docs: update security test count from 136 to 163

Update the documented test count in CLAUDE.md to reflect the current
state after merging PR #100 which added diagnostic warnings for config
loading failures. The test suite now includes additional tests for:
- Empty command name validation in project configs
- Config loading diagnostic warnings

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.claude/commands/create-spec.md

@@ -95,6 +95,27 @@ Ask the user about their involvement preference:
 
 **For Detailed Mode users**, ask specific tech questions about frontend, backend, database, etc.
 
+### Phase 3b: Database Requirements (MANDATORY)
+
+**Always ask this question regardless of mode:**
+
+> "One foundational question about data storage:
+>
+> **Does this application need to store user data persistently?**
+>
+> 1. **Yes, needs a database** - Users create, save, and retrieve data (most apps)
+> 2. **No, stateless** - Pure frontend, no data storage needed (calculators, static sites)
+> 3. **Not sure** - Let me describe what I need and you decide"
+
+**Branching logic:**
+
+- **If "Yes" or "Not sure"**: Continue normally. The spec will include database in tech stack and the initializer will create 5 mandatory Infrastructure features (indices 0-4) to verify database connectivity and persistence.
+
+- **If "No, stateless"**: Note this in the spec. Skip database from tech stack. Infrastructure features will be simplified (no database persistence tests). Mark this clearly:
+  ```xml
+  <database>none - stateless application</database>
+  ```
+
 ## Phase 4: Features (THE MAIN PHASE)
 
 This is where you spend most of your time. Ask questions in plain language that anyone can answer.
@@ -207,12 +228,23 @@ After gathering all features, **you** (the agent) should tally up the testable f
 
 **Typical ranges for reference:**
 
-- **Simple apps** (todo list, calculator, notes): ~20-50 features
+- **Simple apps** (todo list, calculator, notes): ~25-55 features (includes 5 infrastructure)
-- **Medium apps** (blog, task manager with auth): ~100 features
+- **Medium apps** (blog, task manager with auth): ~105 features (includes 5 infrastructure)
-- **Advanced apps** (e-commerce, CRM, full SaaS): ~150-200 features
+- **Advanced apps** (e-commerce, CRM, full SaaS): ~155-205 features (includes 5 infrastructure)
 
 These are just reference points - your actual count should come from the requirements discussed.
 
+**MANDATORY: Infrastructure Features**
+
+If the app requires a database (Phase 3b answer was "Yes" or "Not sure"), you MUST include 5 Infrastructure features (indices 0-4):
+1. Database connection established
+2. Database schema applied correctly
+3. Data persists across server restart
+4. No mock data patterns in codebase
+5. Backend API queries real database
+
+These features ensure the coding agent implements a real database, not mock data or in-memory storage.
+
 **How to count features:**
 For each feature area discussed, estimate the number of discrete, testable behaviors:
 
@@ -225,17 +257,20 @@ For each feature area discussed, estimate the number of discrete, testable behav
 
 > "Based on what we discussed, here's my feature breakdown:
 >
+> - **Infrastructure (required)**: 5 features (database setup, persistence verification)
 > - [Category 1]: ~X features
 > - [Category 2]: ~Y features
 > - [Category 3]: ~Z features
 > - ...
 >
-> **Total: ~N features**
+> **Total: ~N features** (including 5 infrastructure)
 >
 > Does this seem right, or should I adjust?"
 
 Let the user confirm or adjust. This becomes your `feature_count` for the spec.
 
+**Important:** The first 5 features (indices 0-4) created by the initializer MUST be the Infrastructure category with no dependencies. All other features depend on these.
+
 ## Phase 5: Technical Details (DERIVED OR DISCUSSED)
 
 **For Quick Mode users:**

.claude/commands/review-pr.md

@@ -8,8 +8,47 @@ Pull request(s): $ARGUMENTS
 - At least 1 PR is required.
 
 ## TASKS
-- Use the GH CLI tool to retrieve the details (descriptions, divs, comments, feedback, reviews, etc)
+
-- Use 3 deepdive subagents to analyze the impact of the codebase
+1. **Retrieve PR Details**
-- Provide a review on whether the PR is safe to merge as-is
+   - Use the GH CLI tool to retrieve the details (descriptions, diffs, comments, feedback, reviews, etc)
-- Provide any feedback in terms of risk level
+
-- Propose any improments in terms of importance and complexity 
+2. **Assess PR Complexity**
+
+   After retrieving PR details, assess complexity based on:
+   - Number of files changed
+   - Lines added/removed
+   - Number of contributors/commits
+   - Whether changes touch core/architectural files
+
+   ### Complexity Tiers
+
+   **Simple** (no deep dive agents needed):
+   - ≤5 files changed AND ≤100 lines changed AND single author
+   - Review directly without spawning agents
+
+   **Medium** (1-2 deep dive agents):
+   - 6-15 files changed, OR 100-500 lines, OR 2 contributors
+   - Spawn 1 agent for focused areas, 2 if changes span multiple domains
+
+   **Complex** (up to 3 deep dive agents):
+   - >15 files, OR >500 lines, OR >2 contributors, OR touches core architecture
+   - Spawn up to 3 agents to analyze different aspects (e.g., security, performance, architecture)
+
+3. **Analyze Codebase Impact**
+   - Based on the complexity tier determined above, spawn the appropriate number of deep dive subagents
+   - For Simple PRs: analyze directly without spawning agents
+   - For Medium PRs: spawn 1-2 agents focusing on the most impacted areas
+   - For Complex PRs: spawn up to 3 agents to cover security, performance, and architectural concerns
+
+4. **Vision Alignment Check**
+   - Read the project's README.md and CLAUDE.md to understand the application's core purpose
+   - Assess whether this PR aligns with the application's intended functionality
+   - If the changes deviate significantly from the core vision or add functionality that doesn't serve the application's purpose, note this in the review
+   - This is not a blocker, but should be flagged for the reviewer's consideration
+
+5. **Safety Assessment**
+   - Provide a review on whether the PR is safe to merge as-is
+   - Provide any feedback in terms of risk level
+
+6. **Improvements**
+   - Propose any improvements in terms of importance and complexity

.claude/templates/coding_prompt.template.md

@@ -156,6 +156,9 @@ Use browser automation tools:
 - [ ] Deleted the test data - verified it's gone everywhere
 - [ ] NO unexplained data appeared (would indicate mock data)
 - [ ] Dashboard/counts reflect real numbers after my changes
+- [ ] **Ran extended mock data grep (STEP 5.6) - no hits in src/ (excluding tests)**
+- [ ] **Verified no globalThis, devStore, or dev-store patterns**
+- [ ] **Server restart test passed (STEP 5.7) - data persists across restart**
 
 #### Navigation Verification
 
@@ -174,10 +177,92 @@ Use browser automation tools:
 
 ### STEP 5.6: MOCK DATA DETECTION (Before marking passing)
 
-1. **Search code:** `grep -r "mockData\|fakeData\|TODO\|STUB" --include="*.ts" --include="*.tsx"`
+**Run ALL these grep checks. Any hits in src/ (excluding test files) require investigation:**
-2. **Runtime test:** Create unique data (e.g., "TEST_12345") → verify in UI → delete → verify gone
+
-3. **Check database:** All displayed data must come from real DB queries
+```bash
-4. If unexplained data appears, it's mock data - fix before marking passing.
+# Common exclusions for test files
+EXCLUDE="--exclude=*.test.* --exclude=*.spec.* --exclude=*__test__* --exclude=*__mocks__*"
+
+# 1. In-memory storage patterns (CRITICAL - catches dev-store)
+grep -r "globalThis\." --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/
+grep -r "dev-store\|devStore\|DevStore\|mock-db\|mockDb" --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/
+
+# 2. Mock data variables
+grep -r "mockData\|fakeData\|sampleData\|dummyData\|testData" --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/
+
+# 3. TODO/incomplete markers
+grep -r "TODO.*real\|TODO.*database\|TODO.*API\|STUB\|MOCK" --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/
+
+# 4. Development-only conditionals
+grep -r "isDevelopment\|isDev\|process\.env\.NODE_ENV.*development" --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/
+
+# 5. In-memory collections as data stores
+grep -r "new Map\(\)\|new Set\(\)" --include="*.ts" --include="*.tsx" --include="*.js" $EXCLUDE src/ 2>/dev/null
+```
+
+**Rule:** If ANY grep returns results in production code → investigate → FIX before marking passing.
+
+**Runtime verification:**
+1. Create unique data (e.g., "TEST_12345") → verify in UI → delete → verify gone
+2. Check database directly - all displayed data must come from real DB queries
+3. If unexplained data appears, it's mock data - fix before marking passing.
+
+### STEP 5.7: SERVER RESTART PERSISTENCE TEST (MANDATORY for data features)
+
+**When required:** Any feature involving CRUD operations or data persistence.
+
+**This test is NON-NEGOTIABLE. It catches in-memory storage implementations that pass all other tests.**
+
+**Steps:**
+
+1. Create unique test data via UI or API (e.g., item named "RESTART_TEST_12345")
+2. Verify data appears in UI and API response
+
+3. **STOP the server completely:**
+   ```bash
+   # Kill by port (safer - only kills the dev server, not VS Code/Claude Code/etc.)
+   # Unix/macOS:
+   lsof -ti :${PORT:-3000} | xargs kill -TERM 2>/dev/null || true
+   sleep 3
+   lsof -ti :${PORT:-3000} | xargs kill -9 2>/dev/null || true
+   sleep 2
+
+   # Windows alternative (use if lsof not available):
+   # netstat -ano | findstr :${PORT:-3000} | findstr LISTENING
+   # taskkill /F /PID <pid_from_above> 2>nul
+
+   # Verify server is stopped
+   if lsof -ti :${PORT:-3000} > /dev/null 2>&1; then
+     echo "ERROR: Server still running on port ${PORT:-3000}!"
+     exit 1
+   fi
+   ```
+
+4. **RESTART the server:**
+   ```bash
+   ./init.sh &
+   sleep 15  # Allow server to fully start
+   # Verify server is responding
+   if ! curl -f http://localhost:${PORT:-3000}/api/health && ! curl -f http://localhost:${PORT:-3000}; then
+     echo "ERROR: Server failed to start after restart"
+     exit 1
+   fi
+   ```
+
+5. **Query for test data - it MUST still exist**
+   - Via UI: Navigate to data location, verify data appears
+   - Via API: `curl http://localhost:${PORT:-3000}/api/items` - verify data in response
+
+6. **If data is GONE:** Implementation uses in-memory storage → CRITICAL FAIL
+   - Run all grep commands from STEP 5.6 to identify the mock pattern
+   - You MUST fix the in-memory storage implementation before proceeding
+   - Replace in-memory storage with real database queries
+
+7. **Clean up test data** after successful verification
+
+**Why this test exists:** In-memory stores like `globalThis.devStore` pass all other tests because data persists during a single server run. Only a full server restart reveals this bug. Skipping this step WILL allow dev-store implementations to slip through.
+
+**YOLO Mode Note:** Even in YOLO mode, this verification is MANDATORY for data features. Use curl instead of browser automation.
 
 ### STEP 6: UPDATE FEATURE STATUS (CAREFULLY!)
 
@@ -202,17 +287,23 @@ Use the feature_mark_passing tool with feature_id=42
 
 ### STEP 7: COMMIT YOUR PROGRESS
 
-Make a descriptive git commit:
+Make a descriptive git commit.
+
+**Git Commit Rules:**
+- ALWAYS use simple `-m` flag for commit messages
+- NEVER use heredocs (`cat <<EOF` or `<<'EOF'`) - they fail in sandbox mode with "can't create temp file for here document: operation not permitted"
+- For multi-line messages, use multiple `-m` flags:
 
 ```bash
 git add .
-git commit -m "Implement [feature name] - verified end-to-end
+git commit -m "Implement [feature name] - verified end-to-end" -m "- Added [specific changes]" -m "- Tested with browser automation" -m "- Marked feature #X as passing"
+```
 
-- Added [specific changes]
+Or use a single descriptive message:
-- Tested with browser automation
+
-- Marked feature #X as passing
+```bash
-- Screenshots in verification/ directory
+git add .
-"
+git commit -m "feat: implement [feature name] with browser verification"
 ```
 
 ### STEP 8: UPDATE PROGRESS NOTES

.claude/templates/initializer_prompt.template.md

@@ -36,9 +36,9 @@ Use the feature_create_bulk tool to add all features at once. You can create fea
 
 - Feature count must match the `feature_count` specified in app_spec.txt
 - Reference tiers for other projects:
-  - **Simple apps**: ~150 tests
+  - **Simple apps**: ~165 tests (includes 5 infrastructure)
-  - **Medium apps**: ~250 tests
+  - **Medium apps**: ~265 tests (includes 5 infrastructure)
-  - **Complex apps**: ~400+ tests
+  - **Advanced apps**: ~405+ tests (includes 5 infrastructure)
 - Both "functional" and "style" categories
 - Mix of narrow tests (2-5 steps) and comprehensive tests (10+ steps)
 - At least 25 tests MUST have 10+ steps each (more for complex apps)
@@ -60,8 +60,9 @@ Dependencies enable **parallel execution** of independent features. When specifi
 2. **Can only depend on EARLIER features** (index must be less than current position)
 3. **No circular dependencies** allowed
 4. **Maximum 20 dependencies** per feature
-5. **Foundation features (index 0-9)** should have NO dependencies
+5. **Infrastructure features (indices 0-4)** have NO dependencies - they run FIRST
-6. **60% of features after index 10** should have at least one dependency
+6. **ALL features after index 4** MUST depend on `[0, 1, 2, 3, 4]` (infrastructure)
+7. **60% of features after index 10** should have additional dependencies beyond infrastructure
 
 ### Dependency Types
 
@@ -82,30 +83,113 @@ Create WIDE dependency graphs, not linear chains:
 
 ```json
 [
-  // FOUNDATION TIER (indices 0-2, no dependencies) - run first
+  // INFRASTRUCTURE TIER (indices 0-4, no dependencies) - MUST run first
-  { "name": "App loads without errors", "category": "functional" },
+  { "name": "Database connection established", "category": "functional" },
-  { "name": "Navigation bar displays", "category": "style" },
+  { "name": "Database schema applied correctly", "category": "functional" },
-  { "name": "Homepage renders correctly", "category": "functional" },
+  { "name": "Data persists across server restart", "category": "functional" },
+  { "name": "No mock data patterns in codebase", "category": "functional" },
+  { "name": "Backend API queries real database", "category": "functional" },
 
-  // AUTH TIER (indices 3-5, depend on foundation) - run in parallel
+  // FOUNDATION TIER (indices 5-7, depend on infrastructure)
-  { "name": "User can register", "depends_on_indices": [0] },
+  { "name": "App loads without errors", "category": "functional", "depends_on_indices": [0, 1, 2, 3, 4] },
-  { "name": "User can login", "depends_on_indices": [0, 3] },
+  { "name": "Navigation bar displays", "category": "style", "depends_on_indices": [0, 1, 2, 3, 4] },
-  { "name": "User can logout", "depends_on_indices": [4] },
+  { "name": "Homepage renders correctly", "category": "functional", "depends_on_indices": [0, 1, 2, 3, 4] },
 
-  // CORE CRUD TIER (indices 6-9) - WIDE GRAPH: all 4 depend on login
+  // AUTH TIER (indices 8-10, depend on foundation + infrastructure)
-  // All 4 start as soon as login passes!
+  { "name": "User can register", "depends_on_indices": [0, 1, 2, 3, 4, 5] },
-  { "name": "User can create todo", "depends_on_indices": [4] },
+  { "name": "User can login", "depends_on_indices": [0, 1, 2, 3, 4, 5, 8] },
-  { "name": "User can view todos", "depends_on_indices": [4] },
+  { "name": "User can logout", "depends_on_indices": [0, 1, 2, 3, 4, 9] },
-  { "name": "User can edit todo", "depends_on_indices": [4, 6] },
-  { "name": "User can delete todo", "depends_on_indices": [4, 6] },
 
-  // ADVANCED TIER (indices 10-11) - both depend on view, not each other
+  // CORE CRUD TIER (indices 11-14) - WIDE GRAPH: all 4 depend on login
-  { "name": "User can filter todos", "depends_on_indices": [7] },
+  { "name": "User can create todo", "depends_on_indices": [0, 1, 2, 3, 4, 9] },
-  { "name": "User can search todos", "depends_on_indices": [7] }
+  { "name": "User can view todos", "depends_on_indices": [0, 1, 2, 3, 4, 9] },
+  { "name": "User can edit todo", "depends_on_indices": [0, 1, 2, 3, 4, 9, 11] },
+  { "name": "User can delete todo", "depends_on_indices": [0, 1, 2, 3, 4, 9, 11] },
+
+  // ADVANCED TIER (indices 15-16) - both depend on view, not each other
+  { "name": "User can filter todos", "depends_on_indices": [0, 1, 2, 3, 4, 12] },
+  { "name": "User can search todos", "depends_on_indices": [0, 1, 2, 3, 4, 12] }
 ]
 ```
 
