Initial plan

Co-authored-by: Santosh Bhavani <sb@mac-mini-i7.local>

.github/CODEOWNERS

@@ -1,3 +1,3 @@
 # Global code owner
-* @localden
+* @mnriem
 

.github/ISSUE_TEMPLATE/agent_request.yml

@@ -0,0 +1,141 @@
+name: Agent Request
+description: Request support for a new AI agent/assistant in Spec Kit
+title: "[Agent]: Add support for "
+labels: ["agent-request", "enhancement", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for requesting a new agent! Before submitting, please check if the agent is already supported.
+        
+        **Currently supported agents**: Claude Code, Gemini CLI, GitHub Copilot, Cursor, Qwen Code, opencode, Codex CLI, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy, Qoder CLI, Amazon Q Developer CLI, Amp, SHAI, IBM Bob, Antigravity
+
+  - type: input
+    id: agent-name
+    attributes:
+      label: Agent Name
+      description: What is the name of the AI agent/assistant?
+      placeholder: "e.g., SuperCoder AI"
+    validations:
+      required: true
+
+  - type: input
+    id: website
+    attributes:
+      label: Official Website
+      description: Link to the agent's official website or documentation
+      placeholder: "https://..."
+    validations:
+      required: true
+
+  - type: dropdown
+    id: agent-type
+    attributes:
+      label: Agent Type
+      description: How is the agent accessed?
+      options:
+        - CLI tool (command-line interface)
+        - IDE extension/plugin
+        - Both CLI and IDE
+        - Other
+    validations:
+      required: true
+
+  - type: input
+    id: cli-command
+    attributes:
+      label: CLI Command (if applicable)
+      description: What command is used to invoke the agent from terminal?
+      placeholder: "e.g., supercode, ai-assistant"
+
+  - type: input
+    id: install-method
+    attributes:
+      label: Installation Method
+      description: How is the agent installed?
+      placeholder: "e.g., npm install -g supercode, pip install supercode, IDE marketplace"
+    validations:
+      required: true
+
+  - type: textarea
+    id: command-structure
+    attributes:
+      label: Command/Workflow Structure
+      description: How does the agent define custom commands or workflows?
+      placeholder: |
+        - Command file format (Markdown, YAML, TOML, etc.)
+        - Directory location (e.g., .supercode/commands/)
+        - Example command file structure
+    validations:
+      required: true
+
+  - type: textarea
+    id: argument-pattern
+    attributes:
+      label: Argument Passing Pattern
+      description: How does the agent handle arguments in commands?
+      placeholder: |
+        e.g., Uses {{args}}, $ARGUMENTS, %ARGS%, or other placeholder format
+        Example: "Run test suite with {{args}}"
+
+  - type: dropdown
+    id: popularity
+    attributes:
+      label: Popularity/Usage
+      description: How widely is this agent used?
+      options:
+        - Widely used (thousands+ of users)
+        - Growing adoption (hundreds of users)
+        - New/emerging (less than 100 users)
+        - Unknown
+    validations:
+      required: true
+
+  - type: textarea
+    id: documentation
+    attributes:
+      label: Documentation Links
+      description: Links to relevant documentation for custom commands/workflows
+      placeholder: |
+        - Command documentation: https://...
+        - API/CLI reference: https://...
+        - Examples: https://...
+
+  - type: textarea
+    id: use-case
+    attributes:
+      label: Use Case
+      description: Why do you want this agent supported in Spec Kit?
+      placeholder: Explain your workflow and how this agent fits into your development process
+    validations:
+      required: true
+
+  - type: textarea
+    id: example-command
+    attributes:
+      label: Example Command File
+      description: If possible, provide an example of a command file for this agent
+      render: markdown
+      placeholder: |
+        ```toml
+        description = "Example command"
+        prompt = "Do something with {{args}}"
+        ```
+
+  - type: checkboxes
+    id: contribution
+    attributes:
+      label: Contribution
+      description: Are you willing to help implement support for this agent?
+      options:
+        - label: I can help test the integration
+        - label: I can provide example command files
+        - label: I can help with documentation
+        - label: I can submit a pull request for the integration
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Any other relevant information about this agent
+      placeholder: Screenshots, community links, comparison to existing agents, etc.

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,118 @@
+name: Bug Report
+description: Report a bug or unexpected behavior in Specify CLI or Spec Kit
+title: "[Bug]: "
+labels: ["bug", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report a bug! Please fill out the sections below to help us diagnose and fix the issue.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Bug Description
+      description: A clear and concise description of what the bug is.
+      placeholder: What went wrong?
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to Reproduce
+      description: Steps to reproduce the behavior
+      placeholder: |
+        1. Run command '...'
+        2. Execute script '...'
+        3. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+      description: What did you expect to happen?
+      placeholder: Describe the expected outcome
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual Behavior
+      description: What actually happened?
+      placeholder: Describe what happened instead
+    validations:
+      required: true
+
+  - type: input
+    id: version
+    attributes:
+      label: Specify CLI Version
+      description: "Run `specify version` or `pip show spec-kit`"
+      placeholder: "e.g., 1.3.0"
+    validations:
+      required: true
+
+  - type: dropdown
+    id: ai-agent
+    attributes:
+      label: AI Agent
+      description: Which AI agent are you using?
+      options:
+        - Claude Code
+        - Gemini CLI
+        - GitHub Copilot
+        - Cursor
+        - Qwen Code
+        - opencode
+        - Codex CLI
+        - Windsurf
+        - Kilo Code
+        - Auggie CLI
+        - Roo Code
+        - CodeBuddy
+        - Qoder CLI
+        - Amazon Q Developer CLI
+        - Amp
+        - SHAI
+        - IBM Bob
+        - Antigravity
+        - Not applicable
+    validations:
+      required: true
+
+  - type: input
+    id: os
+    attributes:
+      label: Operating System
+      description: Your operating system and version
+      placeholder: "e.g., macOS 14.2, Ubuntu 22.04, Windows 11"
+    validations:
+      required: true
+
+  - type: input
+    id: python
+    attributes:
+      label: Python Version
+      description: "Run `python --version` or `python3 --version`"
+      placeholder: "e.g., Python 3.11.5"
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error Logs
+      description: Please paste any relevant error messages or logs
+      render: shell
+      placeholder: Paste error output here
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Add any other context about the problem
+      placeholder: Screenshots, related issues, workarounds attempted, etc.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,17 @@
+blank_issues_enabled: false
+contact_links:
+  - name: 💬 General Discussion
+    url: https://github.com/github/spec-kit/discussions
+    about: Ask questions, share ideas, or discuss Spec-Driven Development
+  - name: 📖 Documentation
+    url: https://github.com/github/spec-kit/blob/main/README.md
+    about: Read the Spec Kit documentation and guides
+  - name: 🛠️ Extension Development Guide
+    url: https://github.com/manfredseee/spec-kit/blob/main/extensions/EXTENSION-DEVELOPMENT-GUIDE.md
+    about: Learn how to develop and publish Spec Kit extensions
+  - name: 🤝 Contributing Guide
+    url: https://github.com/github/spec-kit/blob/main/CONTRIBUTING.md
+    about: Learn how to contribute to Spec Kit
+  - name: 🔒 Security Issues
+    url: https://github.com/github/spec-kit/blob/main/SECURITY.md
+    about: Report security vulnerabilities privately

.github/ISSUE_TEMPLATE/extension_submission.yml

@@ -0,0 +1,280 @@
+name: Extension Submission
+description: Submit your extension to the Spec Kit catalog
+title: "[Extension]: Add "
+labels: ["extension-submission", "enhancement", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for contributing an extension! This template helps you submit your extension to the community catalog.
+        
+        **Before submitting:**
+        - Review the [Extension Publishing Guide](https://github.com/github/spec-kit/blob/main/extensions/EXTENSION-PUBLISHING-GUIDE.md)
+        - Ensure your extension has a valid `extension.yml` manifest
+        - Create a GitHub release with a version tag (e.g., v1.0.0)
+        - Test installation: `specify extension add --from <your-release-url>`
+
+  - type: input
+    id: extension-id
+    attributes:
+      label: Extension ID
+      description: Unique extension identifier (lowercase with hyphens only)
+      placeholder: "e.g., jira-integration"
+    validations:
+      required: true
+
+  - type: input
+    id: extension-name
+    attributes:
+      label: Extension Name
+      description: Human-readable extension name
+      placeholder: "e.g., Jira Integration"
+    validations:
+      required: true
+
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: Semantic version number
+      placeholder: "e.g., 1.0.0"
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Brief description of what your extension does (under 200 characters)
+      placeholder: Integrates Jira issue tracking with Spec Kit workflows for seamless task management
+    validations:
+      required: true
+
+  - type: input
+    id: author
+    attributes:
+      label: Author
+      description: Your name or organization
+      placeholder: "e.g., John Doe or Acme Corp"
+    validations:
+      required: true
+
+  - type: input
+    id: repository
+    attributes:
+      label: Repository URL
+      description: GitHub repository URL for your extension
+      placeholder: "https://github.com/your-org/spec-kit-your-extension"
+    validations:
+      required: true
+
+  - type: input
+    id: download-url
+    attributes:
+      label: Download URL
+      description: URL to the GitHub release archive (e.g., v1.0.0.zip)
+      placeholder: "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip"
+    validations:
+      required: true
+
+  - type: input
+    id: license
+    attributes:
+      label: License
+      description: Open source license type
+      placeholder: "e.g., MIT, Apache-2.0"
+    validations:
+      required: true
+
+  - type: input
+    id: homepage
+    attributes:
+      label: Homepage (optional)
+      description: Link to extension homepage or documentation site
+      placeholder: "https://..."
+
+  - type: input
+    id: documentation
+    attributes:
+      label: Documentation URL (optional)
+      description: Link to detailed documentation
+      placeholder: "https://github.com/your-org/spec-kit-your-extension/blob/main/docs/"
+
+  - type: input
+    id: changelog
+    attributes:
+      label: Changelog URL (optional)
+      description: Link to changelog file
+      placeholder: "https://github.com/your-org/spec-kit-your-extension/blob/main/CHANGELOG.md"
+
+  - type: input
+    id: speckit-version
+    attributes:
+      label: Required Spec Kit Version
+      description: Minimum Spec Kit version required
+      placeholder: "e.g., >=0.1.0"
+    validations:
+      required: true
+
+  - type: textarea
+    id: required-tools
+    attributes:
+      label: Required Tools (optional)
+      description: List any external tools or dependencies required
+      placeholder: |
+        - jira-cli (>=1.0.0) - required
+        - python (>=3.8) - optional
+      render: markdown
+
+  - type: input
+    id: commands-count
+    attributes:
+      label: Number of Commands
+      description: How many commands does your extension provide?
+      placeholder: "e.g., 3"
+    validations:
+      required: true
+
+  - type: input
+    id: hooks-count
+    attributes:
+      label: Number of Hooks (optional)
+      description: How many hooks does your extension provide?
+      placeholder: "e.g., 0"
+
+  - type: textarea
+    id: tags
+    attributes:
+      label: Tags
+      description: 2-5 relevant tags (lowercase, separated by commas)
+      placeholder: "issue-tracking, jira, atlassian, automation"
+    validations:
+      required: true
+
+  - type: textarea
+    id: features
+    attributes:
+      label: Key Features
+      description: List the main features and capabilities of your extension
+      placeholder: |
+        - Create Jira issues from specs
+        - Sync task status with Jira
+        - Link specs to existing issues
+        - Generate Jira reports
+    validations:
+      required: true
+
+  - type: checkboxes
+    id: testing
+    attributes:
+      label: Testing Checklist
+      description: Confirm that your extension has been tested
+      options:
+        - label: Extension installs successfully via download URL
+          required: true
+        - label: All commands execute without errors
+          required: true
+        - label: Documentation is complete and accurate
+          required: true
+        - label: No security vulnerabilities identified
+          required: true
+        - label: Tested on at least one real project
+          required: true
+
+  - type: checkboxes
+    id: requirements
+    attributes:
+      label: Submission Requirements
+      description: Verify your extension meets all requirements
+      options:
+        - label: Valid `extension.yml` manifest included
+          required: true
+        - label: README.md with installation and usage instructions
+          required: true
+        - label: LICENSE file included
+          required: true
+        - label: GitHub release created with version tag
+          required: true
+        - label: All command files exist and are properly formatted
+          required: true
+        - label: Extension ID follows naming conventions (lowercase-with-hyphens)
+          required: true
+
+  - type: textarea
+    id: testing-details
+    attributes:
+      label: Testing Details
+      description: Describe how you tested your extension
+      placeholder: |
+        **Tested on:**
+        - macOS 14.0 with Spec Kit v0.1.0
+        - Linux Ubuntu 22.04 with Spec Kit v0.1.0
+        
+        **Test project:** [Link or description]
+        
+        **Test scenarios:**
+        1. Installed extension
+        2. Configured settings
+        3. Ran all commands
+        4. Verified outputs
+    validations:
+      required: true
+
+  - type: textarea
+    id: example-usage
+    attributes:
+      label: Example Usage
+      description: Provide a simple example of using your extension
+      render: markdown
+      placeholder: |
+        ```bash
+        # Install extension
+        specify extension add --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+        
+        # Use a command
+        /speckit.your-extension.command-name arg1 arg2
+        ```
+    validations:
+      required: true
+
+  - type: textarea
+    id: catalog-entry
+    attributes:
+      label: Proposed Catalog Entry
+      description: Provide the JSON entry for catalog.json (helps reviewers)
+      render: json
+      placeholder: |
+        {
+          "your-extension": {
+            "name": "Your Extension",
+            "id": "your-extension",
+            "description": "Brief description",
+            "author": "Your Name",
+            "version": "1.0.0",
+            "download_url": "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip",
+            "repository": "https://github.com/your-org/spec-kit-your-extension",
+            "homepage": "https://github.com/your-org/spec-kit-your-extension",
+            "license": "MIT",
+            "requires": {
+              "speckit_version": ">=0.1.0"
+            },
+            "provides": {
+              "commands": 3
+            },
+            "tags": ["category", "tool"],
+            "verified": false,
+            "downloads": 0,
+            "stars": 0,
+            "created_at": "2026-02-20T00:00:00Z",
+            "updated_at": "2026-02-20T00:00:00Z"
+          }
+        }
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Any other information that would help reviewers
+      placeholder: Screenshots, demo videos, links to related projects, etc.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,104 @@
+name: Feature Request
+description: Suggest a new feature or enhancement for Specify CLI or Spec Kit
+title: "[Feature]: "
+labels: ["enhancement", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for suggesting a feature! Please provide details below to help us understand and evaluate your request.
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem Statement
+      description: Is your feature request related to a problem? Please describe.
+      placeholder: "I'm frustrated when..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed Solution
+      description: Describe the solution you'd like
+      placeholder: What would you like to happen?
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: Have you considered any alternative solutions or workarounds?
+      placeholder: What other approaches might work?
+
+  - type: dropdown
+    id: component
+    attributes:
+      label: Component
+      description: Which component does this feature relate to?
+      options:
+        - Specify CLI (initialization, commands)
+        - Spec templates (BDD, Testing Strategy, etc.)
+        - Agent integrations (command files, workflows)
+        - Scripts (Bash/PowerShell utilities)
+        - Documentation
+        - CI/CD workflows
+        - Other
+    validations:
+      required: true
+
+  - type: dropdown
+    id: ai-agent
+    attributes:
+      label: AI Agent (if applicable)
+      description: Does this feature relate to a specific AI agent?
+      options:
+        - All agents
+        - Claude Code
+        - Gemini CLI
+        - GitHub Copilot
+        - Cursor
+        - Qwen Code
+        - opencode
+        - Codex CLI
+        - Windsurf
+        - Kilo Code
+        - Auggie CLI
+        - Roo Code
+        - CodeBuddy
+        - Qoder CLI
+        - Amazon Q Developer CLI
+        - Amp
+        - SHAI
+        - IBM Bob
+        - Antigravity
+        - Not applicable
+
+  - type: textarea
+    id: use-cases
+    attributes:
+      label: Use Cases
+      description: Describe specific use cases where this feature would be valuable
+      placeholder: |
+        1. When working on large projects...
+        2. During spec review...
+        3. When integrating with CI/CD...
+
+  - type: textarea
+    id: acceptance
+    attributes:
+      label: Acceptance Criteria
+      description: How would you know this feature is complete and working?
+      placeholder: |
+        - [ ] Feature does X
+        - [ ] Documentation is updated
+        - [ ] Works with all supported agents
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Add any other context, screenshots, or examples
+      placeholder: Links to similar features, mockups, related discussions, etc.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+## Description
+
+<!-- What does this PR do? Why is it needed? -->
+
+## Testing
+
+<!-- How did you test your changes? -->
+
+- [ ] Tested locally with `uv run specify --help`
+- [ ] Ran existing tests with `uv sync && uv run pytest`
+- [ ] Tested with a sample project (if applicable)
+
+## AI Disclosure
+
+<!-- Per our Contributing guidelines, AI assistance must be disclosed. -->
+<!-- See: https://github.com/github/spec-kit/blob/main/CONTRIBUTING.md#ai-contributions-in-spec-kit -->
+
+- [ ] I **did not** use AI assistance for this contribution
+- [ ] I **did** use AI assistance (describe below)
+
+<!-- If you used AI, briefly describe how (e.g., "Code generated by Copilot", "Consulted ChatGPT for approach"): -->
+

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/codeql.yml

@@ -0,0 +1,32 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'actions', 'python' ]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/lint.yml

@@ -1,4 +1,6 @@
 name: Lint
+permissions:
+  contents: read
 
 on:
   push:
@@ -15,4 +17,6 @@ jobs:
       - name: Run markdownlint-cli2
         uses: DavidAnson/markdownlint-cli2-action@v19
         with:
-          globs: '**/*.md'
+          globs: |
+            '**/*.md'
+            !extensions/**/*.md

.github/workflows/release.yml

@@ -6,6 +6,7 @@ on:
     paths:
       - 'memory/**'
       - 'scripts/**'
+      - 'src/**'
       - 'templates/**'
       - '.github/workflows/**'
   workflow_dispatch:
@@ -57,4 +58,12 @@ jobs:
         run: |
           chmod +x .github/workflows/scripts/update-version.sh
           .github/workflows/scripts/update-version.sh ${{ steps.get_tag.outputs.new_version }}
+      - name: Commit version bump to main
+        if: steps.check_release.outputs.exists == 'false'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add pyproject.toml
+          git diff --cached --quiet || git commit -m "chore: bump version to ${{ steps.get_tag.outputs.new_version }} [skip ci]"
+          git push
 

.github/workflows/scripts/create-github-release.sh

@@ -40,9 +40,19 @@ gh release create "$VERSION" \
   .genreleases/spec-kit-template-roo-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-codebuddy-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-codebuddy-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-qodercli-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-qodercli-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-amp-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-amp-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-shai-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-shai-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-q-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-q-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-agy-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-agy-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-bob-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-bob-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-generic-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-generic-ps-"$VERSION".zip \
   --title "Spec Kit Templates - $VERSION_NO_V" \
   --notes-file release_notes.md

.github/workflows/scripts/create-release-packages.ps1

@@ -0,0 +1,428 @@
+#!/usr/bin/env pwsh
+#requires -Version 7.0
+
+<#
+.SYNOPSIS
+    Build Spec Kit template release archives for each supported AI assistant and script type.
+
+.DESCRIPTION
+    create-release-packages.ps1 (workflow-local)
+    Build Spec Kit template release archives for each supported AI assistant and script type.
+    
+.PARAMETER Version
+    Version string with leading 'v' (e.g., v0.2.0)
+
+.PARAMETER Agents
+    Comma or space separated subset of agents to build (default: all)
+    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, codex, kilocode, auggie, roo, codebuddy, amp, q, bob, qodercli, shai, agy, generic
+
+.PARAMETER Scripts
+    Comma or space separated subset of script types to build (default: both)
+    Valid scripts: sh, ps
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0 -Agents claude,copilot -Scripts sh
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0 -Agents claude -Scripts ps
+#>
+
+param(
+    [Parameter(Mandatory=$true, Position=0)]
+    [string]$Version,
+    
+    [Parameter(Mandatory=$false)]
+    [string]$Agents = "",
+    
+    [Parameter(Mandatory=$false)]
+    [string]$Scripts = ""
+)
+
+$ErrorActionPreference = "Stop"
+
+# Validate version format
+if ($Version -notmatch '^v\d+\.\d+\.\d+$') {
+    Write-Error "Version must look like v0.0.0"
+    exit 1
+}
+
+Write-Host "Building release packages for $Version"
+
+# Create and use .genreleases directory for all build artifacts
+$GenReleasesDir = ".genreleases"
+if (Test-Path $GenReleasesDir) {
+    Remove-Item -Path $GenReleasesDir -Recurse -Force -ErrorAction SilentlyContinue
+}
+New-Item -ItemType Directory -Path $GenReleasesDir -Force | Out-Null
+
+function Rewrite-Paths {
+    param([string]$Content)
+    
+    $Content = $Content -replace '(/?)\bmemory/', '.specify/memory/'
+    $Content = $Content -replace '(/?)\bscripts/', '.specify/scripts/'
+    $Content = $Content -replace '(/?)\btemplates/', '.specify/templates/'
+    return $Content
+}
+
+function Generate-Commands {
+    param(
+        [string]$Agent,
+        [string]$Extension,
+        [string]$ArgFormat,
+        [string]$OutputDir,
+        [string]$ScriptVariant
+    )
+    
+    New-Item -ItemType Directory -Path $OutputDir -Force | Out-Null
+    
+    $templates = Get-ChildItem -Path "templates/commands/*.md" -File -ErrorAction SilentlyContinue
+    
+    foreach ($template in $templates) {
+        $name = [System.IO.Path]::GetFileNameWithoutExtension($template.Name)
+        
+        # Read file content and normalize line endings
+        $fileContent = (Get-Content -Path $template.FullName -Raw) -replace "`r`n", "`n"
+        
+        # Extract description from YAML frontmatter
+        $description = ""
+        if ($fileContent -match '(?m)^description:\s*(.+)$') {
+            $description = $matches[1]
+        }
+        
+        # Extract script command from YAML frontmatter
+        $scriptCommand = ""
+        if ($fileContent -match "(?m)^\s*${ScriptVariant}:\s*(.+)$") {
+            $scriptCommand = $matches[1]
+        }
+        
+        if ([string]::IsNullOrEmpty($scriptCommand)) {
+            Write-Warning "No script command found for $ScriptVariant in $($template.Name)"
+            $scriptCommand = "(Missing script command for $ScriptVariant)"
+        }
+        
+        # Extract agent_script command from YAML frontmatter if present
+        $agentScriptCommand = ""
+        if ($fileContent -match "(?ms)agent_scripts:.*?^\s*${ScriptVariant}:\s*(.+?)$") {
+            $agentScriptCommand = $matches[1].Trim()
+        }
+        
+        # Replace {SCRIPT} placeholder with the script command
+        $body = $fileContent -replace '\{SCRIPT\}', $scriptCommand
+        
+        # Replace {AGENT_SCRIPT} placeholder with the agent script command if found
+        if (-not [string]::IsNullOrEmpty($agentScriptCommand)) {
+            $body = $body -replace '\{AGENT_SCRIPT\}', $agentScriptCommand
+        }
+        
+        # Remove the scripts: and agent_scripts: sections from frontmatter
+        $lines = $body -split "`n"
+        $outputLines = @()
+        $inFrontmatter = $false
+        $skipScripts = $false
+        $dashCount = 0
+        
+        foreach ($line in $lines) {
+            if ($line -match '^---$') {
+                $outputLines += $line
+                $dashCount++
+                if ($dashCount -eq 1) {
+                    $inFrontmatter = $true
+                } else {
+                    $inFrontmatter = $false
+                }
+                continue
+            }
+            
+            if ($inFrontmatter) {
+                if ($line -match '^(scripts|agent_scripts):$') {
+                    $skipScripts = $true
+                    continue
+                }
+                if ($line -match '^[a-zA-Z].*:' -and $skipScripts) {
+                    $skipScripts = $false
+                }
+                if ($skipScripts -and $line -match '^\s+') {
+                    continue
+                }
+            }
+            
+            $outputLines += $line
+        }
+        
+        $body = $outputLines -join "`n"
+        
+        # Apply other substitutions
+        $body = $body -replace '\{ARGS\}', $ArgFormat
+        $body = $body -replace '__AGENT__', $Agent
+        $body = Rewrite-Paths -Content $body
+        
+        # Generate output file based on extension
+        $outputFile = Join-Path $OutputDir "speckit.$name.$Extension"
+        
+        switch ($Extension) {
+            'toml' {
+                $body = $body -replace '\\', '\\'
+                $output = "description = `"$description`"`n`nprompt = `"`"`"`n$body`n`"`"`""
+                Set-Content -Path $outputFile -Value $output -NoNewline
+            }
+            'md' {
+                Set-Content -Path $outputFile -Value $body -NoNewline
+            }
+            'agent.md' {
+                Set-Content -Path $outputFile -Value $body -NoNewline
+            }
+        }
+    }
+}
+
+function Generate-CopilotPrompts {
+    param(
+        [string]$AgentsDir,
+        [string]$PromptsDir
+    )
+    
+    New-Item -ItemType Directory -Path $PromptsDir -Force | Out-Null
+    
+    $agentFiles = Get-ChildItem -Path "$AgentsDir/speckit.*.agent.md" -File -ErrorAction SilentlyContinue
+    
+    foreach ($agentFile in $agentFiles) {
+        $basename = $agentFile.Name -replace '\.agent\.md$', ''
+        $promptFile = Join-Path $PromptsDir "$basename.prompt.md"
+        
+        $content = @"
+---
+agent: $basename
+---
+"@
+        Set-Content -Path $promptFile -Value $content
+    }
+}
+
+function Build-Variant {
+    param(
+        [string]$Agent,
+        [string]$Script
+    )
+    
+    $baseDir = Join-Path $GenReleasesDir "sdd-${Agent}-package-${Script}"
+    Write-Host "Building $Agent ($Script) package..."
+    New-Item -ItemType Directory -Path $baseDir -Force | Out-Null
+    
+    # Copy base structure but filter scripts by variant
+    $specDir = Join-Path $baseDir ".specify"
+    New-Item -ItemType Directory -Path $specDir -Force | Out-Null
+    
+    # Copy memory directory
+    if (Test-Path "memory") {
+        Copy-Item -Path "memory" -Destination $specDir -Recurse -Force
+        Write-Host "Copied memory -> .specify"
+    }
+    
+    # Only copy the relevant script variant directory
+    if (Test-Path "scripts") {
+        $scriptsDestDir = Join-Path $specDir "scripts"
+        New-Item -ItemType Directory -Path $scriptsDestDir -Force | Out-Null
+        
+        switch ($Script) {
+            'sh' {
+                if (Test-Path "scripts/bash") {
+                    Copy-Item -Path "scripts/bash" -Destination $scriptsDestDir -Recurse -Force
+                    Write-Host "Copied scripts/bash -> .specify/scripts"
+                }
+            }
+            'ps' {
+                if (Test-Path "scripts/powershell") {
+                    Copy-Item -Path "scripts/powershell" -Destination $scriptsDestDir -Recurse -Force
+                    Write-Host "Copied scripts/powershell -> .specify/scripts"
+                }
+            }
+        }
+        
+        # Copy any script files that aren't in variant-specific directories
+        Get-ChildItem -Path "scripts" -File -ErrorAction SilentlyContinue | ForEach-Object {
+            Copy-Item -Path $_.FullName -Destination $scriptsDestDir -Force
+        }
+    }
+    
+    # Copy templates (excluding commands directory and vscode-settings.json)
+    if (Test-Path "templates") {
+        $templatesDestDir = Join-Path $specDir "templates"
+        New-Item -ItemType Directory -Path $templatesDestDir -Force | Out-Null
+        
+        Get-ChildItem -Path "templates" -Recurse -File | Where-Object {
+            $_.FullName -notmatch 'templates[/\\]commands[/\\]' -and $_.Name -ne 'vscode-settings.json'
+        } | ForEach-Object {
+            $relativePath = $_.FullName.Substring((Resolve-Path "templates").Path.Length + 1)
+            $destFile = Join-Path $templatesDestDir $relativePath
+            $destFileDir = Split-Path $destFile -Parent
+            New-Item -ItemType Directory -Path $destFileDir -Force | Out-Null
+            Copy-Item -Path $_.FullName -Destination $destFile -Force
+        }
+        Write-Host "Copied templates -> .specify/templates"
+    }
+    
+    # Generate agent-specific command files
+    switch ($Agent) {
+        'claude' {
+            $cmdDir = Join-Path $baseDir ".claude/commands"
+            Generate-Commands -Agent 'claude' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'gemini' {
+            $cmdDir = Join-Path $baseDir ".gemini/commands"
+            Generate-Commands -Agent 'gemini' -Extension 'toml' -ArgFormat '{{args}}' -OutputDir $cmdDir -ScriptVariant $Script
+            if (Test-Path "agent_templates/gemini/GEMINI.md") {
+                Copy-Item -Path "agent_templates/gemini/GEMINI.md" -Destination (Join-Path $baseDir "GEMINI.md")
+            }
+        }
+        'copilot' {
+            $agentsDir = Join-Path $baseDir ".github/agents"
+            Generate-Commands -Agent 'copilot' -Extension 'agent.md' -ArgFormat '$ARGUMENTS' -OutputDir $agentsDir -ScriptVariant $Script
+            
+            # Generate companion prompt files
+            $promptsDir = Join-Path $baseDir ".github/prompts"
+            Generate-CopilotPrompts -AgentsDir $agentsDir -PromptsDir $promptsDir
+            
+            # Create VS Code workspace settings
+            $vscodeDir = Join-Path $baseDir ".vscode"
+            New-Item -ItemType Directory -Path $vscodeDir -Force | Out-Null
+            if (Test-Path "templates/vscode-settings.json") {
+                Copy-Item -Path "templates/vscode-settings.json" -Destination (Join-Path $vscodeDir "settings.json")
+            }
+        }
+        'cursor-agent' {
+            $cmdDir = Join-Path $baseDir ".cursor/commands"
+            Generate-Commands -Agent 'cursor-agent' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'qwen' {
+            $cmdDir = Join-Path $baseDir ".qwen/commands"
+            Generate-Commands -Agent 'qwen' -Extension 'toml' -ArgFormat '{{args}}' -OutputDir $cmdDir -ScriptVariant $Script
+            if (Test-Path "agent_templates/qwen/QWEN.md") {
+                Copy-Item -Path "agent_templates/qwen/QWEN.md" -Destination (Join-Path $baseDir "QWEN.md")
+            }
+        }
+        'opencode' {
+            $cmdDir = Join-Path $baseDir ".opencode/command"
+            Generate-Commands -Agent 'opencode' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'windsurf' {
+            $cmdDir = Join-Path $baseDir ".windsurf/workflows"
+            Generate-Commands -Agent 'windsurf' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'codex' {
+            $cmdDir = Join-Path $baseDir ".codex/prompts"
+            Generate-Commands -Agent 'codex' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'kilocode' {
+            $cmdDir = Join-Path $baseDir ".kilocode/workflows"
+            Generate-Commands -Agent 'kilocode' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'auggie' {
+            $cmdDir = Join-Path $baseDir ".augment/commands"
+            Generate-Commands -Agent 'auggie' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'roo' {
+            $cmdDir = Join-Path $baseDir ".roo/commands"
+            Generate-Commands -Agent 'roo' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'codebuddy' {
+            $cmdDir = Join-Path $baseDir ".codebuddy/commands"
+            Generate-Commands -Agent 'codebuddy' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'amp' {
+            $cmdDir = Join-Path $baseDir ".agents/commands"
+            Generate-Commands -Agent 'amp' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'q' {
+            $cmdDir = Join-Path $baseDir ".amazonq/prompts"
+            Generate-Commands -Agent 'q' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'bob' {
+            $cmdDir = Join-Path $baseDir ".bob/commands"
+            Generate-Commands -Agent 'bob' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'qodercli' {
+            $cmdDir = Join-Path $baseDir ".qoder/commands"
+            Generate-Commands -Agent 'qodercli' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'generic' {
+            $cmdDir = Join-Path $baseDir ".speckit/commands"
+            Generate-Commands -Agent 'generic' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+    }
+    
+    # Create zip archive
+    $zipFile = Join-Path $GenReleasesDir "spec-kit-template-${Agent}-${Script}-${Version}.zip"
+    Compress-Archive -Path "$baseDir/*" -DestinationPath $zipFile -Force
+    Write-Host "Created $zipFile"
+}
+
+# Define all agents and scripts
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'q', 'bob', 'qodercli', 'shai', 'agy', 'generic')
+$AllScripts = @('sh', 'ps')
+
+function Normalize-List {
+    param([string]$Input)
+    
+    if ([string]::IsNullOrEmpty($Input)) {
+        return @()
+    }
+    
+    # Split by comma or space and remove duplicates while preserving order
+    $items = $Input -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
+    return $items
+}
+
+function Validate-Subset {
+    param(
+        [string]$Type,
+        [string[]]$Allowed,
+        [string[]]$Items
+    )
+    
+    $ok = $true
+    foreach ($item in $Items) {
+        if ($item -notin $Allowed) {
+            Write-Error "Unknown $Type '$item' (allowed: $($Allowed -join ', '))"
+            $ok = $false
+        }
+    }
+    return $ok
+}
+
+# Determine agent list
+if (-not [string]::IsNullOrEmpty($Agents)) {
+    $AgentList = Normalize-List -Input $Agents
+    if (-not (Validate-Subset -Type 'agent' -Allowed $AllAgents -Items $AgentList)) {
+        exit 1
+    }
+} else {
+    $AgentList = $AllAgents
+}
+
+# Determine script list
+if (-not [string]::IsNullOrEmpty($Scripts)) {
+    $ScriptList = Normalize-List -Input $Scripts
+    if (-not (Validate-Subset -Type 'script' -Allowed $AllScripts -Items $ScriptList)) {
+        exit 1
+    }
+} else {
+    $ScriptList = $AllScripts
+}
+
+Write-Host "Agents: $($AgentList -join ', ')"
+Write-Host "Scripts: $($ScriptList -join ', ')"
+
+# Build all variants
+foreach ($agent in $AgentList) {
+    foreach ($script in $ScriptList) {
+        Build-Variant -Agent $agent -Script $script
+    }
+}
+
+Write-Host "`nArchives in ${GenReleasesDir}:"
+Get-ChildItem -Path $GenReleasesDir -Filter "spec-kit-template-*-${Version}.zip" | ForEach-Object {
+    Write-Host "  $($_.Name)"
+}

