorder steps based on stepIds array
+    config.steps = stepIds.map((id, index) => {
+      const step = stepMap.get(id)!;
+      return { ...step, order: index, updatedAt: new Date().toISOString() };
+    });
+
+    await this.savePipelineConfig(projectPath, config);
+    logger.info(`Pipeline steps reordered`);
+  }
+
+  /**
+   * Get the next status in the pipeline flow
+   *
+   * Determines what status a feature should transition to based on current status.
+   * Flow: in_progress -> pipeline_step_0 -> pipeline_step_1 -> ... -> final status
+   *
+   * @param currentStatus - Current feature status
+   * @param config - Pipeline configuration (or null if no pipeline)
+   * @param skipTests - Whether to skip tests (affects final status)
+   * @returns The next status in the pipeline flow
+   */
+  getNextStatus(
+    currentStatus: FeatureStatusWithPipeline,
+    config: PipelineConfig | null,
+    skipTests: boolean
+  ): FeatureStatusWithPipeline {
+    const steps = config?.steps || [];
+
+    // Sort steps by order
+    const sortedSteps = [...steps].sort((a, b) => a.order - b.order);
+
+    // If no pipeline steps, use original logic
+    if (sortedSteps.length === 0) {
+      if (currentStatus === 'in_progress') {
+        return skipTests ? 'waiting_approval' : 'verified';
+      }
+      return currentStatus;
+    }
+
+    // Coming from in_progress -> go to first pipeline step
+    if (currentStatus === 'in_progress') {
+      return `pipeline_${sortedSteps[0].id}`;
+    }
+
+    // Coming from a pipeline step -> go to next step or final status
+    if (currentStatus.startsWith('pipeline_')) {
+      const currentStepId = currentStatus.replace('pipeline_', '');
+      const currentIndex = sortedSteps.findIndex((s) => s.id === currentStepId);
+
+      if (currentIndex === -1) {
+        // Step not found, go to final status
+        return skipTests ? 'waiting_approval' : 'verified';
+      }
+
+      if (currentIndex < sortedSteps.length - 1) {
+        // Go to next step
+        return `pipeline_${sortedSteps[currentIndex + 1].id}`;
+      }
+
+      // Last step completed, go to final status
+      return skipTests ? 'waiting_approval' : 'verified';
+    }
+
+    // For other statuses, don't change
+    return currentStatus;
+  }
+
+  /**
+   * Get a specific pipeline step by ID
+   *
+   * @param projectPath - Absolute path to the project
+   * @param stepId - ID of the step to retrieve
+   * @returns The pipeline step or null if not found
+   */
+  async getStep(projectPath: string, stepId: string): Promise<PipelineStep | null> {
+    const config = await this.getPipelineConfig(projectPath);
+    return config.steps.find((s) => s.id === stepId) || null;
+  }
+
+  /**
+   * Check if a status is a pipeline status
+   */
+  isPipelineStatus(status: FeatureStatusWithPipeline): boolean {
+    return status.startsWith('pipeline_');
+  }
+
+  /**
+   * Extract step ID from a pipeline status
+   */
+  getStepIdFromStatus(status: FeatureStatusWithPipeline): string | null {
+    if (!this.isPipelineStatus(status)) {
+      return null;
+    }
+    return status.replace('pipeline_', '');
+  }
+}
+
+// Export singleton instance
+export const pipelineService = new PipelineService();

apps/server/src/services/settings-service.ts

@@ -124,6 +124,8 @@ export class SettingsService {
    * Missing fields are filled in from DEFAULT_GLOBAL_SETTINGS for forward/backward
    * compatibility during schema migrations.
    *
+   * Also applies version-based migrations for breaking changes.
+   *
    * @returns Promise resolving to complete GlobalSettings object
    */
   async getGlobalSettings(): Promise<GlobalSettings> {
@@ -131,7 +133,7 @@ export class SettingsService {
     const settings = await readJsonFile<GlobalSettings>(settingsPath, DEFAULT_GLOBAL_SETTINGS);
 