-**Result:** With 3 parallel agents, this 12-feature project completes in ~5-6 cycles instead of 12 sequential cycles.
+**Result:** With 3 parallel agents, this project completes efficiently with proper database validation first.
+
+---
+
+## MANDATORY INFRASTRUCTURE FEATURES (Indices 0-4)
+
+**CRITICAL:** Create these FIRST, before any functional features. These features ensure the application uses a real database, not mock data or in-memory storage.
+
+| Index | Name | Test Steps |
+|-------|------|------------|
+| 0 | Database connection established | Start server → check logs for DB connection → health endpoint returns DB status |
+| 1 | Database schema applied correctly | Connect to DB directly → list tables → verify schema matches spec |
+| 2 | Data persists across server restart | Create via API → STOP server completely → START server → query API → data still exists |
+| 3 | No mock data patterns in codebase | Run grep for prohibited patterns → must return empty |
+| 4 | Backend API queries real database | Check server logs → SQL/DB queries appear for API calls |
+
+**ALL other features MUST depend on indices [0, 1, 2, 3, 4].**
+
+### Infrastructure Feature Descriptions
+
+**Feature 0 - Database connection established:**
+```text
+Steps:
+1. Start the development server
+2. Check server logs for database connection message
+3. Call health endpoint (e.g., GET /api/health)
+4. Verify response includes database status: connected
+```
+
+**Feature 1 - Database schema applied correctly:**
+```text
+Steps:
+1. Connect to database directly (sqlite3, psql, etc.)
+2. List all tables in the database
+3. Verify tables match what's defined in app_spec.txt
+4. Verify key columns exist on each table
+```
+
+**Feature 2 - Data persists across server restart (CRITICAL):**
+```text
+Steps:
+1. Create unique test data via API (e.g., POST /api/items with name "RESTART_TEST_12345")
+2. Verify data appears in API response (GET /api/items)
+3. STOP the server completely (kill by port to avoid killing unrelated Node processes):
+   - Unix/macOS: lsof -ti :$PORT | xargs kill -9 2>/dev/null || true && sleep 5
+   - Windows: FOR /F "tokens=5" %a IN ('netstat -aon ^| find ":$PORT"') DO taskkill /F /PID %a 2>nul
+   - Note: Replace $PORT with actual port (e.g., 3000)
+4. Verify server is stopped: lsof -ti :$PORT returns nothing (or netstat on Windows)
+5. RESTART the server: ./init.sh & sleep 15
+6. Query API again: GET /api/items
+7. Verify "RESTART_TEST_12345" still exists
+8. If data is GONE → CRITICAL FAILURE (in-memory storage detected)
+9. Clean up test data
+```
+
+**Feature 3 - No mock data patterns in codebase:**
+```text
+Steps:
+1. Run: grep -r "globalThis\." --include="*.ts" --include="*.tsx" --include="*.js" src/
+2. Run: grep -r "dev-store\|devStore\|DevStore\|mock-db\|mockDb" --include="*.ts" --include="*.tsx" --include="*.js" src/
+3. Run: grep -r "mockData\|testData\|fakeData\|sampleData\|dummyData" --include="*.ts" --include="*.tsx" --include="*.js" src/
+4. Run: grep -r "TODO.*real\|TODO.*database\|TODO.*API\|STUB\|MOCK" --include="*.ts" --include="*.tsx" --include="*.js" src/
+5. Run: grep -r "isDevelopment\|isDev\|process\.env\.NODE_ENV.*development" --include="*.ts" --include="*.tsx" --include="*.js" src/
+6. Run: grep -r "new Map\(\)\|new Set\(\)" --include="*.ts" --include="*.tsx" --include="*.js" src/ 2>/dev/null
+7. Run: grep -E "json-server|miragejs|msw" package.json
+8. ALL grep commands must return empty (exit code 1)
+9. If any returns results → investigate and fix before passing
+```
+
+**Feature 4 - Backend API queries real database:**
+```text
+Steps:
+1. Start server with verbose logging
+2. Make API call (e.g., GET /api/items)
+3. Check server logs
+4. Verify SQL query appears (SELECT, INSERT, etc.) or ORM query log
+5. If no DB queries in logs → implementation is using mock data
+```
 
 ---
 
@@ -115,8 +199,9 @@ The feature_list.json **MUST** include tests from ALL 20 categories. Minimum cou
 
 ### Category Distribution by Complexity Tier
 
-| Category                         | Simple  | Medium  | Complex  |
+| Category                         | Simple  | Medium  | Advanced |
 | -------------------------------- | ------- | ------- | -------- |
+| **0. Infrastructure (REQUIRED)** | 5       | 5       | 5        |
 | A. Security & Access Control     | 5       | 20      | 40       |
 | B. Navigation Integrity          | 15      | 25      | 40       |
 | C. Real Data Verification        | 20      | 30      | 50       |
@@ -137,12 +222,14 @@ The feature_list.json **MUST** include tests from ALL 20 categories. Minimum cou
 | R. Concurrency & Race Conditions | 5       | 8       | 15       |
 | S. Export/Import                 | 5       | 6       | 10       |
 | T. Performance                   | 5       | 5       | 10       |
-| **TOTAL**                        | **150** | **250** | **400+** |
+| **TOTAL**                        | **165** | **265** | **405+** |
 
 ---
 
 ### Category Descriptions
 
+**0. Infrastructure (REQUIRED - Priority 0)** - Database connectivity, schema existence, data persistence across server restart, absence of mock patterns. These features MUST pass before any functional features can begin. All tiers require exactly 5 infrastructure features (indices 0-4).
+
 **A. Security & Access Control** - Test unauthorized access blocking, permission enforcement, session management, role-based access, and data isolation between users.
 
 **B. Navigation Integrity** - Test all buttons, links, menus, breadcrumbs, deep links, back button behavior, 404 handling, and post-login/logout redirects.
@@ -205,6 +292,16 @@ The feature_list.json must include tests that **actively verify real data** and
 - `setTimeout` simulating API delays with static data
 - Static returns instead of database queries
 
+**Additional prohibited patterns (in-memory stores):**
+
+- `globalThis.` (in-memory storage pattern)
+- `dev-store`, `devStore`, `DevStore` (development stores)
+- `json-server`, `mirage`, `msw` (mock backends)
+- `Map()` or `Set()` used as primary data store
+- Environment checks like `if (process.env.NODE_ENV === 'development')` for data routing
+
+**Why this matters:** In-memory stores (like `globalThis.devStore`) will pass simple tests because data persists during a single server run. But data is LOST on server restart, which is unacceptable for production. The Infrastructure features (0-4) specifically test for this by requiring data to survive a full server restart.
+
 ---
 
 **CRITICAL INSTRUCTION:**

.env.example

@@ -15,6 +15,13 @@
 # - false: Browser opens a visible window (useful for debugging)
 # PLAYWRIGHT_HEADLESS=true
 
+# Extra Read Paths (Optional)
+# Comma-separated list of absolute paths for read-only access to external directories.
+# The agent can read files from these paths but cannot write to them.
+# Useful for referencing documentation, shared libraries, or other projects.
+# Example: EXTRA_READ_PATHS=/Volumes/Data/dev,/Users/shared/libs
+# EXTRA_READ_PATHS=
+
 # GLM/Alternative API Configuration (Optional)
 # To use Zhipu AI's GLM models instead of Claude, uncomment and set these variables.
 # This only affects AutoCoder - your global Claude Code settings remain unchanged.

CLAUDE.md

@@ -2,6 +2,12 @@
 
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 
+## Prerequisites
+
+- Python 3.11+
+- Node.js 20+ (for UI development)
+- Claude Code CLI
+
 ## Project Overview
 
 This is an autonomous coding agent system with a React-based UI. It uses the Claude Agent SDK to build complete applications over multiple sessions using a two-agent pattern:
@@ -86,6 +92,33 @@ npm run lint     # Run ESLint
 
 **Note:** The `start_ui.bat` script serves the pre-built UI from `ui/dist/`. After making UI changes, run `npm run build` in the `ui/` directory.
 
+## Testing
+
+### Python
+
+```bash
+ruff check .                      # Lint
+mypy .                            # Type check
+python test_security.py           # Security unit tests (163 tests)
+python test_security_integration.py  # Integration tests (9 tests)
+```
+
+### React UI
+
+```bash
+cd ui
+npm run lint          # ESLint
+npm run build         # Type check + build
+npm run test:e2e      # Playwright end-to-end tests
+npm run test:e2e:ui   # Playwright tests with UI
+```
+
+### Code Quality
+
+Configuration in `pyproject.toml`:
+- ruff: Line length 120, Python 3.11 target
+- mypy: Strict return type checking, ignores missing imports
+
 ## Architecture
 
 ### Core Python Modules
@@ -141,7 +174,7 @@ MCP tools available to the agent:
 
 ### React UI (ui/)
 
-- Tech stack: React 18, TypeScript, TanStack Query, Tailwind CSS v4, Radix UI, dagre (graph layout)
+- Tech stack: React 19, TypeScript, TanStack Query, Tailwind CSS v4, Radix UI, dagre (graph layout)
 - `src/App.tsx` - Main app with project selection, kanban board, agent controls
 - `src/hooks/useWebSocket.ts` - Real-time updates via WebSocket (progress, agent status, logs, agent updates)
 - `src/hooks/useProjects.ts` - React Query hooks for API calls
@@ -178,6 +211,46 @@ Defense-in-depth approach configured in `client.py`:
 2. Filesystem restricted to project directory only
 3. Bash commands validated using hierarchical allowlist system
 
+#### Extra Read Paths (Cross-Project File Access)
+
+The agent can optionally read files from directories outside the project folder via the `EXTRA_READ_PATHS` environment variable. This enables referencing documentation, shared libraries, or other projects.
+
+**Configuration:**
+
+```bash
+# Single path
+EXTRA_READ_PATHS=/Users/me/docs
+
+# Multiple paths (comma-separated)
+EXTRA_READ_PATHS=/Users/me/docs,/opt/shared-libs,/Volumes/Data/reference
+```
+
+**Security Controls:**
+
+All paths are validated before being granted read access:
+- Must be absolute paths (not relative)
+- Must exist and be directories
+- Paths are canonicalized via `Path.resolve()` to prevent `..` traversal attacks
+- Sensitive directories are blocked (see blocklist below)
+- Only Read, Glob, and Grep operations are allowed (no Write/Edit)
+
+**Blocked Sensitive Directories:**
+
+The following directories (relative to home) are always blocked:
+- `.ssh`, `.aws`, `.azure`, `.kube` - Cloud/SSH credentials
+- `.gnupg`, `.gpg`, `.password-store` - Encryption keys
+- `.docker`, `.config/gcloud` - Container/cloud configs
+- `.npmrc`, `.pypirc`, `.netrc` - Package manager credentials
+
+**Example Output:**
+
+```
+Created security settings at /path/to/project/.claude_settings.json
+   - Sandbox enabled (OS-level bash isolation)
+   - Filesystem restricted to: /path/to/project
+   - Extra read paths (validated): /Users/me/docs, /opt/shared-libs
+```
+
 #### Per-Project Allowed Commands
 
 The agent's bash command access is controlled through a hierarchical configuration system:
@@ -237,15 +310,6 @@ blocked_commands:
 - Blocklisted commands (sudo, dd, shutdown, etc.) can NEVER be allowed
 - Org-level blocked commands cannot be overridden by project configs
 
-**Testing:**
-```bash
-# Unit tests (136 tests - fast)
-python test_security.py
-
-# Integration tests (9 tests - uses real hooks)
-python test_security_integration.py
-```
-
 **Files:**
 - `security.py` - Command validation logic and hardcoded blocklist
 - `test_security.py` - Unit tests for security system (136 tests)
@@ -334,55 +398,7 @@ The orchestrator enforces strict bounds on concurrent processes:
 - `MAX_PARALLEL_AGENTS = 5` - Maximum concurrent coding agents
 - `MAX_TOTAL_AGENTS = 10` - Hard limit on total agents (coding + testing)
 - Testing agents are capped at `max_concurrency` (same as coding agents)
-
+- Total process count never exceeds 11 Python processes (1 orchestrator + 5 coding + 5 testing)
-**Expected process count during normal operation:**
-- 1 orchestrator process
-- Up to 5 coding agents
-- Up to 5 testing agents
-- Total: never exceeds 11 Python processes
-
-**Stress Test Verification:**
-
-```bash
-# Windows - verify process bounds
-# 1. Note baseline count
-tasklist | findstr python | find /c /v ""
-
-# 2. Start parallel agent (max concurrency)
-python autonomous_agent_demo.py --project-dir test --parallel --max-concurrency 5
-
-# 3. During run - should NEVER exceed baseline + 11
-tasklist | findstr python | find /c /v ""
-
-# 4. After stop via UI - should return to baseline
-tasklist | findstr python | find /c /v ""
-```
-
-```bash
-# macOS/Linux - verify process bounds
-# 1. Note baseline count
-pgrep -c python
-
-# 2. Start parallel agent
-python autonomous_agent_demo.py --project-dir test --parallel --max-concurrency 5
-
-# 3. During run - should NEVER exceed baseline + 11
-pgrep -c python
-
-# 4. After stop - should return to baseline
-pgrep -c python
-```
-
-**Log Verification:**
-
-```bash
-# Check spawn vs completion balance
-grep "Started testing agent" orchestrator_debug.log | wc -l
-grep "Testing agent.*completed\|failed" orchestrator_debug.log | wc -l
-
-# Watch for cap enforcement messages
-grep "at max testing agents\|At max total agents" orchestrator_debug.log
-```
 
 ### Design System
 

api/database.py

@@ -336,12 +336,20 @@ def create_database(project_dir: Path) -> tuple:
     """
     Create database and return engine + session maker.
 
+    Uses a cache to avoid creating new engines for each request, which improves
+    performance by reusing database connections.
+
     Args:
         project_dir: Directory containing the project
 
     Returns:
         Tuple of (engine, SessionLocal)
     """
+    cache_key = project_dir.as_posix()
+
+    if cache_key in _engine_cache:
+        return _engine_cache[cache_key]
+
     db_url = get_database_url(project_dir)
     engine = create_engine(db_url, connect_args={
         "check_same_thread": False,
@@ -369,12 +377,39 @@ def create_database(project_dir: Path) -> tuple:
     _migrate_add_schedules_tables(engine)
 
     SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+    # Cache the engine and session maker
+    _engine_cache[cache_key] = (engine, SessionLocal)
+
     return engine, SessionLocal
 
 
+def dispose_engine(project_dir: Path) -> bool:
+    """Dispose of and remove the cached engine for a project.
+
+    This closes all database connections, releasing file locks on Windows.
+    Should be called before deleting the database file.
+
+    Returns:
+        True if an engine was disposed, False if no engine was cached.
+    """
+    cache_key = project_dir.as_posix()
+
+    if cache_key in _engine_cache:
+        engine, _ = _engine_cache.pop(cache_key)
+        engine.dispose()
+        return True
+
+    return False
+
+
 # Global session maker - will be set when server starts
 _session_maker: Optional[sessionmaker] = None
 
+# Engine cache to avoid creating new engines for each request
+# Key: project directory path (as posix string), Value: (engine, SessionLocal)
+_engine_cache: dict[str, tuple] = {}
+
 
 def set_session_maker(session_maker: sessionmaker) -> None:
     """Set the global session maker."""

api/dependency_resolver.py

@@ -300,15 +300,20 @@ def compute_scheduling_scores(features: list[dict]) -> dict[int, float]:
                 parents[f["id"]].append(dep_id)
 
     # Calculate depths via BFS from roots
+    # Use visited set to prevent infinite loops from circular dependencies
     depths: dict[int, int] = {}
+    visited: set[int] = set()
     roots = [f["id"] for f in features if not parents[f["id"]]]
     queue = [(root, 0) for root in roots]
     while queue:
         node_id, depth = queue.pop(0)
-        if node_id not in depths or depth > depths[node_id]:
+        if node_id in visited:
-            depths[node_id] = depth
+            continue  # Skip already visited nodes (handles cycles)
+        visited.add(node_id)
+        depths[node_id] = depth
         for child_id in children[node_id]:
-            queue.append((child_id, depth + 1))
+            if child_id not in visited:
+                queue.append((child_id, depth + 1))
 
     # Handle orphaned nodes (shouldn't happen but be safe)
     for f in features:

client.py

@@ -42,6 +42,28 @@ API_ENV_VARS = [
     "ANTHROPIC_DEFAULT_HAIKU_MODEL",   # Model override for Haiku
 ]
 
+# Extra read paths for cross-project file access (read-only)
+# Set EXTRA_READ_PATHS environment variable with comma-separated absolute paths
+# Example: EXTRA_READ_PATHS=/Volumes/Data/dev,/Users/shared/libs
+EXTRA_READ_PATHS_VAR = "EXTRA_READ_PATHS"
+
+# Sensitive directories that should never be allowed via EXTRA_READ_PATHS
+# These contain credentials, keys, or system-critical files
+EXTRA_READ_PATHS_BLOCKLIST = {
+    ".ssh",
+    ".aws",
+    ".azure",
+    ".kube",
+    ".gnupg",
+    ".gpg",
+    ".password-store",
+    ".docker",
+    ".config/gcloud",
+    ".npmrc",
+    ".pypirc",
+    ".netrc",
+}
+
 
 def get_playwright_headless() -> bool:
     """
@@ -80,6 +102,79 @@ def get_playwright_browser() -> str:
     return value
 