.github/workflows/scripts/create-release-packages.sh

@@ -6,7 +6,7 @@ set -euo pipefail
 # Usage: .github/workflows/scripts/create-release-packages.sh <version>
 #   Version argument should include leading 'v'.
 #   Optionally set AGENTS and/or SCRIPTS env vars to limit what gets built.
-#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex amp (default: all)
+#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex amp shai bob generic (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -34,7 +34,8 @@ rewrite_paths() {
   sed -E \
     -e 's@(/?)memory/@.specify/memory/@g' \
     -e 's@(/?)scripts/@.specify/scripts/@g' \
-    -e 's@(/?)templates/@.specify/templates/@g'
+    -e 's@(/?)templates/@.specify/templates/@g' \
+    -e 's@\.specify\.specify/@.specify/@g'
 }
 
 generate_commands() {
@@ -95,12 +96,32 @@ generate_commands() {
         { echo "description = \"$description\""; echo; echo "prompt = \"\"\""; echo "$body"; echo "\"\"\""; } > "$output_dir/speckit.$name.$ext" ;;
       md)
         echo "$body" > "$output_dir/speckit.$name.$ext" ;;
-      prompt.md)
+      agent.md)
         echo "$body" > "$output_dir/speckit.$name.$ext" ;;
     esac
   done
 }
 
+generate_copilot_prompts() {
+  local agents_dir=$1 prompts_dir=$2
+  mkdir -p "$prompts_dir"
+  
+  # Generate a .prompt.md file for each .agent.md file
+  for agent_file in "$agents_dir"/speckit.*.agent.md; do
+    [[ -f "$agent_file" ]] || continue
+    
+    local basename=$(basename "$agent_file" .agent.md)
+    local prompt_file="$prompts_dir/${basename}.prompt.md"
+    
+    # Create prompt file with agent frontmatter
+    cat > "$prompt_file" <<EOF
+---
+agent: ${basename}
+---
+EOF
+  done
+}
+
 build_variant() {
   local agent=$1 script=$2
   local base_dir="$GENRELEASES_DIR/sdd-${agent}-package-${script}"
@@ -146,8 +167,10 @@ build_variant() {
       generate_commands gemini toml "{{args}}" "$base_dir/.gemini/commands" "$script"
       [[ -f agent_templates/gemini/GEMINI.md ]] && cp agent_templates/gemini/GEMINI.md "$base_dir/GEMINI.md" ;;
     copilot)
-      mkdir -p "$base_dir/.github/prompts"
-      generate_commands copilot prompt.md "\$ARGUMENTS" "$base_dir/.github/prompts" "$script"
+      mkdir -p "$base_dir/.github/agents"
+      generate_commands copilot agent.md "\$ARGUMENTS" "$base_dir/.github/agents" "$script"
+      # Generate companion prompt files
+      generate_copilot_prompts "$base_dir/.github/agents" "$base_dir/.github/prompts"
       # Create VS Code workspace settings
       mkdir -p "$base_dir/.vscode"
       [[ -f templates/vscode-settings.json ]] && cp templates/vscode-settings.json "$base_dir/.vscode/settings.json"
@@ -180,38 +203,53 @@ build_variant() {
     codebuddy)
       mkdir -p "$base_dir/.codebuddy/commands"
       generate_commands codebuddy md "\$ARGUMENTS" "$base_dir/.codebuddy/commands" "$script" ;;
+    qodercli)
+      mkdir -p "$base_dir/.qoder/commands"
+      generate_commands qodercli md "\$ARGUMENTS" "$base_dir/.qoder/commands" "$script" ;;
     amp)
       mkdir -p "$base_dir/.agents/commands"
       generate_commands amp md "\$ARGUMENTS" "$base_dir/.agents/commands" "$script" ;;
+    shai)
+      mkdir -p "$base_dir/.shai/commands"
+      generate_commands shai md "\$ARGUMENTS" "$base_dir/.shai/commands" "$script" ;;
     q)
       mkdir -p "$base_dir/.amazonq/prompts"
       generate_commands q md "\$ARGUMENTS" "$base_dir/.amazonq/prompts" "$script" ;;
+    agy)
+      mkdir -p "$base_dir/.agent/workflows"
+      generate_commands agy md "\$ARGUMENTS" "$base_dir/.agent/workflows" "$script" ;;
+    bob)
+      mkdir -p "$base_dir/.bob/commands"
+      generate_commands bob md "\$ARGUMENTS" "$base_dir/.bob/commands" "$script" ;;
+    generic)
+      mkdir -p "$base_dir/.speckit/commands"
+      generate_commands generic md "\$ARGUMENTS" "$base_dir/.speckit/commands" "$script" ;;
   esac
   ( cd "$base_dir" && zip -r "../spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip" . )
   echo "Created $GENRELEASES_DIR/spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip"
 }
 
 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp q)
+ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai q agy bob qodercli generic)
 ALL_SCRIPTS=(sh ps)
 
 norm_list() {
-  # convert comma+space separated -> space separated unique while preserving order of first occurrence
-  tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?" ":"") $i)}}}END{printf("\n")}'
+  # convert comma+space separated -> line separated unique while preserving order of first occurrence
+  tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?"\n":"") $i);out=1}}}END{printf("\n")}'
 }
 
 validate_subset() {
   local type=$1; shift; local -n allowed=$1; shift; local items=("$@")
-  local ok=1
+  local invalid=0
   for it in "${items[@]}"; do
     local found=0
     for a in "${allowed[@]}"; do [[ $it == "$a" ]] && { found=1; break; }; done
     if [[ $found -eq 0 ]]; then
       echo "Error: unknown $type '$it' (allowed: ${allowed[*]})" >&2
-      ok=0
+      invalid=1
     fi
   done
-  return $ok
+  return $invalid
 }
 
 if [[ -n ${AGENTS:-} ]]; then

.github/workflows/scripts/generate-release-notes.sh

@@ -30,6 +30,10 @@ fi
 cat > release_notes.md << EOF
 This is the latest set of releases that you can use with your agent of choice. We recommend using the Specify CLI to scaffold your projects, however you can download these independently and manage them yourself.
 
+## Changelog
+
+$COMMITS
+
 EOF
 
 echo "Generated release notes:"

.github/workflows/stale.yml

@@ -0,0 +1,42 @@
+name: 'Close stale issues and PRs'
+
+on:
+  schedule:
+    - cron: '0 0 * * *' # Run daily at midnight UTC
+  workflow_dispatch: # Allow manual triggering
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v10
+        with:
+          # Days of inactivity before an issue or PR becomes stale
+          days-before-stale: 150
+          # Days of inactivity before a stale issue or PR is closed (after being marked stale)
+          days-before-close: 30
+          
+          # Stale issue settings
+          stale-issue-message: 'This issue has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
+          close-issue-message: 'This issue has been automatically closed due to inactivity (180 days total). If you believe this issue is still relevant, please reopen it or create a new issue.'
+          stale-issue-label: 'stale'
+          
+          # Stale PR settings
+          stale-pr-message: 'This pull request has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
+          close-pr-message: 'This pull request has been automatically closed due to inactivity (180 days total). If you believe this PR is still relevant, please reopen it or create a new PR.'
+          stale-pr-label: 'stale'
+          
+          # Exempt issues and PRs with these labels from being marked as stale
+          exempt-issue-labels: 'pinned,security'
+          exempt-pr-labels: 'pinned,security'
+          
+          # Only issues or PRs with all of these labels are checked
+          # Leave empty to check all issues and PRs
+          any-of-labels: ''
+          
+          # Operations per run (helps avoid rate limits)
+          operations-per-run: 100

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: Test & Lint Python
+
+permissions:
+  contents: read
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Run ruff check
+        run: uvx ruff check src/
+
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra test
+
+      - name: Run tests
+        run: uv run pytest

.gitignore

@@ -32,6 +32,7 @@ env/
 *.swp
 *.swo
 .DS_Store
+*.tmp
 
 # Project specific
 *.log
@@ -43,3 +44,9 @@ env/
 .genreleases/
 *.zip
 sdd-*/
+docs/dev
+
+# Extension system
+.specify/extensions/.cache/
+.specify/extensions/.backup/
+.specify/extensions/*/local-config.yml

.markdownlint-cli2.jsonc

@@ -19,6 +19,11 @@
     },
     "MD050": {
       "style": "asterisk"
-    }
-  }
+    },
+    "MD036": false,
+    "MD060": false
+  },
+  "ignores": [
+    ".genreleases/"
+  ]
 }

AGENTS.md

@@ -29,22 +29,26 @@ Specify supports multiple AI agents by generating agent-specific command files a
 
 ### Current Supported Agents
 
-| Agent | Directory | Format | CLI Tool | Description |
-|-------|-----------|---------|----------|-------------|
-| **Claude Code** | `.claude/commands/` | Markdown | `claude` | Anthropic's Claude Code CLI |
-| **Gemini CLI** | `.gemini/commands/` | TOML | `gemini` | Google's Gemini CLI |
-| **GitHub Copilot** | `.github/prompts/` | Markdown | N/A (IDE-based) | GitHub Copilot in VS Code |
-| **Cursor** | `.cursor/commands/` | Markdown | `cursor-agent` | Cursor CLI |
-| **Qwen Code** | `.qwen/commands/` | TOML | `qwen` | Alibaba's Qwen Code CLI |
-| **opencode** | `.opencode/command/` | Markdown | `opencode` | opencode CLI |
-| **Codex CLI** | `.codex/commands/` | Markdown | `codex` | Codex CLI |
-| **Windsurf** | `.windsurf/workflows/` | Markdown | N/A (IDE-based) | Windsurf IDE workflows |
-| **Kilo Code** | `.kilocode/rules/` | Markdown | N/A (IDE-based) | Kilo Code IDE |
-| **Auggie CLI** | `.augment/rules/` | Markdown | `auggie` | Auggie CLI |
-| **Roo Code** | `.roo/rules/` | Markdown | N/A (IDE-based) | Roo Code IDE |
-| **CodeBuddy CLI** | `.codebuddy/commands/` | Markdown | `codebuddy` | CodeBuddy CLI |
-| **Amazon Q Developer CLI** | `.amazonq/prompts/` | Markdown | `q` | Amazon Q Developer CLI |
-| **Amp** | `.agents/commands/` | Markdown | `amp` | Amp CLI |
+| Agent                      | Directory              | Format   | CLI Tool        | Description                 |
+| -------------------------- | ---------------------- | -------- | --------------- | --------------------------- |
+| **Claude Code**            | `.claude/commands/`    | Markdown | `claude`        | Anthropic's Claude Code CLI |
+| **Gemini CLI**             | `.gemini/commands/`    | TOML     | `gemini`        | Google's Gemini CLI         |
+| **GitHub Copilot**         | `.github/agents/`      | Markdown | N/A (IDE-based) | GitHub Copilot in VS Code   |
+| **Cursor**                 | `.cursor/commands/`    | Markdown | `cursor-agent`  | Cursor CLI                  |
+| **Qwen Code**              | `.qwen/commands/`      | TOML     | `qwen`          | Alibaba's Qwen Code CLI     |
+| **opencode**               | `.opencode/command/`   | Markdown | `opencode`      | opencode CLI                |
+| **Codex CLI**              | `.codex/commands/`     | Markdown | `codex`         | Codex CLI                   |
+| **Windsurf**               | `.windsurf/workflows/` | Markdown | N/A (IDE-based) | Windsurf IDE workflows      |
+| **Kilo Code**              | `.kilocode/rules/`     | Markdown | N/A (IDE-based) | Kilo Code IDE               |
+| **Auggie CLI**             | `.augment/rules/`      | Markdown | `auggie`        | Auggie CLI                  |
+| **Roo Code**               | `.roo/rules/`          | Markdown | N/A (IDE-based) | Roo Code IDE                |
+| **CodeBuddy CLI**          | `.codebuddy/commands/` | Markdown | `codebuddy`     | CodeBuddy CLI               |
+| **Qoder CLI**              | `.qoder/commands/`     | Markdown | `qodercli`      | Qoder CLI                   |
+| **Amazon Q Developer CLI** | `.amazonq/prompts/`    | Markdown | `q`             | Amazon Q Developer CLI      |
+| **Amp**                    | `.agents/commands/`    | Markdown | `amp`           | Amp CLI                     |
+| **SHAI**                   | `.shai/commands/`      | Markdown | `shai`          | SHAI CLI                    |
+| **IBM Bob**                | `.bob/commands/`       | Markdown | N/A (IDE-based) | IBM Bob IDE                 |
+| **Generic**                | User-specified via `--ai-commands-dir` | Markdown | N/A | Bring your own agent        |
 
 ### Step-by-Step Integration Guide
 
@@ -62,6 +66,7 @@ AGENT_CONFIG = {
     "new-agent-cli": {  # Use the ACTUAL CLI tool name (what users type in terminal)
         "name": "New Agent Display Name",
         "folder": ".newagent/",  # Directory for agent files
+        "commands_subdir": "commands",  # Subdirectory name for command files (default: "commands")
         "install_url": "https://example.com/install",  # URL for installation docs (or None if IDE-based)
         "requires_cli": True,  # True if CLI tool required, False for IDE-based agents
     },
@@ -79,6 +84,10 @@ This eliminates the need for special-case mappings throughout the codebase.
 
 - `name`: Human-readable display name shown to users
 - `folder`: Directory where agent-specific files are stored (relative to project root)
+- `commands_subdir`: Subdirectory name within the agent folder where command/prompt files are stored (default: `"commands"`)
+  - Most agents use `"commands"` (e.g., `.claude/commands/`)
+  - Some agents use alternative names: `"agents"` (copilot), `"workflows"` (windsurf, kilocode, agy), `"prompts"` (codex, q), `"command"` (opencode - singular)
+  - This field enables `--ai-skills` to locate command templates correctly for skill generation
 - `install_url`: Installation documentation URL (set to `None` for IDE-based agents)
 - `requires_cli`: Whether the agent requires a CLI tool check during initialization
 
@@ -150,7 +159,7 @@ Add to case statement:
 case "$AGENT_TYPE" in
   # ... existing cases ...
   windsurf) update_agent_file "$WINDSURF_FILE" "Windsurf" ;;
-  "") 
+  "")
     # ... existing checks ...
     [ -f "$WINDSURF_FILE" ] && update_agent_file "$WINDSURF_FILE" "Windsurf";
     # Update default creation condition
@@ -304,13 +313,15 @@ echo "✅ Done"
 Require a command-line tool to be installed:
 
 - **Claude Code**: `claude` CLI
-- **Gemini CLI**: `gemini` CLI  
+- **Gemini CLI**: `gemini` CLI
 - **Cursor**: `cursor-agent` CLI
 - **Qwen Code**: `qwen` CLI
 - **opencode**: `opencode` CLI
 - **Amazon Q Developer CLI**: `q` CLI
 - **CodeBuddy CLI**: `codebuddy` CLI
+- **Qoder CLI**: `qodercli` CLI
 - **Amp**: `amp` CLI
+- **SHAI**: `shai` CLI
 
 ### IDE-Based Agents
 
@@ -318,12 +329,15 @@ Work within integrated development environments:
 
 - **GitHub Copilot**: Built into VS Code/compatible editors
 - **Windsurf**: Built into Windsurf IDE
+- **IBM Bob**: Built into IBM Bob IDE
 
 ## Command File Formats
 
 ### Markdown Format
 
-Used by: Claude, Cursor, opencode, Windsurf, Amazon Q Developer, Amp
+Used by: Claude, Cursor, opencode, Windsurf, Amazon Q Developer, Amp, SHAI, IBM Bob
+
+**Standard format:**
 
 ```markdown
 ---
@@ -333,6 +347,17 @@ description: "Command description"
 Command content with {SCRIPT} and $ARGUMENTS placeholders.
 ```
 
+**GitHub Copilot Chat Mode format:**
+
+```markdown
+---
+description: "Command description"
+mode: speckit.command-name
+---
+
+Command content with {SCRIPT} and $ARGUMENTS placeholders.
+```
+
 ### TOML Format
 
 Used by: Gemini, Qwen
@@ -349,7 +374,7 @@ Command content with {SCRIPT} and {{args}} placeholders.
 
 - **CLI agents**: Usually `.<agent-name>/commands/`
 - **IDE agents**: Follow IDE-specific patterns:
-  - Copilot: `.github/prompts/`
+  - Copilot: `.github/agents/`
   - Cursor: `.cursor/commands/`
   - Windsurf: `.windsurf/workflows/`
 

CHANGELOG.md

@@ -2,166 +2,81 @@
 
 <!-- markdownlint-disable MD024 -->
 
-All notable changes to the Specify CLI and templates are documented here.
+Recent changes to the Specify CLI and templates are documented here.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.0.20] - 2025-10-14
-
-### Added
-
-- **Intelligent Branch Naming**: `create-new-feature` scripts now support `--short-name` parameter for custom branch names
-  - When `--short-name` provided: Uses the custom name directly (cleaned and formatted)
-  - When omitted: Automatically generates meaningful names using stop word filtering and length-based filtering
-  - Filters out common stop words (I, want, to, the, for, etc.)
-  - Removes words shorter than 3 characters (unless they're uppercase acronyms)
-  - Takes 3-4 most meaningful words from the description
-  - **Enforces GitHub's 244-byte branch name limit** with automatic truncation and warnings
-  - Examples:
-    - "I want to create user authentication" → `001-create-user-authentication`
-    - "Implement OAuth2 integration for API" → `001-implement-oauth2-integration-api`
-    - "Fix payment processing bug" → `001-fix-payment-processing`
-    - Very long descriptions are automatically truncated at word boundaries to stay within limits
-  - Designed for AI agents to provide semantic short names while maintaining standalone usability
-
-### Changed
-
-- Enhanced help documentation for `create-new-feature.sh` and `create-new-feature.ps1` scripts with examples
-- Branch names now validated against GitHub's 244-byte limit with automatic truncation if needed
-
-## [0.0.19] - 2025-10-10
-
-### Added
-
-- Support for CodeBuddy (thank you to [@lispking](https://github.com/lispking) for the contribution).
-- You can now see Git-sourced errors in the Specify CLI.
-
-### Changed
-
-- Fixed the path to the constitution in `plan.md` (thank you to [@lyzno1](https://github.com/lyzno1) for spotting).
-- Fixed backslash escapes in generated TOML files for Gemini (thank you to [@hsin19](https://github.com/hsin19) for the contribution).
-- Implementation command now ensures that the correct ignore files are added (thank you to [@sigent-amazon](https://github.com/sigent-amazon) for the contribution).
-
-## [0.0.18] - 2025-10-06
-
-### Added
-
-- Support for using `.` as a shorthand for current directory in `specify init .` command, equivalent to `--here` flag but more intuitive for users.
-- Use the `/speckit.` command prefix to easily discover Spec Kit-related commands.
-- Refactor the prompts and templates to simplify their capabilities and how they are tracked. No more polluting things with tests when they are not needed.
-- Ensure that tasks are created per user story (simplifies testing and validation).
-- Add support for Visual Studio Code prompt shortcuts and automatic script execution.
-
-### Changed
-
-- All command files now prefixed with `speckit.` (e.g., `speckit.specify.md`, `speckit.plan.md`) for better discoverability and differentiation in IDE/CLI command palettes and file explorers
-
-## [0.0.17] - 2025-09-22
-
-### Added
-
-- New `/clarify` command template to surface up to 5 targeted clarification questions for an existing spec and persist answers into a Clarifications section in the spec.
-- New `/analyze` command template providing a non-destructive cross-artifact discrepancy and alignment report (spec, clarifications, plan, tasks, constitution) inserted after `/tasks` and before `/implement`.
-  - Note: Constitution rules are explicitly treated as non-negotiable; any conflict is a CRITICAL finding requiring artifact remediation, not weakening of principles.
-
-## [0.0.16] - 2025-09-22
-
-### Added
-
-- `--force` flag for `init` command to bypass confirmation when using `--here` in a non-empty directory and proceed with merging/overwriting files.
-
-## [0.0.15] - 2025-09-21
-
-### Added
-
-- Support for Roo Code.
-
-## [0.0.14] - 2025-09-21
-
-### Changed
-
-- Error messages are now shown consistently.
-
-## [0.0.13] - 2025-09-21
-
-### Added
-
-- Support for Kilo Code. Thank you [@shahrukhkhan489](https://github.com/shahrukhkhan489) with [#394](https://github.com/github/spec-kit/pull/394).
-- Support for Auggie CLI. Thank you [@hungthai1401](https://github.com/hungthai1401) with [#137](https://github.com/github/spec-kit/pull/137).
-- Agent folder security notice displayed after project provisioning completion, warning users that some agents may store credentials or auth tokens in their agent folders and recommending adding relevant folders to `.gitignore` to prevent accidental credential leakage.
-
-### Changed
-
-- Warning displayed to ensure that folks are aware that they might need to add their agent folder to `.gitignore`.
-- Cleaned up the `check` command output.
-
-## [0.0.12] - 2025-09-21
-
-### Changed
-
-- Added additional context for OpenAI Codex users - they need to set an additional environment variable, as described in [#417](https://github.com/github/spec-kit/issues/417).
-
-## [0.0.11] - 2025-09-20
-
-### Added
-
-- Codex CLI support (thank you [@honjo-hiroaki-gtt](https://github.com/honjo-hiroaki-gtt) for the contribution in [#14](https://github.com/github/spec-kit/pull/14))
-- Codex-aware context update tooling (Bash and PowerShell) so feature plans refresh `AGENTS.md` alongside existing assistants without manual edits.
-
-## [0.0.10] - 2025-09-20
+## [0.1.6] - 2026-02-23
 
 ### Fixed
 
-- Addressed [#378](https://github.com/github/spec-kit/issues/378) where a GitHub token may be attached to the request when it was empty.
+- **Parameter Ordering Issues (#1641)**: Fixed CLI parameter parsing issue where option flags were incorrectly consumed as values for preceding options
+  - Added validation to detect when `--ai` or `--ai-commands-dir` incorrectly consume following flags like `--here` or `--ai-skills`
+  - Now provides clear error messages: "Invalid value for --ai: '--here'"
+  - Includes helpful hints suggesting proper usage and listing available agents
+  - Commands like `specify init --ai-skills --ai --here` now fail with actionable feedback instead of confusing "Must specify project name" errors
+  - Added comprehensive test suite (5 new tests) to prevent regressions
 
-## [0.0.9] - 2025-09-19
-
-### Changed
-
-- Improved agent selector UI with cyan highlighting for agent keys and gray parentheses for full names
-
-## [0.0.8] - 2025-09-19
-
-### Added
-
-- Windsurf IDE support as additional AI assistant option (thank you [@raedkit](https://github.com/raedkit) for the work in [#151](https://github.com/github/spec-kit/pull/151))
-- GitHub token support for API requests to handle corporate environments and rate limiting (contributed by [@zryfish](https://github.com/@zryfish) in [#243](https://github.com/github/spec-kit/pull/243))
-
-### Changed
-
-- Updated README with Windsurf examples and GitHub token usage
-- Enhanced release workflow to include Windsurf templates
-
-## [0.0.7] - 2025-09-18
-
-### Changed
-
-- Updated command instructions in the CLI.
-- Cleaned up the code to not render agent-specific information when it's generic.
-
-## [0.0.6] - 2025-09-17
-
-### Added
-
-- opencode support as additional AI assistant option
-
-## [0.0.5] - 2025-09-17
-
-### Added
-
-- Qwen Code support as additional AI assistant option
-
-## [0.0.4] - 2025-09-14
-
-### Added
-
-- SOCKS proxy support for corporate environments via `httpx[socks]` dependency
+## [0.1.5] - 2026-02-21
 
 ### Fixed
 
-N/A
+- **AI Skills Installation Bug (#1658)**: Fixed `--ai-skills` flag not generating skill files for GitHub Copilot and other agents with non-standard command directory structures
+  - Added `commands_subdir` field to `AGENT_CONFIG` to explicitly specify the subdirectory name for each agent
+  - Affected agents now work correctly: copilot (`.github/agents/`), opencode (`.opencode/command/`), windsurf (`.windsurf/workflows/`), codex (`.codex/prompts/`), kilocode (`.kilocode/workflows/`), q (`.amazonq/prompts/`), and agy (`.agent/workflows/`)
+  - The `install_ai_skills()` function now uses the correct path for all agents instead of assuming `commands/` for everyone
 
-### Changed
+## [0.1.4] - 2026-02-20
 
-N/A
+### Fixed
+
+- **Qoder CLI detection**: Renamed `AGENT_CONFIG` key from `"qoder"` to `"qodercli"` to match the actual executable name, fixing `specify check` and `specify init --ai` detection failures
+
+## [0.1.3] - 2026-02-20
+
+### Added
+
+- **Generic Agent Support**: Added `--ai generic` option for unsupported AI agents ("bring your own agent")
+  - Requires `--ai-commands-dir <path>` to specify where the agent reads commands from
+  - Generates Markdown commands with `$ARGUMENTS` format (compatible with most agents)
+  - Example: `specify init my-project --ai generic --ai-commands-dir .myagent/commands/`
+  - Enables users to start with Spec Kit immediately while their agent awaits formal support
+
+## [0.0.102] - 2026-02-20
+
+- fix: include 'src/**' path in release workflow triggers (#1646)
+
+## [0.0.101] - 2026-02-19
+
+- chore(deps): bump github/codeql-action from 3 to 4 (#1635)
+
+## [0.0.100] - 2026-02-19
+
+- Add pytest and Python linting (ruff) to CI (#1637)
+- feat: add pull request template for better contribution guidelines (#1634)
+
+## [0.0.99] - 2026-02-19
+
+- Feat/ai skills (#1632)
+
+## [0.0.98] - 2026-02-19
+
+- chore(deps): bump actions/stale from 9 to 10 (#1623)
+- feat: add dependabot configuration for pip and GitHub Actions updates (#1622)
+
+## [0.0.97] - 2026-02-18
+
+- Remove Maintainers section from README.md (#1618)
+
+## [0.0.96] - 2026-02-17
+
+- fix: typo in plan-template.md (#1446)
+
+## [0.0.95] - 2026-02-12
+
+- Feat: add a new agent: Google Anti Gravity (#1220)
+
+## [0.0.94] - 2026-02-11
+
+- Add stale workflow for 180-day inactive issues and PRs (#1594)

CODE_OF_CONDUCT.md

@@ -23,7 +23,7 @@ include:
 Examples of unacceptable behavior by participants include:
 
 - The use of sexualized language or imagery and unwelcome sexual attention or
-advances
+  advances
 - Trolling, insulting/derogatory comments, and personal or political attacks
 - Public or private harassment
 - Publishing others' private information, such as a physical or electronic

CONTRIBUTING.md

@@ -32,8 +32,8 @@ On [GitHub Codespaces](https://github.com/features/codespaces) it's even simpler
 
 ## Submitting a pull request
 
->[!NOTE]
->If your pull request introduces a large change that materially impacts the work of the CLI or the rest of the repository (e.g., you're introducing new templates, arguments, or otherwise major changes), make sure that it was **discussed and agreed upon** by the project maintainers. Pull requests with large changes that did not have a prior conversation and agreement will be closed.
+> [!NOTE]
+> If your pull request introduces a large change that materially impacts the work of the CLI or the rest of the repository (e.g., you're introducing new templates, arguments, or otherwise major changes), make sure that it was **discussed and agreed upon** by the project maintainers. Pull requests with large changes that did not have a prior conversation and agreement will be closed.
 