     // Apply any missing defaults (for backwards compatibility)
-    return {
+    let result: GlobalSettings = {
       ...DEFAULT_GLOBAL_SETTINGS,
       ...settings,
       keyboardShortcuts: {
@@ -139,6 +141,32 @@ export class SettingsService {
         ...settings.keyboardShortcuts,
       },
     };
+
+    // Version-based migrations
+    const storedVersion = settings.version || 1;
+    let needsSave = false;
+
+    // Migration v1 -> v2: Force enableSandboxMode to false for existing users
+    // Sandbox mode can cause issues on some systems, so we're disabling it by default
+    if (storedVersion < 2) {
+      logger.info('Migrating settings from v1 to v2: disabling sandbox mode');
+      result.enableSandboxMode = false;
+      result.version = SETTINGS_VERSION;
+      needsSave = true;
+    }
+
+    // Save migrated settings if needed
+    if (needsSave) {
+      try {
+        await ensureDataDir(this.dataDir);
+        await atomicWriteJson(settingsPath, result);
+        logger.info('Settings migration complete');
+      } catch (error) {
+        logger.error('Failed to save migrated settings:', error);
+      }
+    }
+
+    return result;
   }
 
   /**

apps/server/src/services/terminal-service.ts

@@ -8,8 +8,18 @@
 import * as pty from 'node-pty';
 import { EventEmitter } from 'events';
 import * as os from 'os';
-import * as fs from 'fs';
 import * as path from 'path';
+// secureFs is used for user-controllable paths (working directory validation)
+// to enforce ALLOWED_ROOT_DIRECTORY security boundary
+import * as secureFs from '../lib/secure-fs.js';
+// System paths module handles shell binary checks and WSL detection
+// These are system paths outside ALLOWED_ROOT_DIRECTORY, centralized for security auditing
+import {
+  systemPathExists,
+  systemPathReadFileSync,
+  getWslVersionPath,
+  getShellPaths,
+} from '@automaker/platform';
 
 // Maximum scrollback buffer size (characters)
 const MAX_SCROLLBACK_SIZE = 50000; // ~50KB per terminal
@@ -60,60 +70,96 @@ export class TerminalService extends EventEmitter {
 
   /**
    * Detect the best shell for the current platform
+   * Uses getShellPaths() to iterate through allowed shell paths
    */
   detectShell(): { shell: string; args: string[] } {
     const platform = os.platform();
+    const shellPaths = getShellPaths();
 
-    // Check if running in WSL
+    // Helper to get basename handling both path separators
+    const getBasename = (shellPath: string): string => {
+      const lastSep = Math.max(shellPath.lastIndexOf('/'), shellPath.lastIndexOf('\\'));
+      return lastSep >= 0 ? shellPath.slice(lastSep + 1) : shellPath;
+    };
+
+    // Helper to get shell args based on shell name
+    const getShellArgs = (shell: string): string[] => {
+      const shellName = getBasename(shell).toLowerCase().replace('.exe', '');
+      // PowerShell and cmd don't need --login
+      if (shellName === 'powershell' || shellName === 'pwsh' || shellName === 'cmd') {
+        return [];
+      }
+      // sh doesn't support --login in all implementations
+      if (shellName === 'sh') {
+        return [];
+      }
+      // bash, zsh, and other POSIX shells support --login
+      return ['--login'];
+    };
+
+    // Check if running in WSL - prefer user's shell or bash with --login
     if (platform === 'linux' && this.isWSL()) {
-      // In WSL, prefer the user's configured shell or bash
-      const userShell = process.env.SHELL || '/bin/bash';
-      if (fs.existsSync(userShell)) {
-        return { shell: userShell, args: ['--login'] };
+      const userShell = process.env.SHELL;
+      if (userShell) {
+        // Try to find userShell in allowed paths
+        for (const allowedShell of shellPaths) {
+          if (allowedShell === userShell || getBasename(allowedShell) === getBasename(userShell)) {
+            try {
+              if (systemPathExists(allowedShell)) {
+                return { shell: allowedShell, args: getShellArgs(allowedShell) };
+              }
+            } catch {
+              // Path not allowed, continue searching
+            }
+          }
+        }
+      }
+      // Fall back to first available POSIX shell
+      for (const shell of shellPaths) {
+        try {
+          if (systemPathExists(shell)) {
+            return { shell, args: getShellArgs(shell) };
+          }
+        } catch {
+          // Path not allowed, continue
+        }
       }
       return { shell: '/bin/bash', args: ['--login'] };
     }
 