 
+def get_extra_read_paths() -> list[Path]:
+    """
+    Get extra read-only paths from EXTRA_READ_PATHS environment variable.
+
+    Parses comma-separated absolute paths and validates each one:
+    - Must be an absolute path
+    - Must exist and be a directory
+    - Cannot be or contain sensitive directories (e.g., .ssh, .aws)
+
+    Returns:
+        List of validated, canonicalized Path objects.
+    """
+    raw_value = os.getenv(EXTRA_READ_PATHS_VAR, "").strip()
+    if not raw_value:
+        return []
+
+    validated_paths: list[Path] = []
+    home_dir = Path.home()
+
+    for path_str in raw_value.split(","):
+        path_str = path_str.strip()
+        if not path_str:
+            continue
+
+        # Parse and canonicalize the path
+        try:
+            path = Path(path_str).resolve()
+        except (OSError, ValueError) as e:
+            print(f"   - Warning: Invalid EXTRA_READ_PATHS path '{path_str}': {e}")
+            continue
+
+        # Must be absolute (resolve() makes it absolute, but check original input)
+        if not Path(path_str).is_absolute():
+            print(f"   - Warning: EXTRA_READ_PATHS requires absolute paths, skipping: {path_str}")
+            continue
+
+        # Must exist
+        if not path.exists():
+            print(f"   - Warning: EXTRA_READ_PATHS path does not exist, skipping: {path_str}")
+            continue
+
+        # Must be a directory
+        if not path.is_dir():
+            print(f"   - Warning: EXTRA_READ_PATHS path is not a directory, skipping: {path_str}")
+            continue
+
+        # Check against sensitive directory blocklist
+        is_blocked = False
+        for sensitive in EXTRA_READ_PATHS_BLOCKLIST:
+            sensitive_path = (home_dir / sensitive).resolve()
+            try:
+                # Block if path IS the sensitive dir or is INSIDE it
+                if path == sensitive_path or path.is_relative_to(sensitive_path):
+                    print(f"   - Warning: EXTRA_READ_PATHS blocked sensitive path: {path_str}")
+                    is_blocked = True
+                    break
+                # Also block if sensitive dir is INSIDE the requested path
+                if sensitive_path.is_relative_to(path):
+                    print(f"   - Warning: EXTRA_READ_PATHS path contains sensitive directory ({sensitive}): {path_str}")
+                    is_blocked = True
+                    break
+            except (OSError, ValueError):
+                # is_relative_to can raise on some edge cases
+                continue
+
+        if is_blocked:
+            continue
+
+        validated_paths.append(path)
+
+    return validated_paths
+
+
 # Feature MCP tools for feature/test management
 FEATURE_MCP_TOOLS = [
     # Core feature operations
@@ -202,6 +297,16 @@ def create_client(
         # Allow Feature MCP tools for feature management
         *FEATURE_MCP_TOOLS,
     ]
+
+    # Add extra read paths from environment variable (read-only access)
+    # Paths are validated, canonicalized, and checked against sensitive blocklist
+    extra_read_paths = get_extra_read_paths()
+    for path in extra_read_paths:
+        # Add read-only permissions for each validated path
+        permissions_list.append(f"Read({path}/**)")
+        permissions_list.append(f"Glob({path}/**)")
+        permissions_list.append(f"Grep({path}/**)")
+
     if not yolo_mode:
         # Allow Playwright MCP tools for browser automation (standard mode only)
         permissions_list.extend(PLAYWRIGHT_TOOLS)
@@ -228,6 +333,8 @@ def create_client(
     print(f"Created security settings at {settings_file}")
     print("   - Sandbox enabled (OS-level bash isolation)")
     print(f"   - Filesystem restricted to: {project_dir.resolve()}")
+    if extra_read_paths:
+        print(f"   - Extra read paths (validated): {', '.join(str(p) for p in extra_read_paths)}")
     print("   - Bash commands restricted to allowlist (see security.py)")
     if yolo_mode:
         print("   - MCP servers: features (database) - YOLO MODE (no Playwright)")

parallel_orchestrator.py

@@ -504,14 +504,20 @@ class ParallelOrchestrator:
             cmd.append("--yolo")
 
         try:
-            proc = subprocess.Popen(
+            # CREATE_NO_WINDOW on Windows prevents console window pop-ups
-                cmd,
+            # stdin=DEVNULL prevents blocking on stdin reads
-                stdout=subprocess.PIPE,
+            popen_kwargs = {
-                stderr=subprocess.STDOUT,
+                "stdin": subprocess.DEVNULL,
-                text=True,
+                "stdout": subprocess.PIPE,
-                cwd=str(AUTOCODER_ROOT),
+                "stderr": subprocess.STDOUT,
-                env={**os.environ, "PYTHONUNBUFFERED": "1"},
+                "text": True,
-            )
+                "cwd": str(AUTOCODER_ROOT),  # Run from autocoder root for proper imports
+                "env": {**os.environ, "PYTHONUNBUFFERED": "1"},
+            }
+            if sys.platform == "win32":
+                popen_kwargs["creationflags"] = subprocess.CREATE_NO_WINDOW
+
+            proc = subprocess.Popen(cmd, **popen_kwargs)
         except Exception as e:
             # Reset in_progress on failure
             session = self.get_session()
@@ -587,14 +593,20 @@ class ParallelOrchestrator:
                 cmd.extend(["--model", self.model])
 
             try:
-                proc = subprocess.Popen(
+                # CREATE_NO_WINDOW on Windows prevents console window pop-ups
-                    cmd,
+                # stdin=DEVNULL prevents blocking on stdin reads
-                    stdout=subprocess.PIPE,
+                popen_kwargs = {
-                    stderr=subprocess.STDOUT,
+                    "stdin": subprocess.DEVNULL,
-                    text=True,
+                    "stdout": subprocess.PIPE,
-                    cwd=str(AUTOCODER_ROOT),
+                    "stderr": subprocess.STDOUT,
-                    env={**os.environ, "PYTHONUNBUFFERED": "1"},
+                    "text": True,
-                )
+                    "cwd": str(AUTOCODER_ROOT),
+                    "env": {**os.environ, "PYTHONUNBUFFERED": "1"},
+                }
+                if sys.platform == "win32":
+                    popen_kwargs["creationflags"] = subprocess.CREATE_NO_WINDOW
+
+                proc = subprocess.Popen(cmd, **popen_kwargs)
             except Exception as e:
                 debug_log.log("TESTING", f"FAILED to spawn testing agent: {e}")
                 return False, f"Failed to start testing agent: {e}"
@@ -638,14 +650,20 @@ class ParallelOrchestrator:
 
         print("Running initializer agent...", flush=True)
 
-        proc = subprocess.Popen(
+        # CREATE_NO_WINDOW on Windows prevents console window pop-ups
-            cmd,
+        # stdin=DEVNULL prevents blocking on stdin reads
-            stdout=subprocess.PIPE,
+        popen_kwargs = {
-            stderr=subprocess.STDOUT,
+            "stdin": subprocess.DEVNULL,
-            text=True,
+            "stdout": subprocess.PIPE,
-            cwd=str(AUTOCODER_ROOT),
+            "stderr": subprocess.STDOUT,
-            env={**os.environ, "PYTHONUNBUFFERED": "1"},
+            "text": True,
-        )
+            "cwd": str(AUTOCODER_ROOT),
+            "env": {**os.environ, "PYTHONUNBUFFERED": "1"},
+        }
+        if sys.platform == "win32":
+            popen_kwargs["creationflags"] = subprocess.CREATE_NO_WINDOW
+
+        proc = subprocess.Popen(cmd, **popen_kwargs)
 
         debug_log.log("INIT", "Initializer subprocess started", pid=proc.pid)
 
@@ -703,6 +721,12 @@ class ParallelOrchestrator:
                     print(f"[Feature #{feature_id}] {line}", flush=True)
             proc.wait()
         finally:
+            # CRITICAL: Kill the process tree to clean up any child processes (e.g., Claude CLI)
+            # This prevents zombie processes from accumulating
+            try:
+                kill_process_tree(proc, timeout=2.0)
+            except Exception as e:
+                debug_log.log("CLEANUP", f"Error killing process tree for {agent_type} agent", error=str(e))
             self._on_agent_complete(feature_id, proc.returncode, agent_type, proc)
 
     def _signal_agent_completed(self):

registry.py

@@ -16,7 +16,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Any
 
-from sqlalchemy import Column, DateTime, String, create_engine
+from sqlalchemy import Column, DateTime, Integer, String, create_engine, text
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
 
@@ -85,6 +85,7 @@ class Project(Base):
     name = Column(String(50), primary_key=True, index=True)
     path = Column(String, nullable=False)  # POSIX format for cross-platform
     created_at = Column(DateTime, nullable=False)
+    default_concurrency = Column(Integer, nullable=False, default=3)
 
 
 class Settings(Base):
@@ -146,12 +147,26 @@ def _get_engine():
                     }
                 )
                 Base.metadata.create_all(bind=_engine)
+                _migrate_add_default_concurrency(_engine)
                 _SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=_engine)
                 logger.debug("Initialized registry database at: %s", db_path)
 
     return _engine, _SessionLocal
 
 
+def _migrate_add_default_concurrency(engine) -> None:
+    """Add default_concurrency column if missing (for existing databases)."""
+    with engine.connect() as conn:
+        result = conn.execute(text("PRAGMA table_info(projects)"))
+        columns = [row[1] for row in result.fetchall()]
+        if "default_concurrency" not in columns:
+            conn.execute(text(
+                "ALTER TABLE projects ADD COLUMN default_concurrency INTEGER DEFAULT 3"
+            ))
+            conn.commit()
+            logger.info("Migrated projects table: added default_concurrency column")
+
+
 @contextmanager
 def _get_session():
     """
@@ -307,7 +322,8 @@ def list_registered_projects() -> dict[str, dict[str, Any]]:
         return {
             p.name: {
                 "path": p.path,
-                "created_at": p.created_at.isoformat() if p.created_at else None
+                "created_at": p.created_at.isoformat() if p.created_at else None,
+                "default_concurrency": getattr(p, 'default_concurrency', 3) or 3
             }
             for p in projects
         }
@@ -333,7 +349,8 @@ def get_project_info(name: str) -> dict[str, Any] | None:
             return None
         return {
             "path": project.path,
-            "created_at": project.created_at.isoformat() if project.created_at else None
+            "created_at": project.created_at.isoformat() if project.created_at else None,
+            "default_concurrency": getattr(project, 'default_concurrency', 3) or 3
         }
     finally:
         session.close()
@@ -362,6 +379,55 @@ def update_project_path(name: str, new_path: Path) -> bool:
     return True
 
 
+def get_project_concurrency(name: str) -> int:
+    """
+    Get project's default concurrency (1-5).
+
+    Args:
+        name: The project name.
+
+    Returns:
+        The default concurrency value (defaults to 3 if not set or project not found).
+    """
+    _, SessionLocal = _get_engine()
+    session = SessionLocal()
+    try:
+        project = session.query(Project).filter(Project.name == name).first()
+        if project is None:
+            return 3
+        return getattr(project, 'default_concurrency', 3) or 3
+    finally:
+        session.close()
+
+
+def set_project_concurrency(name: str, concurrency: int) -> bool:
+    """
+    Set project's default concurrency (1-5).
+
+    Args:
+        name: The project name.
+        concurrency: The concurrency value (1-5).
+
+    Returns:
+        True if updated, False if project wasn't found.
+
+    Raises:
+        ValueError: If concurrency is not between 1 and 5.
+    """
+    if concurrency < 1 or concurrency > 5:
+        raise ValueError("concurrency must be between 1 and 5")
+
+    with _get_session() as session:
+        project = session.query(Project).filter(Project.name == name).first()
+        if not project:
+            return False
+
+        project.default_concurrency = concurrency
+
+    logger.info("Set project '%s' default_concurrency to %d", name, concurrency)
+    return True
+
+
 # =============================================================================
 # Validation Functions
 # =============================================================================

security.py

@@ -6,6 +6,7 @@ Pre-tool-use hooks that validate bash commands for security.
 Uses an allowlist approach - only explicitly permitted commands can run.
 """
 
+import logging
 import os
 import re
 import shlex
@@ -14,6 +15,9 @@ from typing import Optional
 
 import yaml
 
+# Logger for security-related events (fallback parsing, validation failures, etc.)
+logger = logging.getLogger(__name__)
+
 # Regex pattern for valid pkill process names (no regex metacharacters allowed)
 # Matches alphanumeric names with dots, underscores, and hyphens
 VALID_PROCESS_NAME_PATTERN = re.compile(r"^[A-Za-z0-9._-]+$")
@@ -140,6 +144,45 @@ def split_command_segments(command_string: str) -> list[str]:
     return result
 
 
+def _extract_primary_command(segment: str) -> str | None:
+    """
+    Fallback command extraction when shlex fails.
+
+    Extracts the first word that looks like a command, handling cases
+    like complex docker exec commands with nested quotes.
+
+    Args:
+        segment: The command segment to parse
+
+    Returns:
+        The primary command name, or None if extraction fails
+    """
+    # Remove leading whitespace
+    segment = segment.lstrip()
+
+    if not segment:
+        return None
+
+    # Skip env var assignments at start (VAR=value cmd)
+    words = segment.split()
+    while words and "=" in words[0] and not words[0].startswith("="):
+        words = words[1:]
+
+    if not words:
+        return None
+
+    # Extract first token (the command)
+    first_word = words[0]
+
+    # Match valid command characters (alphanumeric, dots, underscores, hyphens, slashes)
+    match = re.match(r"^([a-zA-Z0-9_./-]+)", first_word)
+    if match:
+        cmd = match.group(1)
+        return os.path.basename(cmd)
+
+    return None
+
+
 def extract_commands(command_string: str) -> list[str]:
     """
     Extract command names from a shell command string.
@@ -156,7 +199,6 @@ def extract_commands(command_string: str) -> list[str]:
     commands = []
 
     # shlex doesn't treat ; as a separator, so we need to pre-process
-    import re
 
     # Split on semicolons that aren't inside quotes (simple heuristic)
     # This handles common cases like "echo hello; ls"
@@ -171,8 +213,21 @@ def extract_commands(command_string: str) -> list[str]:
             tokens = shlex.split(segment)
         except ValueError:
             # Malformed command (unclosed quotes, etc.)
-            # Return empty to trigger block (fail-safe)
+            # Try fallback extraction instead of blocking entirely
-            return []
+            fallback_cmd = _extract_primary_command(segment)
+            if fallback_cmd:
+                logger.debug(
+                    "shlex fallback used: segment=%r -> command=%r",
+                    segment,
+                    fallback_cmd,
+                )
+                commands.append(fallback_cmd)
+            else:
+                logger.debug(
+                    "shlex fallback failed: segment=%r (no command extracted)",
+                    segment,
+                )
+            continue
 
         if not tokens:
             continue
@@ -444,58 +499,74 @@ def load_org_config() -> Optional[dict]:
             config = yaml.safe_load(f)
 
         if not config:
+            logger.warning(f"Org config at {config_path} is empty")
             return None
 
         # Validate structure
         if not isinstance(config, dict):
+            logger.warning(f"Org config at {config_path} must be a YAML dictionary")
             return None
 
         if "version" not in config:
+            logger.warning(f"Org config at {config_path} missing required 'version' field")
             return None
 
         # Validate allowed_commands if present
         if "allowed_commands" in config:
             allowed = config["allowed_commands"]
             if not isinstance(allowed, list):
+                logger.warning(f"Org config at {config_path}: 'allowed_commands' must be a list")
                 return None
-            for cmd in allowed:
+            for i, cmd in enumerate(allowed):
                 if not isinstance(cmd, dict):
+                    logger.warning(f"Org config at {config_path}: allowed_commands[{i}] must be a dict")
                     return None
                 if "name" not in cmd:
+                    logger.warning(f"Org config at {config_path}: allowed_commands[{i}] missing 'name'")
                     return None
                 # Validate that name is a non-empty string
                 if not isinstance(cmd["name"], str) or cmd["name"].strip() == "":
+                    logger.warning(f"Org config at {config_path}: allowed_commands[{i}] has invalid 'name'")
                     return None
 
         # Validate blocked_commands if present
         if "blocked_commands" in config:
             blocked = config["blocked_commands"]
             if not isinstance(blocked, list):
+                logger.warning(f"Org config at {config_path}: 'blocked_commands' must be a list")
                 return None
-            for cmd in blocked:
+            for i, cmd in enumerate(blocked):
                 if not isinstance(cmd, str):
+                    logger.warning(f"Org config at {config_path}: blocked_commands[{i}] must be a string")
                     return None
 
         # Validate pkill_processes if present
         if "pkill_processes" in config:
             processes = config["pkill_processes"]
             if not isinstance(processes, list):
+                logger.warning(f"Org config at {config_path}: 'pkill_processes' must be a list")
                 return None
             # Normalize and validate each process name against safe pattern
             normalized = []
-            for proc in processes:
+            for i, proc in enumerate(processes):
                 if not isinstance(proc, str):
+                    logger.warning(f"Org config at {config_path}: pkill_processes[{i}] must be a string")
                     return None
                 proc = proc.strip()
                 # Block empty strings and regex metacharacters
                 if not proc or not VALID_PROCESS_NAME_PATTERN.fullmatch(proc):
+                    logger.warning(f"Org config at {config_path}: pkill_processes[{i}] has invalid value '{proc}'")
                     return None
                 normalized.append(proc)
             config["pkill_processes"] = normalized
 
         return config
 
-    except (yaml.YAMLError, IOError, OSError):
+    except yaml.YAMLError as e:
+        logger.warning(f"Failed to parse org config at {config_path}: {e}")
+        return None
+    except (IOError, OSError) as e:
+        logger.warning(f"Failed to read org config at {config_path}: {e}")
         return None
 