 1. Fork and clone the repository
 1. Configure and install the dependencies: `uv sync`
@@ -62,6 +62,29 @@ When working on spec-kit:
 3. Test script functionality in the `scripts/` directory
 4. Ensure memory files (`memory/constitution.md`) are updated if major process changes are made
 
+### Testing template and command changes locally
+
+Running `uv run specify init` pulls released packages, which won’t include your local changes.  
+To test your templates, commands, and other changes locally, follow these steps:
+
+1. **Create release packages**
+
+   Run the following command to generate the local packages:
+
+   ```bash
+   ./.github/workflows/scripts/create-release-packages.sh v1.0.0
+   ```
+
+2. **Copy the relevant package to your test project**
+
+   ```bash
+   cp -r .genreleases/sdd-copilot-package-sh/. <path-to-test-project>/
+   ```
+
+3. **Open and test the agent**
+
+   Navigate to your test project folder and open the agent to verify your implementation.
+
 ## AI contributions in Spec Kit
 
 > [!IMPORTANT]
@@ -99,7 +122,7 @@ When submitting AI-assisted contributions, please ensure they include:
 
 - **Clear disclosure of AI use** - You are transparent about AI use and degree to which you're using it for the contribution
 - **Human understanding and testing** - You've personally tested the changes and understand what they do
-- **Clear rationale** - You can explain why the change is needed and how it fits within Spec Kit's goals  
+- **Clear rationale** - You can explain why the change is needed and how it fits within Spec Kit's goals
 - **Concrete evidence** - Include test cases, scenarios, or examples that demonstrate the improvement
 - **Your own analysis** - Share your thoughts on the end-to-end developer experience
 

README.md

@@ -1,5 +1,5 @@
 <div align="center">
-    <img src="./media/logo_small.webp" alt="Spec Kit Logo"/>
+    <img src="./media/logo_large.webp" alt="Spec Kit Logo" width="200" height="200"/>
     <h1>🌱 Spec Kit</h1>
     <h3><em>Build high-quality software faster.</em></h3>
 </div>
@@ -31,7 +31,6 @@
 - [📖 Learn More](#-learn-more)
 - [📋 Detailed Process](#-detailed-process)
 - [🔍 Troubleshooting](#-troubleshooting)
-- [👥 Maintainers](#-maintainers)
 - [💬 Support](#-support)
 - [🙏 Acknowledgements](#-acknowledgements)
 - [📄 License](#-license)
@@ -57,11 +56,19 @@ uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 Then use the tool directly:
 
 ```bash
+# Create new project
 specify init <PROJECT_NAME>
+
+# Or initialize in existing project
+specify init . --ai claude
+# or
+specify init --here --ai claude
+
+# Check installed tools
 specify check
 ```
 
-To upgrade specify run:
+To upgrade Specify, see the [Upgrade Guide](./docs/upgrade.md) for detailed instructions. Quick upgrade:
 
 ```bash
 uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
@@ -134,22 +141,28 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 
 ## 🤖 Supported AI Agents
 
-| Agent                                                     | Support | Notes                                             |
-|-----------------------------------------------------------|---------|---------------------------------------------------|
-| [Claude Code](https://www.anthropic.com/claude-code)      | ✅ |                                                   |
-| [GitHub Copilot](https://code.visualstudio.com/)          | ✅ |                                                   |
-| [Gemini CLI](https://github.com/google-gemini/gemini-cli) | ✅ |                                                   |
-| [Cursor](https://cursor.sh/)                              | ✅ |                                                   |
-| [Qwen Code](https://github.com/QwenLM/qwen-code)          | ✅ |                                                   |
-| [opencode](https://opencode.ai/)                          | ✅ |                                                   |
-| [Windsurf](https://windsurf.com/)                         | ✅ |                                                   |
-| [Kilo Code](https://github.com/Kilo-Org/kilocode)         | ✅ |                                                   |
-| [Auggie CLI](https://docs.augmentcode.com/cli/overview)   | ✅ |                                                   |
-| [CodeBuddy CLI](https://www.codebuddy.ai/cli)             | ✅ |                                                   |
-| [Roo Code](https://roocode.com/)                          | ✅ |                                                   |
-| [Codex CLI](https://github.com/openai/codex)              | ✅ |                                                   |
-| [Amazon Q Developer CLI](https://aws.amazon.com/developer/learning/q-developer-cli/) | ⚠️ | Amazon Q Developer CLI [does not support](https://github.com/aws/amazon-q-developer-cli/issues/3064) custom arguments for slash commands. |
-| [Amp](https://ampcode.com/) | ✅ | |
+| Agent                                                                                | Support | Notes                                                                                                                                     |
+| ------------------------------------------------------------------------------------ | ------- | ----------------------------------------------------------------------------------------------------------------------------------------- |
+| [Qoder CLI](https://qoder.com/cli)                                                   | ✅      |                                                                                                                                           |
+| [Amazon Q Developer CLI](https://aws.amazon.com/developer/learning/q-developer-cli/) | ⚠️      | Amazon Q Developer CLI [does not support](https://github.com/aws/amazon-q-developer-cli/issues/3064) custom arguments for slash commands. |
+| [Amp](https://ampcode.com/)                                                          | ✅      |                                                                                                                                           |
+| [Auggie CLI](https://docs.augmentcode.com/cli/overview)                              | ✅      |                                                                                                                                           |
+| [Claude Code](https://www.anthropic.com/claude-code)                                 | ✅      |                                                                                                                                           |
+| [CodeBuddy CLI](https://www.codebuddy.ai/cli)                                        | ✅      |                                                                                                                                           |
+| [Codex CLI](https://github.com/openai/codex)                                         | ✅      |                                                                                                                                           |
+| [Cursor](https://cursor.sh/)                                                         | ✅      |                                                                                                                                           |
+| [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | ✅      |                                                                                                                                           |
+| [GitHub Copilot](https://code.visualstudio.com/)                                     | ✅      |                                                                                                                                           |
+| [IBM Bob](https://www.ibm.com/products/bob)                                          | ✅      | IDE-based agent with slash command support                                                                                                |
+| [Jules](https://jules.google.com/)                                                   | ✅      |                                                                                                                                           |
+| [Kilo Code](https://github.com/Kilo-Org/kilocode)                                    | ✅      |                                                                                                                                           |
+| [opencode](https://opencode.ai/)                                                     | ✅      |                                                                                                                                           |
+| [Qwen Code](https://github.com/QwenLM/qwen-code)                                     | ✅      |                                                                                                                                           |
+| [Roo Code](https://roocode.com/)                                                     | ✅      |                                                                                                                                           |
+| [SHAI (OVHcloud)](https://github.com/ovh/shai)                                       | ✅      |                                                                                                                                           |
+| [Windsurf](https://windsurf.com/)                                                    | ✅      |                                                                                                                                           |
+| [Antigravity (agy)](https://agy.ai/)                                                 | ✅      |                                                                                                                                           |
+| Generic                                                                              | ✅      | Bring your own agent — use `--ai generic --ai-commands-dir <path>` for unsupported agents                                                 |
 
 ## 🔧 Specify CLI Reference
 
@@ -157,25 +170,27 @@ The `specify` command supports the following options:
 
 ### Commands
 
-| Command     | Description                                                    |
-|-------------|----------------------------------------------------------------|
-| `init`      | Initialize a new Specify project from the latest template      |
-| `check`     | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`) |
+| Command | Description                                                                                                                                             |
+| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `init`  | Initialize a new Specify project from the latest template                                                                                               |
+| `check` | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`, `shai`, `qodercli`) |
 
 ### `specify init` Arguments & Options
 
-| Argument/Option        | Type     | Description                                                                  |
-|------------------------|----------|------------------------------------------------------------------------------|
-| `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory) |
-| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, or `q` |
-| `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                 |
-| `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                             |
-| `--no-git`             | Flag     | Skip git repository initialization                                          |
-| `--here`               | Flag     | Initialize project in the current directory instead of creating a new one   |
-| `--force`              | Flag     | Force merge/overwrite when initializing in current directory (skip confirmation) |
-| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                 |
-| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                            |
-| `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)  |
+| Argument/Option        | Type     | Description                                                                                                                                                                                  |
+| ---------------------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory)                                                                                           |
+| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, `shai`, `q`, `agy`, `bob`, `qodercli`, or `generic` (requires `--ai-commands-dir`) |
+| `--ai-commands-dir`    | Option   | Directory for agent command files (required with `--ai generic`, e.g. `.myagent/commands/`)                                                                                                  |
+| `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                                                                                                                                  |
+| `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                                                                                                                                              |
+| `--no-git`             | Flag     | Skip git repository initialization                                                                                                                                                           |
+| `--here`               | Flag     | Initialize project in the current directory instead of creating a new one                                                                                                                    |
+| `--force`              | Flag     | Force merge/overwrite when initializing in current directory (skip confirmation)                                                                                                             |
+| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                  |
+| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                             |
+| `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                    |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                          |
 
 ### Examples
 
@@ -189,12 +204,24 @@ specify init my-project --ai claude
 # Initialize with Cursor support
 specify init my-project --ai cursor-agent
 
+# Initialize with Qoder support
+specify init my-project --ai qodercli
+
 # Initialize with Windsurf support
 specify init my-project --ai windsurf
 
 # Initialize with Amp support
 specify init my-project --ai amp
 
+# Initialize with SHAI support
+specify init my-project --ai shai
+
+# Initialize with IBM Bob support
+specify init my-project --ai bob
+
+# Initialize with an unsupported agent (generic / bring your own agent)
+specify init my-project --ai generic --ai-commands-dir .myagent/commands/
+
 # Initialize with PowerShell scripts (Windows/cross-platform)
 specify init my-project --ai copilot --script ps
 
@@ -205,7 +232,7 @@ specify init --here --ai copilot
 
 # Force merge into current (non-empty) directory without confirmation
 specify init . --force --ai copilot
-# or 
+# or
 specify init --here --force --ai copilot
 
 # Skip git initialization
@@ -217,6 +244,12 @@ specify init my-project --ai claude --debug
 # Use GitHub token for API requests (helpful for corporate environments)
 specify init my-project --ai claude --github-token ghp_your_token_here
 
+# Install agent skills with the project
+specify init my-project --ai claude --ai-skills
+
+# Initialize in current directory with agent skills
+specify init --here --ai gemini --ai-skills
+
 # Check system requirements
 specify check
 ```
@@ -229,29 +262,29 @@ After running `specify init`, your AI coding agent will have access to these sla
 
 Essential commands for the Spec-Driven Development workflow:
 
-| Command                  | Description                                                           |
-|--------------------------|-----------------------------------------------------------------------|
-| `/speckit.constitution`  | Create or update project governing principles and development guidelines |
-| `/speckit.specify`       | Define what you want to build (requirements and user stories)        |
-| `/speckit.plan`          | Create technical implementation plans with your chosen tech stack     |
-| `/speckit.tasks`         | Generate actionable task lists for implementation                     |
-| `/speckit.implement`     | Execute all tasks to build the feature according to the plan         |
+| Command                 | Description                                                              |
+| ----------------------- | ------------------------------------------------------------------------ |
+| `/speckit.constitution` | Create or update project governing principles and development guidelines |
+| `/speckit.specify`      | Define what you want to build (requirements and user stories)            |
+| `/speckit.plan`         | Create technical implementation plans with your chosen tech stack        |
+| `/speckit.tasks`        | Generate actionable task lists for implementation                        |
+| `/speckit.implement`    | Execute all tasks to build the feature according to the plan             |
 
 #### Optional Commands
 
 Additional commands for enhanced quality and validation:
 
-| Command              | Description                                                           |
-|----------------------|-----------------------------------------------------------------------|
-| `/speckit.clarify`   | Clarify underspecified areas (recommended before `/speckit.plan`; formerly `/quizme`) |
-| `/speckit.analyze`   | Cross-artifact consistency & coverage analysis (run after `/speckit.tasks`, before `/speckit.implement`) |
+| Command              | Description                                                                                                                          |
+| -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
+| `/speckit.clarify`   | Clarify underspecified areas (recommended before `/speckit.plan`; formerly `/quizme`)                                                |
+| `/speckit.analyze`   | Cross-artifact consistency & coverage analysis (run after `/speckit.tasks`, before `/speckit.implement`)                             |
 | `/speckit.checklist` | Generate custom quality checklists that validate requirements completeness, clarity, and consistency (like "unit tests for English") |
 
 ### Environment Variables
 
-| Variable         | Description                                                                                    |
-|------------------|------------------------------------------------------------------------------------------------|
-| `SPECIFY_FEATURE` | Override feature detection for non-Git repositories. Set to the feature directory name (e.g., `001-photo-albums`) to work on a specific feature when not using Git branches.<br/>**Must be set in the context of the agent you're working with prior to using `/speckit.plan` or follow-up commands. |
+| Variable          | Description                                                                                                                                                                                                                                                                                            |
+| ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| `SPECIFY_FEATURE` | Override feature detection for non-Git repositories. Set to the feature directory name (e.g., `001-photo-albums`) to work on a specific feature when not using Git branches.<br/>\*\*Must be set in the context of the agent you're working with prior to using `/speckit.plan` or follow-up commands. |
 
 ## 📚 Core Philosophy
 
@@ -264,11 +297,11 @@ Spec-Driven Development is a structured process that emphasizes:
 
 ## 🌟 Development Phases
 
-| Phase | Focus | Key Activities |
-|-------|-------|----------------|
-| **0-to-1 Development** ("Greenfield") | Generate from scratch | <ul><li>Start with high-level requirements</li><li>Generate specifications</li><li>Plan implementation steps</li><li>Build production-ready applications</li></ul> |
-| **Creative Exploration** | Parallel implementations | <ul><li>Explore diverse solutions</li><li>Support multiple technology stacks & architectures</li><li>Experiment with UX patterns</li></ul> |
-| **Iterative Enhancement** ("Brownfield") | Brownfield modernization | <ul><li>Add features iteratively</li><li>Modernize legacy systems</li><li>Adapt processes</li></ul> |
+| Phase                                    | Focus                    | Key Activities                                                                                                                                                     |
+| ---------------------------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **0-to-1 Development** ("Greenfield")    | Generate from scratch    | <ul><li>Start with high-level requirements</li><li>Generate specifications</li><li>Plan implementation steps</li><li>Build production-ready applications</li></ul> |
+| **Creative Exploration**                 | Parallel implementations | <ul><li>Explore diverse solutions</li><li>Support multiple technology stacks & architectures</li><li>Experiment with UX patterns</li></ul>                         |
+| **Iterative Enhancement** ("Brownfield") | Brownfield modernization | <ul><li>Add features iteratively</li><li>Modernize legacy systems</li><li>Adapt processes</li></ul>                                                                |
 
 ## 🎯 Experimental Goals
 
@@ -360,7 +393,7 @@ specify init . --force --ai claude
 specify init --here --force --ai claude
 ```
 
-The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, or Amazon Q Developer CLI installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
+The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, or Amazon Q Developer CLI installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
 
 ```bash
 specify init <project_name> --ai claude --ignore-agent-tools
@@ -386,8 +419,8 @@ This step creates or updates the `.specify/memory/constitution.md` file with you
 
 With your project principles established, you can now create the functional specifications. Use the `/speckit.specify` command and then provide the concrete requirements for the project you want to develop.
 
->[!IMPORTANT]
->Be as explicit as possible about *what* you are trying to build and *why*. **Do not focus on the tech stack at this point**.
+> [!IMPORTANT]
+> Be as explicit as possible about *what* you are trying to build and *why*. **Do not focus on the tech stack at this point**.
 
 An example prompt:
 
@@ -530,8 +563,8 @@ researching .NET Aspire in general and I don't think that's gonna do much for us
 That's way too untargeted research. The research needs to help you solve a specific targeted question.
 ```
 
->[!NOTE]
->Claude Code might be over-eager and add components that you did not ask for. Ask it to clarify the rationale and the source of the change.
+> [!NOTE]
+> Claude Code might be over-eager and add components that you did not ask for. Ask it to clarify the rationale and the source of the change.
 
 ### **STEP 5:** Have Claude Code validate the plan
 
@@ -549,8 +582,8 @@ This helps refine the implementation plan and helps you avoid potential blind sp
 
 You can also ask Claude Code (if you have the [GitHub CLI](https://docs.github.com/en/github-cli/github-cli) installed) to go ahead and create a pull request from your current branch to `main` with a detailed description, to make sure that the effort is properly tracked.
 
->[!NOTE]
->Before you have the agent implement it, it's also worth prompting Claude Code to cross-check the details to see if there are any over-engineered pieces (remember - it can be over-eager). If over-engineered components or decisions exist, you can ask Claude Code to resolve them. Ensure that Claude Code follows the [constitution](base/memory/constitution.md) as the foundational piece that it must adhere to when establishing the plan.
+> [!NOTE]
+> Before you have the agent implement it, it's also worth prompting Claude Code to cross-check the details to see if there are any over-engineered pieces (remember - it can be over-eager). If over-engineered components or decisions exist, you can ask Claude Code to resolve them. Ensure that Claude Code follows the [constitution](base/memory/constitution.md) as the foundational piece that it must adhere to when establishing the plan.
 
 ### **STEP 6:** Generate task breakdown with /speckit.tasks
 
@@ -587,8 +620,8 @@ The `/speckit.implement` command will:
 - Follow the TDD approach defined in your task plan
 - Provide progress updates and handle errors appropriately
 
->[!IMPORTANT]
->The AI agent will execute local CLI commands (such as `dotnet`, `npm`, etc.) - make sure you have the required tools installed on your machine.
+> [!IMPORTANT]
+> The AI agent will execute local CLI commands (such as `dotnet`, `npm`, etc.) - make sure you have the required tools installed on your machine.
 
 Once the implementation is complete, test the application and resolve any runtime errors that may not be visible in CLI logs (e.g., browser console errors). You can copy and paste such errors back to your AI agent for resolution.
 
@@ -615,11 +648,6 @@ echo "Cleaning up..."
 rm gcm-linux_amd64.2.6.1.deb
 ```
 
-## 👥 Maintainers
-
-- Den Delimarsky ([@localden](https://github.com/localden))
-- John Lam ([@jflam](https://github.com/jflam))
-
 ## 💬 Support
 
 For support, please open a [GitHub issue](https://github.com/github/spec-kit/issues/new). We welcome bug reports, feature requests, and questions about using Spec-Driven Development.

docs/index.md

@@ -12,6 +12,7 @@ Spec-Driven Development **flips the script** on traditional software development
 
 - [Installation Guide](installation.md)
 - [Quick Start Guide](quickstart.md)
+- [Upgrade Guide](upgrade.md)
 - [Local Development](local-development.md)
 
 ## Core Philosophy

docs/quickstart.md

@@ -2,16 +2,24 @@
 
 This guide will help you get started with Spec-Driven Development using Spec Kit.
 
-> NEW: All automation scripts now provide both Bash (`.sh`) and PowerShell (`.ps1`) variants. The `specify` CLI auto-selects based on OS unless you pass `--script sh|ps`.
+> [!NOTE]
+> All automation scripts now provide both Bash (`.sh`) and PowerShell (`.ps1`) variants. The `specify` CLI auto-selects based on OS unless you pass `--script sh|ps`.
 
-## The 4-Step Process
+## The 6-Step Process
 
-### 1. Install Specify
+> [!TIP]
+> **Context Awareness**: Spec Kit commands automatically detect the active feature based on your current Git branch (e.g., `001-feature-name`). To switch between different specifications, simply switch Git branches.
 
-Initialize your project depending on the coding agent you're using:
+### Step 1: Install Specify
+
+**In your terminal**, run the `specify` CLI command to initialize your project:
 
 ```bash
+# Create a new project directory
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
+
+# OR initialize in the current directory
+uvx --from git+https://github.com/github/spec-kit.git specify init .
 ```
 
 Pick script type explicitly (optional):
@@ -21,31 +29,74 @@ uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME> --script sh  # Force POSIX shell
 ```
 
-### 2. Create the Spec
+### Step 2: Define Your Constitution
 
-Use the `/speckit.specify` command to describe what you want to build. Focus on the **what** and **why**, not the tech stack.
+**In your AI Agent's chat interface**, use the `/speckit.constitution` slash command to establish the core rules and principles for your project. You should provide your project's specific principles as arguments.
 
-```bash
+```markdown
+/speckit.constitution This project follows a "Library-First" approach. All features must be implemented as standalone libraries first. We use TDD strictly. We prefer functional programming patterns.
+```
+
+### Step 3: Create the Spec
+
+**In the chat**, use the `/speckit.specify` slash command to describe what you want to build. Focus on the **what** and **why**, not the tech stack.
+
+```markdown
 /speckit.specify Build an application that can help me organize my photos in separate photo albums. Albums are grouped by date and can be re-organized by dragging and dropping on the main page. Albums are never in other nested albums. Within each album, photos are previewed in a tile-like interface.
 ```
 
-### 3. Create a Technical Implementation Plan
+### Step 4: Refine the Spec
 
-Use the `/speckit.plan` command to provide your tech stack and architecture choices.
+**In the chat**, use the `/speckit.clarify` slash command to identify and resolve ambiguities in your specification. You can provide specific focus areas as arguments.
 
 ```bash
+/speckit.clarify Focus on security and performance requirements.
+```
+
+### Step 5: Create a Technical Implementation Plan
+
+**In the chat**, use the `/speckit.plan` slash command to provide your tech stack and architecture choices.
+
+```markdown
 /speckit.plan The application uses Vite with minimal number of libraries. Use vanilla HTML, CSS, and JavaScript as much as possible. Images are not uploaded anywhere and metadata is stored in a local SQLite database.
 ```
 
-### 4. Break Down and Implement
+### Step 6: Break Down and Implement
 
-Use `/speckit.tasks` to create an actionable task list, then ask your agent to implement the feature.
+**In the chat**, use the `/speckit.tasks` slash command to create an actionable task list.
+
+```markdown
+/speckit.tasks
+```
+
+Optionally, validate the plan with `/speckit.analyze`:
+
+```markdown
+/speckit.analyze
+```
+
+Then, use the `/speckit.implement` slash command to execute the plan.
+
+```markdown
+/speckit.implement
+```
+
+> [!TIP]
+> **Phased Implementation**: For complex projects, implement in phases to avoid overwhelming the agent's context. Start with core functionality, validate it works, then add features incrementally.
 
 ## Detailed Example: Building Taskify
 
 Here's a complete example of building a team productivity platform:
 
-### Step 1: Define Requirements with `/speckit.specify`
+### Step 1: Define Constitution
+
+Initialize the project's constitution to set ground rules:
+
+```markdown
+/speckit.constitution Taskify is a "Security-First" application. All user inputs must be validated. We use a microservices architecture. Code must be fully documented.
+```
+
+### Step 2: Define Requirements with `/speckit.specify`
 
 ```text
 Develop Taskify, a team productivity platform. It should allow users to create projects, add team members,
@@ -54,60 +105,64 @@ let's call it "Create Taskify," let's have multiple users but the users will be
 I want five users in two different categories, one product manager and four engineers. Let's create three
 different sample projects. Let's have the standard Kanban columns for the status of each task, such as "To Do,"
 "In Progress," "In Review," and "Done." There will be no login for this application as this is just the very
-first testing thing to ensure that our basic features are set up. For each task in the UI for a task card,
-you should be able to change the current status of the task between the different columns in the Kanban work board.
-You should be able to leave an unlimited number of comments for a particular card. You should be able to, from that task
-card, assign one of the valid users. When you first launch Taskify, it's going to give you a list of the five users to pick
-from. There will be no password required. When you click on a user, you go into the main view, which displays the list of
-projects. When you click on a project, you open the Kanban board for that project. You're going to see the columns.
-You'll be able to drag and drop cards back and forth between different columns. You will see any cards that are
-assigned to you, the currently logged in user, in a different color from all the other ones, so you can quickly
-see yours. You can edit any comments that you make, but you can't edit comments that other people made. You can
-delete any comments that you made, but you can't delete comments anybody else made.
+first testing thing to ensure that our basic features are set up.
 ```
 
-### Step 2: Refine the Specification
+### Step 3: Refine the Specification
 
-After the initial specification is created, clarify any missing requirements:
+Use the `/speckit.clarify` command to interactively resolve any ambiguities in your specification. You can also provide specific details you want to ensure are included.
 
-```text
-For each sample project or project that you create there should be a variable number of tasks between 5 and 15
-tasks for each one randomly distributed into different states of completion. Make sure that there's at least
-one task in each stage of completion.
+```bash
+/speckit.clarify I want to clarify the task card details. For each task in the UI for a task card, you should be able to change the current status of the task between the different columns in the Kanban work board. You should be able to leave an unlimited number of comments for a particular card. You should be able to, from that task card, assign one of the valid users.
 ```
 
-Also validate the specification checklist:
+You can continue to refine the spec with more details using `/speckit.clarify`:
 
-```text
-Read the review and acceptance checklist, and check off each item in the checklist if the feature spec meets the criteria. Leave it empty if it does not.
+```bash
+/speckit.clarify When you first launch Taskify, it's going to give you a list of the five users to pick from. There will be no password required. When you click on a user, you go into the main view, which displays the list of projects. When you click on a project, you open the Kanban board for that project. You're going to see the columns. You'll be able to drag and drop cards back and forth between different columns. You will see any cards that are assigned to you, the currently logged in user, in a different color from all the other ones, so you can quickly see yours. You can edit any comments that you make, but you can't edit comments that other people made. You can delete any comments that you made, but you can't delete comments anybody else made.
 ```
 
-### Step 3: Generate Technical Plan with `/speckit.plan`
+### Step 4: Validate the Spec
+
+Validate the specification checklist using the `/speckit.checklist` command:
+
+```bash
+/speckit.checklist
+```
+
+### Step 5: Generate Technical Plan with `/speckit.plan`
 
 Be specific about your tech stack and technical requirements:
 
-```text
-We are going to generate this using .NET Aspire, using Postgres as the database. The frontend should use
-Blazor server with drag-and-drop task boards, real-time updates. There should be a REST API created with a projects API,
-tasks API, and a notifications API.
+```bash
+/speckit.plan We are going to generate this using .NET Aspire, using Postgres as the database. The frontend should use Blazor server with drag-and-drop task boards, real-time updates. There should be a REST API created with a projects API, tasks API, and a notifications API.
 ```
 
-### Step 4: Validate and Implement
+### Step 6: Define Tasks
 
-Have your AI agent audit the implementation plan:
+Generate an actionable task list using the `/speckit.tasks` command:
 
-```text
-Now I want you to go and audit the implementation plan and the implementation detail files.
-Read through it with an eye on determining whether or not there is a sequence of tasks that you need
-to be doing that are obvious from reading this. Because I don't know if there's enough here.
+```bash
+/speckit.tasks
+```
+
+### Step 7: Validate and Implement
+
+Have your AI agent audit the implementation plan using `/speckit.analyze`:
+
+```bash
+/speckit.analyze
 ```
 
 Finally, implement the solution:
 