-    switch (platform) {
-      case 'win32': {
-        // Windows: prefer PowerShell, fall back to cmd
-        const pwsh = 'C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\powershell.exe';
-        const pwshCore = 'C:\\Program Files\\PowerShell\\7\\pwsh.exe';
-
-        if (fs.existsSync(pwshCore)) {
-          return { shell: pwshCore, args: [] };
+    // For all platforms: first try user's shell if set
+    const userShell = process.env.SHELL;
+    if (userShell && platform !== 'win32') {
+      // Try to find userShell in allowed paths
+      for (const allowedShell of shellPaths) {
+        if (allowedShell === userShell || getBasename(allowedShell) === getBasename(userShell)) {
+          try {
+            if (systemPathExists(allowedShell)) {
+              return { shell: allowedShell, args: getShellArgs(allowedShell) };
+            }
+          } catch {
+            // Path not allowed, continue searching
+          }
         }
-        if (fs.existsSync(pwsh)) {
-          return { shell: pwsh, args: [] };
-        }
-        return { shell: 'cmd.exe', args: [] };
-      }
-
-      case 'darwin': {
-        // macOS: prefer user's shell, then zsh, then bash
-        const userShell = process.env.SHELL;
-        if (userShell && fs.existsSync(userShell)) {
-          return { shell: userShell, args: ['--login'] };
-        }
-        if (fs.existsSync('/bin/zsh')) {
-          return { shell: '/bin/zsh', args: ['--login'] };
-        }
-        return { shell: '/bin/bash', args: ['--login'] };
-      }
-
-      case 'linux':
-      default: {
-        // Linux: prefer user's shell, then bash, then sh
-        const userShell = process.env.SHELL;
-        if (userShell && fs.existsSync(userShell)) {
-          return { shell: userShell, args: ['--login'] };
-        }
-        if (fs.existsSync('/bin/bash')) {
-          return { shell: '/bin/bash', args: ['--login'] };
-        }
-        return { shell: '/bin/sh', args: [] };
       }
     }
+
+    // Iterate through allowed shell paths and return first existing one
+    for (const shell of shellPaths) {
+      try {
+        if (systemPathExists(shell)) {
+          return { shell, args: getShellArgs(shell) };
+        }
+      } catch {
+        // Path not allowed or doesn't exist, continue to next
+      }
+    }
+
+    // Ultimate fallbacks based on platform
+    if (platform === 'win32') {
+      return { shell: 'cmd.exe', args: [] };
+    }
+    return { shell: '/bin/sh', args: [] };
   }
 
   /**
@@ -122,8 +168,9 @@ export class TerminalService extends EventEmitter {
   isWSL(): boolean {
     try {
       // Check /proc/version for Microsoft/WSL indicators
-      if (fs.existsSync('/proc/version')) {
-        const version = fs.readFileSync('/proc/version', 'utf-8').toLowerCase();
+      const wslVersionPath = getWslVersionPath();
+      if (systemPathExists(wslVersionPath)) {
+        const version = systemPathReadFileSync(wslVersionPath, 'utf-8').toLowerCase();
         return version.includes('microsoft') || version.includes('wsl');
       }
       // Check for WSL environment variable
@@ -157,8 +204,9 @@ export class TerminalService extends EventEmitter {
   /**
    * Validate and resolve a working directory path
    * Includes basic sanitization against null bytes and path normalization
+   * Uses secureFs to enforce ALLOWED_ROOT_DIRECTORY for user-provided paths
    */
-  private resolveWorkingDirectory(requestedCwd?: string): string {
+  private async resolveWorkingDirectory(requestedCwd?: string): Promise<string> {
     const homeDir = os.homedir();
 
     // If no cwd requested, use home
@@ -187,15 +235,19 @@ export class TerminalService extends EventEmitter {
     }
 