 
@@ -509,7 +580,7 @@ def load_project_commands(project_dir: Path) -> Optional[dict]:
     Returns:
         Dict with parsed YAML config, or None if file doesn't exist or is invalid
     """
-    config_path = project_dir / ".autocoder" / "allowed_commands.yaml"
+    config_path = project_dir.resolve() / ".autocoder" / "allowed_commands.yaml"
 
     if not config_path.exists():
         return None
@@ -519,53 +590,68 @@ def load_project_commands(project_dir: Path) -> Optional[dict]:
             config = yaml.safe_load(f)
 
         if not config:
+            logger.warning(f"Project config at {config_path} is empty")
             return None
 
         # Validate structure
         if not isinstance(config, dict):
+            logger.warning(f"Project config at {config_path} must be a YAML dictionary")
             return None
 
         if "version" not in config:
+            logger.warning(f"Project config at {config_path} missing required 'version' field")
             return None
 
         commands = config.get("commands", [])
         if not isinstance(commands, list):
+            logger.warning(f"Project config at {config_path}: 'commands' must be a list")
             return None
 
         # Enforce 100 command limit
         if len(commands) > 100:
+            logger.warning(f"Project config at {config_path} exceeds 100 command limit ({len(commands)} commands)")
             return None
 
         # Validate each command entry
-        for cmd in commands:
+        for i, cmd in enumerate(commands):
             if not isinstance(cmd, dict):
+                logger.warning(f"Project config at {config_path}: commands[{i}] must be a dict")
                 return None
             if "name" not in cmd:
+                logger.warning(f"Project config at {config_path}: commands[{i}] missing 'name'")
                 return None
-            # Validate name is a string
+            # Validate name is a non-empty string
-            if not isinstance(cmd["name"], str):
+            if not isinstance(cmd["name"], str) or cmd["name"].strip() == "":
+                logger.warning(f"Project config at {config_path}: commands[{i}] has invalid 'name'")
                 return None
 
         # Validate pkill_processes if present
         if "pkill_processes" in config:
             processes = config["pkill_processes"]
             if not isinstance(processes, list):
+                logger.warning(f"Project config at {config_path}: 'pkill_processes' must be a list")
                 return None
             # Normalize and validate each process name against safe pattern
             normalized = []
-            for proc in processes:
+            for i, proc in enumerate(processes):
                 if not isinstance(proc, str):
+                    logger.warning(f"Project config at {config_path}: pkill_processes[{i}] must be a string")
                     return None
                 proc = proc.strip()
                 # Block empty strings and regex metacharacters
                 if not proc or not VALID_PROCESS_NAME_PATTERN.fullmatch(proc):
+                    logger.warning(f"Project config at {config_path}: pkill_processes[{i}] has invalid value '{proc}'")
                     return None
                 normalized.append(proc)
             config["pkill_processes"] = normalized
 
         return config
 
-    except (yaml.YAMLError, IOError, OSError):
+    except yaml.YAMLError as e:
+        logger.warning(f"Failed to parse project config at {config_path}: {e}")
+        return None
+    except (IOError, OSError) as e:
+        logger.warning(f"Failed to read project config at {config_path}: {e}")
         return None
 
 

server/routers/projects.py

@@ -18,6 +18,7 @@ from ..schemas import (
     ProjectDetail,
     ProjectPrompts,
     ProjectPromptsUpdate,
+    ProjectSettingsUpdate,
     ProjectStats,
     ProjectSummary,
 )
@@ -63,13 +64,23 @@ def _get_registry_functions():
         sys.path.insert(0, str(root))
 
     from registry import (
+        get_project_concurrency,
         get_project_path,
         list_registered_projects,
         register_project,
+        set_project_concurrency,
         unregister_project,
         validate_project_path,
     )
-    return register_project, unregister_project, get_project_path, list_registered_projects, validate_project_path
+    return (
+        register_project,
+        unregister_project,
+        get_project_path,
+        list_registered_projects,
+        validate_project_path,
+        get_project_concurrency,
+        set_project_concurrency,
+    )
 
 
 router = APIRouter(prefix="/api/projects", tags=["projects"])
@@ -102,7 +113,8 @@ def get_project_stats(project_dir: Path) -> ProjectStats:
 async def list_projects():
     """List all registered projects."""
     _init_imports()
-    _, _, _, list_registered_projects, validate_project_path = _get_registry_functions()
+    (_, _, _, list_registered_projects, validate_project_path,
+     get_project_concurrency, _) = _get_registry_functions()
 
     projects = list_registered_projects()
     result = []
@@ -123,6 +135,7 @@ async def list_projects():
             path=info["path"],
             has_spec=has_spec,
             stats=stats,
+            default_concurrency=info.get("default_concurrency", 3),
         ))
 
     return result
@@ -132,7 +145,8 @@ async def list_projects():
 async def create_project(project: ProjectCreate):
     """Create a new project at the specified path."""
     _init_imports()
-    register_project, _, get_project_path, list_registered_projects, _ = _get_registry_functions()
+    (register_project, _, get_project_path, list_registered_projects,
+     _, _, _) = _get_registry_functions()
 
     name = validate_project_name(project.name)
     project_path = Path(project.path).resolve()
@@ -203,6 +217,7 @@ async def create_project(project: ProjectCreate):
         path=project_path.as_posix(),
         has_spec=False,  # Just created, no spec yet
         stats=ProjectStats(passing=0, total=0, percentage=0.0),
+        default_concurrency=3,
     )
 
 
@@ -210,7 +225,7 @@ async def create_project(project: ProjectCreate):
 async def get_project(name: str):
     """Get detailed information about a project."""
     _init_imports()
-    _, _, get_project_path, _, _ = _get_registry_functions()
+    (_, _, get_project_path, _, _, get_project_concurrency, _) = _get_registry_functions()
 
     name = validate_project_name(name)
     project_dir = get_project_path(name)
@@ -231,6 +246,7 @@ async def get_project(name: str):
         has_spec=has_spec,
         stats=stats,
         prompts_dir=str(prompts_dir),
+        default_concurrency=get_project_concurrency(name),
     )
 
 
@@ -244,7 +260,7 @@ async def delete_project(name: str, delete_files: bool = False):
         delete_files: If True, also delete the project directory and files
     """
     _init_imports()
-    _, unregister_project, get_project_path, _, _ = _get_registry_functions()
+    (_, unregister_project, get_project_path, _, _, _, _) = _get_registry_functions()
 
     name = validate_project_name(name)
     project_dir = get_project_path(name)
@@ -280,7 +296,7 @@ async def delete_project(name: str, delete_files: bool = False):
 async def get_project_prompts(name: str):
     """Get the content of project prompt files."""
     _init_imports()
-    _, _, get_project_path, _, _ = _get_registry_functions()
+    (_, _, get_project_path, _, _, _, _) = _get_registry_functions()
 
     name = validate_project_name(name)
     project_dir = get_project_path(name)
@@ -313,7 +329,7 @@ async def get_project_prompts(name: str):
 async def update_project_prompts(name: str, prompts: ProjectPromptsUpdate):
     """Update project prompt files."""
     _init_imports()
-    _, _, get_project_path, _, _ = _get_registry_functions()
+    (_, _, get_project_path, _, _, _, _) = _get_registry_functions()
 
     name = validate_project_name(name)
     project_dir = get_project_path(name)
@@ -343,7 +359,7 @@ async def update_project_prompts(name: str, prompts: ProjectPromptsUpdate):
 async def get_project_stats_endpoint(name: str):
     """Get current progress statistics for a project."""
     _init_imports()
-    _, _, get_project_path, _, _ = _get_registry_functions()
+    (_, _, get_project_path, _, _, _, _) = _get_registry_functions()
 
     name = validate_project_name(name)
     project_dir = get_project_path(name)
@@ -355,3 +371,121 @@ async def get_project_stats_endpoint(name: str):
         raise HTTPException(status_code=404, detail="Project directory not found")
 
     return get_project_stats(project_dir)
+
+
+@router.post("/{name}/reset")
+async def reset_project(name: str, full_reset: bool = False):
+    """
+    Reset a project to its initial state.
+
+    Args:
+        name: Project name to reset
+        full_reset: If True, also delete prompts/ directory (triggers setup wizard)
+
+    Returns:
+        Dictionary with list of deleted files and reset type
+    """
+    _init_imports()
+    (_, _, get_project_path, _, _, _, _) = _get_registry_functions()
+
+    name = validate_project_name(name)
+    project_dir = get_project_path(name)
+
+    if not project_dir:
+        raise HTTPException(status_code=404, detail=f"Project '{name}' not found")
+
+    if not project_dir.exists():
+        raise HTTPException(status_code=404, detail="Project directory not found")
+
+    # Check if agent is running
+    lock_file = project_dir / ".agent.lock"
+    if lock_file.exists():
+        raise HTTPException(
+            status_code=409,
+            detail="Cannot reset project while agent is running. Stop the agent first."
+        )
+
+    # Dispose of database engines to release file locks (required on Windows)
+    # Import here to avoid circular imports
+    from api.database import dispose_engine as dispose_features_engine
+    from server.services.assistant_database import dispose_engine as dispose_assistant_engine
+
+    dispose_features_engine(project_dir)
+    dispose_assistant_engine(project_dir)
+
+    deleted_files: list[str] = []
+
+    # Files to delete in quick reset
+    quick_reset_files = [
+        "features.db",
+        "features.db-wal",  # WAL mode journal file
+        "features.db-shm",  # WAL mode shared memory file
+        "assistant.db",
+        "assistant.db-wal",
+        "assistant.db-shm",
+        ".claude_settings.json",
+        ".claude_assistant_settings.json",
+    ]
+
+    for filename in quick_reset_files:
+        file_path = project_dir / filename
+        if file_path.exists():
+            try:
+                file_path.unlink()
+                deleted_files.append(filename)
+            except Exception as e:
+                raise HTTPException(status_code=500, detail=f"Failed to delete {filename}: {e}")
+
+    # Full reset: also delete prompts directory
+    if full_reset:
+        prompts_dir = project_dir / "prompts"
+        if prompts_dir.exists():
+            try:
+                shutil.rmtree(prompts_dir)
+                deleted_files.append("prompts/")
+            except Exception as e:
+                raise HTTPException(status_code=500, detail=f"Failed to delete prompts/: {e}")
+
+    return {
+        "success": True,
+        "reset_type": "full" if full_reset else "quick",
+        "deleted_files": deleted_files,
+        "message": f"Project '{name}' has been reset" + (" (full reset)" if full_reset else " (quick reset)")
+    }
+
+
+@router.patch("/{name}/settings", response_model=ProjectDetail)
+async def update_project_settings(name: str, settings: ProjectSettingsUpdate):
+    """Update project-level settings (concurrency, etc.)."""
+    _init_imports()
+    (_, _, get_project_path, _, _, get_project_concurrency,
+     set_project_concurrency) = _get_registry_functions()
+
+    name = validate_project_name(name)
+    project_dir = get_project_path(name)
+
+    if not project_dir:
+        raise HTTPException(status_code=404, detail=f"Project '{name}' not found")
+
+    if not project_dir.exists():
+        raise HTTPException(status_code=404, detail="Project directory not found")
+
+    # Update concurrency if provided
+    if settings.default_concurrency is not None:
+        success = set_project_concurrency(name, settings.default_concurrency)
+        if not success:
+            raise HTTPException(status_code=500, detail="Failed to update concurrency")
+
+    # Return updated project details
+    has_spec = _check_spec_exists(project_dir)
+    stats = get_project_stats(project_dir)
+    prompts_dir = _get_project_prompts_dir(project_dir)
+
+    return ProjectDetail(
+        name=name,
+        path=project_dir.as_posix(),
+        has_spec=has_spec,
+        stats=stats,
+        prompts_dir=str(prompts_dir),
+        default_concurrency=get_project_concurrency(name),
+    )

server/schemas.py

@@ -45,6 +45,7 @@ class ProjectSummary(BaseModel):
     path: str
     has_spec: bool
     stats: ProjectStats
+    default_concurrency: int = 3
 
 
 class ProjectDetail(BaseModel):
@@ -54,6 +55,7 @@ class ProjectDetail(BaseModel):
     has_spec: bool
     stats: ProjectStats
     prompts_dir: str
+    default_concurrency: int = 3
 
 
 class ProjectPrompts(BaseModel):
@@ -70,6 +72,18 @@ class ProjectPromptsUpdate(BaseModel):
     coding_prompt: str | None = None
 
 
+class ProjectSettingsUpdate(BaseModel):
+    """Request schema for updating project-level settings."""
+    default_concurrency: int | None = None
+
+    @field_validator('default_concurrency')
+    @classmethod
+    def validate_concurrency(cls, v: int | None) -> int | None:
+        if v is not None and (v < 1 or v > 5):
+            raise ValueError("default_concurrency must be between 1 and 5")
+        return v
+
+
 # ============================================================================
 # Feature Schemas
 # ============================================================================

server/services/assistant_database.py

@@ -79,6 +79,26 @@ def get_engine(project_dir: Path):
     return _engine_cache[cache_key]
 
 
+def dispose_engine(project_dir: Path) -> bool:
+    """Dispose of and remove the cached engine for a project.
+
+    This closes all database connections, releasing file locks on Windows.
+    Should be called before deleting the database file.
+
+    Returns:
+        True if an engine was disposed, False if no engine was cached.
+    """
+    cache_key = project_dir.as_posix()
+
+    if cache_key in _engine_cache:
+        engine = _engine_cache.pop(cache_key)
+        engine.dispose()
+        logger.debug(f"Disposed database engine for {cache_key}")
+        return True
+
+    return False
+
+
 def get_session(project_dir: Path):
     """Get a new database session for a project."""
     engine = get_engine(project_dir)

server/services/expand_chat_session.py

@@ -10,8 +10,8 @@ import asyncio
 import json
 import logging
 import os
-import re
 import shutil
+import sys
 import threading
 import uuid
 from datetime import datetime
@@ -38,6 +38,13 @@ API_ENV_VARS = [
     "ANTHROPIC_DEFAULT_HAIKU_MODEL",
 ]
 
+# Feature MCP tools needed for expand session
+EXPAND_FEATURE_TOOLS = [
+    "mcp__features__feature_create",
+    "mcp__features__feature_create_bulk",
+    "mcp__features__feature_get_stats",
+]
+
 
 async def _make_multimodal_message(content_blocks: list[dict]) -> AsyncGenerator[dict, None]:
     """
@@ -61,9 +68,8 @@ class ExpandChatSession:
 
     Unlike SpecChatSession which writes spec files, this session:
     1. Reads existing app_spec.txt for context
-    2. Parses feature definitions from Claude's output
+    2. Chats with the user to define new features
-    3. Creates features via REST API
+    3. Claude creates features via the feature_create_bulk MCP tool
-    4. Tracks which features were created during the session
     """
 
     def __init__(self, project_name: str, project_dir: Path):
@@ -145,10 +151,14 @@ class ExpandChatSession:
             return
 
         # Create temporary security settings file (unique per session to avoid conflicts)
+        # Note: permission_mode="bypassPermissions" is safe here because:
+        # 1. Only Read/Glob file tools are allowed (no Write/Edit)
+        # 2. MCP tools are restricted to feature creation only
+        # 3. No Bash access - cannot execute arbitrary commands
         security_settings = {
             "sandbox": {"enabled": True},
             "permissions": {
-                "defaultMode": "acceptEdits",
+                "defaultMode": "bypassPermissions",
                 "allow": [
                     "Read(./**)",
                     "Glob(./**)",
@@ -171,6 +181,18 @@ class ExpandChatSession:
         # This allows using alternative APIs (e.g., GLM via z.ai) that may not support Claude model names
         model = os.getenv("ANTHROPIC_DEFAULT_OPUS_MODEL", "claude-opus-4-5-20251101")
 
+        # Build MCP servers config for feature creation
+        mcp_servers = {
+            "features": {
+                "command": sys.executable,
+                "args": ["-m", "mcp_server.feature_mcp"],
+                "env": {
+                    "PROJECT_DIR": str(self.project_dir.resolve()),
+                    "PYTHONPATH": str(ROOT_DIR.resolve()),
+                },
+            },
+        }
+
         # Create Claude SDK client
         try:
             self.client = ClaudeSDKClient(
@@ -181,8 +203,10 @@ class ExpandChatSession:
                     allowed_tools=[
                         "Read",
                         "Glob",
+                        *EXPAND_FEATURE_TOOLS,
                     ],
-                    permission_mode="acceptEdits",
+                    mcp_servers=mcp_servers,
+                    permission_mode="bypassPermissions",
                     max_turns=100,
                     cwd=str(self.project_dir.resolve()),
                     settings=str(settings_file.resolve()),
@@ -267,7 +291,8 @@ class ExpandChatSession:
         """
         Internal method to query Claude and stream responses.
 