-```text
-implement specs/002-create-taskify/plan.md
+```bash
+/speckit.implement
 ```
 
+> [!TIP]
+> **Phased Implementation**: For large projects like Taskify, consider implementing in phases (e.g., Phase 1: Basic project/task structure, Phase 2: Kanban functionality, Phase 3: Comments and assignments). This prevents context saturation and allows for validation at each stage.
+
 ## Key Principles
 
 - **Be explicit** about what you're building and why
@@ -118,6 +173,6 @@ implement specs/002-create-taskify/plan.md
 
 ## Next Steps
 
-- Read the complete methodology for in-depth guidance
-- Check out more examples in the repository
-- Explore the source code on GitHub
+- Read the [complete methodology](../spec-driven.md) for in-depth guidance
+- Check out [more examples](../templates) in the repository
+- Explore the [source code on GitHub](https://github.com/github/spec-kit)

docs/toc.yml

@@ -9,10 +9,11 @@
       href: installation.md
     - name: Quick Start
       href: quickstart.md
+    - name: Upgrade
+      href: upgrade.md
 
 # Development workflows
 - name: Development
   items:
     - name: Local Development
       href: local-development.md
-

docs/upgrade.md

@@ -0,0 +1,444 @@
+# Upgrade Guide
+
+> You have Spec Kit installed and want to upgrade to the latest version to get new features, bug fixes, or updated slash commands. This guide covers both upgrading the CLI tool and updating your project files.
+
+---
+
+## Quick Reference
+
+| What to Upgrade | Command | When to Use |
+|----------------|---------|-------------|
+| **CLI Tool Only** | `uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git` | Get latest CLI features without touching project files |
+| **Project Files** | `specify init --here --force --ai <your-agent>` | Update slash commands, templates, and scripts in your project |
+| **Both** | Run CLI upgrade, then project update | Recommended for major version updates |
+
+---
+
+## Part 1: Upgrade the CLI Tool
+
+The CLI tool (`specify`) is separate from your project files. Upgrade it to get the latest features and bug fixes.
+
+### If you installed with `uv tool install`
+
+```bash
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+```
+
+### If you use one-shot `uvx` commands
+
+No upgrade needed—`uvx` always fetches the latest version. Just run your commands as normal:
+
+```bash
+uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai copilot
+```
+
+### Verify the upgrade
+
+```bash
+specify check
+```
+
+This shows installed tools and confirms the CLI is working.
+
+---
+
+## Part 2: Updating Project Files
+
+When Spec Kit releases new features (like new slash commands or updated templates), you need to refresh your project's Spec Kit files.
+
+### What gets updated?
+
+Running `specify init --here --force` will update:
+
+- ✅ **Slash command files** (`.claude/commands/`, `.github/prompts/`, etc.)
+- ✅ **Script files** (`.specify/scripts/`)
+- ✅ **Template files** (`.specify/templates/`)
+- ✅ **Shared memory files** (`.specify/memory/`) - **⚠️ See warnings below**
+
+### What stays safe?
+
+These files are **never touched** by the upgrade—the template packages don't even contain them:
+
+- ✅ **Your specifications** (`specs/001-my-feature/spec.md`, etc.) - **CONFIRMED SAFE**
+- ✅ **Your implementation plans** (`specs/001-my-feature/plan.md`, `tasks.md`, etc.) - **CONFIRMED SAFE**
+- ✅ **Your source code** - **CONFIRMED SAFE**
+- ✅ **Your git history** - **CONFIRMED SAFE**
+
+The `specs/` directory is completely excluded from template packages and will never be modified during upgrades.
+
+### Update command
+
+Run this inside your project directory:
+
+```bash
+specify init --here --force --ai <your-agent>
+```
+
+Replace `<your-agent>` with your AI assistant. Refer to this list of [Supported AI Agents](../README.md#-supported-ai-agents)
+
+**Example:**
+
+```bash
+specify init --here --force --ai copilot
+```
+
+### Understanding the `--force` flag
+
+Without `--force`, the CLI warns you and asks for confirmation:
+
+```text
+Warning: Current directory is not empty (25 items)
+Template files will be merged with existing content and may overwrite existing files
+Proceed? [y/N]
+```
+
+With `--force`, it skips the confirmation and proceeds immediately.
+
+**Important: Your `specs/` directory is always safe.** The `--force` flag only affects template files (commands, scripts, templates, memory). Your feature specifications, plans, and tasks in `specs/` are never included in upgrade packages and cannot be overwritten.
+
+---
+
+## ⚠️ Important Warnings
+
+### 1. Constitution file will be overwritten
+
+**Known issue:** `specify init --here --force` currently overwrites `.specify/memory/constitution.md` with the default template, erasing any customizations you made.
+
+**Workaround:**
+
+```bash
+# 1. Back up your constitution before upgrading
+cp .specify/memory/constitution.md .specify/memory/constitution-backup.md
+
+# 2. Run the upgrade
+specify init --here --force --ai copilot
+
+# 3. Restore your customized constitution
+mv .specify/memory/constitution-backup.md .specify/memory/constitution.md
+```
+
+Or use git to restore it:
+
+```bash
+# After upgrade, restore from git history
+git restore .specify/memory/constitution.md
+```
+
+### 2. Custom template modifications
+
+If you customized any templates in `.specify/templates/`, the upgrade will overwrite them. Back them up first:
+
+```bash
+# Back up custom templates
+cp -r .specify/templates .specify/templates-backup
+
+# After upgrade, merge your changes back manually
+```
+
+### 3. Duplicate slash commands (IDE-based agents)
+
+Some IDE-based agents (like Kilo Code, Windsurf) may show **duplicate slash commands** after upgrading—both old and new versions appear.
+
+**Solution:** Manually delete the old command files from your agent's folder.
+
+**Example for Kilo Code:**
+
+```bash
+# Navigate to the agent's commands folder
+cd .kilocode/rules/
+
+# List files and identify duplicates
+ls -la
+
+# Delete old versions (example filenames - yours may differ)
+rm speckit.specify-old.md
+rm speckit.plan-v1.md
+```
+
+Restart your IDE to refresh the command list.
+
+---
+
+## Common Scenarios
+
+### Scenario 1: "I just want new slash commands"
+
+```bash
+# Upgrade CLI (if using persistent install)
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+
+# Update project files to get new commands
+specify init --here --force --ai copilot
+
+# Restore your constitution if customized
+git restore .specify/memory/constitution.md
+```
+
+### Scenario 2: "I customized templates and constitution"
+
+```bash
+# 1. Back up customizations
+cp .specify/memory/constitution.md /tmp/constitution-backup.md
+cp -r .specify/templates /tmp/templates-backup
+
+# 2. Upgrade CLI
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+
+# 3. Update project
+specify init --here --force --ai copilot
+
+# 4. Restore customizations
+mv /tmp/constitution-backup.md .specify/memory/constitution.md
+# Manually merge template changes if needed
+```
+
+### Scenario 3: "I see duplicate slash commands in my IDE"
+
+This happens with IDE-based agents (Kilo Code, Windsurf, Roo Code, etc.).
+
+```bash
+# Find the agent folder (example: .kilocode/rules/)
+cd .kilocode/rules/
+
+# List all files
+ls -la
+
+# Delete old command files
+rm speckit.old-command-name.md
+
+# Restart your IDE
+```
+
+### Scenario 4: "I'm working on a project without Git"
+
+If you initialized your project with `--no-git`, you can still upgrade:
+
+```bash
+# Manually back up files you customized
+cp .specify/memory/constitution.md /tmp/constitution-backup.md
+
+# Run upgrade
+specify init --here --force --ai copilot --no-git
+
+# Restore customizations
+mv /tmp/constitution-backup.md .specify/memory/constitution.md
+```
+
+The `--no-git` flag skips git initialization but doesn't affect file updates.
+
+---
+
+## Using `--no-git` Flag
+
+The `--no-git` flag tells Spec Kit to **skip git repository initialization**. This is useful when:
+
+- You manage version control differently (Mercurial, SVN, etc.)
+- Your project is part of a larger monorepo with existing git setup
+- You're experimenting and don't want version control yet
+
+**During initial setup:**
+
+```bash
+specify init my-project --ai copilot --no-git
+```
+
+**During upgrade:**
+
+```bash
+specify init --here --force --ai copilot --no-git
+```
+
+### What `--no-git` does NOT do
+
+❌ Does NOT prevent file updates
+❌ Does NOT skip slash command installation
+❌ Does NOT affect template merging
+
+It **only** skips running `git init` and creating the initial commit.
+
+### Working without Git
+
+If you use `--no-git`, you'll need to manage feature directories manually:
+
+**Set the `SPECIFY_FEATURE` environment variable** before using planning commands:
+
+```bash
+# Bash/Zsh
+export SPECIFY_FEATURE="001-my-feature"
+
+# PowerShell
+$env:SPECIFY_FEATURE = "001-my-feature"
+```
+
+This tells Spec Kit which feature directory to use when creating specs, plans, and tasks.
+
+**Why this matters:** Without git, Spec Kit can't detect your current branch name to determine the active feature. The environment variable provides that context manually.
+
+---
+
+## Troubleshooting
+
+### "Slash commands not showing up after upgrade"
+
+**Cause:** Agent didn't reload the command files.
+
+**Fix:**
+
+1. **Restart your IDE/editor** completely (not just reload window)
+2. **For CLI-based agents**, verify files exist:
+
+   ```bash
+   ls -la .claude/commands/      # Claude Code
+   ls -la .gemini/commands/       # Gemini
+   ls -la .cursor/commands/       # Cursor
+   ```
+
+3. **Check agent-specific setup:**
+   - Codex requires `CODEX_HOME` environment variable
+   - Some agents need workspace restart or cache clearing
+
+### "I lost my constitution customizations"
+
+**Fix:** Restore from git or backup:
+
+```bash
+# If you committed before upgrading
+git restore .specify/memory/constitution.md
+
+# If you backed up manually
+cp /tmp/constitution-backup.md .specify/memory/constitution.md
+```
+
+**Prevention:** Always commit or back up `constitution.md` before upgrading.
+
+### "Warning: Current directory is not empty"
+
+**Full warning message:**
+
+```text
+Warning: Current directory is not empty (25 items)
+Template files will be merged with existing content and may overwrite existing files
+Do you want to continue? [y/N]
+```
+
+**What this means:**
+
+This warning appears when you run `specify init --here` (or `specify init .`) in a directory that already has files. It's telling you:
+
+1. **The directory has existing content** - In the example, 25 files/folders
+2. **Files will be merged** - New template files will be added alongside your existing files
+3. **Some files may be overwritten** - If you already have Spec Kit files (`.claude/`, `.specify/`, etc.), they'll be replaced with the new versions
+
+**What gets overwritten:**
+
+Only Spec Kit infrastructure files:
+
+- Agent command files (`.claude/commands/`, `.github/prompts/`, etc.)
+- Scripts in `.specify/scripts/`
+- Templates in `.specify/templates/`
+- Memory files in `.specify/memory/` (including constitution)
+
+**What stays untouched:**
+
+- Your `specs/` directory (specifications, plans, tasks)
+- Your source code files
+- Your `.git/` directory and git history
+- Any other files not part of Spec Kit templates
+
+**How to respond:**
+
+- **Type `y` and press Enter** - Proceed with the merge (recommended if upgrading)
+- **Type `n` and press Enter** - Cancel the operation
+- **Use `--force` flag** - Skip this confirmation entirely:
+
+  ```bash
+  specify init --here --force --ai copilot
+  ```
+
+**When you see this warning:**
+
+- ✅ **Expected** when upgrading an existing Spec Kit project
+- ✅ **Expected** when adding Spec Kit to an existing codebase
+- ⚠️ **Unexpected** if you thought you were creating a new project in an empty directory
+
+**Prevention tip:** Before upgrading, commit or back up your `.specify/memory/constitution.md` if you customized it.
+
+### "CLI upgrade doesn't seem to work"
+
+Verify the installation:
+
+```bash
+# Check installed tools
+uv tool list
+
+# Should show specify-cli
+
+# Verify path
+which specify
+
+# Should point to the uv tool installation directory
+```
+
+If not found, reinstall:
+
+```bash
+uv tool uninstall specify-cli
+uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
+```
+
+### "Do I need to run specify every time I open my project?"
+
+**Short answer:** No, you only run `specify init` once per project (or when upgrading).
+
+**Explanation:**
+
+The `specify` CLI tool is used for:
+
+- **Initial setup:** `specify init` to bootstrap Spec Kit in your project
+- **Upgrades:** `specify init --here --force` to update templates and commands
+- **Diagnostics:** `specify check` to verify tool installation
+
+Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/speckit.plan`, etc.) are **permanently installed** in your project's agent folder (`.claude/`, `.github/prompts/`, etc.). Your AI assistant reads these command files directly—no need to run `specify` again.
+
+**If your agent isn't recognizing slash commands:**
+
+1. **Verify command files exist:**
+
+   ```bash
+   # For GitHub Copilot
+   ls -la .github/prompts/
+
+   # For Claude
+   ls -la .claude/commands/
+   ```
+
+2. **Restart your IDE/editor completely** (not just reload window)
+
+3. **Check you're in the correct directory** where you ran `specify init`
+
+4. **For some agents**, you may need to reload the workspace or clear cache
+
+**Related issue:** If Copilot can't open local files or uses PowerShell commands unexpectedly, this is typically an IDE context issue, not related to `specify`. Try:
+
+- Restarting VS Code
+- Checking file permissions
+- Ensuring the workspace folder is properly opened
+
+---
+
+## Version Compatibility
+
+Spec Kit follows semantic versioning for major releases. The CLI and project files are designed to be compatible within the same major version.
+
+**Best practice:** Keep both CLI and project files in sync by upgrading both together during major version changes.
+
+---
+
+## Next Steps
+
+After upgrading:
+
+- **Test new slash commands:** Run `/speckit.constitution` or another command to verify everything works
+- **Review release notes:** Check [GitHub Releases](https://github.com/github/spec-kit/releases) for new features and breaking changes
+- **Update workflows:** If new commands were added, update your team's development workflows
+- **Check documentation:** Visit [github.io/spec-kit](https://github.github.io/spec-kit/) for updated guides

extensions/EXTENSION-API-REFERENCE.md

@@ -0,0 +1,714 @@
+# Extension API Reference
+
+Technical reference for Spec Kit extension system APIs and manifest schema.
+
+## Table of Contents
+
+1. [Extension Manifest](#extension-manifest)
+2. [Python API](#python-api)
+3. [Command File Format](#command-file-format)
+4. [Configuration Schema](#configuration-schema)
+5. [Hook System](#hook-system)
+6. [CLI Commands](#cli-commands)
+
+---
+
+## Extension Manifest
+
+### Schema Version 1.0
+
+File: `extension.yml`
+
+```yaml
+schema_version: "1.0"  # Required
+
+extension:
+  id: string           # Required, pattern: ^[a-z0-9-]+$
+  name: string         # Required, human-readable name
+  version: string      # Required, semantic version (X.Y.Z)
+  description: string  # Required, brief description (<200 chars)
+  author: string       # Required
+  repository: string   # Required, valid URL
+  license: string      # Required (e.g., "MIT", "Apache-2.0")
+  homepage: string     # Optional, valid URL
+
+requires:
+  speckit_version: string  # Required, version specifier (>=X.Y.Z)
+  tools:                   # Optional, array of tool requirements
+    - name: string         # Tool name
+      version: string      # Optional, version specifier
+      required: boolean    # Optional, default: false
+
+provides:
+  commands:              # Required, at least one command
+    - name: string       # Required, pattern: ^speckit\.[a-z0-9-]+\.[a-z0-9-]+$
+      file: string       # Required, relative path to command file
+      description: string # Required
+      aliases: [string]  # Optional, array of alternate names
+
+  config:                # Optional, array of config files
+    - name: string       # Config file name
+      template: string   # Template file path
+      description: string
+      required: boolean  # Default: false
+
+hooks:                   # Optional, event hooks
+  event_name:            # e.g., "after_tasks", "after_implement"
+    command: string      # Command to execute
+    optional: boolean    # Default: true
+    prompt: string       # Prompt text for optional hooks
+    description: string  # Hook description
+    condition: string    # Optional, condition expression
+
+tags:                    # Optional, array of tags (2-10 recommended)
+  - string
+
+defaults:                # Optional, default configuration values
+  key: value             # Any YAML structure
+```
+
+### Field Specifications
+
+#### `extension.id`
+
+- **Type**: string
+- **Pattern**: `^[a-z0-9-]+$`
+- **Description**: Unique extension identifier
+- **Examples**: `jira`, `linear`, `azure-devops`
+- **Invalid**: `Jira`, `my_extension`, `extension.id`
+
+#### `extension.version`
+
+- **Type**: string
+- **Format**: Semantic versioning (X.Y.Z)
+- **Description**: Extension version
+- **Examples**: `1.0.0`, `0.9.5`, `2.1.3`
+- **Invalid**: `v1.0`, `1.0`, `1.0.0-beta`
+
+#### `requires.speckit_version`
+
+- **Type**: string
+- **Format**: Version specifier
+- **Description**: Required spec-kit version range
+- **Examples**:
+  - `>=0.1.0` - Any version 0.1.0 or higher
+  - `>=0.1.0,<2.0.0` - Version 0.1.x or 1.x
+  - `==0.1.0` - Exactly 0.1.0
+- **Invalid**: `0.1.0`, `>= 0.1.0` (space), `latest`
+
+#### `provides.commands[].name`
+
+- **Type**: string
+- **Pattern**: `^speckit\.[a-z0-9-]+\.[a-z0-9-]+$`
+- **Description**: Namespaced command name
+- **Format**:  `speckit.{extension-id}.{command-name}`
+- **Examples**: `speckit.jira.specstoissues`, `speckit.linear.sync`
+- **Invalid**: `jira.specstoissues`, `speckit.command`, `speckit.jira.CreateIssues`
+
+#### `hooks`
+
+- **Type**: object
+- **Keys**: Event names (e.g., `after_tasks`, `after_implement`, `before_commit`)
+- **Description**: Hooks that execute at lifecycle events
+- **Events**: Defined by core spec-kit commands
+
+---
+
+## Python API
+
+### ExtensionManifest
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionManifest
+
+manifest = ExtensionManifest(Path("extension.yml"))
+```
+
+**Properties**:
+
+```python
+manifest.id                        # str: Extension ID
+manifest.name                      # str: Extension name
+manifest.version                   # str: Version
+manifest.description               # str: Description
+manifest.requires_speckit_version  # str: Required spec-kit version
+manifest.commands                  # List[Dict]: Command definitions
+manifest.hooks                     # Dict: Hook definitions
+```
+
+**Methods**:
+
+```python
+manifest.get_hash()  # str: SHA256 hash of manifest file
+```
+
+**Exceptions**:
+
+```python
+ValidationError       # Invalid manifest structure
+CompatibilityError    # Incompatible with current spec-kit version
+```
+
+### ExtensionRegistry
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionRegistry
+
+registry = ExtensionRegistry(extensions_dir)
+```
+
+**Methods**:
+
+```python
+# Add extension to registry
+registry.add(extension_id: str, metadata: dict)
+
+# Remove extension from registry
+registry.remove(extension_id: str)
+
+# Get extension metadata
+metadata = registry.get(extension_id: str)  # Optional[dict]
+
+# List all extensions
+extensions = registry.list()  # Dict[str, dict]
+
+# Check if installed
+is_installed = registry.is_installed(extension_id: str)  # bool
+```
+
+**Registry Format**:
+
+```json
+{
+  "schema_version": "1.0",
+  "extensions": {
+    "jira": {
+      "version": "1.0.0",
+      "source": "catalog",
+      "manifest_hash": "sha256...",
+      "enabled": true,
+      "registered_commands": ["speckit.jira.specstoissues", ...],
+      "installed_at": "2026-01-28T..."
+    }
+  }
+}
+```
+
+### ExtensionManager
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionManager
+
+manager = ExtensionManager(project_root)
+```
+
+**Methods**:
+
+```python
+# Install from directory
+manifest = manager.install_from_directory(
+    source_dir: Path,
+    speckit_version: str,
+    register_commands: bool = True
+)  # Returns: ExtensionManifest
+
+# Install from ZIP
+manifest = manager.install_from_zip(
+    zip_path: Path,
+    speckit_version: str
+)  # Returns: ExtensionManifest
+
+# Remove extension
+success = manager.remove(
+    extension_id: str,
+    keep_config: bool = False
+)  # Returns: bool
+
+# List installed extensions
+extensions = manager.list_installed()  # List[Dict]
+
+# Get extension manifest
+manifest = manager.get_extension(extension_id: str)  # Optional[ExtensionManifest]
+
+# Check compatibility
+manager.check_compatibility(
+    manifest: ExtensionManifest,
+    speckit_version: str
+)  # Raises: CompatibilityError if incompatible
+```
+
+### ExtensionCatalog
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionCatalog
+
+catalog = ExtensionCatalog(project_root)
+```
+
+**Methods**:
+
+```python
+# Fetch catalog
+catalog_data = catalog.fetch_catalog(force_refresh: bool = False)  # Dict
+
+# Search extensions
+results = catalog.search(
+    query: Optional[str] = None,
+    tag: Optional[str] = None,
+    author: Optional[str] = None,
+    verified_only: bool = False
+)  # Returns: List[Dict]
+
+# Get extension info
+ext_info = catalog.get_extension_info(extension_id: str)  # Optional[Dict]
+
+# Check cache validity
+is_valid = catalog.is_cache_valid()  # bool
+
+# Clear cache
+catalog.clear_cache()
+```
+
+### HookExecutor
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import HookExecutor
+
+hook_executor = HookExecutor(project_root)
+```
+
+**Methods**:
+
+```python
+# Get project config
+config = hook_executor.get_project_config()  # Dict
+
+# Save project config
+hook_executor.save_project_config(config: Dict)
+
+# Register hooks
+hook_executor.register_hooks(manifest: ExtensionManifest)
+
+# Unregister hooks
+hook_executor.unregister_hooks(extension_id: str)
+
+# Get hooks for event
+hooks = hook_executor.get_hooks_for_event(event_name: str)  # List[Dict]
+
+# Check if hook should execute
+should_run = hook_executor.should_execute_hook(hook: Dict)  # bool
+
+# Format hook message
+message = hook_executor.format_hook_message(
+    event_name: str,
+    hooks: List[Dict]
+)  # str
+```
+
+### CommandRegistrar
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import CommandRegistrar
+
+registrar = CommandRegistrar()
+```
+
+**Methods**:
+
+```python
+# Register commands for Claude Code
+registered = registrar.register_commands_for_claude(
+    manifest: ExtensionManifest,
+    extension_dir: Path,
+    project_root: Path
+)  # Returns: List[str] (command names)
+
+# Parse frontmatter
+frontmatter, body = registrar.parse_frontmatter(content: str)
+
+# Render frontmatter
+yaml_text = registrar.render_frontmatter(frontmatter: Dict)  # str
+```
+
+---
+
+## Command File Format
+
+### Universal Command Format
+
+**File**: `commands/{command-name}.md`
+
+```markdown
+---
+description: "Command description"
+tools:
+  - 'mcp-server/tool_name'
+  - 'other-mcp-server/other_tool'
+---
+
+# Command Title
+
+Command documentation in Markdown.
+
+## Prerequisites
+
+1. Requirement 1
+2. Requirement 2
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+### Step 1: Description
+
+Instruction text...
+
+\`\`\`bash
+# Shell commands
+\`\`\`
+
+### Step 2: Another Step
+
+More instructions...
+
+## Configuration Reference
+
+Information about configuration options.
+
+## Notes
+
+Additional notes and tips.
+```
+
+### Frontmatter Fields
+
+```yaml
+description: string   # Required, brief command description
+tools: [string]       # Optional, MCP tools required
+```
+
+### Special Variables
+
+- `$ARGUMENTS` - Placeholder for user-provided arguments
+- Extension context automatically injected:
+
+  ```markdown
+  <!-- Extension: {extension-id} -->
+  <!-- Config: .specify/extensions/{extension-id}/ -->
+  ```
+
+---
+
+## Configuration Schema
+
+### Extension Config File
+
+**File**: `.specify/extensions/{extension-id}/{extension-id}-config.yml`
+
+Extensions define their own config schema. Common patterns:
+
+```yaml
+# Connection settings
+connection:
+  url: string
+  api_key: string
+
+# Project settings
+project:
+  key: string
+  workspace: string
+
+# Feature flags
+features:
+  enabled: boolean
+  auto_sync: boolean
+
+# Defaults
+defaults:
+  labels: [string]
+  assignee: string
+
+# Custom fields
+field_mappings:
+  internal_name: "external_field_id"
+```
+
+### Config Layers
+
+1. **Extension Defaults** (from `extension.yml` `defaults` section)
+2. **Project Config** (`{extension-id}-config.yml`)
+3. **Local Override** (`{extension-id}-config.local.yml`, gitignored)
+4. **Environment Variables** (`SPECKIT_{EXTENSION}_*`)
+
+### Environment Variable Pattern
+
+Format: `SPECKIT_{EXTENSION}_{KEY}`
+
+Examples:
+
+- `SPECKIT_JIRA_PROJECT_KEY`
+- `SPECKIT_LINEAR_API_KEY`
+- `SPECKIT_GITHUB_TOKEN`
+
+---
+
+## Hook System
+
+### Hook Definition
+
+**In extension.yml**:
+
+```yaml
+hooks:
+  after_tasks:
+    command: "speckit.jira.specstoissues"
+    optional: true
+    prompt: "Create Jira issues from tasks?"
+    description: "Automatically create Jira hierarchy"
+    condition: null
+```
+
+### Hook Events
+
+Standard events (defined by core):
+
+- `after_tasks` - After task generation
+- `after_implement` - After implementation
+- `before_commit` - Before git commit
+- `after_commit` - After git commit
+
+### Hook Configuration
+
+**In `.specify/extensions.yml`**:
+
+```yaml
+hooks:
+  after_tasks:
+    - extension: jira
+      command: speckit.jira.specstoissues
+      enabled: true
+      optional: true
+      prompt: "Create Jira issues from tasks?"
+      description: "..."
+      condition: null
+```
+
+### Hook Message Format
+
+```markdown
+## Extension Hooks
+
+**Optional Hook**: {extension}
+Command: `/{command}`
+Description: {description}
+
+Prompt: {prompt}
+To execute: `/{command}`
+```
+
+Or for mandatory hooks:
+
+```markdown
+**Automatic Hook**: {extension}
+Executing: `/{command}`
+EXECUTE_COMMAND: {command}
+```
+
+---
+
+## CLI Commands
+
+### extension list
+
+**Usage**: `specify extension list [OPTIONS]`
+
+**Options**:
+
+- `--available` - Show available extensions from catalog
+- `--all` - Show both installed and available
+
+**Output**: List of installed extensions with metadata
+
+### extension add
+
+**Usage**: `specify extension add EXTENSION [OPTIONS]`
+
+**Options**:
+
+- `--from URL` - Install from custom URL
+- `--dev PATH` - Install from local directory
+- `--version VERSION` - Install specific version
+- `--no-register` - Skip command registration
+
+**Arguments**:
+
+- `EXTENSION` - Extension name or URL
+
+### extension remove
+
+**Usage**: `specify extension remove EXTENSION [OPTIONS]`
+
+**Options**:
+
+- `--keep-config` - Preserve config files
+- `--force` - Skip confirmation
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension search
+
+**Usage**: `specify extension search [QUERY] [OPTIONS]`
+
+**Options**:
+
+- `--tag TAG` - Filter by tag
+- `--author AUTHOR` - Filter by author
+- `--verified` - Show only verified extensions
+
+**Arguments**:
+
+- `QUERY` - Optional search query
+
+### extension info
+
+**Usage**: `specify extension info EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension update
+
+**Usage**: `specify extension update [EXTENSION]`
+
+**Arguments**:
+
+- `EXTENSION` - Optional, extension ID (default: all)
+
+### extension enable
+
+**Usage**: `specify extension enable EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension disable
+
+**Usage**: `specify extension disable EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+---
+
+## Exceptions
+
+### ValidationError
+
+Raised when extension manifest validation fails.
+
+```python
+from specify_cli.extensions import ValidationError
+
+try:
+    manifest = ExtensionManifest(path)
+except ValidationError as e:
+    print(f"Invalid manifest: {e}")
+```
+
+### CompatibilityError
+
+Raised when extension is incompatible with current spec-kit version.
+
+```python
+from specify_cli.extensions import CompatibilityError
+
+try:
+    manager.check_compatibility(manifest, "0.1.0")
+except CompatibilityError as e:
+    print(f"Incompatible: {e}")
+```
+
+### ExtensionError
+
+Base exception for all extension-related errors.
+
+```python
+from specify_cli.extensions import ExtensionError
+
+try:
+    manager.install_from_directory(path, "0.1.0")
+except ExtensionError as e:
+    print(f"Extension error: {e}")
+```
+
+---
+
+## Version Functions
+
+### version_satisfies
+
+Check if a version satisfies a specifier.
+
+```python
+from specify_cli.extensions import version_satisfies
+
+# True if 1.2.3 satisfies >=1.0.0,<2.0.0
+satisfied = version_satisfies("1.2.3", ">=1.0.0,<2.0.0")  # bool
+```
+
+---
+
+## File System Layout
+
+```text
+.specify/
+├── extensions/
+│   ├── .registry               # Extension registry (JSON)
+│   ├── .cache/                 # Catalog cache
+│   │   ├── catalog.json
+│   │   └── catalog-metadata.json
+│   ├── .backup/                # Config backups
+│   │   └── {ext}-{config}.yml
+│   ├── {extension-id}/         # Extension directory
+│   │   ├── extension.yml       # Manifest
+│   │   ├── {ext}-config.yml    # User config
+│   │   ├── {ext}-config.local.yml  # Local overrides (gitignored)
+│   │   ├── {ext}-config.template.yml  # Template
+│   │   ├── commands/           # Command files
+│   │   │   └── *.md
+│   │   ├── scripts/            # Helper scripts
+│   │   │   └── *.sh
+│   │   ├── docs/               # Documentation
+│   │   └── README.md
+│   └── extensions.yml          # Project extension config
+└── scripts/                    # (existing spec-kit)
+
+.claude/
+└── commands/
+    └── speckit.{ext}.{cmd}.md  # Registered commands
+```
+
+---
+
+*Last Updated: 2026-01-28*
+*API Version: 1.0*
+*Spec Kit Version: 0.1.0*

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -0,0 +1,649 @@
+# Extension Development Guide
+
+A guide for creating Spec Kit extensions.
+
+---
+
+## Quick Start
+
+### 1. Create Extension Directory
+
+```bash
+mkdir my-extension
+cd my-extension
+```
+
+### 2. Create `extension.yml` Manifest
+
+```yaml
+schema_version: "1.0"
+
+extension:
+  id: "my-ext"                          # Lowercase, alphanumeric + hyphens only
+  name: "My Extension"
+  version: "1.0.0"                      # Semantic versioning
+  description: "My custom extension"
+  author: "Your Name"
+  repository: "https://github.com/you/spec-kit-my-ext"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"            # Minimum spec-kit version
+  tools:                                # Optional: External tools required
+    - name: "my-tool"
+      required: true
+      version: ">=1.0.0"
+  commands:                             # Optional: Core commands needed
+    - "speckit.tasks"
+
+provides:
+  commands:
+    - name: "speckit.my-ext.hello"      # Must follow pattern: speckit.{ext-id}.{cmd}
+      file: "commands/hello.md"
+      description: "Say hello"
+      aliases: ["speckit.hello"]        # Optional aliases
+
+  config:                               # Optional: Config files
+    - name: "my-ext-config.yml"
+      template: "my-ext-config.template.yml"
+      description: "Extension configuration"
+      required: false
+
+hooks:                                  # Optional: Integration hooks
+  after_tasks:
+    command: "speckit.my-ext.hello"
+    optional: true
+    prompt: "Run hello command?"
+
+tags:                                   # Optional: For catalog search
+  - "example"
+  - "utility"
+```
+
+### 3. Create Commands Directory
+
+```bash
+mkdir commands
+```
+
+### 4. Create Command File
+
+**File**: `commands/hello.md`
+
+```markdown
+---
+description: "Say hello command"
+tools:                              # Optional: AI tools this command uses
+  - 'some-tool/function'
+scripts:                            # Optional: Helper scripts
+  sh: ../../scripts/bash/helper.sh
+  ps: ../../scripts/powershell/helper.ps1
+---
+
+# Hello Command
+
+This command says hello!
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+1. Greet the user
+2. Show extension is working
+
+```bash
+echo "Hello from my extension!"
+echo "Arguments: $ARGUMENTS"
+```
+
+## Extension Configuration
+
+Load extension config from `.specify/extensions/my-ext/my-ext-config.yml`.
+
+### 5. Test Locally
+
+```bash
+cd /path/to/spec-kit-project
+specify extension add --dev /path/to/my-extension
+```
+
+### 6. Verify Installation
+
+```bash
+specify extension list
+
+# Should show:
+#  ✓ My Extension (v1.0.0)
+#     My custom extension
+#     Commands: 1 | Hooks: 1 | Status: Enabled
+```
+
+### 7. Test Command
+
+If using Claude:
+
+```bash
+claude
+> /speckit.my-ext.hello world
+```
+
+The command will be available in `.claude/commands/speckit.my-ext.hello.md`.
+
+---
+
+## Manifest Schema Reference
+
+### Required Fields
+
+#### `schema_version`
+
+Extension manifest schema version. Currently: `"1.0"`
+
+#### `extension`
+
+Extension metadata block.
+
+**Required sub-fields**:
+
+- `id`: Extension identifier (lowercase, alphanumeric, hyphens)
+- `name`: Human-readable name
+- `version`: Semantic version (e.g., "1.0.0")
+- `description`: Short description
+
+**Optional sub-fields**:
+
+- `author`: Extension author
+- `repository`: Source code URL
+- `license`: SPDX license identifier
+- `homepage`: Extension homepage URL
+
+#### `requires`
+
+Compatibility requirements.
+
+**Required sub-fields**:
+
+- `speckit_version`: Semantic version specifier (e.g., ">=0.1.0,<2.0.0")
+
+**Optional sub-fields**:
+
+- `tools`: External tools required (array of tool objects)
+- `commands`: Core spec-kit commands needed (array of command names)
+- `scripts`: Core scripts required (array of script names)
+
+#### `provides`
+
+What the extension provides.
+
+**Required sub-fields**:
+
+- `commands`: Array of command objects (must have at least one)
+
+**Command object**:
+
+- `name`: Command name (must match `speckit.{ext-id}.{command}`)
+- `file`: Path to command file (relative to extension root)
+- `description`: Command description (optional)
+- `aliases`: Alternative command names (optional, array)
+
+### Optional Fields
+
+#### `hooks`
+
+Integration hooks for automatic execution.
+
+Available hook points:
+
+- `after_tasks`: After `/speckit.tasks` completes
+- `after_implement`: After `/speckit.implement` completes (future)
+
+Hook object:
+
+- `command`: Command to execute (must be in `provides.commands`)
+- `optional`: If true, prompt user before executing
+- `prompt`: Prompt text for optional hooks
+- `description`: Hook description
+- `condition`: Execution condition (future)
+
+#### `tags`
+
+Array of tags for catalog discovery.
+
+#### `defaults`
+
+Default extension configuration values.
+
+#### `config_schema`
+
+JSON Schema for validating extension configuration.
+
+---
+
+## Command File Format
+
+### Frontmatter (YAML)
+
+```yaml
+---
+description: "Command description"          # Required
+tools:                                      # Optional
+  - 'tool-name/function'
+scripts:                                    # Optional
+  sh: ../../scripts/bash/helper.sh
+  ps: ../../scripts/powershell/helper.ps1
+---
+```
+
+### Body (Markdown)
+
+Use standard Markdown with special placeholders:
+
+- `$ARGUMENTS`: User-provided arguments
+- `{SCRIPT}`: Replaced with script path during registration
+
+**Example**:
+
+````markdown
+## Steps
+
+1. Parse arguments
+2. Execute logic
+
+```bash
+args="$ARGUMENTS"
+echo "Running with args: $args"
+```
+````
+
+### Script Path Rewriting
+
+Extension commands use relative paths that get rewritten during registration:
+
+**In extension**:
+
+```yaml
+scripts:
+  sh: ../../scripts/bash/helper.sh
+```
+
+**After registration**:
+
+```yaml
+scripts:
+  sh: .specify/scripts/bash/helper.sh
+```
+
+This allows scripts to reference core spec-kit scripts.
+
+---
+
+## Configuration Files
+
+### Config Template
+
+**File**: `my-ext-config.template.yml`
+
+```yaml
+# My Extension Configuration
+# Copy this to my-ext-config.yml and customize
+
+# Example configuration
+api:
+  endpoint: "https://api.example.com"
+  timeout: 30
+
+features:
+  feature_a: true
+  feature_b: false
+
+credentials:
+  # DO NOT commit credentials!
+  # Use environment variables instead
+  api_key: "${MY_EXT_API_KEY}"
+```
+
+### Config Loading
+
+In your command, load config with layered precedence:
+
+1. Extension defaults (`extension.yml` → `defaults`)
+2. Project config (`.specify/extensions/my-ext/my-ext-config.yml`)
+3. Local overrides (`.specify/extensions/my-ext/my-ext-config.local.yml` - gitignored)
+4. Environment variables (`SPECKIT_MY_EXT_*`)
+
+**Example loading script**:
+
+```bash
+#!/usr/bin/env bash
+EXT_DIR=".specify/extensions/my-ext"
+
+# Load and merge config
+config=$(yq eval '.' "$EXT_DIR/my-ext-config.yml" -o=json)
+
+# Apply env overrides
+if [ -n "${SPECKIT_MY_EXT_API_KEY:-}" ]; then
+  config=$(echo "$config" | jq ".api.api_key = \"$SPECKIT_MY_EXT_API_KEY\"")
+fi
+
+echo "$config"
+```
+
+---
+
+## Validation Rules
+
+### Extension ID
+
+- **Pattern**: `^[a-z0-9-]+$`
+- **Valid**: `my-ext`, `tool-123`, `awesome-plugin`
+- **Invalid**: `MyExt` (uppercase), `my_ext` (underscore), `my ext` (space)
+
+### Extension Version
+
+- **Format**: Semantic versioning (MAJOR.MINOR.PATCH)
+- **Valid**: `1.0.0`, `0.1.0`, `2.5.3`
+- **Invalid**: `1.0`, `v1.0.0`, `1.0.0-beta`
+
+### Command Name
+
+- **Pattern**: `^speckit\.[a-z0-9-]+\.[a-z0-9-]+$`
+- **Valid**: `speckit.my-ext.hello`, `speckit.tool.cmd`
+- **Invalid**: `my-ext.hello` (missing prefix), `speckit.hello` (no extension namespace)
+
+### Command File Path
+
+- **Must be** relative to extension root
+- **Valid**: `commands/hello.md`, `commands/subdir/cmd.md`
+- **Invalid**: `/absolute/path.md`, `../outside.md`
+
+---
+
+## Testing Extensions
+
+### Manual Testing
+
+1. **Create test extension**
+2. **Install locally**:
+
+   ```bash
+   specify extension add --dev /path/to/extension
+   ```
+
+3. **Verify installation**:
+
+   ```bash
+   specify extension list
+   ```
+
+4. **Test commands** with your AI agent
+5. **Check command registration**:
+
+   ```bash
+   ls .claude/commands/speckit.my-ext.*
+   ```
+
+6. **Remove extension**:
+
+   ```bash
+   specify extension remove my-ext
+   ```
+
+### Automated Testing
+
+Create tests for your extension:
+
+```python
+# tests/test_my_extension.py
+import pytest
+from pathlib import Path
+from specify_cli.extensions import ExtensionManifest
+
+def test_manifest_valid():
+    """Test extension manifest is valid."""
+    manifest = ExtensionManifest(Path("extension.yml"))
+    assert manifest.id == "my-ext"
+    assert len(manifest.commands) >= 1
+
+def test_command_files_exist():
+    """Test all command files exist."""
+    manifest = ExtensionManifest(Path("extension.yml"))
+    for cmd in manifest.commands:
+        cmd_file = Path(cmd["file"])
+        assert cmd_file.exists(), f"Command file not found: {cmd_file}"
+```
+
+---
+
+## Distribution
+
+### Option 1: GitHub Repository
+
+1. **Create repository**: `spec-kit-my-ext`
+2. **Add files**:
+
+   ```text
+   spec-kit-my-ext/
+   ├── extension.yml
+   ├── commands/
+   ├── scripts/
+   ├── docs/
+   ├── README.md
+   ├── LICENSE
+   └── CHANGELOG.md
+   ```
+
+3. **Create release**: Tag with version (e.g., `v1.0.0`)
+4. **Install from repo**:
+
+   ```bash
+   git clone https://github.com/you/spec-kit-my-ext
+   specify extension add --dev spec-kit-my-ext/
+   ```
+
+### Option 2: ZIP Archive (Future)
+
+Create ZIP archive and host on GitHub Releases:
+
+```bash
+zip -r spec-kit-my-ext-1.0.0.zip extension.yml commands/ scripts/ docs/
+```
+
+Users install with:
+
+```bash
+specify extension add --from https://github.com/.../spec-kit-my-ext-1.0.0.zip
+```
+
+### Option 3: Extension Catalog (Future)
+
+Submit to official catalog:
+
+1. **Fork** spec-kit repository
+2. **Add entry** to `extensions/catalog.json`
+3. **Create PR**
+4. **After merge**, users can install with:
+
+   ```bash
+   specify extension add my-ext  # No URL needed!
+   ```
+
+---
+
+## Best Practices
+
+### Naming Conventions
+
+- **Extension ID**: Use descriptive, hyphenated names (`jira-integration`, not `ji`)
+- **Commands**: Use verb-noun pattern (`create-issue`, `sync-status`)