     // Check if path exists and is a directory
+    // Using secureFs.stat to enforce ALLOWED_ROOT_DIRECTORY security boundary
+    // This prevents terminals from being opened in directories outside the allowed workspace
     try {
-      const stat = fs.statSync(cwd);
-      if (stat.isDirectory()) {
+      const statResult = await secureFs.stat(cwd);
+      if (statResult.isDirectory()) {
         return cwd;
       }
       console.warn(`[Terminal] Path exists but is not a directory: ${cwd}, falling back to home`);
       return homeDir;
     } catch {
-      console.warn(`[Terminal] Working directory does not exist: ${cwd}, falling back to home`);
+      console.warn(
+        `[Terminal] Working directory does not exist or not allowed: ${cwd}, falling back to home`
+      );
       return homeDir;
     }
   }
@@ -228,7 +280,7 @@ export class TerminalService extends EventEmitter {
    * Create a new terminal session
    * Returns null if the maximum session limit has been reached
    */
-  createSession(options: TerminalOptions = {}): TerminalSession | null {
+  async createSession(options: TerminalOptions = {}): Promise<TerminalSession | null> {
     // Check session limit
     if (this.sessions.size >= maxSessions) {
       console.error(`[Terminal] Max sessions (${maxSessions}) reached, refusing new session`);
@@ -241,12 +293,23 @@ export class TerminalService extends EventEmitter {
     const shell = options.shell || detectedShell;
 
     // Validate and resolve working directory
-    const cwd = this.resolveWorkingDirectory(options.cwd);
+    // Uses secureFs internally to enforce ALLOWED_ROOT_DIRECTORY
+    const cwd = await this.resolveWorkingDirectory(options.cwd);
 
     // Build environment with some useful defaults
     // These settings ensure consistent terminal behavior across platforms
+    // First, create a clean copy of process.env excluding Automaker-specific variables
+    // that could pollute user shells (e.g., PORT would affect Next.js/other dev servers)
+    const automakerEnvVars = ['PORT', 'DATA_DIR', 'AUTOMAKER_API_KEY', 'NODE_PATH'];
+    const cleanEnv: Record<string, string> = {};
+    for (const [key, value] of Object.entries(process.env)) {
+      if (value !== undefined && !automakerEnvVars.includes(key)) {
+        cleanEnv[key] = value;
+      }
+    }
+
     const env: Record<string, string> = {
-      ...process.env,
+      ...cleanEnv,
       TERM: 'xterm-256color',
       COLORTERM: 'truecolor',
       TERM_PROGRAM: 'automaker-terminal',

apps/server/tests/integration/helpers/git-test-repo.ts

@@ -22,13 +22,21 @@ export async function createTestGitRepo(): Promise<TestRepo> {
 
   // Initialize git repo
   await execAsync('git init', { cwd: tmpDir });
-  await execAsync('git config user.email "test@example.com"', { cwd: tmpDir });
-  await execAsync('git config user.name "Test User"', { cwd: tmpDir });
+
+  // Use environment variables instead of git config to avoid affecting user's git config
+  // These env vars override git config without modifying it
+  const gitEnv = {
+    ...process.env,
+    GIT_AUTHOR_NAME: 'Test User',
+    GIT_AUTHOR_EMAIL: 'test@example.com',
+    GIT_COMMITTER_NAME: 'Test User',
+    GIT_COMMITTER_EMAIL: 'test@example.com',
+  };
 
   // Create initial commit
   await fs.writeFile(path.join(tmpDir, 'README.md'), '# Test Project\n');
-  await execAsync('git add .', { cwd: tmpDir });
-  await execAsync('git commit -m "Initial commit"', { cwd: tmpDir });
+  await execAsync('git add .', { cwd: tmpDir, env: gitEnv });
+  await execAsync('git commit -m "Initial commit"', { cwd: tmpDir, env: gitEnv });
 
   // Create main branch explicitly
   await execAsync('git branch -M main', { cwd: tmpDir });

apps/server/tests/integration/routes/worktree/create.integration.test.ts

@@ -15,10 +15,8 @@ describe('worktree create route - repositories without commits', () => {
   async function initRepoWithoutCommit() {
     repoPath = await fs.mkdtemp(path.join(os.tmpdir(), 'automaker-no-commit-'));
     await execAsync('git init', { cwd: repoPath });
-    await execAsync('git config user.email "test@example.com"', {
-      cwd: repoPath,
-    });
-    await execAsync('git config user.name "Test User"', { cwd: repoPath });
+    // Don't set git config - use environment variables in commit operations instead
+    // to avoid affecting user's git config
     // Intentionally skip creating an initial commit
   }