-        Handles text responses and detects feature creation blocks.
+        Feature creation is handled by Claude calling the feature_create_bulk
+        MCP tool directly -- no text parsing needed.
         """
         if not self.client:
             return
@@ -291,9 +316,6 @@ class ExpandChatSession:
         else:
             await self.client.query(message)
 
-        # Accumulate full response to detect feature blocks
-        full_response = ""
-
         # Stream the response
         async for msg in self.client.receive_response():
             msg_type = type(msg).__name__
@@ -305,7 +327,6 @@ class ExpandChatSession:
                     if block_type == "TextBlock" and hasattr(block, "text"):
                         text = block.text
                         if text:
-                            full_response += text
                             yield {"type": "text", "content": text}
 
                             self.messages.append({
@@ -314,123 +335,6 @@ class ExpandChatSession:
                                 "timestamp": datetime.now().isoformat()
                             })
 
-        # Check for feature creation blocks in full response (handle multiple blocks)
-        features_matches = re.findall(
-            r'<features_to_create>\s*(\[[\s\S]*?\])\s*</features_to_create>',
-            full_response
-        )
-
-        if features_matches:
-            # Collect all features from all blocks, deduplicating by name
-            all_features: list[dict] = []
-            seen_names: set[str] = set()
-
-            for features_json in features_matches:
-                try:
-                    features_data = json.loads(features_json)
-
-                    if features_data and isinstance(features_data, list):
-                        for feature in features_data:
-                            name = feature.get("name", "")
-                            if name and name not in seen_names:
-                                seen_names.add(name)
-                                all_features.append(feature)
-                except json.JSONDecodeError as e:
-                    logger.error(f"Failed to parse features JSON block: {e}")
-                    # Continue processing other blocks
-
-            if all_features:
-                try:
-                    # Create all deduplicated features
-                    created = await self._create_features_bulk(all_features)
-
-                    if created:
-                        self.features_created += len(created)
-                        self.created_feature_ids.extend([f["id"] for f in created])
-
-                        yield {
-                            "type": "features_created",
-                            "count": len(created),
-                            "features": created
-                        }
-
-                        logger.info(f"Created {len(created)} features for {self.project_name}")
-                except Exception:
-                    logger.exception("Failed to create features")
-                    yield {
-                        "type": "error",
-                        "content": "Failed to create features"
-                    }
-
-    async def _create_features_bulk(self, features: list[dict]) -> list[dict]:
-        """
-        Create features directly in the database.
-
-        Args:
-            features: List of feature dictionaries with category, name, description, steps
-
-        Returns:
-            List of created feature dictionaries with IDs
-
-        Note:
-            Uses flush() to get IDs immediately without re-querying by priority range,
-            which could pick up rows from concurrent writers.
-        """
-        # Import database classes
-        import sys
-        root = Path(__file__).parent.parent.parent
-        if str(root) not in sys.path:
-            sys.path.insert(0, str(root))
-
-        from api.database import Feature, create_database
-
-        # Get database session
-        _, SessionLocal = create_database(self.project_dir)
-        session = SessionLocal()
-
-        try:
-            # Determine starting priority
-            max_priority_feature = session.query(Feature).order_by(Feature.priority.desc()).first()
-            current_priority = (max_priority_feature.priority + 1) if max_priority_feature else 1
-
-            created_rows: list = []
-
-            for f in features:
-                db_feature = Feature(
-                    priority=current_priority,
-                    category=f.get("category", "functional"),
-                    name=f.get("name", "Unnamed feature"),
-                    description=f.get("description", ""),
-                    steps=f.get("steps", []),
-                    passes=False,
-                    in_progress=False,
-                )
-                session.add(db_feature)
-                created_rows.append(db_feature)
-                current_priority += 1
-
-            # Flush to get IDs without relying on priority range query
-            session.flush()
-
-            # Build result from the flushed objects (IDs are now populated)
-            created_features = [
-                {
-                    "id": db_feature.id,
-                    "name": db_feature.name,
-                    "category": db_feature.category,
-                }
-                for db_feature in created_rows
-            ]
-
-            session.commit()
-            return created_features
-
-        except Exception:
-            session.rollback()
-            raise
-        finally:
-            session.close()
-
     def get_features_created(self) -> int:
         """Get the total number of features created in this session."""
         return self.features_created

server/services/process_manager.py

@@ -349,14 +349,20 @@ class AgentProcessManager:
         try:
             # Start subprocess with piped stdout/stderr
             # Use project_dir as cwd so Claude SDK sandbox allows access to project files
-            # IMPORTANT: Set PYTHONUNBUFFERED to ensure output isn't delayed
+            # stdin=DEVNULL prevents blocking if Claude CLI or child process tries to read stdin
-            self.process = subprocess.Popen(
+            # CREATE_NO_WINDOW on Windows prevents console window pop-ups
-                cmd,
+            # PYTHONUNBUFFERED ensures output isn't delayed
-                stdout=subprocess.PIPE,
+            popen_kwargs = {
-                stderr=subprocess.STDOUT,
+                "stdin": subprocess.DEVNULL,
-                cwd=str(self.project_dir),
+                "stdout": subprocess.PIPE,
-                env={**os.environ, "PYTHONUNBUFFERED": "1"},
+                "stderr": subprocess.STDOUT,
-            )
+                "cwd": str(self.project_dir),
+                "env": {**os.environ, "PYTHONUNBUFFERED": "1"},
+            }
+            if sys.platform == "win32":
+                popen_kwargs["creationflags"] = subprocess.CREATE_NO_WINDOW
+
+            self.process = subprocess.Popen(cmd, **popen_kwargs)
 
             # Atomic lock creation - if it fails, another process beat us
             if not self._create_lock():

start_ui.bat

@@ -39,5 +39,3 @@ pip install -r requirements.txt --quiet
 
 REM Run the Python launcher
 python "%~dp0start_ui.py" %*
-
-pause

start_ui.py

@@ -137,10 +137,25 @@ def check_node() -> bool:
 
 
 def install_npm_deps() -> bool:
-    """Install npm dependencies if node_modules doesn't exist."""
+    """Install npm dependencies if node_modules doesn't exist or is stale."""
     node_modules = UI_DIR / "node_modules"
+    package_json = UI_DIR / "package.json"
+    package_lock = UI_DIR / "package-lock.json"
 
-    if node_modules.exists():
+    # Check if npm install is needed
+    needs_install = False
+
+    if not node_modules.exists():
+        needs_install = True
+    elif package_json.exists():
+        # If package.json or package-lock.json is newer than node_modules, reinstall
+        node_modules_mtime = node_modules.stat().st_mtime
+        if package_json.stat().st_mtime > node_modules_mtime:
+            needs_install = True
+        elif package_lock.exists() and package_lock.stat().st_mtime > node_modules_mtime:
+            needs_install = True
+
+    if not needs_install:
         print("  npm dependencies already installed")
         return True
 

test_dependency_resolver.py

@@ -0,0 +1,426 @@
+#!/usr/bin/env python3
+"""
+Dependency Resolver Tests
+=========================
+
+Tests for the dependency resolver functions including cycle detection.
+Run with: python test_dependency_resolver.py
+"""
+
+import sys
+import time
+from concurrent.futures import ThreadPoolExecutor
+from concurrent.futures import TimeoutError as FuturesTimeoutError
+
+from api.dependency_resolver import (
+    are_dependencies_satisfied,
+    compute_scheduling_scores,
+    get_blocked_features,
+    get_blocking_dependencies,
+    get_ready_features,
+    resolve_dependencies,
+    would_create_circular_dependency,
+)
+
+
+def test_compute_scheduling_scores_simple_chain():
+    """Test scheduling scores for a simple linear dependency chain."""
+    print("\nTesting compute_scheduling_scores with simple chain:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": []},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [2]},
+    ]
+
+    scores = compute_scheduling_scores(features)
+
+    # All features should have scores
+    passed = True
+    for f in features:
+        if f["id"] not in scores:
+            print(f"  FAIL: Feature {f['id']} missing from scores")
+            passed = False
+
+    if passed:
+        # Root feature (1) should have highest score (unblocks most)
+        if scores[1] > scores[2] > scores[3]:
+            print("  PASS: Root feature has highest score, leaf has lowest")
+        else:
+            print(f"  FAIL: Expected scores[1] > scores[2] > scores[3], got {scores}")
+            passed = False
+
+    return passed
+
+
+def test_compute_scheduling_scores_with_cycle():
+    """Test that compute_scheduling_scores handles circular dependencies without hanging."""
+    print("\nTesting compute_scheduling_scores with circular dependencies:")
+
+    # Create a cycle: 1 -> 2 -> 3 -> 1
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [3]},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [2]},
+    ]
+
+    # Use timeout to detect infinite loop
+    def compute_with_timeout():
+        return compute_scheduling_scores(features)
+
+    start = time.time()
+    try:
+        with ThreadPoolExecutor(max_workers=1) as executor:
+            future = executor.submit(compute_with_timeout)
+            scores = future.result(timeout=5.0)  # 5 second timeout
+
+        elapsed = time.time() - start
+
+        # Should complete quickly (< 1 second for 3 features)
+        if elapsed > 1.0:
+            print(f"  FAIL: Took {elapsed:.2f}s (expected < 1s)")
+            return False
+
+        # All features should have scores (even cyclic ones)
+        if len(scores) == 3:
+            print(f"  PASS: Completed in {elapsed:.3f}s with {len(scores)} scores")
+            return True
+        else:
+            print(f"  FAIL: Expected 3 scores, got {len(scores)}")
+            return False
+
+    except FuturesTimeoutError:
+        print("  FAIL: Infinite loop detected (timed out after 5s)")
+        return False
+
+
+def test_compute_scheduling_scores_self_reference():
+    """Test scheduling scores with self-referencing dependency."""
+    print("\nTesting compute_scheduling_scores with self-reference:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [1]},  # Self-reference
+        {"id": 2, "priority": 2, "dependencies": []},
+    ]
+
+    start = time.time()
+    try:
+        with ThreadPoolExecutor(max_workers=1) as executor:
+            future = executor.submit(lambda: compute_scheduling_scores(features))
+            scores = future.result(timeout=5.0)
+
+        elapsed = time.time() - start
+
+        if elapsed > 1.0:
+            print(f"  FAIL: Took {elapsed:.2f}s (expected < 1s)")
+            return False
+
+        if len(scores) == 2:
+            print(f"  PASS: Completed in {elapsed:.3f}s with {len(scores)} scores")
+            return True
+        else:
+            print(f"  FAIL: Expected 2 scores, got {len(scores)}")
+            return False
+
+    except FuturesTimeoutError:
+        print("  FAIL: Infinite loop detected (timed out after 5s)")
+        return False
+
+
+def test_compute_scheduling_scores_complex_cycle():
+    """Test scheduling scores with complex circular dependencies."""
+    print("\nTesting compute_scheduling_scores with complex cycle:")
+
+    # Features 1-3 form a cycle, feature 4 depends on 1
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [3]},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [2]},
+        {"id": 4, "priority": 4, "dependencies": [1]},  # Outside cycle
+    ]
+
+    start = time.time()
+    try:
+        with ThreadPoolExecutor(max_workers=1) as executor:
+            future = executor.submit(lambda: compute_scheduling_scores(features))
+            scores = future.result(timeout=5.0)
+
+        elapsed = time.time() - start
+
+        if elapsed > 1.0:
+            print(f"  FAIL: Took {elapsed:.2f}s (expected < 1s)")
+            return False
+
+        if len(scores) == 4:
+            print(f"  PASS: Completed in {elapsed:.3f}s with {len(scores)} scores")
+            return True
+        else:
+            print(f"  FAIL: Expected 4 scores, got {len(scores)}")
+            return False
+
+    except FuturesTimeoutError:
+        print("  FAIL: Infinite loop detected (timed out after 5s)")
+        return False
+
+
+def test_compute_scheduling_scores_diamond():
+    """Test scheduling scores with diamond dependency pattern."""
+    print("\nTesting compute_scheduling_scores with diamond pattern:")
+
+    #     1
+    #    / \
+    #   2   3
+    #    \ /
+    #     4
+    features = [
+        {"id": 1, "priority": 1, "dependencies": []},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [1]},
+        {"id": 4, "priority": 4, "dependencies": [2, 3]},
+    ]
+
+    scores = compute_scheduling_scores(features)
+
+    # Feature 1 should have highest score (unblocks 2, 3, and transitively 4)
+    if scores[1] > scores[2] and scores[1] > scores[3] and scores[1] > scores[4]:
+        # Feature 4 should have lowest score (leaf, unblocks nothing)
+        if scores[4] < scores[2] and scores[4] < scores[3]:
+            print("  PASS: Root has highest score, leaf has lowest")
+            return True
+        else:
+            print(f"  FAIL: Leaf should have lowest score. Scores: {scores}")
+            return False
+    else:
+        print(f"  FAIL: Root should have highest score. Scores: {scores}")
+        return False
+
+
+def test_compute_scheduling_scores_empty():
+    """Test scheduling scores with empty feature list."""
+    print("\nTesting compute_scheduling_scores with empty list:")
+
+    scores = compute_scheduling_scores([])
+
+    if scores == {}:
+        print("  PASS: Returns empty dict for empty input")
+        return True
+    else:
+        print(f"  FAIL: Expected empty dict, got {scores}")
+        return False
+
+
+def test_would_create_circular_dependency():
+    """Test cycle detection for new dependencies."""
+    print("\nTesting would_create_circular_dependency:")
+
+    # Current dependencies: 2 depends on 1, 3 depends on 2
+    # Dependency chain: 3 -> 2 -> 1 (arrows mean "depends on")
+    features = [
+        {"id": 1, "priority": 1, "dependencies": []},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [2]},
+    ]
+
+    passed = True
+
+    # source_id gains dependency on target_id
+    # Adding "1 depends on 3" would create cycle: 1 -> 3 -> 2 -> 1
+    if would_create_circular_dependency(features, 1, 3):
+        print("  PASS: Detected cycle when adding 1 depends on 3")
+    else:
+        print("  FAIL: Should detect cycle when adding 1 depends on 3")
+        passed = False
+
+    # Adding "3 depends on 1" would NOT create cycle (redundant but not circular)
+    if not would_create_circular_dependency(features, 3, 1):
+        print("  PASS: No false positive for 3 depends on 1")
+    else:
+        print("  FAIL: False positive for 3 depends on 1")
+        passed = False
+
+    # Self-reference should be detected
+    if would_create_circular_dependency(features, 1, 1):
+        print("  PASS: Detected self-reference")
+    else:
+        print("  FAIL: Should detect self-reference")
+        passed = False
+
+    return passed
+
+
+def test_resolve_dependencies_with_cycle():
+    """Test resolve_dependencies detects and reports cycles."""
+    print("\nTesting resolve_dependencies with cycle:")
+
+    # Create a cycle: 1 -> 2 -> 3 -> 1
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [3]},
+        {"id": 2, "priority": 2, "dependencies": [1]},
+        {"id": 3, "priority": 3, "dependencies": [2]},
+    ]
+
+    result = resolve_dependencies(features)
+
+    # Should report circular dependencies
+    if result["circular_dependencies"]:
+        print(f"  PASS: Detected cycle: {result['circular_dependencies']}")
+        return True
+    else:
+        print("  FAIL: Should report circular dependencies")
+        return False
+
+
+def test_are_dependencies_satisfied():
+    """Test dependency satisfaction checking."""
+    print("\nTesting are_dependencies_satisfied:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [], "passes": True},
+        {"id": 2, "priority": 2, "dependencies": [1], "passes": False},
+        {"id": 3, "priority": 3, "dependencies": [2], "passes": False},
+    ]
+
+    passed = True
+
+    # Feature 1 has no deps, should be satisfied
+    if are_dependencies_satisfied(features[0], features):
+        print("  PASS: Feature 1 (no deps) is satisfied")
+    else:
+        print("  FAIL: Feature 1 should be satisfied")
+        passed = False
+
+    # Feature 2 depends on 1 which passes, should be satisfied
+    if are_dependencies_satisfied(features[1], features):
+        print("  PASS: Feature 2 (dep on passing) is satisfied")
+    else:
+        print("  FAIL: Feature 2 should be satisfied")
+        passed = False
+
+    # Feature 3 depends on 2 which doesn't pass, should NOT be satisfied
+    if not are_dependencies_satisfied(features[2], features):
+        print("  PASS: Feature 3 (dep on non-passing) is not satisfied")
+    else:
+        print("  FAIL: Feature 3 should not be satisfied")
+        passed = False
+
+    return passed
+
+
+def test_get_blocking_dependencies():
+    """Test getting blocking dependency IDs."""
+    print("\nTesting get_blocking_dependencies:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [], "passes": True},
+        {"id": 2, "priority": 2, "dependencies": [], "passes": False},
+        {"id": 3, "priority": 3, "dependencies": [1, 2], "passes": False},
+    ]
+
+    blocking = get_blocking_dependencies(features[2], features)
+
+    # Only feature 2 should be blocking (1 passes)
+    if blocking == [2]:
+        print("  PASS: Correctly identified blocking dependency")
+        return True
+    else:
+        print(f"  FAIL: Expected [2], got {blocking}")
+        return False
+
+
+def test_get_ready_features():
+    """Test getting ready features."""
+    print("\nTesting get_ready_features:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [], "passes": True},
+        {"id": 2, "priority": 2, "dependencies": [], "passes": False, "in_progress": False},
+        {"id": 3, "priority": 3, "dependencies": [1], "passes": False, "in_progress": False},
+        {"id": 4, "priority": 4, "dependencies": [2], "passes": False, "in_progress": False},
+    ]
+
+    ready = get_ready_features(features)
+
+    # Features 2 and 3 should be ready
+    # Feature 1 passes, feature 4 blocked by 2
+    ready_ids = [f["id"] for f in ready]
+
+    if 2 in ready_ids and 3 in ready_ids:
+        if 1 not in ready_ids and 4 not in ready_ids:
+            print(f"  PASS: Ready features: {ready_ids}")
+            return True
+        else:
+            print(f"  FAIL: Should not include passing/blocked. Got: {ready_ids}")
+            return False
+    else:
+        print(f"  FAIL: Should include 2 and 3. Got: {ready_ids}")
+        return False
+
+
+def test_get_blocked_features():
+    """Test getting blocked features."""
+    print("\nTesting get_blocked_features:")
+
+    features = [
+        {"id": 1, "priority": 1, "dependencies": [], "passes": False},
+        {"id": 2, "priority": 2, "dependencies": [1], "passes": False},
+    ]
+
+    blocked = get_blocked_features(features)
+
+    # Feature 2 should be blocked by 1
+    if len(blocked) == 1 and blocked[0]["id"] == 2:
+        if blocked[0]["blocked_by"] == [1]:
+            print("  PASS: Correctly identified blocked feature")
+            return True
+        else:
+            print(f"  FAIL: Wrong blocked_by: {blocked[0]['blocked_by']}")
+            return False
+    else:
+        print(f"  FAIL: Expected feature 2 blocked, got: {blocked}")
+        return False
+
+
+def run_all_tests():
+    """Run all tests and report results."""
+    print("=" * 60)
+    print("Dependency Resolver Tests")
+    print("=" * 60)
+
+    tests = [
+        test_compute_scheduling_scores_simple_chain,
+        test_compute_scheduling_scores_with_cycle,
+        test_compute_scheduling_scores_self_reference,
+        test_compute_scheduling_scores_complex_cycle,
+        test_compute_scheduling_scores_diamond,
+        test_compute_scheduling_scores_empty,
+        test_would_create_circular_dependency,
+        test_resolve_dependencies_with_cycle,
+        test_are_dependencies_satisfied,
+        test_get_blocking_dependencies,
+        test_get_ready_features,
+        test_get_blocked_features,
+    ]
+
+    passed = 0
+    failed = 0
+
+    for test in tests:
+        try:
+            if test():
+                passed += 1
+            else:
+                failed += 1
+        except Exception as e:
+            print(f"  ERROR: {e}")
+            failed += 1
+
+    print("\n" + "=" * 60)
+    print(f"Results: {passed} passed, {failed} failed")
+    print("=" * 60)
+
+    return failed == 0
+
+
+if __name__ == "__main__":
+    success = run_all_tests()
+    sys.exit(0 if success else 1)