+- **Config files**: Match extension ID (`jira-config.yml`)
+
+### Documentation
+
+- **README.md**: Overview, installation, usage
+- **CHANGELOG.md**: Version history
+- **docs/**: Detailed guides
+- **Command descriptions**: Clear, concise
+
+### Versioning
+
+- **Follow SemVer**: `MAJOR.MINOR.PATCH`
+- **MAJOR**: Breaking changes
+- **MINOR**: New features
+- **PATCH**: Bug fixes
+
+### Security
+
+- **Never commit secrets**: Use environment variables
+- **Validate input**: Sanitize user arguments
+- **Document permissions**: What files/APIs are accessed
+
+### Compatibility
+
+- **Specify version range**: Don't require exact version
+- **Test with multiple versions**: Ensure compatibility
+- **Graceful degradation**: Handle missing features
+
+---
+
+## Example Extensions
+
+### Minimal Extension
+
+Smallest possible extension:
+
+```yaml
+# extension.yml
+schema_version: "1.0"
+extension:
+  id: "minimal"
+  name: "Minimal Extension"
+  version: "1.0.0"
+  description: "Minimal example"
+requires:
+  speckit_version: ">=0.1.0"
+provides:
+  commands:
+    - name: "speckit.minimal.hello"
+      file: "commands/hello.md"
+```
+
+````markdown
+<!-- commands/hello.md -->
+---
+description: "Hello command"
+---
+
+# Hello World
+
+```bash
+echo "Hello, $ARGUMENTS!"
+```
+````
+
+### Extension with Config
+
+Extension using configuration:
+
+```yaml
+# extension.yml
+# ... metadata ...
+provides:
+  config:
+    - name: "tool-config.yml"
+      template: "tool-config.template.yml"
+      required: true
+```
+
+```yaml
+# tool-config.template.yml
+api_endpoint: "https://api.example.com"
+timeout: 30
+```
+
+````markdown
+<!-- commands/use-config.md -->
+# Use Config
+
+Load config:
+```bash
+config_file=".specify/extensions/tool/tool-config.yml"
+endpoint=$(yq eval '.api_endpoint' "$config_file")
+echo "Using endpoint: $endpoint"
+```
+````
+
+### Extension with Hooks
+
+Extension that runs automatically:
+
+```yaml
+# extension.yml
+hooks:
+  after_tasks:
+    command: "speckit.auto.analyze"
+    optional: false  # Always run
+    description: "Analyze tasks after generation"
+```
+
+---
+
+## Troubleshooting
+
+### Extension won't install
+
+**Error**: `Invalid extension ID`
+
+- **Fix**: Use lowercase, alphanumeric + hyphens only
+
+**Error**: `Extension requires spec-kit >=0.2.0`
+
+- **Fix**: Update spec-kit with `uv tool install specify-cli --force`
+
+**Error**: `Command file not found`
+
+- **Fix**: Ensure command files exist at paths specified in manifest
+
+### Commands not registered
+
+**Symptom**: Commands don't appear in AI agent
+
+**Check**:
+
+1. `.claude/commands/` directory exists
+2. Extension installed successfully
+3. Commands registered in registry:
+
+   ```bash
+   cat .specify/extensions/.registry
+   ```
+
+**Fix**: Reinstall extension to trigger registration
+
+### Config not loading
+
+**Check**:
+
+1. Config file exists: `.specify/extensions/{ext-id}/{ext-id}-config.yml`
+2. YAML syntax is valid: `yq eval '.' config.yml`
+3. Environment variables set correctly
+
+---
+
+## Getting Help
+
+- **Issues**: Report bugs at GitHub repository
+- **Discussions**: Ask questions in GitHub Discussions
+- **Examples**: See `spec-kit-jira` for full-featured example (Phase B)
+
+---
+
+## Next Steps
+
+1. **Create your extension** following this guide
+2. **Test locally** with `--dev` flag
+3. **Share with community** (GitHub, catalog)
+4. **Iterate** based on feedback
+
+Happy extending! 🚀

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -0,0 +1,530 @@
+# Extension Publishing Guide
+
+This guide explains how to publish your extension to the Spec Kit extension catalog, making it discoverable by `specify extension search`.
+
+## Table of Contents
+
+1. [Prerequisites](#prerequisites)
+2. [Prepare Your Extension](#prepare-your-extension)
+3. [Submit to Catalog](#submit-to-catalog)
+4. [Verification Process](#verification-process)
+5. [Release Workflow](#release-workflow)
+6. [Best Practices](#best-practices)
+
+---
+
+## Prerequisites
+
+Before publishing an extension, ensure you have:
+
+1. **Valid Extension**: A working extension with a valid `extension.yml` manifest
+2. **Git Repository**: Extension hosted on GitHub (or other public git hosting)
+3. **Documentation**: README.md with installation and usage instructions
+4. **License**: Open source license file (MIT, Apache 2.0, etc.)
+5. **Versioning**: Semantic versioning (e.g., 1.0.0)
+6. **Testing**: Extension tested on real projects
+
+---
+
+## Prepare Your Extension
+
+### 1. Extension Structure
+
+Ensure your extension follows the standard structure:
+
+```text
+your-extension/
+├── extension.yml              # Required: Extension manifest
+├── README.md                  # Required: Documentation
+├── LICENSE                    # Required: License file
+├── CHANGELOG.md               # Recommended: Version history
+├── .gitignore                 # Recommended: Git ignore rules
+│
+├── commands/                  # Extension commands
+│   ├── command1.md
+│   └── command2.md
+│
+├── config-template.yml        # Config template (if needed)
+│
+└── docs/                      # Additional documentation
+    ├── usage.md
+    └── examples/
+```
+
+### 2. extension.yml Validation
+
+Verify your manifest is valid:
+
+```yaml
+schema_version: "1.0"
+
+extension:
+  id: "your-extension"           # Unique lowercase-hyphenated ID
+  name: "Your Extension Name"     # Human-readable name
+  version: "1.0.0"                # Semantic version
+  description: "Brief description (one sentence)"
+  author: "Your Name or Organization"
+  repository: "https://github.com/your-org/spec-kit-your-extension"
+  license: "MIT"
+  homepage: "https://github.com/your-org/spec-kit-your-extension"
+
+requires:
+  speckit_version: ">=0.1.0"    # Required spec-kit version
+
+provides:
+  commands:                       # List all commands
+    - name: "speckit.your-extension.command"
+      file: "commands/command.md"
+      description: "Command description"
+
+tags:                             # 2-5 relevant tags
+  - "category"
+  - "tool-name"
+```
+
+**Validation Checklist**:
+
+- ✅ `id` is lowercase with hyphens only (no underscores, spaces, or special characters)
+- ✅ `version` follows semantic versioning (X.Y.Z)
+- ✅ `description` is concise (under 100 characters)
+- ✅ `repository` URL is valid and public
+- ✅ All command files exist in the extension directory
+- ✅ Tags are lowercase and descriptive
+
+### 3. Create GitHub Release
+
+Create a GitHub release for your extension version:
+
+```bash
+# Tag the release
+git tag v1.0.0
+git push origin v1.0.0
+
+# Create release on GitHub
+# Go to: https://github.com/your-org/spec-kit-your-extension/releases/new
+# - Tag: v1.0.0
+# - Title: v1.0.0 - Release Name
+# - Description: Changelog/release notes
+```
+
+The release archive URL will be:
+
+```text
+https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+```
+
+### 4. Test Installation
+
+Test that users can install from your release:
+
+```bash
+# Test dev installation
+specify extension add --dev /path/to/your-extension
+
+# Test from GitHub archive
+specify extension add --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+```
+
+---
+
+## Submit to Catalog
+
+### 1. Fork the spec-kit Repository
+
+```bash
+# Fork on GitHub
+# https://github.com/statsperform/spec-kit/fork
+
+# Clone your fork
+git clone https://github.com/YOUR-USERNAME/spec-kit.git
+cd spec-kit
+```
+
+### 2. Add Extension to Catalog
+
+Edit `extensions/catalog.json` and add your extension:
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-01-28T15:54:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/statsperform/spec-kit/main/extensions/catalog.json",
+  "extensions": {
+    "your-extension": {
+      "name": "Your Extension Name",
+      "id": "your-extension",
+      "description": "Brief description of your extension",
+      "author": "Your Name",
+      "version": "1.0.0",
+      "download_url": "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-your-extension",
+      "homepage": "https://github.com/your-org/spec-kit-your-extension",
+      "documentation": "https://github.com/your-org/spec-kit-your-extension/blob/main/docs/",
+      "changelog": "https://github.com/your-org/spec-kit-your-extension/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "required-mcp-tool",
+            "version": ">=1.0.0",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": [
+        "category",
+        "tool-name",
+        "feature"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-01-28T00:00:00Z",
+      "updated_at": "2026-01-28T00:00:00Z"
+    }
+  }
+}
+```
+
+**Important**:
+
+- Set `verified: false` (maintainers will verify)
+- Set `downloads: 0` and `stars: 0` (auto-updated later)
+- Use current timestamp for `created_at` and `updated_at`
+- Update the top-level `updated_at` to current time
+
+### 3. Submit Pull Request
+
+```bash
+# Create a branch
+git checkout -b add-your-extension
+
+# Commit your changes
+git add extensions/catalog.json
+git commit -m "Add your-extension to catalog
+
+- Extension ID: your-extension
+- Version: 1.0.0
+- Author: Your Name
+- Description: Brief description
+"
+
+# Push to your fork
+git push origin add-your-extension
+
+# Create Pull Request on GitHub
+# https://github.com/statsperform/spec-kit/compare
+```
+
+**Pull Request Template**:
+
+```markdown
+## Extension Submission
+
+**Extension Name**: Your Extension Name
+**Extension ID**: your-extension
+**Version**: 1.0.0
+**Author**: Your Name
+**Repository**: https://github.com/your-org/spec-kit-your-extension
+
+### Description
+Brief description of what your extension does.
+
+### Checklist
+- [x] Valid extension.yml manifest
+- [x] README.md with installation and usage docs
+- [x] LICENSE file included
+- [x] GitHub release created (v1.0.0)
+- [x] Extension tested on real project
+- [x] All commands working
+- [x] No security vulnerabilities
+
+### Testing
+Tested on:
+- macOS 13.0+ with spec-kit 0.1.0
+- Project: [Your test project]
+
+### Additional Notes
+Any additional context or notes for reviewers.
+```
+
+---
+
+## Verification Process
+
+### What Happens After Submission
+
+1. **Automated Checks** (if available):
+   - Manifest validation
+   - Download URL accessibility
+   - Repository existence
+   - License file presence
+
+2. **Manual Review**:
+   - Code quality review
+   - Security audit
+   - Functionality testing
+   - Documentation review
+
+3. **Verification**:
+   - If approved, `verified: true` is set
+   - Extension appears in `specify extension search --verified`
+
+### Verification Criteria
+
+To be verified, your extension must:
+
+✅ **Functionality**:
+
+- Works as described in documentation
+- All commands execute without errors
+- No breaking changes to user workflows
+
+✅ **Security**:
+
+- No known vulnerabilities
+- No malicious code
+- Safe handling of user data
+- Proper validation of inputs
+
+✅ **Code Quality**:
+
+- Clean, readable code
+- Follows extension best practices
+- Proper error handling
+- Helpful error messages
+
+✅ **Documentation**:
+
+- Clear installation instructions
+- Usage examples
+- Troubleshooting section
+- Accurate description
+
+✅ **Maintenance**:
+
+- Active repository
+- Responsive to issues
+- Regular updates
+- Semantic versioning followed
+
+### Typical Review Timeline
+
+- **Automated checks**: Immediate (if implemented)
+- **Manual review**: 3-7 business days
+- **Verification**: After successful review
+
+---
+
+## Release Workflow
+
+### Publishing New Versions
+
+When releasing a new version:
+
+1. **Update version** in `extension.yml`:
+
+   ```yaml
+   extension:
+     version: "1.1.0"  # Updated version
+   ```
+
+2. **Update CHANGELOG.md**:
+
+   ```markdown
+   ## [1.1.0] - 2026-02-15
+
+   ### Added
+   - New feature X
+
+   ### Fixed
+   - Bug fix Y
+   ```
+
+3. **Create GitHub release**:
+
+   ```bash
+   git tag v1.1.0
+   git push origin v1.1.0
+   # Create release on GitHub
+   ```
+
+4. **Update catalog**:
+
+   ```bash
+   # Fork spec-kit repo (or update existing fork)
+   cd spec-kit
+
+   # Update extensions/catalog.json
+   jq '.extensions["your-extension"].version = "1.1.0"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.extensions["your-extension"].download_url = "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.1.0.zip"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.extensions["your-extension"].updated_at = "2026-02-15T00:00:00Z"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.updated_at = "2026-02-15T00:00:00Z"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+
+   # Submit PR
+   git checkout -b update-your-extension-v1.1.0
+   git add extensions/catalog.json
+   git commit -m "Update your-extension to v1.1.0"
+   git push origin update-your-extension-v1.1.0
+   ```
+
+5. **Submit update PR** with changelog in description
+
+---
+
+## Best Practices
+
+### Extension Design
+
+1. **Single Responsibility**: Each extension should focus on one tool/integration
+2. **Clear Naming**: Use descriptive, unambiguous names
+3. **Minimal Dependencies**: Avoid unnecessary dependencies
+4. **Backward Compatibility**: Follow semantic versioning strictly
+
+### Documentation
+
+1. **README.md Structure**:
+   - Overview and features
+   - Installation instructions
+   - Configuration guide
+   - Usage examples
+   - Troubleshooting
+   - Contributing guidelines
+
+2. **Command Documentation**:
+   - Clear description
+   - Prerequisites listed
+   - Step-by-step instructions
+   - Error handling guidance
+   - Examples
+
+3. **Configuration**:
+   - Provide template file
+   - Document all options
+   - Include examples
+   - Explain defaults
+
+### Security
+
+1. **Input Validation**: Validate all user inputs
+2. **No Hardcoded Secrets**: Never include credentials
+3. **Safe Dependencies**: Only use trusted dependencies
+4. **Audit Regularly**: Check for vulnerabilities
+
+### Maintenance
+
+1. **Respond to Issues**: Address issues within 1-2 weeks
+2. **Regular Updates**: Keep dependencies updated
+3. **Changelog**: Maintain detailed changelog
+4. **Deprecation**: Give advance notice for breaking changes
+
+### Community
+
+1. **License**: Use permissive open-source license (MIT, Apache 2.0)
+2. **Contributing**: Welcome contributions
+3. **Code of Conduct**: Be respectful and inclusive
+4. **Support**: Provide ways to get help (issues, discussions, email)
+
+---
+
+## FAQ
+
+### Q: Can I publish private/proprietary extensions?
+
+A: The main catalog is for public extensions only. For private extensions:
+
+- Host your own catalog.json file
+- Users add your catalog: `specify extension add-catalog https://your-domain.com/catalog.json`
+- Not yet implemented - coming in Phase 4
+
+### Q: How long does verification take?
+
+A: Typically 3-7 business days for initial review. Updates to verified extensions are usually faster.
+
+### Q: What if my extension is rejected?
+
+A: You'll receive feedback on what needs to be fixed. Make the changes and resubmit.
+
+### Q: Can I update my extension anytime?
+
+A: Yes, submit a PR to update the catalog with your new version. Verified status may be re-evaluated for major changes.
+
+### Q: Do I need to be verified to be in the catalog?
+
+A: No, unverified extensions are still searchable. Verification just adds trust and visibility.
+
+### Q: Can extensions have paid features?
+
+A: Extensions should be free and open-source. Commercial support/services are allowed, but core functionality must be free.
+
+---
+
+## Support
+
+- **Catalog Issues**: <https://github.com/statsperform/spec-kit/issues>
+- **Extension Template**: <https://github.com/statsperform/spec-kit-extension-template> (coming soon)
+- **Development Guide**: See EXTENSION-DEVELOPMENT-GUIDE.md
+- **Community**: Discussions and Q&A
+
+---
+
+## Appendix: Catalog Schema
+
+### Complete Catalog Entry Schema
+
+```json
+{
+  "name": "string (required)",
+  "id": "string (required, unique)",
+  "description": "string (required, <200 chars)",
+  "author": "string (required)",
+  "version": "string (required, semver)",
+  "download_url": "string (required, valid URL)",
+  "repository": "string (required, valid URL)",
+  "homepage": "string (optional, valid URL)",
+  "documentation": "string (optional, valid URL)",
+  "changelog": "string (optional, valid URL)",
+  "license": "string (required)",
+  "requires": {
+    "speckit_version": "string (required, version specifier)",
+    "tools": [
+      {
+        "name": "string (required)",
+        "version": "string (optional, version specifier)",
+        "required": "boolean (default: false)"
+      }
+    ]
+  },
+  "provides": {
+    "commands": "integer (optional)",
+    "hooks": "integer (optional)"
+  },
+  "tags": ["array of strings (2-10 tags)"],
+  "verified": "boolean (default: false)",
+  "downloads": "integer (auto-updated)",
+  "stars": "integer (auto-updated)",
+  "created_at": "string (ISO 8601 datetime)",
+  "updated_at": "string (ISO 8601 datetime)"
+}
+```
+
+### Valid Tags
+
+Recommended tag categories:
+
+- **Integration**: jira, linear, github, gitlab, azure-devops
+- **Category**: issue-tracking, vcs, ci-cd, documentation, testing
+- **Platform**: atlassian, microsoft, google
+- **Feature**: automation, reporting, deployment, monitoring
+
+Use 2-5 tags that best describe your extension.
+
+---
+
+*Last Updated: 2026-01-28*
+*Catalog Format Version: 1.0*

extensions/EXTENSION-USER-GUIDE.md

@@ -0,0 +1,885 @@
+# Extension User Guide
+
+Complete guide for using Spec Kit extensions to enhance your workflow.
+
+## Table of Contents
+
+1. [Introduction](#introduction)
+2. [Getting Started](#getting-started)
+3. [Finding Extensions](#finding-extensions)
+4. [Installing Extensions](#installing-extensions)
+5. [Using Extensions](#using-extensions)
+6. [Managing Extensions](#managing-extensions)
+7. [Configuration](#configuration)
+8. [Troubleshooting](#troubleshooting)
+9. [Best Practices](#best-practices)
+
+---
+
+## Introduction
+
+### What are Extensions?
+
+Extensions are modular packages that add new commands and functionality to Spec Kit without bloating the core framework. They allow you to:
+
+- **Integrate** with external tools (Jira, Linear, GitHub, etc.)
+- **Automate** repetitive tasks with hooks
+- **Customize** workflows for your team
+- **Share** solutions across projects
+
+### Why Use Extensions?
+
+- **Clean Core**: Keeps spec-kit lightweight and focused
+- **Optional Features**: Only install what you need
+- **Community Driven**: Anyone can create and share extensions
+- **Version Controlled**: Extensions are versioned independently
+
+---
+
+## Getting Started
+
+### Prerequisites
+
+- Spec Kit version 0.1.0 or higher
+- A spec-kit project (directory with `.specify/` folder)
+
+### Check Your Version
+
+```bash
+specify version
+# Should show 0.1.0 or higher
+```
+
+### First Extension
+
+Let's install the Jira extension as an example:
+
+```bash
+# 1. Search for the extension
+specify extension search jira
+
+# 2. Get detailed information
+specify extension info jira
+
+# 3. Install it
+specify extension add jira
+
+# 4. Configure it
+vim .specify/extensions/jira/jira-config.yml
+
+# 5. Use it
+# (Commands are now available in Claude Code)
+/speckit.jira.specstoissues
+```
+
+---
+
+## Finding Extensions
+
+### Browse All Extensions
+
+```bash
+specify extension search
+```
+
+Shows all available extensions in the catalog.
+
+### Search by Keyword
+
+```bash
+# Search for "jira"
+specify extension search jira
+
+# Search for "issue tracking"
+specify extension search issue
+```
+
+### Filter by Tag
+
+```bash
+# Find all issue-tracking extensions
+specify extension search --tag issue-tracking
+
+# Find all Atlassian tools
+specify extension search --tag atlassian
+```
+
+### Filter by Author
+
+```bash
+# Extensions by Stats Perform
+specify extension search --author "Stats Perform"
+```
+
+### Show Verified Only
+
+```bash
+# Only show verified extensions
+specify extension search --verified
+```
+
+### Get Extension Details
+
+```bash
+# Detailed information
+specify extension info jira
+```
+
+Shows:
+
+- Description
+- Requirements
+- Commands provided
+- Hooks available
+- Links (documentation, repository, changelog)
+- Installation status
+
+---
+
+## Installing Extensions
+
+### Install from Catalog
+
+```bash
+# By name (from catalog)
+specify extension add jira
+```
+
+This will:
+
+1. Download the extension from GitHub
+2. Validate the manifest
+3. Check compatibility with your spec-kit version
+4. Install to `.specify/extensions/jira/`
+5. Register commands with your AI agent
+6. Create config template
+
+### Install from URL
+
+```bash
+# From GitHub release
+specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
+```
+
+### Install from Local Directory (Development)
+
+```bash
+# For testing or development
+specify extension add --dev /path/to/extension
+```
+
+### Installation Output
+
+```text
+✓ Extension installed successfully!
+
+Jira Integration (v1.0.0)
+  Create Jira Epics, Stories, and Issues from spec-kit artifacts
+
+Provided commands:
+  • speckit.jira.specstoissues - Create Jira hierarchy from spec and tasks
+  • speckit.jira.discover-fields - Discover Jira custom fields for configuration
+  • speckit.jira.sync-status - Sync task completion status to Jira
+
+⚠  Configuration may be required
+   Check: .specify/extensions/jira/
+```
+
+---
+
+## Using Extensions
+
+### Using Extension Commands
+
+Extensions add commands that appear in your AI agent (Claude Code):
+
+```text
+# In Claude Code
+> /speckit.jira.specstoissues
+
+# Or use short alias (if provided)
+> /speckit.specstoissues
+```
+
+### Extension Configuration
+
+Most extensions require configuration:
+
+```bash
+# 1. Find the config file
+ls .specify/extensions/jira/
+
+# 2. Copy template to config
+cp .specify/extensions/jira/jira-config.template.yml \
+   .specify/extensions/jira/jira-config.yml
+
+# 3. Edit configuration
+vim .specify/extensions/jira/jira-config.yml
+
+# 4. Use the extension
+# (Commands will now work with your config)
+```
+
+### Extension Hooks
+
+Some extensions provide hooks that execute after core commands:
+
+**Example**: Jira extension hooks into `/speckit.tasks`
+
+```text
+# Run core command
+> /speckit.tasks
+
+# Output includes:
+## Extension Hooks
+
+**Optional Hook**: jira
+Command: `/speckit.jira.specstoissues`
+Description: Automatically create Jira hierarchy after task generation
+
+Prompt: Create Jira issues from tasks?
+To execute: `/speckit.jira.specstoissues`
+```
+
+You can then choose to run the hook or skip it.
+
+---
+
+## Managing Extensions
+
+### List Installed Extensions
+
+```bash
+specify extension list
+```
+
+Output:
+
+```text
+Installed Extensions:
+
+  ✓ Jira Integration (v1.0.0)
+     Create Jira Epics, Stories, and Issues from spec-kit artifacts
+     Commands: 3 | Hooks: 1 | Status: Enabled
+```
+
+### Update Extensions
+
+```bash
+# Check for updates (all extensions)
+specify extension update
+
+# Update specific extension
+specify extension update jira
+```
+
+Output:
+
+```text
+🔄 Checking for updates...
+
+Updates available:
+
+  • jira: 1.0.0 → 1.1.0
+
+Update these extensions? [y/N]:
+```
+
+### Disable Extension Temporarily
+
+```bash
+# Disable without removing
+specify extension disable jira
+
+✓ Extension 'jira' disabled
+
+Commands will no longer be available. Hooks will not execute.
+To re-enable: specify extension enable jira
+```
+
+### Re-enable Extension
+
+```bash
+specify extension enable jira
+
+✓ Extension 'jira' enabled
+```
+
+### Remove Extension
+
+```bash
+# Remove extension (with confirmation)
+specify extension remove jira
+
+# Keep configuration when removing
+specify extension remove jira --keep-config
+
+# Force removal (no confirmation)
+specify extension remove jira --force
+```
+
+---
+
+## Configuration
+
+### Configuration Files
+
+Extensions can have multiple configuration files:
+
+```text
+.specify/extensions/jira/
+├── jira-config.yml           # Main config (version controlled)
+├── jira-config.local.yml     # Local overrides (gitignored)
+└── jira-config.template.yml  # Template (reference)
+```
+
+### Configuration Layers
+
+Configuration is merged in this order (highest priority last):
+
+1. **Extension defaults** (from `extension.yml`)
+2. **Project config** (`jira-config.yml`)
+3. **Local overrides** (`jira-config.local.yml`)
+4. **Environment variables** (`SPECKIT_JIRA_*`)
+
+### Example: Jira Configuration
+
+**Project config** (`.specify/extensions/jira/jira-config.yml`):
+
+```yaml
+project:
+  key: "MSATS"
+
+defaults:
+  epic:
+    labels: ["spec-driven"]
+```
+
+**Local override** (`.specify/extensions/jira/jira-config.local.yml`):
+
+```yaml
+project:
+  key: "MYTEST"  # Override for local development
+```
+
+**Environment variable**:
+
+```bash
+export SPECKIT_JIRA_PROJECT_KEY="DEVTEST"
+```
+
+Final resolved config uses `DEVTEST` from environment variable.
+
+### Project-Wide Extension Settings
+
+File: `.specify/extensions.yml`
+
+```yaml
+# Extensions installed in this project
+installed:
+  - jira
+  - linear
+
+# Global settings
+settings:
+  auto_execute_hooks: true
+
+# Hook configuration
+hooks:
+  after_tasks:
+    - extension: jira
+      command: speckit.jira.specstoissues
+      enabled: true
+      optional: true
+      prompt: "Create Jira issues from tasks?"
+```
+
+### Core Environment Variables
+
+In addition to extension-specific environment variables (`SPECKIT_{EXT_ID}_*`), spec-kit supports core environment variables:
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `SPECKIT_CATALOG_URL`       | Override the extension catalog URL | GitHub-hosted catalog |
+| `GH_TOKEN` / `GITHUB_TOKEN` | GitHub API token for downloads     | None                  |
+
+#### Example: Using a custom catalog for testing
+
+```bash
+# Point to a local or alternative catalog
+export SPECKIT_CATALOG_URL="http://localhost:8000/catalog.json"
+
+# Or use a staging catalog
+export SPECKIT_CATALOG_URL="https://example.com/staging/catalog.json"
+```
+
+---
+
+## Organization Catalog Customization
+
+### Why the Default Catalog is Empty
+
+The default spec-kit catalog ships empty by design. This allows organizations to:
+
+- **Control available extensions** - Curate which extensions your team can install
+- **Host private extensions** - Internal tools that shouldn't be public
+- **Customize for compliance** - Meet security/audit requirements
+- **Support air-gapped environments** - Work without internet access
+
+### Setting Up a Custom Catalog
+
+#### 1. Create Your Catalog File
+
+Create a `catalog.json` file with your extensions:
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-03T00:00:00Z",
+  "catalog_url": "https://your-org.com/spec-kit/catalog.json",
+  "extensions": {
+    "jira": {
+      "name": "Jira Integration",
+      "id": "jira",
+      "description": "Create Jira issues from spec-kit artifacts",
+      "author": "Your Organization",
+      "version": "2.1.0",
+      "download_url": "https://github.com/your-org/spec-kit-jira/archive/refs/tags/v2.1.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-jira",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {"name": "atlassian-mcp-server", "required": true}
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": ["jira", "atlassian", "issue-tracking"],
+      "verified": true
+    },
+    "internal-tool": {
+      "name": "Internal Tool Integration",
+      "id": "internal-tool",
+      "description": "Connect to internal company systems",
+      "author": "Your Organization",
+      "version": "1.0.0",
+      "download_url": "https://internal.your-org.com/extensions/internal-tool-1.0.0.zip",
+      "repository": "https://github.internal.your-org.com/spec-kit-internal",
+      "license": "Proprietary",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 2
+      },
+      "tags": ["internal", "proprietary"],
+      "verified": true
+    }
+  }
+}
+```
+
+#### 2. Host the Catalog
+
+Options for hosting your catalog:
+
+| Method | URL Example | Use Case |
+| ------ | ----------- | -------- |
+| GitHub Pages | `https://your-org.github.io/spec-kit-catalog/catalog.json` | Public or org-visible |
+| Internal web server | `https://internal.company.com/spec-kit/catalog.json` | Corporate network |
+| S3/Cloud storage | `https://s3.amazonaws.com/your-bucket/catalog.json` | Cloud-hosted teams |
+| Local file server | `http://localhost:8000/catalog.json` | Development/testing |
+
+**Security requirement**: URLs must use HTTPS (except `localhost` for testing).
+
+#### 3. Configure Your Environment
+
+##### Option A: Environment variable (recommended for CI/CD)
+
+```bash
+# In ~/.bashrc, ~/.zshrc, or CI pipeline
+export SPECKIT_CATALOG_URL="https://your-org.com/spec-kit/catalog.json"
+```
+
+##### Option B: Per-project configuration
+
+Create `.env` or set in your shell before running spec-kit commands:
+
+```bash
+SPECKIT_CATALOG_URL="https://your-org.com/spec-kit/catalog.json" specify extension search
+```
+
+#### 4. Verify Configuration
+
+```bash
+# Search should now show your catalog's extensions
+specify extension search
+
+# Install from your catalog
+specify extension add jira
+```
+
+### Catalog JSON Schema
+
+Required fields for each extension entry:
+
+| Field | Type | Required | Description |
+| ----- | ---- | -------- | ----------- |
+| `name` | string | Yes | Human-readable name |
+| `id` | string | Yes | Unique identifier (lowercase, hyphens) |
+| `version` | string | Yes | Semantic version (X.Y.Z) |
+| `download_url` | string | Yes | URL to ZIP archive |
+| `repository` | string | Yes | Source code URL |
+| `description` | string | No | Brief description |
+| `author` | string | No | Author/organization |
+| `license` | string | No | SPDX license identifier |
+| `requires.speckit_version` | string | No | Version constraint |
+| `requires.tools` | array | No | Required external tools |
+| `provides.commands` | number | No | Number of commands |
+| `provides.hooks` | number | No | Number of hooks |
+| `tags` | array | No | Search tags |
+| `verified` | boolean | No | Verification status |
+
+### Use Cases
+
+#### Private/Internal Extensions
+
+Host proprietary extensions that integrate with internal systems:
+
+```json
+{
+  "internal-auth": {
+    "name": "Internal SSO Integration",
+    "download_url": "https://artifactory.company.com/spec-kit/internal-auth-1.0.0.zip",
+    "verified": true
+  }
+}
+```
+
+#### Curated Team Catalog
+
+Limit which extensions your team can install:
+
+```json
+{
+  "extensions": {
+    "jira": { "..." },
+    "github": { "..." }
+  }
+}
+```
+
+Only `jira` and `github` will appear in `specify extension search`.
+
+#### Air-Gapped Environments
+
+For networks without internet access:
+
+1. Download extension ZIPs to internal file server
+2. Create catalog pointing to internal URLs
+3. Host catalog on internal web server
+
+```json
+{
+  "jira": {
+    "download_url": "https://files.internal/spec-kit/jira-2.1.0.zip"
+  }
+}
+```
+
+#### Development/Testing
+
+Test new extensions before publishing:
+
+```bash
+# Start local server
+python -m http.server 8000 --directory ./my-catalog/
+
+# Point spec-kit to local catalog
+export SPECKIT_CATALOG_URL="http://localhost:8000/catalog.json"
+
+# Test installation
+specify extension add my-new-extension
+```
+
+### Combining with Direct Installation
+
+You can still install extensions not in your catalog using `--from`:
+
+```bash
+# From catalog
+specify extension add jira
+
+# Direct URL (bypasses catalog)
+specify extension add --from https://github.com/someone/spec-kit-ext/archive/v1.0.0.zip
+
+# Local development
+specify extension add --dev /path/to/extension
+```
+
+**Note**: Direct URL installation shows a security warning since the extension isn't from your configured catalog.
+
+---
+
+## Troubleshooting
+
+### Extension Not Found
+
+**Error**: `Extension 'jira' not found in catalog
+
+**Solutions**:
+
+1. Check spelling: `specify extension search jira`
+2. Refresh catalog: `specify extension search --help`
+3. Check internet connection
+4. Extension may not be published yet
+
+### Configuration Not Found
+
+**Error**: `Jira configuration not found`
+
+**Solutions**:
+
+1. Check if extension is installed: `specify extension list`
+2. Create config from template:
+
+   ```bash
+   cp .specify/extensions/jira/jira-config.template.yml \
+      .specify/extensions/jira/jira-config.yml
+   ```
+
+3. Reinstall extension: `specify extension remove jira && specify extension add jira`
+
+### Command Not Available
+
+**Issue**: Extension command not appearing in AI agent
+
+**Solutions**:
+
+1. Check extension is enabled: `specify extension list`
+2. Restart AI agent (Claude Code)
+3. Check command file exists:
+
+   ```bash
+   ls .claude/commands/speckit.jira.*.md
+   ```
+
+4. Reinstall extension
+
+### Incompatible Version
+
+**Error**: `Extension requires spec-kit >=0.2.0, but you have 0.1.0`
+
+**Solutions**:
+
+1. Upgrade spec-kit:
+
+   ```bash
+   uv tool upgrade specify-cli
+   ```
+
+2. Install older version of extension:
+
+   ```bash
+   specify extension add --from https://github.com/org/ext/archive/v1.0.0.zip
+   ```
+
+### MCP Tool Not Available
+
+**Error**: `Tool 'jira-mcp-server/epic_create' not found`
+
+**Solutions**:
+
+1. Check MCP server is installed
+2. Check AI agent MCP configuration
+3. Restart AI agent
+4. Check extension requirements: `specify extension info jira`
+
+### Permission Denied
+
+**Error**: `Permission denied` when accessing Jira
+
+**Solutions**:
+
+1. Check Jira credentials in MCP server config
+2. Verify project permissions in Jira
+3. Test MCP server connection independently
+
+---
+
+## Best Practices
+
+### 1. Version Control
+
+**Do commit**:
+
+- `.specify/extensions.yml` (project extension config)
+- `.specify/extensions/*/jira-config.yml` (project config)
+
+**Don't commit**:
+
+- `.specify/extensions/.cache/` (catalog cache)
+- `.specify/extensions/.backup/` (config backups)
+- `.specify/extensions/*/*.local.yml` (local overrides)
+- `.specify/extensions/.registry` (installation state)
+
+Add to `.gitignore`:
+
+```gitignore
+.specify/extensions/.cache/
+.specify/extensions/.backup/
+.specify/extensions/*/*.local.yml
+.specify/extensions/.registry
+```
+
+### 2. Team Workflows
+
+**For teams**:
+
+1. Agree on which extensions to use
+2. Commit extension configuration
+3. Document extension usage in README
+4. Keep extensions updated together
+
+**Example README section**:
+
+```markdown
+## Extensions
+
+This project uses:
+- **jira** (v1.0.0) - Jira integration
+  - Config: `.specify/extensions/jira/jira-config.yml`
+  - Requires: jira-mcp-server
+
+To install: `specify extension add jira`
+```
+
+### 3. Local Development
+
+Use local config for development:
+
+```yaml
+# .specify/extensions/jira/jira-config.local.yml
+project:
+  key: "DEVTEST"  # Your test project
+
+defaults:
+  task:
+    custom_fields:
+      customfield_10002: 1  # Lower story points for testing
+```
+
+### 4. Environment-Specific Config
+
+Use environment variables for CI/CD:
+
+```bash
+# .github/workflows/deploy.yml
+env:
+  SPECKIT_JIRA_PROJECT_KEY: ${{ secrets.JIRA_PROJECT }}
+
+- name: Create Jira Issues
+  run: specify extension add jira && ...
+```
+
+### 5. Extension Updates
+
+**Check for updates regularly**:
+
+```bash
+# Weekly or before major releases
+specify extension update
+```
+
+**Pin versions for stability**:
+
+```yaml
+# .specify/extensions.yml
+installed:
+  - id: jira
+    version: "1.0.0"  # Pin to specific version
+```
+
+### 6. Minimal Extensions
+
+Only install extensions you actively use:
+
+- Reduces complexity
+- Faster command loading
+- Less configuration
+
+### 7. Documentation
+
+Document extension usage in your project:
+
+```markdown
+# PROJECT.md
+
+## Working with Jira
+
+After creating tasks, sync to Jira:
+1. Run `/speckit.tasks` to generate tasks
+2. Run `/speckit.jira.specstoissues` to create Jira issues
+3. Run `/speckit.jira.sync-status` to update status
+```
+
+---
+
+## FAQ
+
+### Q: Can I use multiple extensions at once?
+
+**A**: Yes! Extensions are designed to work together. Install as many as you need.
+
+### Q: Do extensions slow down spec-kit?
+
+**A**: No. Extensions are loaded on-demand and only when their commands are used.
+
+### Q: Can I create private extensions?
+
+**A**: Yes. Install with `--dev` or `--from` and keep private. Public catalog submission is optional.
+
+### Q: How do I know if an extension is safe?
+
+**A**: Look for the ✓ Verified badge. Verified extensions are reviewed by maintainers. Always review extension code before installing.
+
+### Q: Can extensions modify spec-kit core?
+
+**A**: No. Extensions can only add commands and hooks. They cannot modify core functionality.
+
+### Q: What happens if two extensions have the same command name?
+
+**A**: Extensions use namespaced commands (`speckit.{extension}.{command}`), so conflicts are very rare. The extension system will warn you if conflicts occur.
+
+### Q: Can I contribute to existing extensions?
+
+**A**: Yes! Most extensions are open source. Check the repository link in `specify extension info {extension}`.
+
+### Q: How do I report extension bugs?
+
+**A**: Go to the extension's repository (shown in `specify extension info`) and create an issue.
+
+### Q: Can extensions work offline?
+
+**A**: Once installed, extensions work offline. However, some extensions may require internet for their functionality (e.g., Jira requires Jira API access).
+
+### Q: How do I backup my extension configuration?
+
+**A**: Extension configs are in `.specify/extensions/{extension}/`. Back up this directory or commit configs to git.
+
+---
+
+## Support
+
+- **Extension Issues**: Report to extension repository (see `specify extension info`)
+- **Spec Kit Issues**: <https://github.com/statsperform/spec-kit/issues>
+- **Extension Catalog**: <https://github.com/statsperform/spec-kit/tree/main/extensions>
+- **Documentation**: See EXTENSION-DEVELOPMENT-GUIDE.md and EXTENSION-PUBLISHING-GUIDE.md
+
+---
+
+*Last Updated: 2026-01-28*
+*Spec Kit Version: 0.1.0*

extensions/README.md

@@ -0,0 +1,14 @@
+# Spec Kit Community Extensions
+
+Community-contributed extensions for [Spec Kit](https://github.com/github/spec-kit).
+
+## Available Extensions
+
+| Extension | Purpose | URL |
+|-----------|---------|-----|
+| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
+| Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
+
+## Adding Your Extension
+
+See the [Extension Publishing Guide](EXTENSION-PUBLISHING-GUIDE.md) for instructions on how to submit your extension to the community catalog.

extensions/catalog.community.json

@@ -0,0 +1,85 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-24T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
+  "extensions": {
+    "cleanup": {
+      "name": "Cleanup Extension",
+      "id": "cleanup",
+      "description": "Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues.",
+      "author": "dsrednicki",
+      "version": "1.0.0",
+      "download_url": "https://github.com/dsrednicki/spec-kit-cleanup/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/dsrednicki/spec-kit-cleanup",
+      "homepage": "https://github.com/dsrednicki/spec-kit-cleanup",
+      "documentation": "https://github.com/dsrednicki/spec-kit-cleanup/blob/main/README.md",
+      "changelog": "https://github.com/dsrednicki/spec-kit-cleanup/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 1
+      },
+      "tags": ["quality", "tech-debt", "review", "cleanup", "scout-rule"],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-02-22T00:00:00Z",
+      "updated_at": "2026-02-22T00:00:00Z"
+    },
+    "retrospective": {
+      "name": "Retrospective Extension",
+      "id": "retrospective",
+      "description": "Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates.",
+      "author": "emi-dm",
+      "version": "1.0.0",
+      "download_url": "https://github.com/emi-dm/spec-kit-retrospective/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/emi-dm/spec-kit-retrospective",
+      "homepage": "https://github.com/emi-dm/spec-kit-retrospective",
+      "documentation": "https://github.com/emi-dm/spec-kit-retrospective/blob/main/README.md",
+      "changelog": "https://github.com/emi-dm/spec-kit-retrospective/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 1
+      },
+      "tags": ["retrospective", "spec-drift", "quality", "analysis", "governance"],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-02-24T00:00:00Z",
+      "updated_at": "2026-02-24T00:00:00Z"
+    },
+    "v-model": {
+      "name": "V-Model Extension Pack",
+      "id": "v-model",