test_security.py

@@ -107,6 +107,8 @@ def test_extract_commands():
         ("/usr/bin/node script.js", ["node"]),
         ("VAR=value ls", ["ls"]),
         ("git status || git init", ["git", "git"]),
+        # Fallback parser test: complex nested quotes that break shlex
+        ('docker exec container php -r "echo \\"test\\";"', ["docker"]),
     ]
 
     for cmd, expected in test_cases:
@@ -453,6 +455,21 @@ commands:
             print("  FAIL: Non-allowed command 'rustc' should be blocked")
             failed += 1
 
+        # Test 4: Empty command name is rejected
+        config_path.write_text("""version: 1
+commands:
+  - name: ""
+    description: Empty name should be rejected
+""")
+        result = load_project_commands(project_dir)
+        if result is None:
+            print("  PASS: Empty command name rejected in project config")
+            passed += 1
+        else:
+            print("  FAIL: Empty command name should be rejected in project config")
+            print(f"         Got: {result}")
+            failed += 1
+
     return passed, failed
 
 

ui/package-lock.json

@@ -3024,7 +3024,7 @@
       "version": "19.2.9",
       "resolved": "https://registry.npmjs.org/@types/react/-/react-19.2.9.tgz",
       "integrity": "sha512-Lpo8kgb/igvMIPeNV2rsYKTgaORYdO1XGVZ4Qz3akwOj0ySGYMPlQWa8BaLn0G63D1aSaAQ5ldR06wCpChQCjA==",
-      "dev": true,
+      "devOptional": true,
       "license": "MIT",
       "dependencies": {
         "csstype": "^3.2.2"
@@ -3034,7 +3034,7 @@
       "version": "19.2.3",
       "resolved": "https://registry.npmjs.org/@types/react-dom/-/react-dom-19.2.3.tgz",
       "integrity": "sha512-jp2L/eY6fn+KgVVQAOqYItbF0VY/YApe5Mz2F0aykSO8gx31bYCZyvSeYxCHKvzHG5eZjc+zyaS5BrBWya2+kQ==",
-      "dev": true,
+      "devOptional": true,
       "license": "MIT",
       "peerDependencies": {
         "@types/react": "^19.2.0"
@@ -3658,7 +3658,7 @@
       "version": "3.2.3",
       "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.2.3.tgz",
       "integrity": "sha512-z1HGKcYy2xA8AGQfwrn0PAy+PB7X/GSj3UVJW9qKyn43xWa+gl5nXmU4qqLMRzWVLFC8KusUX8T/0kCiOYpAIQ==",
-      "dev": true,
+      "devOptional": true,
       "license": "MIT"
     },
     "node_modules/d3-color": {

ui/src/App.tsx

@@ -26,8 +26,10 @@ import { ViewToggle, type ViewMode } from './components/ViewToggle'
 import { DependencyGraph } from './components/DependencyGraph'
 import { KeyboardShortcutsHelp } from './components/KeyboardShortcutsHelp'
 import { ThemeSelector } from './components/ThemeSelector'
+import { ResetProjectModal } from './components/ResetProjectModal'
+import { ProjectSetupRequired } from './components/ProjectSetupRequired'
 import { getDependencyGraph } from './lib/api'
-import { Loader2, Settings, Moon, Sun } from 'lucide-react'
+import { Loader2, Settings, Moon, Sun, RotateCcw } from 'lucide-react'
 import type { Feature } from './lib/types'
 import { Button } from '@/components/ui/button'
 import { Card, CardContent } from '@/components/ui/card'
@@ -36,6 +38,9 @@ import { Badge } from '@/components/ui/badge'
 const STORAGE_KEY = 'autocoder-selected-project'
 const VIEW_MODE_KEY = 'autocoder-view-mode'
 
+// Bottom padding for main content when debug panel is collapsed (40px header + 8px margin)
+const COLLAPSED_DEBUG_PANEL_CLEARANCE = 48
+
 function App() {
   // Initialize selected project from localStorage
   const [selectedProject, setSelectedProject] = useState<string | null>(() => {
@@ -56,6 +61,7 @@ function App() {
   const [showSettings, setShowSettings] = useState(false)
   const [showKeyboardHelp, setShowKeyboardHelp] = useState(false)
   const [isSpecCreating, setIsSpecCreating] = useState(false)
+  const [showResetModal, setShowResetModal] = useState(false)
   const [showSpecChat, setShowSpecChat] = useState(false)  // For "Create Spec" button in empty kanban
   const [viewMode, setViewMode] = useState<ViewMode>(() => {
     try {
@@ -200,10 +206,18 @@ function App() {
         setShowKeyboardHelp(true)
       }
 
+      // R : Open reset modal (when project selected and agent not running)
+      if ((e.key === 'r' || e.key === 'R') && selectedProject && wsState.agentStatus !== 'running') {
+        e.preventDefault()
+        setShowResetModal(true)
+      }
+
       // Escape : Close modals
       if (e.key === 'Escape') {
         if (showKeyboardHelp) {
           setShowKeyboardHelp(false)
+        } else if (showResetModal) {
+          setShowResetModal(false)
         } else if (showExpandProject) {
           setShowExpandProject(false)
         } else if (showSettings) {
@@ -222,7 +236,7 @@ function App() {
 
     window.addEventListener('keydown', handleKeyDown)
     return () => window.removeEventListener('keydown', handleKeyDown)
-  }, [selectedProject, showAddFeature, showExpandProject, selectedFeature, debugOpen, debugActiveTab, assistantOpen, features, showSettings, showKeyboardHelp, isSpecCreating, viewMode])
+  }, [selectedProject, showAddFeature, showExpandProject, selectedFeature, debugOpen, debugActiveTab, assistantOpen, features, showSettings, showKeyboardHelp, isSpecCreating, viewMode, showResetModal, wsState.agentStatus])
 
   // Combine WebSocket progress with feature data
   const progress = wsState.progress.total > 0 ? wsState.progress : {
@@ -242,7 +256,7 @@ function App() {
   return (
     <div className="min-h-screen bg-background">
       {/* Header */}
-      <header className="bg-card text-foreground border-b-2 border-border">
+      <header className="sticky top-0 z-50 bg-card/80 backdrop-blur-md text-foreground border-b-2 border-border">
         <div className="max-w-7xl mx-auto px-4 py-4">
           <div className="flex items-center justify-between">
             {/* Logo and Title */}
@@ -265,6 +279,7 @@ function App() {
                   <AgentControl
                     projectName={selectedProject}
                     status={wsState.agentStatus}
+                    defaultConcurrency={selectedProjectData?.default_concurrency}
                   />
 
                   <DevServerControl
@@ -283,6 +298,17 @@ function App() {
                     <Settings size={18} />
                   </Button>
 
+                  <Button
+                    onClick={() => setShowResetModal(true)}
+                    variant="outline"
+                    size="sm"
+                    title="Reset Project (R)"
+                    aria-label="Reset Project"
+                    disabled={wsState.agentStatus === 'running'}
+                  >
+                    <RotateCcw size={18} />
+                  </Button>
+
                   {/* Ollama Mode Indicator */}
                   {settings?.ollama_mode && (
                     <div
@@ -331,7 +357,7 @@ function App() {
       {/* Main Content */}
       <main
         className="max-w-7xl mx-auto px-4 py-8"
-        style={{ paddingBottom: debugOpen ? debugPanelHeight + 32 : undefined }}
+        style={{ paddingBottom: debugOpen ? debugPanelHeight + 32 : COLLAPSED_DEBUG_PANEL_CLEARANCE }}
       >
         {!selectedProject ? (
           <div className="text-center mt-12">
@@ -342,6 +368,16 @@ function App() {
               Select a project from the dropdown above or create a new one to get started.
             </p>
           </div>
+        ) : !hasSpec ? (
+          <ProjectSetupRequired
+            projectName={selectedProject}
+            projectPath={selectedProjectData?.path}
+            onCreateWithClaude={() => setShowSpecChat(true)}
+            onEditManually={() => {
+              // Open debug panel for the user to see the project path
+              setDebugOpen(true)
+            }}
+          />
         ) : (
           <div className="space-y-8">
             {/* Progress Dashboard */}
@@ -508,6 +544,21 @@ function App() {
       {/* Keyboard Shortcuts Help */}
       <KeyboardShortcutsHelp isOpen={showKeyboardHelp} onClose={() => setShowKeyboardHelp(false)} />
 
+      {/* Reset Project Modal */}
+      {showResetModal && selectedProject && (
+        <ResetProjectModal
+          isOpen={showResetModal}
+          projectName={selectedProject}
+          onClose={() => setShowResetModal(false)}
+          onResetComplete={(wasFullReset) => {
+            // If full reset, the spec was deleted - show spec creation chat
+            if (wasFullReset) {
+              setShowSpecChat(true)
+            }
+          }}
+        />
+      )}
+
       {/* Celebration Overlay - shows when a feature is completed by an agent */}
       {wsState.celebration && (
         <CelebrationOverlay

ui/src/components/AgentControl.tsx

@@ -1,9 +1,10 @@
-import { useState } from 'react'
+import { useState, useEffect, useRef, useCallback } from 'react'
 import { Play, Square, Loader2, GitBranch, Clock } from 'lucide-react'
 import {
   useStartAgent,
   useStopAgent,
   useSettings,
+  useUpdateProjectSettings,
 } from '../hooks/useProjects'
 import { useNextScheduledRun } from '../hooks/useSchedules'
 import { formatNextRun, formatEndTime } from '../lib/timeUtils'
@@ -15,14 +16,47 @@ import { Badge } from '@/components/ui/badge'
 interface AgentControlProps {
   projectName: string
   status: AgentStatus
+  defaultConcurrency?: number
 }
 
-export function AgentControl({ projectName, status }: AgentControlProps) {
+export function AgentControl({ projectName, status, defaultConcurrency = 3 }: AgentControlProps) {
   const { data: settings } = useSettings()
   const yoloMode = settings?.yolo_mode ?? false
 
   // Concurrency: 1 = single agent, 2-5 = parallel
-  const [concurrency, setConcurrency] = useState(3)
+  const [concurrency, setConcurrency] = useState(defaultConcurrency)
+
+  // Sync concurrency when project changes or defaultConcurrency updates
+  useEffect(() => {
+    setConcurrency(defaultConcurrency)
+  }, [defaultConcurrency])
+
+  // Debounced save for concurrency changes
+  const updateProjectSettings = useUpdateProjectSettings(projectName)
+  const saveTimeoutRef = useRef<ReturnType<typeof setTimeout> | null>(null)
+
+  const handleConcurrencyChange = useCallback((newConcurrency: number) => {
+    setConcurrency(newConcurrency)
+
+    // Clear previous timeout
+    if (saveTimeoutRef.current) {
+      clearTimeout(saveTimeoutRef.current)
+    }
+
+    // Debounce save (500ms)
+    saveTimeoutRef.current = setTimeout(() => {
+      updateProjectSettings.mutate({ default_concurrency: newConcurrency })
+    }, 500)
+  }, [updateProjectSettings])
+
+  // Cleanup timeout on unmount
+  useEffect(() => {
+    return () => {
+      if (saveTimeoutRef.current) {
+        clearTimeout(saveTimeoutRef.current)
+      }
+    }
+  }, [])
 
   const startAgent = useStartAgent(projectName)
   const stopAgent = useStopAgent(projectName)
@@ -57,7 +91,7 @@ export function AgentControl({ projectName, status }: AgentControlProps) {
               min={1}
               max={5}
               value={concurrency}
-              onChange={(e) => setConcurrency(Number(e.target.value))}
+              onChange={(e) => handleConcurrencyChange(Number(e.target.value))}
               disabled={isLoading}
               className="w-16 h-2 accent-primary cursor-pointer"
               title={`${concurrency} concurrent agent${concurrency > 1 ? 's' : ''}`}

ui/src/components/AssistantChat.tsx

@@ -12,6 +12,7 @@ import { useAssistantChat } from '../hooks/useAssistantChat'
 import { ChatMessage as ChatMessageComponent } from './ChatMessage'
 import { ConversationHistory } from './ConversationHistory'
 import type { ChatMessage } from '../lib/types'
+import { isSubmitEnter } from '../lib/keyboard'
 import { Button } from '@/components/ui/button'
 import { Textarea } from '@/components/ui/textarea'
 
@@ -134,7 +135,7 @@ export function AssistantChat({
   }
 
   const handleKeyDown = (e: React.KeyboardEvent<HTMLTextAreaElement>) => {
-    if (e.key === 'Enter' && !e.shiftKey) {
+    if (isSubmitEnter(e)) {
       e.preventDefault()
       handleSend()
     }

ui/src/components/AssistantPanel.tsx

@@ -50,11 +50,23 @@ export function AssistantPanel({ projectName, isOpen, onClose }: AssistantPanelP
   )
 
   // Fetch conversation details when we have an ID
-  const { data: conversationDetail, isLoading: isLoadingConversation } = useConversation(
+  const { data: conversationDetail, isLoading: isLoadingConversation, error: conversationError } = useConversation(
     projectName,
     conversationId
   )
 
+  // Clear stored conversation ID if it no longer exists (404 error)
+  useEffect(() => {
+    if (conversationError && conversationId) {
+      const message = conversationError.message.toLowerCase()
+      // Only clear for 404 errors, not transient network issues
+      if (message.includes('not found') || message.includes('404')) {
+        console.warn(`Conversation ${conversationId} not found, clearing stored ID`)
+        setConversationId(null)
+      }
+    }
+  }, [conversationError, conversationId])
+
   // Convert API messages to ChatMessage format for the chat component
   const initialMessages: ChatMessage[] | undefined = conversationDetail?.messages.map((msg) => ({
     id: `db-${msg.id}`,

ui/src/components/ConversationHistory.tsx

@@ -168,7 +168,7 @@ export function ConversationHistory({
                     <Button
                       variant="ghost"
                       size="icon"
-                      onClick={(e) => handleDeleteClick(e, conversation)}
+                      onClick={(e: React.MouseEvent) => handleDeleteClick(e, conversation)}
                       className={`h-8 w-8 mr-2 ${
                         isCurrent
                           ? 'opacity-60 hover:opacity-100'

ui/src/components/DebugLogViewer.tsx

@@ -349,7 +349,7 @@ export function DebugLogViewer({
               <Button
                 variant={activeTab === 'agent' ? 'secondary' : 'ghost'}
                 size="sm"
-                onClick={(e) => {
+                onClick={(e: React.MouseEvent) => {
                   e.stopPropagation()
                   setActiveTab('agent')
                 }}
@@ -366,7 +366,7 @@ export function DebugLogViewer({
               <Button
                 variant={activeTab === 'devserver' ? 'secondary' : 'ghost'}
                 size="sm"
-                onClick={(e) => {
+                onClick={(e: React.MouseEvent) => {
                   e.stopPropagation()
                   setActiveTab('devserver')
                 }}
@@ -383,7 +383,7 @@ export function DebugLogViewer({
               <Button
                 variant={activeTab === 'terminal' ? 'secondary' : 'ghost'}
                 size="sm"
-                onClick={(e) => {
+                onClick={(e: React.MouseEvent) => {
                   e.stopPropagation()
                   setActiveTab('terminal')
                 }}
@@ -421,7 +421,7 @@ export function DebugLogViewer({
             <Button
               variant="ghost"
               size="icon"
-              onClick={(e) => {
+              onClick={(e: React.MouseEvent) => {
                 e.stopPropagation()
                 handleClear()
               }}

ui/src/components/ExpandProjectChat.tsx

@@ -11,6 +11,7 @@ import { useExpandChat } from '../hooks/useExpandChat'
 import { ChatMessage } from './ChatMessage'
 import { TypingIndicator } from './TypingIndicator'
 import type { ImageAttachment } from '../lib/types'
+import { isSubmitEnter } from '../lib/keyboard'
 import { Button } from '@/components/ui/button'
 import { Input } from '@/components/ui/input'
 import { Card, CardContent } from '@/components/ui/card'
@@ -88,7 +89,7 @@ export function ExpandProjectChat({
   }
 
   const handleKeyDown = (e: React.KeyboardEvent) => {
-    if (e.key === 'Enter' && !e.shiftKey) {
+    if (isSubmitEnter(e)) {
       e.preventDefault()
       handleSendMessage()
     }

ui/src/components/FolderBrowser.tsx

@@ -18,6 +18,7 @@ import {
   ArrowLeft,
 } from 'lucide-react'
 import * as api from '../lib/api'
+import { isSubmitEnter } from '../lib/keyboard'
 import type { DirectoryEntry, DriveInfo } from '../lib/types'
 import { Button } from '@/components/ui/button'
 import { Input } from '@/components/ui/input'
@@ -269,7 +270,7 @@ export function FolderBrowser({ onSelect, onCancel, initialPath }: FolderBrowser
                     className="flex-1"
                     autoFocus
                     onKeyDown={(e) => {
-                      if (e.key === 'Enter') handleCreateFolder()
+                      if (isSubmitEnter(e, false)) handleCreateFolder()
                       if (e.key === 'Escape') {
                         setIsCreatingFolder(false)
                         setNewFolderName('')

ui/src/components/OrchestratorStatusCard.tsx

@@ -36,7 +36,7 @@ function getStateColor(state: OrchestratorState): string {
     case 'complete':
       return 'text-primary'
     case 'spawning':
-      return 'text-violet-600 dark:text-violet-400'
+      return 'text-primary'
     case 'scheduling':
     case 'monitoring':
       return 'text-primary'
@@ -65,7 +65,7 @@ export function OrchestratorStatusCard({ status }: OrchestratorStatusCardProps)
   const [showEvents, setShowEvents] = useState(false)
 
   return (
-    <Card className="mb-4 bg-gradient-to-r from-violet-50 to-purple-50 dark:from-violet-950/30 dark:to-purple-950/30 border-violet-200 dark:border-violet-800/50 py-4">
+    <Card className="mb-4 bg-primary/10 border-primary/30 py-4">
       <CardContent className="p-4">
         <div className="flex items-start gap-4">
           {/* Avatar */}
@@ -75,7 +75,7 @@ export function OrchestratorStatusCard({ status }: OrchestratorStatusCardProps)
           <div className="flex-1 min-w-0">
             {/* Header row */}
             <div className="flex items-center gap-2 mb-1">
-              <span className="font-semibold text-lg text-violet-700 dark:text-violet-300">
+              <span className="font-semibold text-lg text-primary">
                 Maestro
               </span>
               <span className={`text-sm font-medium ${getStateColor(status.state)}`}>
@@ -124,7 +124,7 @@ export function OrchestratorStatusCard({ status }: OrchestratorStatusCardProps)
               variant="ghost"
               size="sm"
               onClick={() => setShowEvents(!showEvents)}
-              className="text-violet-600 dark:text-violet-400 hover:bg-violet-100 dark:hover:bg-violet-900/30"
+              className="text-primary hover:bg-primary/10"
             >
               <Sparkles size={12} />
               Activity
@@ -135,14 +135,14 @@ export function OrchestratorStatusCard({ status }: OrchestratorStatusCardProps)
 
         {/* Collapsible recent events */}
         {showEvents && status.recentEvents.length > 0 && (
-          <div className="mt-3 pt-3 border-t border-violet-200 dark:border-violet-800/50">
+          <div className="mt-3 pt-3 border-t border-primary/20">
             <div className="space-y-1.5">
               {status.recentEvents.map((event, idx) => (
                 <div
                   key={`${event.timestamp}-${idx}`}
                   className="flex items-start gap-2 text-xs"
                 >
-                  <span className="text-violet-500 dark:text-violet-400 shrink-0 font-mono">
+                  <span className="text-primary shrink-0 font-mono">
                     {formatRelativeTime(event.timestamp)}
                   </span>
                   <span className="text-foreground">

ui/src/components/ProjectSelector.tsx

@@ -120,7 +120,7 @@ export function ProjectSelector({
                   <Button
                     variant="ghost"
                     size="icon-xs"
-                    onClick={(e) => handleDeleteClick(e, project.name)}
+                    onClick={(e: React.MouseEvent) => handleDeleteClick(e, project.name)}
                     className="text-muted-foreground hover:text-destructive"
                   >
                     <Trash2 size={14} />

ui/src/components/ProjectSetupRequired.tsx

@@ -0,0 +1,90 @@
+import { Sparkles, FileEdit, FolderOpen } from 'lucide-react'
+import { Button } from '@/components/ui/button'
+import { Card, CardContent, CardDescription, CardHeader, CardTitle } from '@/components/ui/card'
+
+interface ProjectSetupRequiredProps {
+  projectName: string
+  projectPath?: string
+  onCreateWithClaude: () => void
+  onEditManually: () => void
+}
+
+export function ProjectSetupRequired({
+  projectName,
+  projectPath,
+  onCreateWithClaude,
+  onEditManually,
+}: ProjectSetupRequiredProps) {
+  return (
+    <div className="max-w-2xl mx-auto mt-8">
+      <Card className="border-2">
+        <CardHeader className="text-center">
+          <CardTitle className="text-2xl font-display">
+            Project Setup Required
+          </CardTitle>
+          <CardDescription className="text-base">
+            <span className="font-semibold">{projectName}</span> needs an app spec to get started
+          </CardDescription>
+          {projectPath && (
+            <div className="flex items-center justify-center gap-2 text-sm text-muted-foreground mt-2">
+              <FolderOpen size={14} />
+              <code className="bg-muted px-2 py-0.5 rounded text-xs">{projectPath}</code>
+            </div>
+          )}
+        </CardHeader>
+        <CardContent className="space-y-4">
+          <p className="text-center text-muted-foreground">
+            Choose how you want to create your app specification:
+          </p>
+
+          <div className="grid gap-4 md:grid-cols-2">
+            {/* Create with Claude Option */}
+            <Card
+              className="cursor-pointer border-2 transition-all hover:border-primary hover:shadow-md"
+              onClick={onCreateWithClaude}
+            >
+              <CardContent className="pt-6 text-center space-y-3">
+                <div className="w-12 h-12 mx-auto bg-primary/10 rounded-full flex items-center justify-center">
+                  <Sparkles className="text-primary" size={24} />
+                </div>
+                <h3 className="font-semibold text-lg">Create with Claude</h3>
+                <p className="text-sm text-muted-foreground">
+                  Describe your app idea and Claude will help create a detailed specification
+                </p>
+                <Button className="w-full">
+                  <Sparkles size={16} className="mr-2" />
+                  Start Chat
+                </Button>
+              </CardContent>
+            </Card>
+
+            {/* Edit Manually Option */}
+            <Card
+              className="cursor-pointer border-2 transition-all hover:border-primary hover:shadow-md"
+              onClick={onEditManually}
+            >
+              <CardContent className="pt-6 text-center space-y-3">
+                <div className="w-12 h-12 mx-auto bg-muted rounded-full flex items-center justify-center">
+                  <FileEdit className="text-muted-foreground" size={24} />
+                </div>
+                <h3 className="font-semibold text-lg">Edit Templates Manually</h3>
+                <p className="text-sm text-muted-foreground">
+                  Create the prompts directory and edit template files yourself
+                </p>
+                <Button variant="outline" className="w-full">
+                  <FileEdit size={16} className="mr-2" />
+                  View Templates
+                </Button>
+              </CardContent>
+            </Card>
+          </div>
+
+          <p className="text-center text-xs text-muted-foreground pt-4">
+            The app spec tells the agent what to build. It includes the application name,
+            description, tech stack, and feature requirements.
+          </p>
+        </CardContent>
+      </Card>
+    </div>
+  )
+}

ui/src/components/ResetProjectModal.tsx

@@ -0,0 +1,194 @@
+import { useState } from 'react'
+import { Loader2, AlertTriangle, RotateCcw, Trash2, Check, X } from 'lucide-react'
+import { useResetProject } from '../hooks/useProjects'
+import {
+  Dialog,
+  DialogContent,
+  DialogHeader,
+  DialogTitle,
+  DialogDescription,
+  DialogFooter,
+} from '@/components/ui/dialog'
+import { Button } from '@/components/ui/button'
+import { Alert, AlertDescription } from '@/components/ui/alert'
+
+interface ResetProjectModalProps {
+  isOpen: boolean
+  projectName: string
+  onClose: () => void
+  onResetComplete?: (wasFullReset: boolean) => void
+}
+
+export function ResetProjectModal({
+  isOpen,
+  projectName,
+  onClose,
+  onResetComplete,
+}: ResetProjectModalProps) {
+  const [resetType, setResetType] = useState<'quick' | 'full'>('quick')
+  const resetProject = useResetProject(projectName)
+
+  const handleReset = async () => {
+    const isFullReset = resetType === 'full'
+    try {
+      await resetProject.mutateAsync(isFullReset)
+      onResetComplete?.(isFullReset)
+      onClose()
+    } catch {
+      // Error is handled by the mutation state
+    }
+  }
+
+  const handleClose = () => {
+    if (!resetProject.isPending) {
+      resetProject.reset()
+      setResetType('quick')
+      onClose()
+    }
+  }
+
+  return (
+    <Dialog open={isOpen} onOpenChange={(open) => !open && handleClose()}>
+      <DialogContent className="sm:max-w-md">
+        <DialogHeader>
+          <DialogTitle className="flex items-center gap-2">
+            <RotateCcw size={20} />
+            Reset Project
+          </DialogTitle>
+          <DialogDescription>
+            Reset <span className="font-semibold">{projectName}</span> to start fresh
+          </DialogDescription>
+        </DialogHeader>
+
+        <div className="space-y-4 py-4">
+          {/* Reset Type Toggle */}
+          <div className="flex rounded-lg border-2 border-border overflow-hidden">
+            <button
+              onClick={() => setResetType('quick')}
+              disabled={resetProject.isPending}
+              className={`flex-1 py-3 px-4 text-sm font-medium transition-colors flex items-center justify-center gap-2 ${
+                resetType === 'quick'
+                  ? 'bg-primary text-primary-foreground'
+                  : 'bg-background text-foreground hover:bg-muted'
+              } ${resetProject.isPending ? 'opacity-50 cursor-not-allowed' : ''}`}
+            >
+              <RotateCcw size={16} />
+              Quick Reset
+            </button>
+            <button
+              onClick={() => setResetType('full')}
+              disabled={resetProject.isPending}
+              className={`flex-1 py-3 px-4 text-sm font-medium transition-colors flex items-center justify-center gap-2 ${
+                resetType === 'full'
+                  ? 'bg-destructive text-destructive-foreground'
+                  : 'bg-background text-foreground hover:bg-muted'
+              } ${resetProject.isPending ? 'opacity-50 cursor-not-allowed' : ''}`}
+            >
+              <Trash2 size={16} />
+              Full Reset
+            </button>
+          </div>
+
+          {/* Warning Box */}
+          <Alert variant={resetType === 'full' ? 'destructive' : 'default'} className="border-2">
+            <AlertTriangle className="h-4 w-4" />
+            <AlertDescription>
+              <div className="font-semibold mb-2">
+                {resetType === 'quick' ? 'What will be deleted:' : 'What will be deleted:'}
+              </div>
+              <ul className="list-none space-y-1 text-sm">
+                <li className="flex items-center gap-2">
+                  <X size={14} className="text-destructive" />
+                  All features and progress
+                </li>
+                <li className="flex items-center gap-2">
+                  <X size={14} className="text-destructive" />
+                  Assistant chat history
+                </li>
+                <li className="flex items-center gap-2">
+                  <X size={14} className="text-destructive" />
+                  Agent settings
+                </li>
+                {resetType === 'full' && (
+                  <li className="flex items-center gap-2">
+                    <X size={14} className="text-destructive" />
+                    App spec and prompts
+                  </li>
+                )}
+              </ul>
+            </AlertDescription>
+          </Alert>
+
+          {/* What will be preserved */}
+          <div className="bg-muted/50 rounded-lg border-2 border-border p-3">
+            <div className="font-semibold mb-2 text-sm">
+              {resetType === 'quick' ? 'What will be preserved:' : 'What will be preserved:'}
+            </div>
+            <ul className="list-none space-y-1 text-sm text-muted-foreground">
+              {resetType === 'quick' ? (
+                <>
+                  <li className="flex items-center gap-2">
+                    <Check size={14} className="text-green-600" />
+                    App spec and prompts
+                  </li>
+                  <li className="flex items-center gap-2">
+                    <Check size={14} className="text-green-600" />
+                    Project code and files
+                  </li>
+                </>
+              ) : (
+                <>
+                  <li className="flex items-center gap-2">
+                    <Check size={14} className="text-green-600" />
+                    Project code and files
+                  </li>
+                  <li className="flex items-center gap-2 text-muted-foreground/70">
+                    <AlertTriangle size={14} />
+                    Setup wizard will appear
+                  </li>
+                </>
+              )}
+            </ul>
+          </div>
+
+          {/* Error Message */}
+          {resetProject.isError && (
+            <Alert variant="destructive">
+              <AlertDescription>
+                {resetProject.error instanceof Error
+                  ? resetProject.error.message
+                  : 'Failed to reset project. Please try again.'}
+              </AlertDescription>
+            </Alert>
+          )}
+        </div>
+
+        <DialogFooter className="gap-2">
+          <Button
+            variant="outline"
+            onClick={handleClose}
+            disabled={resetProject.isPending}
+          >
+            Cancel
+          </Button>
+          <Button
+            variant={resetType === 'full' ? 'destructive' : 'default'}
+            onClick={handleReset}
+            disabled={resetProject.isPending}
+          >
+            {resetProject.isPending ? (
+              <>
+                <Loader2 className="animate-spin mr-2" size={16} />
+                Resetting...
+              </>
+            ) : (
+              <>
+                {resetType === 'quick' ? 'Quick Reset' : 'Full Reset'}
+              </>
+            )}
+          </Button>
+        </DialogFooter>
+      </DialogContent>
+    </Dialog>
+  )
+}

ui/src/components/ScheduleModal.tsx

@@ -335,7 +335,7 @@ export function ScheduleModal({ projectName, isOpen, onClose }: ScheduleModalPro
               <Checkbox
                 id="yolo-mode"
                 checked={newSchedule.yolo_mode}
-                onCheckedChange={(checked) =>
+                onCheckedChange={(checked: boolean | 'indeterminate') =>
                   setNewSchedule((prev) => ({ ...prev, yolo_mode: checked === true }))
                 }
               />

ui/src/components/SpecCreationChat.tsx

@@ -12,6 +12,7 @@ import { ChatMessage } from './ChatMessage'
 import { QuestionOptions } from './QuestionOptions'
 import { TypingIndicator } from './TypingIndicator'
 import type { ImageAttachment } from '../lib/types'
+import { isSubmitEnter } from '../lib/keyboard'
 import { Button } from '@/components/ui/button'
 import { Textarea } from '@/components/ui/textarea'
 import { Card, CardContent } from '@/components/ui/card'
@@ -127,7 +128,7 @@ export function SpecCreationChat({
   }
 
   const handleKeyDown = (e: React.KeyboardEvent) => {
-    if (e.key === 'Enter' && !e.shiftKey) {
+    if (isSubmitEnter(e)) {
       e.preventDefault()
       handleSendMessage()
     }

ui/src/components/TerminalTabs.tsx

@@ -8,6 +8,7 @@
 import { useState, useRef, useEffect, useCallback } from 'react'
 import { Plus, X } from 'lucide-react'
 import type { TerminalInfo } from '@/lib/types'
+import { isSubmitEnter } from '@/lib/keyboard'
 import { Button } from '@/components/ui/button'
 import { Input } from '@/components/ui/input'
 
@@ -96,7 +97,7 @@ export function TerminalTabs({
   // Handle key events during editing
   const handleKeyDown = useCallback(
     (e: React.KeyboardEvent) => {
-      if (e.key === 'Enter') {
+      if (isSubmitEnter(e, false)) {
         e.preventDefault()
         submitEdit()
       } else if (e.key === 'Escape') {

ui/src/components/ThemeSelector.tsx

@@ -13,7 +13,7 @@ export function ThemeSelector({ themes, currentTheme, onThemeChange }: ThemeSele
   const [isOpen, setIsOpen] = useState(false)
   const [previewTheme, setPreviewTheme] = useState<ThemeId | null>(null)
   const containerRef = useRef<HTMLDivElement>(null)
-  const timeoutRef = useRef<NodeJS.Timeout | null>(null)
+  const timeoutRef = useRef<ReturnType<typeof setTimeout> | null>(null)
 