+      "description": "Enforces V-Model paired generation of development specs and test specs with full traceability.",
+      "author": "leocamello",
+      "version": "0.4.0",
+      "download_url": "https://github.com/leocamello/spec-kit-v-model/archive/refs/tags/v0.4.0.zip",
+      "repository": "https://github.com/leocamello/spec-kit-v-model",
+      "homepage": "https://github.com/leocamello/spec-kit-v-model",
+      "documentation": "https://github.com/leocamello/spec-kit-v-model/blob/main/README.md",
+      "changelog": "https://github.com/leocamello/spec-kit-v-model/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 9,
+        "hooks": 1
+      },
+      "tags": ["v-model", "traceability", "testing", "compliance", "safety-critical"],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-02-20T00:00:00Z",
+      "updated_at": "2026-02-22T00:00:00Z"
+    }
+  }
+}

extensions/catalog.json

@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-03T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.json",
+  "extensions": {}
+}

extensions/template/.gitignore

@@ -0,0 +1,39 @@
+# Local configuration overrides
+*-config.local.yml
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log
+
+# Build artifacts
+dist/
+build/
+*.egg-info/
+
+# Temporary files
+*.tmp
+.cache/

extensions/template/CHANGELOG.md

@@ -0,0 +1,39 @@
+# Changelog
+
+All notable changes to this extension will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to  [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Planned
+
+- Feature ideas for future versions
+- Enhancements
+- Bug fixes
+
+## [1.0.0] - YYYY-MM-DD
+
+### Added
+
+- Initial release of extension
+- Command: `/speckit.my-extension.example` - Example command functionality
+- Configuration system with template
+- Documentation and examples
+
+### Features
+
+- Feature 1 description
+- Feature 2 description
+- Feature 3 description
+
+### Requirements
+
+- Spec Kit: >=0.1.0
+- External dependencies (if any)
+
+---
+
+[Unreleased]: https://github.com/your-org/spec-kit-my-extension/compare/v1.0.0...HEAD
+[1.0.0]: https://github.com/your-org/spec-kit-my-extension/releases/tag/v1.0.0

extensions/template/EXAMPLE-README.md

@@ -0,0 +1,158 @@
+# EXAMPLE: Extension README
+
+This is an example of what your extension README should look like after customization.
+**Delete this file and replace README.md with content similar to this.**
+
+---
+
+# My Extension
+
+<!-- CUSTOMIZE: Replace with your extension description -->
+
+Brief description of what your extension does and why it's useful.
+
+## Features
+
+<!-- CUSTOMIZE: List key features -->
+
+- Feature 1: Description
+- Feature 2: Description
+- Feature 3: Description
+
+## Installation
+
+```bash
+# Install from catalog
+specify extension add my-extension
+
+# Or install from local development directory
+specify extension add --dev /path/to/my-extension
+```
+
+## Configuration
+
+1. Create configuration file:
+
+   ```bash
+   cp .specify/extensions/my-extension/config-template.yml \
+      .specify/extensions/my-extension/my-extension-config.yml
+   ```
+
+2. Edit configuration:
+
+   ```bash
+   vim .specify/extensions/my-extension/my-extension-config.yml
+   ```
+
+3. Set required values:
+   <!-- CUSTOMIZE: List required configuration -->
+   ```yaml
+   connection:
+     url: "https://api.example.com"
+     api_key: "your-api-key"
+
+   project:
+     id: "your-project-id"
+   ```
+
+## Usage
+
+<!-- CUSTOMIZE: Add usage examples -->
+
+### Command: example
+
+Description of what this command does.
+
+```bash
+# In Claude Code
+> /speckit.my-extension.example
+```
+
+**Prerequisites**:
+
+- Prerequisite 1
+- Prerequisite 2
+
+**Output**:
+
+- What this command produces
+- Where results are saved
+
+## Configuration Reference
+
+<!-- CUSTOMIZE: Document all configuration options -->
+
+### Connection Settings
+
+| Setting | Type | Required | Description |
+|---------|------|----------|-------------|
+| `connection.url` | string | Yes | API endpoint URL |
+| `connection.api_key` | string | Yes | API authentication key |
+
+### Project Settings
+
+| Setting | Type | Required | Description |
+|---------|------|----------|-------------|
+| `project.id` | string | Yes | Project identifier |
+| `project.workspace` | string | No | Workspace or organization |
+
+## Environment Variables
+
+Override configuration with environment variables:
+
+```bash
+# Override connection settings
+export SPECKIT_MY_EXTENSION_CONNECTION_URL="https://custom-api.com"
+export SPECKIT_MY_EXTENSION_CONNECTION_API_KEY="custom-key"
+```
+
+## Examples
+
+<!-- CUSTOMIZE: Add real-world examples -->
+
+### Example 1: Basic Workflow
+
+```bash
+# Step 1: Create specification
+> /speckit.spec
+
+# Step 2: Generate tasks
+> /speckit.tasks
+
+# Step 3: Use extension
+> /speckit.my-extension.example
+```
+
+## Troubleshooting
+
+<!-- CUSTOMIZE: Add common issues -->
+
+### Issue: Configuration not found
+
+**Solution**: Create config from template (see Configuration section)
+
+### Issue: Command not available
+
+**Solutions**:
+
+1. Check extension is installed: `specify extension list`
+2. Restart AI agent
+3. Reinstall extension
+
+## License
+
+MIT License - see LICENSE file
+
+## Support
+
+- **Issues**: <https://github.com/your-org/spec-kit-my-extension/issues>
+- **Spec Kit Docs**: <https://github.com/statsperform/spec-kit>
+
+## Changelog
+
+See [CHANGELOG.md](CHANGELOG.md) for version history.
+
+---
+
+*Extension Version: 1.0.0*
+*Spec Kit: >=0.1.0*

extensions/template/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 [Your Name or Organization]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/template/README.md

@@ -0,0 +1,79 @@
+# Extension Template
+
+Starter template for creating a Spec Kit extension.
+
+## Quick Start
+
+1. **Copy this template**:
+
+   ```bash
+   cp -r extensions/template my-extension
+   cd my-extension
+   ```
+
+2. **Customize `extension.yml`**:
+   - Change extension ID, name, description
+   - Update author and repository
+   - Define your commands
+
+3. **Create commands**:
+   - Add command files in `commands/` directory
+   - Use Markdown format with YAML frontmatter
+
+4. **Create config template**:
+   - Define configuration options
+   - Document all settings
+
+5. **Write documentation**:
+   - Update README.md with usage instructions
+   - Add examples
+
+6. **Test locally**:
+
+   ```bash
+   cd /path/to/spec-kit-project
+   specify extension add --dev /path/to/my-extension
+   ```
+
+7. **Publish** (optional):
+   - Create GitHub repository
+   - Create release
+   - Submit to catalog (see EXTENSION-PUBLISHING-GUIDE.md)
+
+## Files in This Template
+
+- `extension.yml` - Extension manifest (CUSTOMIZE THIS)
+- `config-template.yml` - Configuration template (CUSTOMIZE THIS)
+- `commands/example.md` - Example command (REPLACE THIS)
+- `README.md` - Extension documentation (REPLACE THIS)
+- `LICENSE` - MIT License (REVIEW THIS)
+- `CHANGELOG.md` - Version history (UPDATE THIS)
+- `.gitignore` - Git ignore rules
+
+## Customization Checklist
+
+- [ ] Update `extension.yml` with your extension details
+- [ ] Change extension ID to your extension name
+- [ ] Update author information
+- [ ] Define your commands
+- [ ] Create command files in `commands/`
+- [ ] Update config template
+- [ ] Write README with usage instructions
+- [ ] Add examples
+- [ ] Update LICENSE if needed
+- [ ] Test extension locally
+- [ ] Create git repository
+- [ ] Create first release
+
+## Need Help?
+
+- **Development Guide**: See EXTENSION-DEVELOPMENT-GUIDE.md
+- **API Reference**: See EXTENSION-API-REFERENCE.md
+- **Publishing Guide**: See EXTENSION-PUBLISHING-GUIDE.md
+- **User Guide**: See EXTENSION-USER-GUIDE.md
+
+## Template Version
+
+- Version: 1.0.0
+- Last Updated: 2026-01-28
+- Compatible with Spec Kit: >=0.1.0

extensions/template/commands/example.md

@@ -0,0 +1,210 @@
+---
+description: "Example command that demonstrates extension functionality"
+# CUSTOMIZE: List MCP tools this command uses
+tools:
+  - 'example-mcp-server/example_tool'
+---
+
+# Example Command
+
+<!-- CUSTOMIZE: Replace this entire file with your command documentation -->
+
+This is an example command that demonstrates how to create commands for Spec Kit extensions.
+
+## Purpose
+
+Describe what this command does and when to use it.
+
+## Prerequisites
+
+List requirements before using this command:
+
+1. Prerequisite 1 (e.g., "MCP server configured")
+2. Prerequisite 2 (e.g., "Configuration file exists")
+3. Prerequisite 3 (e.g., "Valid API credentials")
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+### Step 1: Load Configuration
+
+<!-- CUSTOMIZE: Replace with your actual steps -->
+
+Load extension configuration from the project:
+
+``bash
+config_file=".specify/extensions/my-extension/my-extension-config.yml"
+
+if [ ! -f "$config_file" ]; then
+  echo "❌ Error: Configuration not found at $config_file"
+  echo "Run 'specify extension add my-extension' to install and configure"
+  exit 1
+fi
+
+# Read configuration values
+
+setting_value=$(yq eval '.settings.key' "$config_file")
+
+# Apply environment variable overrides
+
+setting_value="${SPECKIT_MY_EXTENSION_KEY:-$setting_value}"
+
+# Validate configuration
+
+if [ -z "$setting_value" ]; then
+  echo "❌ Error: Configuration value not set"
+  echo "Edit $config_file and set 'settings.key'"
+  exit 1
+fi
+
+echo "📋 Configuration loaded: $setting_value"
+``
+
+### Step 2: Perform Main Action
+
+<!-- CUSTOMIZE: Replace with your command logic -->
+
+Describe what this step does:
+
+``markdown
+Use MCP tools to perform the main action:
+
+- Tool: example-mcp-server example_tool
+- Parameters: { "key": "$setting_value" }
+
+This calls the MCP server tool to execute the operation.
+``
+
+### Step 3: Process Results
+
+<!-- CUSTOMIZE: Add more steps as needed -->
+
+Process the results and provide output:
+
+`` bash
+echo ""
+echo "✅ Command completed successfully!"
+echo ""
+echo "Results:"
+echo "  • Item 1: Value"
+echo "  • Item 2: Value"
+echo ""
+``
+
+### Step 4: Save Output (Optional)
+
+Save results to a file if needed:
+
+``bash
+output_file=".specify/my-extension-output.json"
+
+cat > "$output_file" <<EOF
+{
+  "timestamp": "$(date -u +"%Y-%m-%dT%H:%M:%SZ")",
+  "setting": "$setting_value",
+  "results": []
+}
+EOF
+
+echo "💾 Output saved to $output_file"
+``
+
+## Configuration Reference
+
+<!-- CUSTOMIZE: Document configuration options -->
+
+This command uses the following configuration from `my-extension-config.yml`:
+
+- **settings.key**: Description of what this setting does
+  - Type: string
+  - Required: Yes
+  - Example: `"example-value"`
+
+- **settings.another_key**: Description of another setting
+  - Type: boolean
+  - Required: No
+  - Default: `false`
+  - Example: `true`
+
+## Environment Variables
+
+<!-- CUSTOMIZE: Document environment variable overrides -->
+
+Configuration can be overridden with environment variables:
+
+- `SPECKIT_MY_EXTENSION_KEY` - Overrides `settings.key`
+- `SPECKIT_MY_EXTENSION_ANOTHER_KEY` - Overrides `settings.another_key`
+
+Example:
+``bash
+export SPECKIT_MY_EXTENSION_KEY="override-value"
+``
+
+## Troubleshooting
+
+<!-- CUSTOMIZE: Add common issues and solutions -->
+
+### "Configuration not found"
+
+**Solution**: Install the extension and create configuration:
+``bash
+specify extension add my-extension
+cp .specify/extensions/my-extension/config-template.yml \
+   .specify/extensions/my-extension/my-extension-config.yml
+``
+
+### "MCP tool not available"
+
+**Solution**: Ensure MCP server is configured in your AI agent settings.
+
+### "Permission denied"
+
+**Solution**: Check credentials and permissions in the external service.
+
+## Notes
+
+<!-- CUSTOMIZE: Add helpful notes and tips -->
+
+- This command requires an active connection to the external service
+- Results are cached for performance
+- Re-run the command to refresh data
+
+## Examples
+
+<!-- CUSTOMIZE: Add usage examples -->
+
+### Example 1: Basic Usage
+
+``bash
+
+# Run with default configuration
+>
+> /speckit.my-extension.example
+``
+
+### Example 2: With Environment Override
+
+``bash
+
+# Override configuration with environment variable
+
+export SPECKIT_MY_EXTENSION_KEY="custom-value"
+> /speckit.my-extension.example
+``
+
+### Example 3: After Core Command
+
+``bash
+
+# Use as part of a workflow
+>
+> /speckit.tasks
+> /speckit.my-extension.example
+``
+
+---
+
+*For more information, see the extension README or run `specify extension info my-extension`*

extensions/template/config-template.yml

@@ -0,0 +1,75 @@
+# Extension Configuration Template
+# Copy this to my-extension-config.yml and customize for your project
+
+# CUSTOMIZE: Add your configuration sections below
+
+# Example: Connection settings
+connection:
+  # URL to external service
+  url: ""  # REQUIRED: e.g., "https://api.example.com"
+
+  # API key or token
+  api_key: ""  # REQUIRED: Your API key
+
+# Example: Project settings
+project:
+  # Project identifier
+  id: ""  # REQUIRED: e.g., "my-project"
+
+  # Workspace or organization
+  workspace: ""  # OPTIONAL: e.g., "my-org"
+
+# Example: Feature flags
+features:
+  # Enable/disable main functionality
+  enabled: true
+
+  # Automatic synchronization
+  auto_sync: false
+
+  # Verbose logging
+  verbose: false
+
+# Example: Default values
+defaults:
+  # Labels to apply
+  labels: []  # e.g., ["automated", "spec-kit"]
+
+  # Priority level
+  priority: "medium"  # Options: "low", "medium", "high"
+
+  # Assignee
+  assignee: ""  # OPTIONAL: Default assignee
+
+# Example: Field mappings
+# Map internal names to external field IDs
+field_mappings:
+  # Example mappings
+  # internal_field: "external_field_id"
+  # status: "customfield_10001"
+
+# Example: Advanced settings
+advanced:
+  # Timeout in seconds
+  timeout: 30
+
+  # Retry attempts
+  retry_count: 3
+
+  # Cache duration in seconds
+  cache_duration: 3600
+
+# Environment Variable Overrides:
+# You can override any setting with environment variables  using this pattern:
+# SPECKIT_MY_EXTENSION_{SECTION}_{KEY}
+#
+# Examples:
+# - SPECKIT_MY_EXTENSION_CONNECTION_API_KEY: Override connection.api_key
+# - SPECKIT_MY_EXTENSION_PROJECT_ID: Override project.id
+# - SPECKIT_MY_EXTENSION_FEATURES_ENABLED: Override features.enabled
+#
+# Note: Use uppercase and replace dots with underscores
+
+# Local Overrides:
+# For local development, create my-extension-config.local.yml (gitignored)
+# to override settings without affecting the team configuration

extensions/template/extension.yml

@@ -0,0 +1,97 @@
+schema_version: "1.0"
+
+extension:
+  # CUSTOMIZE: Change 'my-extension' to your extension ID (lowercase, hyphen-separated)
+  id: "my-extension"
+
+  # CUSTOMIZE: Human-readable name for your extension
+  name: "My Extension"
+
+  # CUSTOMIZE: Update version when releasing (semantic versioning: X.Y.Z)
+  version: "1.0.0"
+
+  # CUSTOMIZE: Brief description (under 200 characters)
+  description: "Brief description of what your extension does"
+
+  # CUSTOMIZE: Your name or organization name
+  author: "Your Name"
+
+  # CUSTOMIZE: GitHub repository URL (create before publishing)
+  repository: "https://github.com/your-org/spec-kit-my-extension"
+
+  # REVIEW: License (MIT is recommended for open source)
+  license: "MIT"
+
+  # CUSTOMIZE: Extension homepage (can be same as repository)
+  homepage: "https://github.com/your-org/spec-kit-my-extension"
+
+# Requirements for this extension
+requires:
+  # CUSTOMIZE: Minimum spec-kit version required
+  # Use >=X.Y.Z for minimum version
+  # Use >=X.Y.Z,<Y.0.0 for version range
+  speckit_version: ">=0.1.0"
+
+  # CUSTOMIZE: Add MCP tools or other dependencies
+  # Remove if no external tools required
+  tools:
+    - name: "example-mcp-server"
+      version: ">=1.0.0"
+      required: true
+
+# Commands provided by this extension
+provides:
+  commands:
+    # CUSTOMIZE: Define your commands
+    # Pattern: speckit.{extension-id}.{command-name}
+    - name: "speckit.my-extension.example"
+      file: "commands/example.md"
+      description: "Example command that demonstrates functionality"
+      # Optional: Add aliases for shorter command names
+      aliases: ["speckit.example"]
+
+    # ADD MORE COMMANDS: Copy this block for each command
+    # - name: "speckit.my-extension.another-command"
+    #   file: "commands/another-command.md"
+    #   description: "Another command"
+
+  # CUSTOMIZE: Define configuration files
+  config:
+    - name: "my-extension-config.yml"
+      template: "config-template.yml"
+      description: "Extension configuration"
+      required: true # Set to false if config is optional
+
+# CUSTOMIZE: Define hooks (optional)
+# Remove if no hooks needed
+hooks:
+  # Hook that runs after /speckit.tasks
+  after_tasks:
+    command: "speckit.my-extension.example"
+    optional: true # User will be prompted
+    prompt: "Run example command?"
+    description: "Demonstrates hook functionality"
+    condition: null # Future: conditional execution
+
+  # ADD MORE HOOKS: Copy this block for other events
+  # after_implement:
+  #   command: "speckit.my-extension.another"
+  #   optional: false  # Auto-execute without prompting
+  #   description: "Runs automatically after implementation"
+
+# CUSTOMIZE: Add relevant tags (2-5 recommended)
+# Used for discovery in catalog
+tags:
+  - "example"
+  - "template"
+  # ADD MORE: "category", "tool-name", etc.
+
+# CUSTOMIZE: Default configuration values (optional)
+# These are merged with user config
+defaults:
+  # Example default values
+  feature:
+    enabled: true
+    auto_sync: false
+
+  # ADD MORE: Any default settings for your extension

pyproject.toml

@@ -1,15 +1,18 @@
 [project]
 name = "specify-cli"
-version = "0.0.20"
+version = "0.1.6"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
     "typer",
+    "click>=8.1",
     "rich",
     "httpx[socks]",
     "platformdirs",
     "readchar",
     "truststore>=0.10.4",
+    "pyyaml>=6.0",
+    "packaging>=23.0",
 ]
 
 [project.scripts]
@@ -22,3 +25,30 @@ build-backend = "hatchling.build"
 [tool.hatch.build.targets.wheel]
 packages = ["src/specify_cli"]
 
+[project.optional-dependencies]
+test = [
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--strict-markers",
+    "--tb=short",
+]
+
+[tool.coverage.run]
+source = ["src"]
+omit = ["*/tests/*", "*/__pycache__/*"]
+
+[tool.coverage.report]
+precision = 2
+show_missing = true
+skip_covered = false
+
+

scripts/bash/check-prerequisites.sh

@@ -75,7 +75,7 @@ EOF
 done
 
 # Source common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths and validate branch

scripts/bash/common.sh

@@ -7,7 +7,7 @@ get_repo_root() {
         git rev-parse --show-toplevel
     else
         # Fall back to script location for non-git repos
-        local script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+        local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
         (cd "$script_dir/../../.." && pwd)
     fi
 }

scripts/bash/create-new-feature.sh

@@ -4,6 +4,7 @@ set -e
 
 JSON_MODE=false
 SHORT_NAME=""
+BRANCH_NUMBER=""
 ARGS=()
 i=1
 while [ $i -le $# ]; do
@@ -26,17 +27,31 @@ while [ $i -le $# ]; do
             fi
             SHORT_NAME="$next_arg"
             ;;
+        --number)
+            if [ $((i + 1)) -gt $# ]; then
+                echo 'Error: --number requires a value' >&2
+                exit 1
+            fi
+            i=$((i + 1))
+            next_arg="${!i}"
+            if [[ "$next_arg" == --* ]]; then
+                echo 'Error: --number requires a value' >&2
+                exit 1
+            fi
+            BRANCH_NUMBER="$next_arg"
+            ;;
         --help|-h) 
-            echo "Usage: $0 [--json] [--short-name <name>] <feature_description>"
+            echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>"
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
             echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
+            echo "  --number N          Specify branch number manually (overrides auto-detection)"
             echo "  --help, -h          Show this help message"
             echo ""
             echo "Examples:"
             echo "  $0 'Add user authentication system' --short-name 'user-auth'"
-            echo "  $0 'Implement OAuth2 integration for API'"
+            echo "  $0 'Implement OAuth2 integration for API' --number 5"
             exit 0
             ;;
         *) 
@@ -48,7 +63,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>" >&2
     exit 1
 fi
 
@@ -65,10 +80,85 @@ find_repo_root() {
     return 1
 }
 
+# Function to get highest number from specs directory
+get_highest_from_specs() {
+    local specs_dir="$1"
+    local highest=0
+    
+    if [ -d "$specs_dir" ]; then
+        for dir in "$specs_dir"/*; do
+            [ -d "$dir" ] || continue
+            dirname=$(basename "$dir")
+            number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
+            number=$((10#$number))
+            if [ "$number" -gt "$highest" ]; then
+                highest=$number
+            fi
+        done
+    fi
+    
+    echo "$highest"
+}
+
+# Function to get highest number from git branches
+get_highest_from_branches() {
+    local highest=0
+    
+    # Get all branches (local and remote)
+    branches=$(git branch -a 2>/dev/null || echo "")
+    
+    if [ -n "$branches" ]; then
+        while IFS= read -r branch; do
+            # Clean branch name: remove leading markers and remote prefixes
+            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
+            
+            # Extract feature number if branch matches pattern ###-*
+            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
+                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
+                number=$((10#$number))
+                if [ "$number" -gt "$highest" ]; then
+                    highest=$number
+                fi
+            fi
+        done <<< "$branches"
+    fi
+    
+    echo "$highest"
+}
+
+# Function to check existing branches (local and remote) and return next available number
+check_existing_branches() {
+    local specs_dir="$1"
+
+    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
+    git fetch --all --prune 2>/dev/null || true
+
+    # Get highest number from ALL branches (not just matching short name)
+    local highest_branch=$(get_highest_from_branches)
+
+    # Get highest number from ALL specs (not just matching short name)
+    local highest_spec=$(get_highest_from_specs "$specs_dir")
+
+    # Take the maximum of both
+    local max_num=$highest_branch
+    if [ "$highest_spec" -gt "$max_num" ]; then
+        max_num=$highest_spec
+    fi
+
+    # Return next number
+    echo $((max_num + 1))
+}
+
+# Function to clean and format a branch name
+clean_branch_name() {
+    local name="$1"
+    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
+}
+
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 if git rev-parse --show-toplevel >/dev/null 2>&1; then
     REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -87,20 +177,6 @@ cd "$REPO_ROOT"
 SPECS_DIR="$REPO_ROOT/specs"
 mkdir -p "$SPECS_DIR"
 
-HIGHEST=0
-if [ -d "$SPECS_DIR" ]; then
-    for dir in "$SPECS_DIR"/*; do
-        [ -d "$dir" ] || continue
-        dirname=$(basename "$dir")
-        number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
-        number=$((10#$number))
-        if [ "$number" -gt "$HIGHEST" ]; then HIGHEST=$number; fi
-    done
-fi
-
-NEXT=$((HIGHEST + 1))
-FEATURE_NUM=$(printf "%03d" "$NEXT")
-
 # Function to generate branch name with stop word filtering and length filtering
 generate_branch_name() {
     local description="$1"
@@ -144,19 +220,34 @@ generate_branch_name() {
         echo "$result"
     else
         # Fallback to original logic if no meaningful words found
-        echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//' | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
+        local cleaned=$(clean_branch_name "$description")
+        echo "$cleaned" | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
     fi
 }
 
 # Generate branch name
 if [ -n "$SHORT_NAME" ]; then
     # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(echo "$SHORT_NAME" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//')
+    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
 else
     # Generate from description with smart filtering
     BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
 fi
 
+# Determine branch number
+if [ -z "$BRANCH_NUMBER" ]; then
+    if [ "$HAS_GIT" = true ]; then
+        # Check existing branches on remotes
+        BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
+    else
+        # Fall back to local directory check
+        HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
+        BRANCH_NUMBER=$((HIGHEST + 1))
+    fi
+fi
+
+# Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
+FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
 BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
 
 # GitHub enforces a 244-byte limit on branch names

scripts/bash/setup-plan.sh

@@ -24,7 +24,7 @@ for arg in "$@"; do
 done
 
 # Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions

scripts/bash/update-agent-context.sh

@@ -30,12 +30,12 @@
 #
 # 5. Multi-Agent Support
 #    - Handles agent-specific file paths and naming conventions
-#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Amp, or Amazon Q Developer CLI
+#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Amazon Q Developer CLI, or Antigravity
 #    - Can update single agents or all existing agent files
 #    - Creates default Claude file if no agent files exist
 #
 # Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|q
+# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|agy|bob|qodercli
 # Leave empty to update all existing agent files
 
 set -e
@@ -49,7 +49,7 @@ set -o pipefail
 #==============================================================================
 
 # Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
@@ -61,7 +61,7 @@ AGENT_TYPE="${1:-}"
 # Agent-specific file paths  
 CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
 GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/copilot-instructions.md"
+COPILOT_FILE="$REPO_ROOT/.github/agents/copilot-instructions.md"
 CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
 QWEN_FILE="$REPO_ROOT/QWEN.md"
 AGENTS_FILE="$REPO_ROOT/AGENTS.md"
@@ -70,8 +70,12 @@ KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
 AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
 ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
 CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
+QODER_FILE="$REPO_ROOT/QODER.md"
 AMP_FILE="$REPO_ROOT/AGENTS.md"
+SHAI_FILE="$REPO_ROOT/SHAI.md"
 Q_FILE="$REPO_ROOT/AGENTS.md"
+AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
+BOB_FILE="$REPO_ROOT/AGENTS.md"
 
 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -391,12 +395,25 @@ update_existing_agent_file() {
         new_change_entry="- $CURRENT_BRANCH: Added $NEW_DB"
     fi
     
+    # Check if sections exist in the file
+    local has_active_technologies=0
+    local has_recent_changes=0
+    
+    if grep -q "^## Active Technologies" "$target_file" 2>/dev/null; then
+        has_active_technologies=1
+    fi
+    
+    if grep -q "^## Recent Changes" "$target_file" 2>/dev/null; then
+        has_recent_changes=1
+    fi
+    
     # Process file line by line
     local in_tech_section=false
     local in_changes_section=false
     local tech_entries_added=false
     local changes_entries_added=false
     local existing_changes_count=0
+    local file_ended=false
     
     while IFS= read -r line || [[ -n "$line" ]]; do
         # Handle Active Technologies section
@@ -457,6 +474,22 @@ update_existing_agent_file() {
     # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
     if [[ $in_tech_section == true ]] && [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
         printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
+        tech_entries_added=true
+    fi
+    
+    # If sections don't exist, add them at the end of the file
+    if [[ $has_active_technologies -eq 0 ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
+        echo "" >> "$temp_file"
+        echo "## Active Technologies" >> "$temp_file"
+        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
+        tech_entries_added=true
+    fi
+    
+    if [[ $has_recent_changes -eq 0 ]] && [[ -n "$new_change_entry" ]]; then
+        echo "" >> "$temp_file"
+        echo "## Recent Changes" >> "$temp_file"
+        echo "$new_change_entry" >> "$temp_file"
+        changes_entries_added=true
     fi
     
     # Move temp file to target atomically
@@ -586,15 +619,30 @@ update_specific_agent() {
         codebuddy)
             update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
             ;;
+        qodercli)
+            update_agent_file "$QODER_FILE" "Qoder CLI"
+            ;;
         amp)
             update_agent_file "$AMP_FILE" "Amp"
             ;;
+        shai)
+            update_agent_file "$SHAI_FILE" "SHAI"
+            ;;
         q)
             update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
             ;;
+        agy)
+            update_agent_file "$AGY_FILE" "Antigravity"
+            ;;
+        bob)
+            update_agent_file "$BOB_FILE" "IBM Bob"
+            ;;
+        generic)
+            log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
+            ;;
         *)
             log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|amp|q"
+            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|agy|bob|qodercli|generic"
             exit 1
             ;;
     esac
@@ -659,10 +707,29 @@ update_all_existing_agents() {
         found_agent=true
     fi
 
+    if [[ -f "$SHAI_FILE" ]]; then
+        update_agent_file "$SHAI_FILE" "SHAI"
+        found_agent=true
+    fi
+
+    if [[ -f "$QODER_FILE" ]]; then
+        update_agent_file "$QODER_FILE" "Qoder CLI"
+        found_agent=true
+    fi
+
     if [[ -f "$Q_FILE" ]]; then
         update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
         found_agent=true
     fi
+
+    if [[ -f "$AGY_FILE" ]]; then
+        update_agent_file "$AGY_FILE" "Antigravity"
+        found_agent=true
+    fi
+    if [[ -f "$BOB_FILE" ]]; then
+        update_agent_file "$BOB_FILE" "IBM Bob"
+        found_agent=true
+    fi
     
     # If no agent files exist, create a default Claude file
     if [[ "$found_agent" == false ]]; then
@@ -688,7 +755,7 @@ print_summary() {
     
     echo
 
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|codebuddy|q]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|agy|bob|qodercli]"
 }
 
 #==============================================================================

scripts/powershell/create-new-feature.ps1

@@ -4,6 +4,7 @@
 param(
     [switch]$Json,
     [string]$ShortName,
+    [int]$Number = 0,
     [switch]$Help,
     [Parameter(ValueFromRemainingArguments = $true)]
     [string[]]$FeatureDescription
@@ -12,11 +13,12 @@ $ErrorActionPreference = 'Stop'
 
 # Show help if requested
 if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] <feature description>"
+    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] <feature description>"
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
+    Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
     Write-Host "  -Help               Show this help message"
     Write-Host ""
     Write-Host "Examples:"
@@ -56,6 +58,77 @@ function Find-RepositoryRoot {
         $current = $parent
     }
 }
+
+function Get-HighestNumberFromSpecs {
+    param([string]$SpecsDir)
+    
+    $highest = 0
+    if (Test-Path $SpecsDir) {
+        Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
+            if ($_.Name -match '^(\d+)') {
+                $num = [int]$matches[1]
+                if ($num -gt $highest) { $highest = $num }
+            }
+        }
+    }
+    return $highest
+}
+
+function Get-HighestNumberFromBranches {
+    param()
+    
+    $highest = 0
+    try {
+        $branches = git branch -a 2>$null
+        if ($LASTEXITCODE -eq 0) {
+            foreach ($branch in $branches) {
+                # Clean branch name: remove leading markers and remote prefixes
+                $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
+                
+                # Extract feature number if branch matches pattern ###-*
+                if ($cleanBranch -match '^(\d+)-') {
+                    $num = [int]$matches[1]
+                    if ($num -gt $highest) { $highest = $num }
+                }
+            }
+        }
+    } catch {
+        # If git command fails, return 0
+        Write-Verbose "Could not check Git branches: $_"
+    }
+    return $highest
+}
+
+function Get-NextBranchNumber {
+    param(
+        [string]$SpecsDir
+    )
+
+    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
+    try {
+        git fetch --all --prune 2>$null | Out-Null
+    } catch {
+        # Ignore fetch errors
+    }
+
+    # Get highest number from ALL branches (not just matching short name)
+    $highestBranch = Get-HighestNumberFromBranches
+
+    # Get highest number from ALL specs (not just matching short name)
+    $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
+
+    # Take the maximum of both
+    $maxNum = [Math]::Max($highestBranch, $highestSpec)
+
+    # Return next number
+    return $maxNum + 1
+}
+
+function ConvertTo-CleanBranchName {
+    param([string]$Name)
+    
+    return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+}
 $fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
 if (-not $fallbackRoot) {
     Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
@@ -79,18 +152,6 @@ Set-Location $repoRoot
 $specsDir = Join-Path $repoRoot 'specs'
 New-Item -ItemType Directory -Path $specsDir -Force | Out-Null
 
-$highest = 0
-if (Test-Path $specsDir) {
-    Get-ChildItem -Path $specsDir -Directory | ForEach-Object {
-        if ($_.Name -match '^(\d{3})') {
-            $num = [int]$matches[1]
-            if ($num -gt $highest) { $highest = $num }
-        }
-    }
-}
-$next = $highest + 1
-$featureNum = ('{0:000}' -f $next)
-
 # Function to generate branch name with stop word filtering and length filtering
 function Get-BranchName {
     param([string]$Description)
@@ -130,7 +191,7 @@ function Get-BranchName {
         return $result
     } else {
         # Fallback to original logic if no meaningful words found
-        $result = $Description.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+        $result = ConvertTo-CleanBranchName -Name $Description
         $fallbackWords = ($result -split '-') | Where-Object { $_ } | Select-Object -First 3
         return [string]::Join('-', $fallbackWords)
     }
@@ -139,12 +200,24 @@ function Get-BranchName {
 # Generate branch name
 if ($ShortName) {
     # Use provided short name, just clean it up
-    $branchSuffix = $ShortName.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+    $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
 } else {
     # Generate from description with smart filtering
     $branchSuffix = Get-BranchName -Description $featureDesc
 }
 
+# Determine branch number
+if ($Number -eq 0) {
+    if ($hasGit) {
+        # Check existing branches on remotes
+        $Number = Get-NextBranchNumber -SpecsDir $specsDir
+    } else {
+        # Fall back to local directory check
+        $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
+    }
+}
+
+$featureNum = ('{0:000}' -f $Number)
 $branchName = "$featureNum-$branchSuffix"
 
 # GitHub enforces a 244-byte limit on branch names

scripts/powershell/setup-plan.ps1

@@ -59,4 +59,3 @@ if ($Json) {
     Write-Output "BRANCH: $($paths.CURRENT_BRANCH)"
     Write-Output "HAS_GIT: $($paths.HAS_GIT)"
 }
-

scripts/powershell/update-agent-context.ps1

@@ -9,7 +9,7 @@ Mirrors the behavior of scripts/bash/update-agent-context.sh:
  2. Plan Data Extraction
  3. Agent File Management (create from template or update existing)
  4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, amp, q)
+ 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, q, agy, bob, qodercli)
 
 .PARAMETER AgentType
 Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
@@ -25,7 +25,7 @@ Relies on common helper functions in common.ps1
 #>
 param(
     [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','q')]
+    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','q','agy','bob','qodercli','generic')]
     [string]$AgentType
 )
 
@@ -46,7 +46,7 @@ $NEW_PLAN = $IMPL_PLAN
 # Agent file paths
 $CLAUDE_FILE   = Join-Path $REPO_ROOT 'CLAUDE.md'
 $GEMINI_FILE   = Join-Path $REPO_ROOT 'GEMINI.md'
-$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/copilot-instructions.md'
+$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/agents/copilot-instructions.md'
 $CURSOR_FILE   = Join-Path $REPO_ROOT '.cursor/rules/specify-rules.mdc'
 $QWEN_FILE     = Join-Path $REPO_ROOT 'QWEN.md'
 $AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'
@@ -55,8 +55,12 @@ $KILOCODE_FILE = Join-Path $REPO_ROOT '.kilocode/rules/specify-rules.md'
 $AUGGIE_FILE   = Join-Path $REPO_ROOT '.augment/rules/specify-rules.md'
 $ROO_FILE      = Join-Path $REPO_ROOT '.roo/rules/specify-rules.md'
 $CODEBUDDY_FILE = Join-Path $REPO_ROOT 'CODEBUDDY.md'
+$QODER_FILE    = Join-Path $REPO_ROOT 'QODER.md'
 $AMP_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
+$SHAI_FILE     = Join-Path $REPO_ROOT 'SHAI.md'
 $Q_FILE        = Join-Path $REPO_ROOT 'AGENTS.md'
+$AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
+$BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 
 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
 
@@ -380,9 +384,14 @@ function Update-SpecificAgent {
         'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
         'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
         'codebuddy' { Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI' }
+        'qodercli' { Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI' }
         'amp'      { Update-AgentFile -TargetFile $AMP_FILE      -AgentName 'Amp' }
+        'shai'     { Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI' }
         'q'        { Update-AgentFile -TargetFile $Q_FILE        -AgentName 'Amazon Q Developer CLI' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|q'; return $false }
+        'agy'      { Update-AgentFile -TargetFile $AGY_FILE      -AgentName 'Antigravity' }
+        'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
+        'generic'  { Write-Info 'Generic agent: no predefined context file. Use the agent-specific update script for your agent.' }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|agy|bob|qodercli|generic'; return $false }
     }
 }
 
@@ -400,7 +409,11 @@ function Update-AllExistingAgents {
     if (Test-Path $AUGGIE_FILE)   { if (-not (Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI')) { $ok = $false }; $found = $true }
     if (Test-Path $ROO_FILE)      { if (-not (Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code')) { $ok = $false }; $found = $true }
     if (Test-Path $CODEBUDDY_FILE) { if (-not (Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $QODER_FILE)    { if (-not (Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $SHAI_FILE)     { if (-not (Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI')) { $ok = $false }; $found = $true }
     if (Test-Path $Q_FILE)        { if (-not (Update-AgentFile -TargetFile $Q_FILE        -AgentName 'Amazon Q Developer CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $AGY_FILE)      { if (-not (Update-AgentFile -TargetFile $AGY_FILE      -AgentName 'Antigravity')) { $ok = $false }; $found = $true }
+    if (Test-Path $BOB_FILE)      { if (-not (Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob')) { $ok = $false }; $found = $true }
     if (-not $found) {
         Write-Info 'No existing agent files found, creating default Claude file...'
         if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
@@ -415,7 +428,7 @@ function Print-Summary {
     if ($NEW_FRAMEWORK) { Write-Host "  - Added framework: $NEW_FRAMEWORK" }
     if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Host "  - Added database: $NEW_DB" }
     Write-Host ''
-    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|q]'
+    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|agy|bob|qodercli|generic]'
 }
 
 function Main {

spec-driven.md

@@ -195,6 +195,7 @@ The templates include comprehensive checklists that act as "unit tests" for the
 