   // Close dropdown when clicking outside
   useEffect(() => {
@@ -32,7 +32,7 @@ export function ThemeSelector({ themes, currentTheme, onThemeChange }: ThemeSele
   useEffect(() => {
     if (previewTheme) {
       const root = document.documentElement
-      root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora')
+      root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora', 'theme-business')
       if (previewTheme === 'claude') {
         root.classList.add('theme-claude')
       } else if (previewTheme === 'neo-brutalism') {
@@ -41,6 +41,8 @@ export function ThemeSelector({ themes, currentTheme, onThemeChange }: ThemeSele
         root.classList.add('theme-retro-arcade')
       } else if (previewTheme === 'aurora') {
         root.classList.add('theme-aurora')
+      } else if (previewTheme === 'business') {
+        root.classList.add('theme-business')
       }
     }
 
@@ -48,7 +50,7 @@ export function ThemeSelector({ themes, currentTheme, onThemeChange }: ThemeSele
     return () => {
       if (previewTheme) {
         const root = document.documentElement
-        root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora')
+        root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora', 'theme-business')
         if (currentTheme === 'claude') {
           root.classList.add('theme-claude')
         } else if (currentTheme === 'neo-brutalism') {
@@ -57,6 +59,8 @@ export function ThemeSelector({ themes, currentTheme, onThemeChange }: ThemeSele
           root.classList.add('theme-retro-arcade')
         } else if (currentTheme === 'aurora') {
           root.classList.add('theme-aurora')
+        } else if (currentTheme === 'business') {
+          root.classList.add('theme-business')
         }
       }
     }

ui/src/hooks/useConversations.ts

@@ -26,6 +26,16 @@ export function useConversation(projectName: string | null, conversationId: numb
     queryFn: () => api.getAssistantConversation(projectName!, conversationId!),
     enabled: !!projectName && !!conversationId,
     staleTime: 30_000, // Cache for 30 seconds
+    retry: (failureCount, error) => {
+      // Don't retry on "not found" errors (404) - conversation doesn't exist
+      if (error instanceof Error && (
+        error.message.toLowerCase().includes('not found') ||
+        error.message === 'HTTP 404'
+      )) {
+        return false
+      }
+      return failureCount < 3
+    },
   })
 }
 

ui/src/hooks/useProjects.ts

@@ -4,7 +4,7 @@
 
 import { useQuery, useMutation, useQueryClient } from '@tanstack/react-query'
 import * as api from '../lib/api'
-import type { FeatureCreate, FeatureUpdate, ModelsResponse, Settings, SettingsUpdate } from '../lib/types'
+import type { FeatureCreate, FeatureUpdate, ModelsResponse, ProjectSettingsUpdate, Settings, SettingsUpdate } from '../lib/types'
 
 // ============================================================================
 // Projects
@@ -48,6 +48,33 @@ export function useDeleteProject() {
   })
 }
 
+export function useResetProject(projectName: string) {
+  const queryClient = useQueryClient()
+
+  return useMutation({
+    mutationFn: (fullReset: boolean) => api.resetProject(projectName, fullReset),
+    onSuccess: () => {
+      queryClient.invalidateQueries({ queryKey: ['projects'] })
+      queryClient.invalidateQueries({ queryKey: ['project', projectName] })
+      queryClient.invalidateQueries({ queryKey: ['features', projectName] })
+      queryClient.invalidateQueries({ queryKey: ['agent-status', projectName] })
+    },
+  })
+}
+
+export function useUpdateProjectSettings(projectName: string) {
+  const queryClient = useQueryClient()
+
+  return useMutation({
+    mutationFn: (settings: ProjectSettingsUpdate) =>
+      api.updateProjectSettings(projectName, settings),
+    onSuccess: () => {
+      queryClient.invalidateQueries({ queryKey: ['projects'] })
+      queryClient.invalidateQueries({ queryKey: ['project', projectName] })
+    },
+  })
+}
+
 // ============================================================================
 // Features
 // ============================================================================

ui/src/hooks/useTheme.ts

@@ -1,6 +1,6 @@
 import { useState, useEffect, useCallback } from 'react'
 
-export type ThemeId = 'twitter' | 'claude' | 'neo-brutalism' | 'retro-arcade' | 'aurora'
+export type ThemeId = 'twitter' | 'claude' | 'neo-brutalism' | 'retro-arcade' | 'aurora' | 'business'
 
 export interface ThemeOption {
   id: ThemeId
@@ -43,6 +43,12 @@ export const THEMES: ThemeOption[] = [
     name: 'Aurora',
     description: 'Deep violet and teal, like northern lights',
     previewColors: { primary: '#8b5cf6', background: '#faf8ff', accent: '#2dd4bf' }
+  },
+  {
+    id: 'business',
+    name: 'Business',
+    description: 'Deep navy (#000e4e) and gray monochrome',
+    previewColors: { primary: '#000e4e', background: '#eaecef', accent: '#6b7280' }
   }
 ]
 
@@ -61,6 +67,8 @@ function getThemeClass(themeId: ThemeId): string {
       return 'theme-retro-arcade'
     case 'aurora':
       return 'theme-aurora'
+    case 'business':
+      return 'theme-business'
     default:
       return ''
   }
@@ -70,7 +78,7 @@ export function useTheme() {
   const [theme, setThemeState] = useState<ThemeId>(() => {
     try {
       const stored = localStorage.getItem(THEME_STORAGE_KEY)
-      if (stored === 'twitter' || stored === 'claude' || stored === 'neo-brutalism' || stored === 'retro-arcade' || stored === 'aurora') {
+      if (stored === 'twitter' || stored === 'claude' || stored === 'neo-brutalism' || stored === 'retro-arcade' || stored === 'aurora' || stored === 'business') {
         return stored
       }
     } catch {
@@ -92,7 +100,7 @@ export function useTheme() {
     const root = document.documentElement
 
     // Remove all theme classes
-    root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora')
+    root.classList.remove('theme-claude', 'theme-neo-brutalism', 'theme-retro-arcade', 'theme-aurora', 'theme-business')
 
     // Add current theme class (if not twitter/default)
     const themeClass = getThemeClass(theme)

ui/src/lib/api.ts

@@ -6,6 +6,7 @@ import type {
   ProjectSummary,
   ProjectDetail,
   ProjectPrompts,
+  ProjectSettingsUpdate,
   FeatureListResponse,
   Feature,
   FeatureCreate,
@@ -100,6 +101,33 @@ export async function updateProjectPrompts(
   })
 }
 
+export async function updateProjectSettings(
+  name: string,
+  settings: ProjectSettingsUpdate
+): Promise<ProjectDetail> {
+  return fetchJSON(`/projects/${encodeURIComponent(name)}/settings`, {
+    method: 'PATCH',
+    body: JSON.stringify(settings),
+  })
+}
+
+export interface ResetProjectResponse {
+  success: boolean
+  reset_type: 'quick' | 'full'
+  deleted_files: string[]
+  message: string
+}
+
+export async function resetProject(
+  name: string,
+  fullReset: boolean = false
+): Promise<ResetProjectResponse> {
+  const params = fullReset ? '?full_reset=true' : ''
+  return fetchJSON(`/projects/${encodeURIComponent(name)}/reset${params}`, {
+    method: 'POST',
+  })
+}
+
 // ============================================================================
 // Features API
 // ============================================================================

ui/src/lib/keyboard.ts

@@ -0,0 +1,38 @@
+/**
+ * Keyboard event utilities
+ *
+ * Helpers for handling keyboard events, particularly for IME-aware input handling.
+ */
+
+/**
+ * Check if an Enter keypress should trigger form submission.
+ *
+ * Returns false during IME composition (e.g., Japanese, Chinese, Korean input)
+ * to prevent accidental submission while selecting characters.
+ *
+ * @param e - The keyboard event from React
+ * @param allowShiftEnter - If true, Shift+Enter returns false (for multiline input)
+ * @returns true if Enter should submit, false if it should be ignored
+ *
+ * @example
+ * // In a chat input (Shift+Enter for newline)
+ * if (isSubmitEnter(e)) {
+ *   e.preventDefault()
+ *   handleSend()
+ * }
+ *
+ * @example
+ * // In a single-line input (Enter always submits)
+ * if (isSubmitEnter(e, false)) {
+ *   handleSubmit()
+ * }
+ */
+export function isSubmitEnter(
+  e: React.KeyboardEvent,
+  allowShiftEnter: boolean = true
+): boolean {
+  if (e.key !== 'Enter') return false
+  if (allowShiftEnter && e.shiftKey) return false
+  if (e.nativeEvent.isComposing) return false
+  return true
+}

ui/src/lib/types.ts

@@ -15,6 +15,7 @@ export interface ProjectSummary {
   path: string
   has_spec: boolean
   stats: ProjectStats
+  default_concurrency: number
 }
 
 export interface ProjectDetail extends ProjectSummary {
@@ -536,6 +537,10 @@ export interface SettingsUpdate {
   testing_agent_ratio?: number
 }
 
+export interface ProjectSettingsUpdate {
+  default_concurrency?: number
+}
+
 // ============================================================================
 // Schedule Types
 // ============================================================================

ui/src/styles/globals.css

@@ -1,5 +1,5 @@
 @import "tailwindcss";
-@import "tw-animate-css";
+@import url("tw-animate-css");
 
 /* Enable class-based dark mode in Tailwind v4 */
 @custom-variant dark (&:where(.dark, .dark *));
@@ -590,6 +590,139 @@
   --color-status-done: oklch(0.4500 0.1500 285);
 }
 
+/* ============================================================================
+   Theme: Business
+   Professional deep navy (#000e4e) and gray palette for corporate use
+   Designed for trust, readability, and modern depth with card shadows
+   ============================================================================ */
+
+.theme-business {
+  --radius: 0.5rem;
+  /* Concrete-like blue-gray background */
+  --background: oklch(0.9500 0.0080 265);
+  /* Deep navy foreground #000e4e */
+  --foreground: oklch(0.1700 0.0900 265);
+  /* White cards with shadow depth */
+  --card: oklch(1.0000 0 0);
+  --card-foreground: oklch(0.1700 0.0900 265);
+  --popover: oklch(1.0000 0 0);
+  --popover-foreground: oklch(0.1700 0.0900 265);
+  /* Primary: Deep navy #000e4e */
+  --primary: oklch(0.1700 0.0900 265);
+  --primary-foreground: oklch(1.0000 0 0);
+  /* Secondary: Light gray */
+  --secondary: oklch(0.9500 0.0020 265);
+  --secondary-foreground: oklch(0.1700 0.0900 265);
+  /* Muted: Soft gray */
+  --muted: oklch(0.9300 0.0020 265);
+  --muted-foreground: oklch(0.4500 0.0100 265);
+  /* Accent: Medium gray (no teal) */
+  --accent: oklch(0.5500 0.0100 265);
+  --accent-foreground: oklch(1.0000 0 0);
+  --destructive: oklch(0.5800 0.2000 25);
+  --destructive-foreground: oklch(1.0000 0 0);
+  /* Border: Subtle gray */
+  --border: oklch(0.8800 0.0030 265);
+  --input: oklch(0.9300 0.0020 265);
+  --ring: oklch(0.1700 0.0900 265);
+  /* Chart colors: Navy-gray monochrome scale */
+  --chart-1: oklch(0.1700 0.0900 265);
+  --chart-2: oklch(0.3500 0.0600 265);
+  --chart-3: oklch(0.5000 0.0400 265);
+  --chart-4: oklch(0.6500 0.0200 265);
+  --chart-5: oklch(0.8000 0.0100 265);
+  --sidebar: oklch(0.9300 0.0100 265);
+  --sidebar-foreground: oklch(0.1700 0.0900 265);
+  --sidebar-primary: oklch(0.1700 0.0900 265);
+  --sidebar-primary-foreground: oklch(1.0000 0 0);
+  --sidebar-accent: oklch(0.5500 0.0100 265);
+  --sidebar-accent-foreground: oklch(1.0000 0 0);
+  --sidebar-border: oklch(0.8800 0.0030 265);
+  --sidebar-ring: oklch(0.1700 0.0900 265);
+
+  /* Shadow variables - pronounced for card depth (2026 trend) */
+  --shadow-sm: 0 1px 3px 0 rgb(0 14 78 / 0.06), 0 1px 2px -1px rgb(0 14 78 / 0.04);
+  --shadow: 0 2px 8px 0 rgb(0 14 78 / 0.08), 0 1px 3px -1px rgb(0 14 78 / 0.06);
+  --shadow-md: 0 6px 16px -2px rgb(0 14 78 / 0.10), 0 3px 6px -3px rgb(0 14 78 / 0.08);
+  --shadow-lg: 0 12px 32px -4px rgb(0 14 78 / 0.12), 0 6px 12px -6px rgb(0 14 78 / 0.10);
+
+  /* Log level colors - professional muted tones */
+  --color-log-error: #dc2626;
+  --color-log-warning: #d97706;
+  --color-log-info: #000e4e;
+  --color-log-debug: #6b7280;
+  --color-log-success: #059669;
+
+  /* Status colors for Kanban - gray-navy scale */
+  --color-status-pending: oklch(0.9300 0.0030 265);
+  --color-status-progress: oklch(0.8500 0.0200 265);
+  --color-status-done: oklch(0.7500 0.0400 265);
+
+  /* Font stacks - system fonts for professional feel */
+  --font-sans: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+  --font-mono: 'SF Mono', SFMono-Regular, ui-monospace, Consolas, 'Liberation Mono', monospace;
+}
+
+.theme-business.dark {
+  /* Very dark navy background */
+  --background: oklch(0.1200 0.0400 265);
+  --foreground: oklch(0.9400 0.0050 265);
+  /* Dark navy cards with elevation */
+  --card: oklch(0.1600 0.0500 265);
+  --card-foreground: oklch(0.9400 0.0050 265);
+  --popover: oklch(0.1400 0.0450 265);
+  --popover-foreground: oklch(0.9400 0.0050 265);
+  /* Primary: Lighter navy for dark mode */
+  --primary: oklch(0.5500 0.1200 265);
+  --primary-foreground: oklch(0.9800 0 0);
+  /* Secondary: Dark gray */
+  --secondary: oklch(0.2200 0.0200 265);
+  --secondary-foreground: oklch(0.9400 0.0050 265);
+  /* Muted: Medium-dark gray */
+  --muted: oklch(0.2500 0.0150 265);
+  --muted-foreground: oklch(0.6000 0.0100 265);
+  /* Accent: Light gray */
+  --accent: oklch(0.6500 0.0100 265);
+  --accent-foreground: oklch(0.1200 0.0400 265);
+  --destructive: oklch(0.6500 0.2000 25);
+  --destructive-foreground: oklch(1.0000 0 0);
+  --border: oklch(0.2800 0.0200 265);
+  --input: oklch(0.2200 0.0200 265);
+  --ring: oklch(0.5500 0.1200 265);
+  /* Chart colors: Navy-gray scale for dark mode */
+  --chart-1: oklch(0.5500 0.1200 265);
+  --chart-2: oklch(0.6500 0.0800 265);
+  --chart-3: oklch(0.7500 0.0400 265);
+  --chart-4: oklch(0.5000 0.0600 265);
+  --chart-5: oklch(0.4000 0.0400 265);
+  --sidebar: oklch(0.1000 0.0350 265);
+  --sidebar-foreground: oklch(0.9400 0.0050 265);
+  --sidebar-primary: oklch(0.5500 0.1200 265);
+  --sidebar-primary-foreground: oklch(0.9800 0 0);
+  --sidebar-accent: oklch(0.6500 0.0100 265);
+  --sidebar-accent-foreground: oklch(0.1200 0.0400 265);
+  --sidebar-border: oklch(0.2600 0.0180 265);
+  --sidebar-ring: oklch(0.5500 0.1200 265);
+
+  /* Shadow variables - dark mode with stronger depth */
+  --shadow-sm: 0 1px 3px 0 rgb(0 0 0 / 0.4), 0 1px 2px -1px rgb(0 0 0 / 0.3);
+  --shadow: 0 2px 8px 0 rgb(0 0 0 / 0.5), 0 1px 3px -1px rgb(0 0 0 / 0.4);
+  --shadow-md: 0 6px 16px -2px rgb(0 0 0 / 0.6), 0 3px 6px -3px rgb(0 0 0 / 0.5);
+  --shadow-lg: 0 12px 32px -4px rgb(0 0 0 / 0.7), 0 6px 12px -6px rgb(0 0 0 / 0.6);
+
+  /* Log level colors - dark mode */
+  --color-log-error: #f87171;
+  --color-log-warning: #fbbf24;
+  --color-log-info: #93c5fd;
+  --color-log-debug: #9ca3af;
+  --color-log-success: #34d399;
+
+  /* Status colors for Kanban - dark mode */
+  --color-status-pending: oklch(0.2500 0.0200 265);
+  --color-status-progress: oklch(0.3500 0.0400 265);
+  --color-status-done: oklch(0.4500 0.0600 265);
+}
+
 /* ============================================================================
    ShadCN Tailwind v4 Theme Integration
    ============================================================================ */

ui/tsconfig.node.json

@@ -4,6 +4,7 @@
     "lib": ["ES2023"],
     "module": "ESNext",
     "skipLibCheck": true,
+    "types": ["node"],
 
     /* Bundler mode */
     "moduleResolution": "bundler",