 ```markdown
 ### Requirement Completeness
+
 - [ ] No [NEEDS CLARIFICATION] markers remain
 - [ ] Requirements are testable and unambiguous
 - [ ] Success criteria are measurable
@@ -208,10 +209,14 @@ The implementation plan template enforces architectural principles through phase
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
+
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 ```
@@ -347,15 +352,19 @@ The implementation plan template operationalizes these articles through concrete
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
 
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 
 #### Integration-First Gate (Article IX)
+
 - [ ] Contracts defined?
 - [ ] Contract tests written?
 ```

spec-kit.code-workspace

@@ -0,0 +1,8 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}

templates/commands/clarify.md

@@ -1,5 +1,9 @@
 ---
 description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
+handoffs: 
+  - label: Build Technical Plan
+    agent: speckit.plan
+    prompt: Create a plan for the spec. I am building with...
 scripts:
    sh: scripts/bash/check-prerequisites.sh --json --paths-only
    ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly

templates/commands/constitution.md

@@ -1,5 +1,9 @@
 ---
-description: Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync
+description: Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.
+handoffs: 
+  - label: Build Specification
+    agent: speckit.specify
+    prompt: Implement the feature specification based on the updated constitution. I want to build...
 ---
 
 ## User Input
@@ -12,11 +16,13 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 ## Outline
 
-You are updating the project constitution at `/memory/constitution.md`. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. `[PROJECT_NAME]`, `[PRINCIPLE_1_NAME]`). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.
+You are updating the project constitution at `.specify/memory/constitution.md`. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. `[PROJECT_NAME]`, `[PRINCIPLE_1_NAME]`). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.
+
+**Note**: If `.specify/memory/constitution.md` does not exist yet, it should have been initialized from `.specify/templates/constitution-template.md` during project setup. If it's missing, copy the template first.
 
 Follow this execution flow:
 
-1. Load the existing constitution template at `/memory/constitution.md`.
+1. Load the existing constitution at `.specify/memory/constitution.md`.
    - Identify every placeholder token of the form `[ALL_CAPS_IDENTIFIER]`.
    **IMPORTANT**: The user might require less or more principles than the ones used in the template. If a number is specified, respect that - follow the general template. You will update the doc accordingly.
 
@@ -37,10 +43,10 @@ Follow this execution flow:
    - Ensure Governance section lists amendment procedure, versioning policy, and compliance review expectations.
 
 4. Consistency propagation checklist (convert prior checklist into active validations):
-   - Read `/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
-   - Read `/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
-   - Read `/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
-   - Read each command file in `/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
+   - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
+   - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
+   - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
+   - Read each command file in `.specify/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
    - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
 
 5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):
@@ -57,7 +63,7 @@ Follow this execution flow:
    - Dates ISO format YYYY-MM-DD.
    - Principles are declarative, testable, and free of vague language ("should" → replace with MUST/SHOULD rationale where appropriate).
 
-7. Write the completed constitution back to `/memory/constitution.md` (overwrite).
+7. Write the completed constitution back to `.specify/memory/constitution.md` (overwrite).
 
 8. Output a final summary to the user with:
    - New version and bump rationale.
@@ -75,4 +81,4 @@ If the user supplies partial updates (e.g., only one principle revision), still
 
 If critical info missing (e.g., ratification date truly unknown), insert `TODO(<FIELD_NAME>): explanation` and include in the Sync Impact Report under deferred items.
 
-Do not create a new template; always operate on the existing `/memory/constitution.md` file.
+Do not create a new template; always operate on the existing `.specify/memory/constitution.md` file.

templates/commands/implement.md

@@ -67,7 +67,8 @@ You **MUST** consider the user input before proceeding (if not empty).
      ```
 
    - Check if Dockerfile* exists or Docker in plan.md → create/verify .dockerignore
-   - Check if .eslintrc*or eslint.config.* exists → create/verify .eslintignore
+   - Check if .eslintrc* exists → create/verify .eslintignore
+   - Check if eslint.config.* exists → ensure the config's `ignores` entries cover required patterns
    - Check if .prettierrc* exists → create/verify .prettierignore
    - Check if .npmrc or package.json exists → create/verify .npmignore (if publishing)
    - Check if terraform files (*.tf) exist → create/verify .terraformignore
@@ -135,4 +136,3 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Report final status with summary of completed work
 
 Note: This command assumes a complete task breakdown exists in tasks.md. If tasks are incomplete or missing, suggest running `/speckit.tasks` first to regenerate the task list.
-

templates/commands/plan.md

@@ -1,5 +1,13 @@
 ---
 description: Execute the implementation planning workflow using the plan template to generate design artifacts.
+handoffs: 
+  - label: Create Tasks
+    agent: speckit.tasks
+    prompt: Break the plan into tasks
+    send: true
+  - label: Create Checklist
+    agent: speckit.checklist
+    prompt: Create a checklist for the following domain...
 scripts:
   sh: scripts/bash/setup-plan.sh --json
   ps: scripts/powershell/setup-plan.ps1 -Json
@@ -67,10 +75,11 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Validation rules from requirements
    - State transitions if applicable
 
-2. **Generate API contracts** from functional requirements:
-   - For each user action → endpoint
-   - Use standard REST/GraphQL patterns
-   - Output OpenAPI/GraphQL schema to `/contracts/`
+2. **Define interface contracts** (if project has external interfaces) → `/contracts/`:
+   - Identify what interfaces the project exposes to users or other systems
+   - Document the contract format appropriate for the project type
+   - Examples: public APIs for libraries, command schemas for CLI tools, endpoints for web services, grammars for parsers, UI contracts for applications
+   - Skip if project is purely internal (build scripts, one-off tools, etc.)
 
 3. **Agent context update**:
    - Run `{AGENT_SCRIPT}`

templates/commands/specify.md

@@ -1,5 +1,13 @@
 ---
 description: Create or update the feature specification from a natural language feature description.
+handoffs: 
+  - label: Build Technical Plan
+    agent: speckit.plan
+    prompt: Create a plan for the spec. I am building with...
+  - label: Clarify Spec Requirements
+    agent: speckit.clarify
+    prompt: Clarify specification requirements
+    send: true
 scripts:
   sh: scripts/bash/create-new-feature.sh --json "{ARGS}"
   ps: scripts/powershell/create-new-feature.ps1 -Json "{ARGS}"
@@ -31,16 +39,37 @@ Given that feature description, do this:
      - "Create a dashboard for analytics" → "analytics-dashboard"
      - "Fix payment processing timeout bug" → "fix-payment-timeout"
 
-2. Run the script `{SCRIPT}` from repo root **with the short-name argument** and parse its JSON output for BRANCH_NAME and SPEC_FILE. All file paths must be absolute.
+2. **Check for existing branches before creating new one**:
+
+   a. First, fetch all remote branches to ensure we have the latest information:
+
+      ```bash
+      git fetch --all --prune
+      ```
+
+   b. Find the highest feature number across all sources for the short-name:
+      - Remote branches: `git ls-remote --heads origin | grep -E 'refs/heads/[0-9]+-<short-name>$'`
+      - Local branches: `git branch | grep -E '^[* ]*[0-9]+-<short-name>$'`
+      - Specs directories: Check for directories matching `specs/[0-9]+-<short-name>`
+
+   c. Determine the next available number:
+      - Extract all numbers from all three sources
+      - Find the highest number N
+      - Use N+1 for the new branch number
+
+   d. Run the script `{SCRIPT}` with the calculated number and short-name:
+      - Pass `--number N+1` and `--short-name "your-short-name"` along with the feature description
+      - Bash example: `{SCRIPT} --json --number 5 --short-name "user-auth" "Add user authentication"`
+      - PowerShell example: `{SCRIPT} -Json -Number 5 -ShortName "user-auth" "Add user authentication"`
 
    **IMPORTANT**:
-
-   - Append the short-name argument to the `{SCRIPT}` command with the 2-4 word short name you created in step 1
-   - Bash: `--short-name "your-generated-short-name"`
-   - PowerShell: `-ShortName "your-generated-short-name"`
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
-   - You must only ever run this script once
+   - Check all three sources (remote branches, local branches, specs directories) to find the highest number
+   - Only match branches/directories with the exact short-name pattern
+   - If no existing branches/directories found with this short-name, start with number 1
+   - You must only ever run this script once per feature
    - The JSON is provided in the terminal as output - always refer to it to get the actual content you're looking for
+   - The JSON output will contain BRANCH_NAME and SPEC_FILE paths
+   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
 
 3. Load `templates/spec-template.md` to understand required sections.
 
@@ -206,7 +235,7 @@ When creating this spec from a user prompt:
 - Performance targets: Standard web/mobile app expectations unless specified
 - Error handling: User-friendly messages with appropriate fallbacks
 - Authentication method: Standard session-based or OAuth2 for web apps
-- Integration patterns: RESTful APIs unless specified otherwise
+- Integration patterns: Use project-appropriate patterns (REST/GraphQL for web services, function calls for libraries, CLI args for tools, etc.)
 
 ### Success Criteria Guidelines
 

templates/commands/tasks.md

@@ -1,5 +1,14 @@
 ---
 description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
+handoffs: 
+  - label: Analyze For Consistency
+    agent: speckit.analyze
+    prompt: Run a project analysis for consistency
+    send: true
+  - label: Implement Project
+    agent: speckit.implement
+    prompt: Start the implementation in phases
+    send: true
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json
   ps: scripts/powershell/check-prerequisites.ps1 -Json
@@ -19,21 +28,21 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 2. **Load design documents**: Read from FEATURE_DIR:
    - **Required**: plan.md (tech stack, libraries, structure), spec.md (user stories with priorities)
-   - **Optional**: data-model.md (entities), contracts/ (API endpoints), research.md (decisions), quickstart.md (test scenarios)
+   - **Optional**: data-model.md (entities), contracts/ (interface contracts), research.md (decisions), quickstart.md (test scenarios)
    - Note: Not all projects have all documents. Generate tasks based on what's available.
 
 3. **Execute task generation workflow**:
    - Load plan.md and extract tech stack, libraries, project structure
    - Load spec.md and extract user stories with their priorities (P1, P2, P3, etc.)
    - If data-model.md exists: Extract entities and map to user stories
-   - If contracts/ exists: Map endpoints to user stories
+   - If contracts/ exists: Map interface contracts to user stories
    - If research.md exists: Extract decisions for setup tasks
    - Generate tasks organized by user story (see Task Generation Rules below)
    - Generate dependency graph showing user story completion order
    - Create parallel execution examples per user story
    - Validate task completeness (each user story has all needed tasks, independently testable)
 
-4. **Generate tasks.md**: Use `.specify/templates/tasks-template.md` as structure, fill with:
+4. **Generate tasks.md**: Use `templates/tasks-template.md` as structure, fill with:
    - Correct feature name from plan.md
    - Phase 1: Setup tasks (project initialization)
    - Phase 2: Foundational tasks (blocking prerequisites for all user stories)
@@ -103,13 +112,13 @@ Every task MUST strictly follow this format:
    - Map all related components to their story:
      - Models needed for that story
      - Services needed for that story
-     - Endpoints/UI needed for that story
+     - Interfaces/UI needed for that story
      - If tests requested: Tests specific to that story
    - Mark story dependencies (most stories should be independent)
 
 2. **From Contracts**:
-   - Map each contract/endpoint → to the user story it serves
-   - If tests requested: Each contract → contract test task [P] before implementation in that story's phase
+   - Map each interface contract → to the user story it serves
+   - If tests requested: Each interface contract → contract test task [P] before implementation in that story's phase
 
 3. **From Data Model**:
    - Map each entity to the user story(ies) that need it

templates/commands/taskstoissues.md

@@ -0,0 +1,33 @@
+---
+description: Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts.
+tools: ['github/github-mcp-server/issue_write']
+scripts:
+  sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
+  ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+---
+
+## User Input
+
+```text
+$ARGUMENTS
+```
+
+You **MUST** consider the user input before proceeding (if not empty).
+
+## Outline
+
+1. Run `{SCRIPT}` from repo root and parse FEATURE_DIR and AVAILABLE_DOCS list. All paths must be absolute. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
+1. From the executed script, extract the path to **tasks**.
+1. Get the Git remote by running:
+
+```bash
+git config --get remote.origin.url
+```
+
+> [!CAUTION]
+> ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL
+
+1. For each task in the list, use the GitHub MCP server to create a new issue in the repository that is representative of the Git remote.
+
+> [!CAUTION]
+> UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL

templates/plan-template.md

@@ -3,7 +3,7 @@
 **Branch**: `[###-feature-name]` | **Date**: [DATE] | **Spec**: [link]
 **Input**: Feature specification from `/specs/[###-feature-name]/spec.md`
 
-**Note**: This template is filled in by the `/speckit.plan` command. See `.specify/templates/commands/plan.md` for the execution workflow.
+**Note**: This template is filled in by the `/speckit.plan` command. See `.specify/templates/plan-template.md` for the execution workflow.
 
 ## Summary
 
@@ -22,7 +22,7 @@
 **Storage**: [if applicable, e.g., PostgreSQL, CoreData, files or N/A]  
 **Testing**: [e.g., pytest, XCTest, cargo test or NEEDS CLARIFICATION]  
 **Target Platform**: [e.g., Linux server, iOS 15+, WASM or NEEDS CLARIFICATION]
-**Project Type**: [single/web/mobile - determines source structure]  
+**Project Type**: [e.g., library/cli/web-service/mobile-app/compiler/desktop-app or NEEDS CLARIFICATION]  
 **Performance Goals**: [domain-specific, e.g., 1000 req/s, 10k lines/sec, 60 fps or NEEDS CLARIFICATION]  
 **Constraints**: [domain-specific, e.g., <200ms p95, <100MB memory, offline-capable or NEEDS CLARIFICATION]  
 **Scale/Scope**: [domain-specific, e.g., 10k users, 1M LOC, 50 screens or NEEDS CLARIFICATION]

tests/__init__.py

@@ -0,0 +1 @@
+"""Unit tests for Spec Kit."""

tests/test_ai_skills.py

@@ -0,0 +1,694 @@
+"""
+Unit tests for AI agent skills installation.
+
+Tests cover:
+- Skills directory resolution for different agents (_get_skills_dir)
+- YAML frontmatter parsing and SKILL.md generation (install_ai_skills)
+- Cleanup of duplicate command files when --ai-skills is used
+- Missing templates directory handling
+- Malformed template error handling
+- CLI validation: --ai-skills requires --ai
+"""
+
+import re
+import pytest
+import tempfile
+import shutil
+import yaml
+from pathlib import Path
+from unittest.mock import patch
+
+import specify_cli
+
+from specify_cli import (
+    _get_skills_dir,
+    install_ai_skills,
+    AGENT_SKILLS_DIR_OVERRIDES,
+    DEFAULT_SKILLS_DIR,
+    SKILL_DESCRIPTIONS,
+    AGENT_CONFIG,
+    app,
+)
+
+
+# ===== Fixtures =====
+
+@pytest.fixture
+def temp_dir():
+    """Create a temporary directory for tests."""
+    tmpdir = tempfile.mkdtemp()
+    yield Path(tmpdir)
+    shutil.rmtree(tmpdir)
+
+
+@pytest.fixture
+def project_dir(temp_dir):
+    """Create a mock project directory."""
+    proj_dir = temp_dir / "test-project"
+    proj_dir.mkdir()
+    return proj_dir
+
+
+@pytest.fixture
+def templates_dir(project_dir):
+    """Create mock command templates in the project's agent commands directory.
+
+    This simulates what download_and_extract_template() does: it places
+    command .md files into project_path/<agent_folder>/commands/.
+    install_ai_skills() now reads from here instead of from the repo
+    source tree.
+    """
+    tpl_root = project_dir / ".claude" / "commands"
+    tpl_root.mkdir(parents=True, exist_ok=True)
+
+    # Template with valid YAML frontmatter
+    (tpl_root / "specify.md").write_text(
+        "---\n"
+        "description: Create or update the feature specification.\n"
+        "handoffs:\n"
+        "  - label: Build Plan\n"
+        "    agent: speckit.plan\n"
+        "scripts:\n"
+        "  sh: scripts/bash/create-new-feature.sh\n"
+        "---\n"
+        "\n"
+        "# Specify Command\n"
+        "\n"
+        "Run this to create a spec.\n",
+        encoding="utf-8",
+    )
+
+    # Template with minimal frontmatter
+    (tpl_root / "plan.md").write_text(
+        "---\n"
+        "description: Generate implementation plan.\n"
+        "---\n"
+        "\n"
+        "# Plan Command\n"
+        "\n"
+        "Plan body content.\n",
+        encoding="utf-8",
+    )
+
+    # Template with no frontmatter
+    (tpl_root / "tasks.md").write_text(
+        "# Tasks Command\n"
+        "\n"
+        "Body without frontmatter.\n",
+        encoding="utf-8",
+    )
+
+    # Template with empty YAML frontmatter (yaml.safe_load returns None)
+    (tpl_root / "empty_fm.md").write_text(
+        "---\n"
+        "---\n"
+        "\n"
+        "# Empty Frontmatter Command\n"
+        "\n"
+        "Body with empty frontmatter.\n",
+        encoding="utf-8",
+    )
+
+    return tpl_root
+
+
+@pytest.fixture
+def commands_dir_claude(project_dir):
+    """Create a populated .claude/commands directory simulating template extraction."""
+    cmd_dir = project_dir / ".claude" / "commands"
+    cmd_dir.mkdir(parents=True, exist_ok=True)
+    for name in ["speckit.specify.md", "speckit.plan.md", "speckit.tasks.md"]:
+        (cmd_dir / name).write_text(f"# {name}\nContent here\n")
+    return cmd_dir
+
+
+@pytest.fixture
+def commands_dir_gemini(project_dir):
+    """Create a populated .gemini/commands directory (TOML format)."""
+    cmd_dir = project_dir / ".gemini" / "commands"
+    cmd_dir.mkdir(parents=True)
+    for name in ["speckit.specify.toml", "speckit.plan.toml", "speckit.tasks.toml"]:
+        (cmd_dir / name).write_text(f'[command]\nname = "{name}"\n')
+    return cmd_dir
+
+
+# ===== _get_skills_dir Tests =====
+
+class TestGetSkillsDir:
+    """Test the _get_skills_dir() helper function."""
+
+    def test_claude_skills_dir(self, project_dir):
+        """Claude should use .claude/skills/."""
+        result = _get_skills_dir(project_dir, "claude")
+        assert result == project_dir / ".claude" / "skills"
+
+    def test_gemini_skills_dir(self, project_dir):
+        """Gemini should use .gemini/skills/."""
+        result = _get_skills_dir(project_dir, "gemini")
+        assert result == project_dir / ".gemini" / "skills"
+
+    def test_copilot_skills_dir(self, project_dir):
+        """Copilot should use .github/skills/."""
+        result = _get_skills_dir(project_dir, "copilot")
+        assert result == project_dir / ".github" / "skills"
+
+    def test_codex_uses_override(self, project_dir):
+        """Codex should use the AGENT_SKILLS_DIR_OVERRIDES value."""
+        result = _get_skills_dir(project_dir, "codex")
+        assert result == project_dir / ".agents" / "skills"
+
+    def test_cursor_agent_skills_dir(self, project_dir):
+        """Cursor should use .cursor/skills/."""
+        result = _get_skills_dir(project_dir, "cursor-agent")
+        assert result == project_dir / ".cursor" / "skills"
+
+    def test_unknown_agent_uses_default(self, project_dir):
+        """Unknown agents should fall back to DEFAULT_SKILLS_DIR."""
+        result = _get_skills_dir(project_dir, "nonexistent-agent")
+        assert result == project_dir / DEFAULT_SKILLS_DIR
+
+    def test_all_configured_agents_resolve(self, project_dir):
+        """Every agent in AGENT_CONFIG should resolve to a valid path."""
+        for agent_key in AGENT_CONFIG:
+            result = _get_skills_dir(project_dir, agent_key)
+            assert result is not None
+            assert str(result).startswith(str(project_dir))
+            # Should always end with "skills"
+            assert result.name == "skills"
+
+    def test_override_takes_precedence_over_config(self, project_dir):
+        """AGENT_SKILLS_DIR_OVERRIDES should take precedence over AGENT_CONFIG."""
+        for agent_key in AGENT_SKILLS_DIR_OVERRIDES:
+            result = _get_skills_dir(project_dir, agent_key)
+            expected = project_dir / AGENT_SKILLS_DIR_OVERRIDES[agent_key]
+            assert result == expected
+
+
+# ===== install_ai_skills Tests =====
+
+class TestInstallAiSkills:
+    """Test SKILL.md generation and installation logic."""
+
+    def test_skills_installed_with_correct_structure(self, project_dir, templates_dir):
+        """Verify SKILL.md files have correct agentskills.io structure."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+
+        skills_dir = project_dir / ".claude" / "skills"
+        assert skills_dir.exists()
+
+        # Check that skill directories were created
+        skill_dirs = sorted([d.name for d in skills_dir.iterdir() if d.is_dir()])
+        assert "speckit-plan" in skill_dirs
+        assert "speckit-specify" in skill_dirs
+        assert "speckit-tasks" in skill_dirs
+        assert "speckit-empty_fm" in skill_dirs
+
+        # Verify SKILL.md content for speckit-specify
+        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+
+        # Check agentskills.io frontmatter
+        assert content.startswith("---\n")
+        assert "name: speckit-specify" in content
+        assert "description:" in content
+        assert "compatibility:" in content
+        assert "metadata:" in content
+        assert "author: github-spec-kit" in content
+        assert "source: templates/commands/specify.md" in content
+
+        # Check body content is included
+        assert "# Speckit Specify Skill" in content
+        assert "Run this to create a spec." in content
+
+    def test_generated_skill_has_parseable_yaml(self, project_dir, templates_dir):
+        """Generated SKILL.md should contain valid, parseable YAML frontmatter."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-specify" / "SKILL.md"
+        content = skill_file.read_text()
+
+        # Extract and parse frontmatter
+        assert content.startswith("---\n")
+        parts = content.split("---", 2)
+        assert len(parts) >= 3
+        parsed = yaml.safe_load(parts[1])
+        assert isinstance(parsed, dict)
+        assert "name" in parsed
+        assert parsed["name"] == "speckit-specify"
+        assert "description" in parsed
+
+    def test_empty_yaml_frontmatter(self, project_dir, templates_dir):
+        """Templates with empty YAML frontmatter (---\\n---) should not crash."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-empty_fm" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+        assert "name: speckit-empty_fm" in content
+        assert "Body with empty frontmatter." in content
+
+    def test_enhanced_descriptions_used_when_available(self, project_dir, templates_dir):
+        """SKILL_DESCRIPTIONS take precedence over template frontmatter descriptions."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-specify" / "SKILL.md"
+        content = skill_file.read_text()
+
+        # Parse the generated YAML to compare the description value
+        # (yaml.safe_dump may wrap long strings across multiple lines)
+        parts = content.split("---", 2)
+        parsed = yaml.safe_load(parts[1])
+
+        if "specify" in SKILL_DESCRIPTIONS:
+            assert parsed["description"] == SKILL_DESCRIPTIONS["specify"]
+
+    def test_template_without_frontmatter(self, project_dir, templates_dir):
+        """Templates without YAML frontmatter should still produce valid skills."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-tasks" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+
+        # Should still have valid SKILL.md structure
+        assert "name: speckit-tasks" in content
+        assert "Body without frontmatter." in content
+
+    def test_missing_templates_directory(self, project_dir):
+        """Returns False when no command templates exist anywhere."""
+        # No .claude/commands/ exists, and __file__ fallback won't find anything
+        fake_init = project_dir / "nonexistent" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            result = install_ai_skills(project_dir, "claude")
+
+        assert result is False
+
+        # Skills directory should not exist
+        skills_dir = project_dir / ".claude" / "skills"
+        assert not skills_dir.exists()
+
+    def test_empty_templates_directory(self, project_dir):
+        """Returns False when commands directory has no .md files."""
+        # Create empty .claude/commands/
+        empty_cmds = project_dir / ".claude" / "commands"
+        empty_cmds.mkdir(parents=True)
+
+        # Block the __file__ fallback so it can't find real templates
+        fake_init = project_dir / "nowhere" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            result = install_ai_skills(project_dir, "claude")
+
+        assert result is False
+
+    def test_malformed_yaml_frontmatter(self, project_dir):
+        """Malformed YAML in a template should be handled gracefully, not crash."""
+        # Create .claude/commands/ with a broken template
+        cmds_dir = project_dir / ".claude" / "commands"
+        cmds_dir.mkdir(parents=True)
+
+        (cmds_dir / "broken.md").write_text(
+            "---\n"
+            "description: [unclosed bracket\n"
+            "  invalid: yaml: content: here\n"
+            "---\n"
+            "\n"
+            "# Broken\n",
+            encoding="utf-8",
+        )
+
+        # Should not raise — errors are caught per-file
+        result = install_ai_skills(project_dir, "claude")
+
+        # The broken template should be skipped but not crash the process
+        assert result is False
+
+    def test_additive_does_not_overwrite_other_files(self, project_dir, templates_dir):
+        """Installing skills should not remove non-speckit files in the skills dir."""
+        # Pre-create a custom skill
+        custom_dir = project_dir / ".claude" / "skills" / "my-custom-skill"
+        custom_dir.mkdir(parents=True)
+        custom_file = custom_dir / "SKILL.md"
+        custom_file.write_text("# My Custom Skill\n")
+
+        install_ai_skills(project_dir, "claude")
+
+        # Custom skill should still exist
+        assert custom_file.exists()
+        assert custom_file.read_text() == "# My Custom Skill\n"
+
+    def test_return_value(self, project_dir, templates_dir):
+        """install_ai_skills returns True when skills installed, False otherwise."""
+        assert install_ai_skills(project_dir, "claude") is True
+
+    def test_return_false_when_no_templates(self, project_dir):
+        """install_ai_skills returns False when no templates found."""
+        fake_init = project_dir / "missing" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            assert install_ai_skills(project_dir, "claude") is False
+
+    def test_non_md_commands_dir_falls_back(self, project_dir):
+        """When extracted commands are .toml (e.g. gemini), fall back to repo templates."""
+        # Simulate gemini template extraction: .gemini/commands/ with .toml files only
+        cmds_dir = project_dir / ".gemini" / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.toml").write_text('[command]\nname = "specify"\n')
+        (cmds_dir / "speckit.plan.toml").write_text('[command]\nname = "plan"\n')
+
+        # The __file__ fallback should find the real repo templates/commands/*.md
+        result = install_ai_skills(project_dir, "gemini")
+
+        assert result is True
+        skills_dir = project_dir / ".gemini" / "skills"
+        assert skills_dir.exists()
+        # Should have installed skills from the fallback .md templates
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert len(skill_dirs) >= 1
+        # .toml commands should be untouched
+        assert (cmds_dir / "speckit.specify.toml").exists()
+
+    @pytest.mark.parametrize("agent_key", [k for k in AGENT_CONFIG.keys() if k != "generic"])
+    def test_skills_install_for_all_agents(self, temp_dir, agent_key):
+        """install_ai_skills should produce skills for every configured agent."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        # Place .md templates in the agent's commands directory
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        cmds_dir = proj / agent_folder.rstrip("/") / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "specify.md").write_text(
+            "---\ndescription: Test command\n---\n\n# Test\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-specify" in skill_dirs
+        assert (skills_dir / "speckit-specify" / "SKILL.md").exists()
+
+
+
+class TestCommandCoexistence:
+    """Verify install_ai_skills never touches command files.
+
+    Cleanup of freshly-extracted commands for NEW projects is handled
+    in init(), not in install_ai_skills().  These tests confirm that
+    install_ai_skills leaves existing commands intact.
+    """
+
+    def test_existing_commands_preserved_claude(self, project_dir, templates_dir, commands_dir_claude):
+        """install_ai_skills must NOT remove pre-existing .claude/commands files."""
+        # Verify commands exist before
+        assert len(list(commands_dir_claude.glob("speckit.*"))) == 3
+
+        install_ai_skills(project_dir, "claude")
+
+        # Commands must still be there — install_ai_skills never touches them
+        remaining = list(commands_dir_claude.glob("speckit.*"))
+        assert len(remaining) == 3
+
+    def test_existing_commands_preserved_gemini(self, project_dir, templates_dir, commands_dir_gemini):
+        """install_ai_skills must NOT remove pre-existing .gemini/commands files."""
+        assert len(list(commands_dir_gemini.glob("speckit.*"))) == 3
+
+        install_ai_skills(project_dir, "gemini")
+
+        remaining = list(commands_dir_gemini.glob("speckit.*"))
+        assert len(remaining) == 3
+
+    def test_commands_dir_not_removed(self, project_dir, templates_dir, commands_dir_claude):
+        """install_ai_skills must not remove the commands directory."""
+        install_ai_skills(project_dir, "claude")
+
+        assert commands_dir_claude.exists()
+
+    def test_no_commands_dir_no_error(self, project_dir, templates_dir):
+        """No error when installing skills — commands dir has templates and is preserved."""
+        result = install_ai_skills(project_dir, "claude")
+
+        # Should succeed since templates are in .claude/commands/ via fixture
+        assert result is True
+
+
+# ===== New-Project Command Skip Tests =====
+
+class TestNewProjectCommandSkip:
+    """Test that init() removes extracted commands for new projects only.
+
+    These tests run init() end-to-end via CliRunner with
+    download_and_extract_template patched to create local fixtures.
+    """
+
+    def _fake_extract(self, agent, project_path, **_kwargs):
+        """Simulate template extraction: create agent commands dir."""
+        agent_cfg = AGENT_CONFIG.get(agent, {})
+        agent_folder = agent_cfg.get("folder", "")
+        if agent_folder:
+            cmds_dir = project_path / agent_folder.rstrip("/") / "commands"
+            cmds_dir.mkdir(parents=True, exist_ok=True)
+            (cmds_dir / "speckit.specify.md").write_text("# spec")
+
+    def test_new_project_commands_removed_after_skills_succeed(self, tmp_path):
+        """For new projects, commands should be removed when skills succeed."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "new-proj"
+
+        def fake_download(project_path, *args, **kwargs):
+            self._fake_extract("claude", project_path)
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=True) as mock_skills, \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", str(target), "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Skills should have been called
+        mock_skills.assert_called_once()
+
+        # Commands dir should have been removed after skills succeeded
+        cmds_dir = target / ".claude" / "commands"
+        assert not cmds_dir.exists()
+
+    def test_commands_preserved_when_skills_fail(self, tmp_path):
+        """If skills fail, commands should NOT be removed (safety net)."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "fail-proj"
+
+        def fake_download(project_path, *args, **kwargs):
+            self._fake_extract("claude", project_path)
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=False), \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", str(target), "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Commands should still exist since skills failed
+        cmds_dir = target / ".claude" / "commands"
+        assert cmds_dir.exists()
+        assert (cmds_dir / "speckit.specify.md").exists()
+
+    def test_here_mode_commands_preserved(self, tmp_path, monkeypatch):
+        """For --here on existing repos, commands must NOT be removed."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        # Create a mock existing project with commands already present
+        target = tmp_path / "existing"
+        target.mkdir()
+        agent_folder = AGENT_CONFIG["claude"]["folder"]
+        cmds_dir = target / agent_folder.rstrip("/") / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.md").write_text("# spec")
+
+        # --here uses CWD, so chdir into the target
+        monkeypatch.chdir(target)
+
+        def fake_download(project_path, *args, **kwargs):
+            pass  # commands already exist, no need to re-create
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=True), \
+             patch("specify_cli.is_git_repo", return_value=True), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", "--here", "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Commands must remain for --here
+        assert cmds_dir.exists()
+        assert (cmds_dir / "speckit.specify.md").exists()
+
+
+# ===== Skip-If-Exists Tests =====
+
+class TestSkipIfExists:
+    """Test that install_ai_skills does not overwrite existing SKILL.md files."""
+
+    def test_existing_skill_not_overwritten(self, project_dir, templates_dir):
+        """Pre-existing SKILL.md should not be replaced on re-run."""
+        # Pre-create a custom SKILL.md for speckit-specify
+        skill_dir = project_dir / ".claude" / "skills" / "speckit-specify"
+        skill_dir.mkdir(parents=True)
+        custom_content = "# My Custom Specify Skill\nUser-modified content\n"
+        (skill_dir / "SKILL.md").write_text(custom_content)
+
+        result = install_ai_skills(project_dir, "claude")
+
+        # The custom SKILL.md should be untouched
+        assert (skill_dir / "SKILL.md").read_text() == custom_content
+
+        # But other skills should still be installed
+        assert result is True
+        assert (project_dir / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        assert (project_dir / ".claude" / "skills" / "speckit-tasks" / "SKILL.md").exists()
+
+    def test_fresh_install_writes_all_skills(self, project_dir, templates_dir):
+        """On first install (no pre-existing skills), all should be written."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+        skills_dir = project_dir / ".claude" / "skills"
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        # All 4 templates should produce skills (specify, plan, tasks, empty_fm)
+        assert len(skill_dirs) == 4
+
+
+# ===== SKILL_DESCRIPTIONS Coverage Tests =====
+
+class TestSkillDescriptions:
+    """Test SKILL_DESCRIPTIONS constants."""
+
+    def test_all_known_commands_have_descriptions(self):
+        """All standard spec-kit commands should have enhanced descriptions."""
+        expected_commands = [
+            "specify", "plan", "tasks", "implement", "analyze",
+            "clarify", "constitution", "checklist", "taskstoissues",
+        ]
+        for cmd in expected_commands:
+            assert cmd in SKILL_DESCRIPTIONS, f"Missing description for '{cmd}'"
+            assert len(SKILL_DESCRIPTIONS[cmd]) > 20, f"Description for '{cmd}' is too short"
+
+
+# ===== CLI Validation Tests =====
+
+class TestCliValidation:
+    """Test --ai-skills CLI flag validation."""
+
+    def test_ai_skills_without_ai_fails(self):
+        """--ai-skills without --ai should fail with exit code 1."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "test-proj", "--ai-skills"])
+
+        assert result.exit_code == 1
+        assert "--ai-skills requires --ai" in result.output
+
+    def test_ai_skills_without_ai_shows_usage(self):
+        """Error message should include usage hint."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "test-proj", "--ai-skills"])
+
+        assert "Usage:" in result.output
+        assert "--ai" in result.output
+
+    def test_ai_skills_flag_appears_in_help(self):
+        """--ai-skills should appear in init --help output."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "--help"])
+
+        plain = re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        assert "--ai-skills" in plain
+        assert "agent skills" in plain.lower()
+
+
+class TestParameterOrderingIssue:
+    """Test fix for GitHub issue #1641: parameter ordering issues."""
+
+    def test_ai_flag_consuming_here_flag(self):
+        """--ai without value should not consume --here flag (issue #1641)."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        # This used to fail with "Must specify project name" because --here was consumed by --ai
+        result = runner.invoke(app, ["init", "--ai-skills", "--ai", "--here"])
+
+        assert result.exit_code == 1
+        assert "Invalid value for --ai" in result.output
+        assert "--here" in result.output  # Should mention the invalid value
+
+    def test_ai_flag_consuming_ai_skills_flag(self):
+        """--ai without value should not consume --ai-skills flag."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        # This should fail with helpful error about missing --ai value
+        result = runner.invoke(app, ["init", "--here", "--ai", "--ai-skills"])
+
+        assert result.exit_code == 1
+        assert "Invalid value for --ai" in result.output
+        assert "--ai-skills" in result.output  # Should mention the invalid value
+
+    def test_error_message_provides_hint(self):
+        """Error message should provide helpful hint about missing value."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "--ai", "--here"])
+
+        assert result.exit_code == 1
+        assert "Hint:" in result.output or "hint" in result.output.lower()
+        assert "forget to provide a value" in result.output.lower()
+
+    def test_error_message_lists_available_agents(self):
+        """Error message should list available agents."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "--ai", "--here"])
+
+        assert result.exit_code == 1
+        # Should mention some known agents
+        output_lower = result.output.lower()
+        assert any(agent in output_lower for agent in ["claude", "copilot", "gemini"])
+
+    def test_ai_commands_dir_consuming_flag(self):
+        """--ai-commands-dir without value should not consume next flag."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "myproject", "--ai", "generic", "--ai-commands-dir", "--here"])
+
+        assert result.exit_code == 1
+        assert "Invalid value for --ai-commands-dir" in result.output
+        assert "--here" in result.output

tests/test_extensions.py

@@ -0,0 +1,989 @@
+"""
+Unit tests for the extension system.
+
+Tests cover:
+- Extension manifest validation
+- Extension registry operations
+- Extension manager installation/removal
+- Command registration
+"""
+
+import pytest
+import json
+import tempfile
+import shutil
+from pathlib import Path
+from datetime import datetime, timezone
+
+from specify_cli.extensions import (
+    ExtensionManifest,
+    ExtensionRegistry,
+    ExtensionManager,
+    CommandRegistrar,
+    ExtensionCatalog,
+    ExtensionError,
+    ValidationError,
+    CompatibilityError,
+    version_satisfies,
+)
+
+
+# ===== Fixtures =====
+
+@pytest.fixture
+def temp_dir():
+    """Create a temporary directory for tests."""
+    tmpdir = tempfile.mkdtemp()
+    yield Path(tmpdir)
+    shutil.rmtree(tmpdir)
+
+
+@pytest.fixture
+def valid_manifest_data():
+    """Valid extension manifest data."""
+    return {
+        "schema_version": "1.0",
+        "extension": {
+            "id": "test-ext",
+            "name": "Test Extension",
+            "version": "1.0.0",
+            "description": "A test extension",
+            "author": "Test Author",
+            "repository": "https://github.com/test/test-ext",
+            "license": "MIT",
+        },
+        "requires": {
+            "speckit_version": ">=0.1.0",
+            "commands": ["speckit.tasks"],
+        },
+        "provides": {
+            "commands": [
+                {
+                    "name": "speckit.test.hello",
+                    "file": "commands/hello.md",
+                    "description": "Test command",
+                }
+            ]
+        },
+        "hooks": {
+            "after_tasks": {
+                "command": "speckit.test.hello",
+                "optional": True,
+                "prompt": "Run test?",
+            }
+        },
+        "tags": ["testing", "example"],
+    }
+
+
+@pytest.fixture
+def extension_dir(temp_dir, valid_manifest_data):
+    """Create a complete extension directory structure."""
+    ext_dir = temp_dir / "test-ext"
+    ext_dir.mkdir()
+
+    # Write manifest
+    import yaml
+    manifest_path = ext_dir / "extension.yml"
+    with open(manifest_path, 'w') as f:
+        yaml.dump(valid_manifest_data, f)
+
+    # Create commands directory
+    commands_dir = ext_dir / "commands"
+    commands_dir.mkdir()
+
+    # Write command file
+    cmd_file = commands_dir / "hello.md"
+    cmd_file.write_text("""---
+description: "Test hello command"
+---
+
+# Test Hello Command
+
+$ARGUMENTS
+""")
+
+    return ext_dir
+
+
+@pytest.fixture
+def project_dir(temp_dir):
+    """Create a mock spec-kit project directory."""
+    proj_dir = temp_dir / "project"
+    proj_dir.mkdir()
+
+    # Create .specify directory
+    specify_dir = proj_dir / ".specify"
+    specify_dir.mkdir()
+
+    return proj_dir
+
+
+# ===== ExtensionManifest Tests =====
+
+class TestExtensionManifest:
+    """Test ExtensionManifest validation and parsing."""
+
+    def test_valid_manifest(self, extension_dir):
+        """Test loading a valid manifest."""
+        manifest_path = extension_dir / "extension.yml"
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.id == "test-ext"
+        assert manifest.name == "Test Extension"
+        assert manifest.version == "1.0.0"
+        assert manifest.description == "A test extension"
+        assert len(manifest.commands) == 1
+        assert manifest.commands[0]["name"] == "speckit.test.hello"
+
+    def test_missing_required_field(self, temp_dir):
+        """Test manifest missing required field."""
+        import yaml
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump({"schema_version": "1.0"}, f)  # Missing 'extension'
+
+        with pytest.raises(ValidationError, match="Missing required field"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_extension_id(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid extension ID format."""
+        import yaml
+
+        valid_manifest_data["extension"]["id"] = "Invalid_ID"  # Uppercase not allowed
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid extension ID"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_version(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid semantic version."""
+        import yaml
+
+        valid_manifest_data["extension"]["version"] = "invalid"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid version"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_command_name(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid command name format."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"][0]["name"] = "invalid-name"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid command name"):
+            ExtensionManifest(manifest_path)
+
+    def test_no_commands(self, temp_dir, valid_manifest_data):
+        """Test manifest with no commands provided."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"] = []
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="must provide at least one command"):
+            ExtensionManifest(manifest_path)
+
+    def test_manifest_hash(self, extension_dir):
+        """Test manifest hash calculation."""
+        manifest_path = extension_dir / "extension.yml"
+        manifest = ExtensionManifest(manifest_path)
+
+        hash_value = manifest.get_hash()
+        assert hash_value.startswith("sha256:")
+        assert len(hash_value) > 10
+
+
+# ===== ExtensionRegistry Tests =====
+
+class TestExtensionRegistry:
+    """Test ExtensionRegistry operations."""
+
+    def test_empty_registry(self, temp_dir):
+        """Test creating a new empty registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        assert registry.data["schema_version"] == "1.0"
+        assert registry.data["extensions"] == {}
+        assert len(registry.list()) == 0
+
+    def test_add_extension(self, temp_dir):
+        """Test adding an extension to registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        metadata = {
+            "version": "1.0.0",
+            "source": "local",
+            "enabled": True,
+        }
+        registry.add("test-ext", metadata)
+
+        assert registry.is_installed("test-ext")
+        ext_data = registry.get("test-ext")
+        assert ext_data["version"] == "1.0.0"
+        assert "installed_at" in ext_data
+
+    def test_remove_extension(self, temp_dir):
+        """Test removing an extension from registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("test-ext", {"version": "1.0.0"})
+
+        assert registry.is_installed("test-ext")
+
+        registry.remove("test-ext")
+
+        assert not registry.is_installed("test-ext")
+        assert registry.get("test-ext") is None
+
+    def test_registry_persistence(self, temp_dir):
+        """Test that registry persists to disk."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        # Create registry and add extension
+        registry1 = ExtensionRegistry(extensions_dir)
+        registry1.add("test-ext", {"version": "1.0.0"})
+
+        # Load new registry instance
+        registry2 = ExtensionRegistry(extensions_dir)
+
+        # Should still have the extension
+        assert registry2.is_installed("test-ext")
+        assert registry2.get("test-ext")["version"] == "1.0.0"
+
+
+# ===== ExtensionManager Tests =====
+
+class TestExtensionManager:
+    """Test ExtensionManager installation and removal."""
+
+    def test_check_compatibility_valid(self, extension_dir, project_dir):
+        """Test compatibility check with valid version."""
+        manager = ExtensionManager(project_dir)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        # Should not raise
+        result = manager.check_compatibility(manifest, "0.1.0")
+        assert result is True
+
+    def test_check_compatibility_invalid(self, extension_dir, project_dir):
+        """Test compatibility check with invalid version."""
+        manager = ExtensionManager(project_dir)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        # Requires >=0.1.0, but we have 0.0.1
+        with pytest.raises(CompatibilityError, match="Extension requires spec-kit"):
+            manager.check_compatibility(manifest, "0.0.1")
+
+    def test_install_from_directory(self, extension_dir, project_dir):
+        """Test installing extension from directory."""
+        manager = ExtensionManager(project_dir)
+
+        manifest = manager.install_from_directory(
+            extension_dir,
+            "0.1.0",
+            register_commands=False  # Skip command registration for now
+        )
+
+        assert manifest.id == "test-ext"
+        assert manager.registry.is_installed("test-ext")
+
+        # Check extension directory was copied
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        assert ext_dir.exists()
+        assert (ext_dir / "extension.yml").exists()
+        assert (ext_dir / "commands" / "hello.md").exists()
+
+    def test_install_duplicate(self, extension_dir, project_dir):
+        """Test installing already installed extension."""
+        manager = ExtensionManager(project_dir)
+
+        # Install once
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Try to install again
+        with pytest.raises(ExtensionError, match="already installed"):
+            manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+    def test_remove_extension(self, extension_dir, project_dir):
+        """Test removing an installed extension."""
+        manager = ExtensionManager(project_dir)
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        assert ext_dir.exists()
+
+        # Remove extension
+        result = manager.remove("test-ext", keep_config=False)
+
+        assert result is True
+        assert not manager.registry.is_installed("test-ext")
+        assert not ext_dir.exists()
+
+    def test_remove_nonexistent(self, project_dir):
+        """Test removing non-existent extension."""
+        manager = ExtensionManager(project_dir)
+
+        result = manager.remove("nonexistent")
+        assert result is False
+
+    def test_list_installed(self, extension_dir, project_dir):
+        """Test listing installed extensions."""
+        manager = ExtensionManager(project_dir)
+
+        # Initially empty
+        assert len(manager.list_installed()) == 0
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Should have one extension
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "test-ext"
+        assert installed[0]["name"] == "Test Extension"
+        assert installed[0]["version"] == "1.0.0"
+        assert installed[0]["command_count"] == 1
+        assert installed[0]["hook_count"] == 1
+
+    def test_config_backup_on_remove(self, extension_dir, project_dir):
+        """Test that config files are backed up on removal."""
+        manager = ExtensionManager(project_dir)
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Create a config file
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        config_file = ext_dir / "test-ext-config.yml"
+        config_file.write_text("test: config")
+
+        # Remove extension (without keep_config)
+        manager.remove("test-ext", keep_config=False)
+
+        # Check backup was created (now in subdirectory per extension)
+        backup_dir = project_dir / ".specify" / "extensions" / ".backup" / "test-ext"
+        backup_file = backup_dir / "test-ext-config.yml"
+        assert backup_file.exists()
+        assert backup_file.read_text() == "test: config"
+
+
+# ===== CommandRegistrar Tests =====
+
+class TestCommandRegistrar:
+    """Test CommandRegistrar command registration."""
+
+    def test_parse_frontmatter_valid(self):
+        """Test parsing valid YAML frontmatter."""
+        content = """---
+description: "Test command"
+tools:
+  - tool1
+  - tool2
+---
+
+# Command body
+$ARGUMENTS
+"""
+        registrar = CommandRegistrar()
+        frontmatter, body = registrar.parse_frontmatter(content)
+
+        assert frontmatter["description"] == "Test command"
+        assert frontmatter["tools"] == ["tool1", "tool2"]
+        assert "Command body" in body
+        assert "$ARGUMENTS" in body
+
+    def test_parse_frontmatter_no_frontmatter(self):
+        """Test parsing content without frontmatter."""
+        content = "# Just a command\n$ARGUMENTS"
+
+        registrar = CommandRegistrar()
+        frontmatter, body = registrar.parse_frontmatter(content)
+
+        assert frontmatter == {}
+        assert body == content
+
+    def test_render_frontmatter(self):
+        """Test rendering frontmatter to YAML."""
+        frontmatter = {
+            "description": "Test command",
+            "tools": ["tool1", "tool2"]
+        }
+
+        registrar = CommandRegistrar()
+        output = registrar.render_frontmatter(frontmatter)
+
+        assert output.startswith("---\n")
+        assert output.endswith("---\n")
+        assert "description: Test command" in output
+
+    def test_register_commands_for_claude(self, extension_dir, project_dir):
+        """Test registering commands for Claude agent."""
+        # Create .claude directory
+        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir.mkdir(parents=True)
+
+        ExtensionManager(project_dir)  # Initialize manager (side effects only)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_claude(
+            manifest,
+            extension_dir,
+            project_dir
+        )
+
+        assert len(registered) == 1
+        assert "speckit.test.hello" in registered
+
+        # Check command file was created
+        cmd_file = claude_dir / "speckit.test.hello.md"
+        assert cmd_file.exists()
+
+        content = cmd_file.read_text()
+        assert "description: Test hello command" in content
+        assert "<!-- Extension: test-ext -->" in content
+        assert "<!-- Config: .specify/extensions/test-ext/ -->" in content
+
+    def test_command_with_aliases(self, project_dir, temp_dir):
+        """Test registering a command with aliases."""
+        import yaml
+
+        # Create extension with command alias
+        ext_dir = temp_dir / "ext-alias"
+        ext_dir.mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-alias",
+                "name": "Extension with Alias",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {
+                "speckit_version": ">=0.1.0",
+            },
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.alias.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shortcut"],
+                    }
+                ]
+            },
+        }
+
+        with open(ext_dir / "extension.yml", 'w') as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nTest")
+
+        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_claude(manifest, ext_dir, project_dir)
+
+        assert len(registered) == 2
+        assert "speckit.alias.cmd" in registered
+        assert "speckit.shortcut" in registered
+        assert (claude_dir / "speckit.alias.cmd.md").exists()
+        assert (claude_dir / "speckit.shortcut.md").exists()
+
+
+# ===== Utility Function Tests =====
+
+class TestVersionSatisfies:
+    """Test version_satisfies utility function."""
+
+    def test_version_satisfies_simple(self):
+        """Test simple version comparison."""
+        assert version_satisfies("1.0.0", ">=1.0.0")
+        assert version_satisfies("1.0.1", ">=1.0.0")
+        assert not version_satisfies("0.9.9", ">=1.0.0")
+
+    def test_version_satisfies_range(self):
+        """Test version range."""
+        assert version_satisfies("1.5.0", ">=1.0.0,<2.0.0")
+        assert not version_satisfies("2.0.0", ">=1.0.0,<2.0.0")
+        assert not version_satisfies("0.9.0", ">=1.0.0,<2.0.0")
+
+    def test_version_satisfies_complex(self):
+        """Test complex version specifier."""
+        assert version_satisfies("1.0.5", ">=1.0.0,!=1.0.3")
+        assert not version_satisfies("1.0.3", ">=1.0.0,!=1.0.3")
+
+    def test_version_satisfies_invalid(self):
+        """Test invalid version strings."""
+        assert not version_satisfies("invalid", ">=1.0.0")
+        assert not version_satisfies("1.0.0", "invalid specifier")
+
+
+# ===== Integration Tests =====
+
+class TestIntegration:
+    """Integration tests for complete workflows."""
+
+    def test_full_install_and_remove_workflow(self, extension_dir, project_dir):
+        """Test complete installation and removal workflow."""
+        # Create Claude directory
+        (project_dir / ".claude" / "commands").mkdir(parents=True)
+
+        manager = ExtensionManager(project_dir)
+
+        # Install
+        manager.install_from_directory(
+            extension_dir,
+            "0.1.0",
+            register_commands=True
+        )
+
+        # Verify installation
+        assert manager.registry.is_installed("test-ext")
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "test-ext"
+
+        # Verify command registered
+        cmd_file = project_dir / ".claude" / "commands" / "speckit.test.hello.md"
+        assert cmd_file.exists()
+
+        # Verify registry has registered commands (now a dict keyed by agent)
+        metadata = manager.registry.get("test-ext")
+        registered_commands = metadata["registered_commands"]
+        # Check that the command is registered for at least one agent
+        assert any(
+            "speckit.test.hello" in cmds
+            for cmds in registered_commands.values()
+        )
+
+        # Remove
+        result = manager.remove("test-ext")
+        assert result is True
+
+        # Verify removal
+        assert not manager.registry.is_installed("test-ext")
+        assert not cmd_file.exists()
+        assert len(manager.list_installed()) == 0
+
+    def test_multiple_extensions(self, temp_dir, project_dir):
+        """Test installing multiple extensions."""
+        import yaml
+
+        # Create two extensions
+        for i in range(1, 3):
+            ext_dir = temp_dir / f"ext{i}"
+            ext_dir.mkdir()
+
+            manifest_data = {
+                "schema_version": "1.0",
+                "extension": {
+                    "id": f"ext{i}",
+                    "name": f"Extension {i}",
+                    "version": "1.0.0",
+                    "description": f"Extension {i}",
+                },
+                "requires": {"speckit_version": ">=0.1.0"},
+                "provides": {
+                    "commands": [
+                        {
+                            "name": f"speckit.ext{i}.cmd",
+                            "file": "commands/cmd.md",
+                        }
+                    ]
+                },
+            }
+
+            with open(ext_dir / "extension.yml", 'w') as f:
+                yaml.dump(manifest_data, f)
+
+            (ext_dir / "commands").mkdir()
+            (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\nTest")
+
+        manager = ExtensionManager(project_dir)
+
+        # Install both
+        manager.install_from_directory(temp_dir / "ext1", "0.1.0", register_commands=False)
+        manager.install_from_directory(temp_dir / "ext2", "0.1.0", register_commands=False)
+
+        # Verify both installed
+        installed = manager.list_installed()
+        assert len(installed) == 2
+        assert {ext["id"] for ext in installed} == {"ext1", "ext2"}
+
+        # Remove first
+        manager.remove("ext1")
+
+        # Verify only second remains
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "ext2"
+
+
+# ===== Extension Catalog Tests =====
+
+
+class TestExtensionCatalog:
+    """Test extension catalog functionality."""
+
+    def test_catalog_initialization(self, temp_dir):
+        """Test catalog initialization."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        assert catalog.project_root == project_dir
+        assert catalog.cache_dir == project_dir / ".specify" / "extensions" / ".cache"
+
+    def test_cache_directory_creation(self, temp_dir):
+        """Test catalog cache directory is created when fetching."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog data
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "test-ext": {
+                    "name": "Test Extension",
+                    "id": "test-ext",
+                    "version": "1.0.0",
+                    "description": "Test",
+                }
+            },
+        }
+
+        # Manually save to cache to test cache reading
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com/catalog.json",
+                }
+            )
+        )
+
+        # Should use cache
+        result = catalog.fetch_catalog()
+        assert result == catalog_data
+
+    def test_cache_expiration(self, temp_dir):
+        """Test that expired cache is not used."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create expired cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog_data = {"schema_version": "1.0", "extensions": {}}
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+
+        # Set cache time to 2 hours ago (expired)
+        expired_time = datetime.now(timezone.utc).timestamp() - 7200
+        expired_datetime = datetime.fromtimestamp(expired_time, tz=timezone.utc)
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": expired_datetime.isoformat(),
+                    "catalog_url": "http://test.com/catalog.json",
+                }
+            )
+        )
+
+        # Cache should be invalid
+        assert not catalog.is_cache_valid()
+
+    def test_search_all_extensions(self, temp_dir):
+        """Test searching all extensions without filters."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira integration",
+                    "author": "Stats Perform",
+                    "tags": ["issue-tracking", "jira"],
+                    "verified": True,
+                },
+                "linear": {
+                    "name": "Linear Integration",
+                    "id": "linear",
+                    "version": "0.9.0",
+                    "description": "Linear integration",
+                    "author": "Community",
+                    "tags": ["issue-tracking"],
+                    "verified": False,
+                },
+            },
+        }
+
+        # Save to cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search without filters
+        results = catalog.search()
+        assert len(results) == 2
+
+    def test_search_by_query(self, temp_dir):
+        """Test searching by query text."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira issue tracking",
+                    "tags": ["jira"],
+                },
+                "linear": {
+                    "name": "Linear Integration",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear project management",
+                    "tags": ["linear"],
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search for "jira"
+        results = catalog.search(query="jira")
+        assert len(results) == 1
+        assert results[0]["id"] == "jira"
+
+    def test_search_by_tag(self, temp_dir):
+        """Test searching by tag."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira",
+                    "tags": ["issue-tracking", "jira"],
+                },
+                "linear": {
+                    "name": "Linear",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear",
+                    "tags": ["issue-tracking", "linear"],
+                },
+                "github": {
+                    "name": "GitHub",
+                    "id": "github",
+                    "version": "1.0.0",
+                    "description": "GitHub",
+                    "tags": ["vcs", "github"],
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search by tag "issue-tracking"
+        results = catalog.search(tag="issue-tracking")
+        assert len(results) == 2
+        assert {r["id"] for r in results} == {"jira", "linear"}
+
+    def test_search_verified_only(self, temp_dir):
+        """Test searching verified extensions only."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira",
+                    "verified": True,
+                },
+                "linear": {
+                    "name": "Linear",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear",
+                    "verified": False,
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search verified only
+        results = catalog.search(verified_only=True)
+        assert len(results) == 1
+        assert results[0]["id"] == "jira"
+
+    def test_get_extension_info(self, temp_dir):
+        """Test getting specific extension info."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira integration",
+                    "author": "Stats Perform",
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Get extension info
+        info = catalog.get_extension_info("jira")
+        assert info is not None
+        assert info["id"] == "jira"
+        assert info["name"] == "Jira Integration"
+
+        # Non-existent extension
+        info = catalog.get_extension_info("nonexistent")
+        assert info is None
+
+    def test_clear_cache(self, temp_dir):
+        """Test clearing catalog cache."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text("{}")
+        catalog.cache_metadata_file.write_text("{}")
+
+        assert catalog.cache_file.exists()
+        assert catalog.cache_metadata_file.exists()
+
+        # Clear cache
+        catalog.clear_cache()
+
+        assert not catalog.cache_file.exists()
+        assert not catalog.cache_metadata_file.exists()