chore(deps): bump actions/setup-python from 5 to 6 (#1710)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.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/workflows/docs.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0 # Fetch all history for git info
 

.github/workflows/lint.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Run markdownlint-cli2
         uses: DavidAnson/markdownlint-cli2-action@v19

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

@@ -19,7 +19,7 @@ jobs:
         uses: astral-sh/setup-uv@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -39,7 +39,7 @@ jobs:
         uses: astral-sh/setup-uv@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

AGENTS.md

@@ -66,6 +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
     },
@@ -83,6 +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
 

CHANGELOG.md

@@ -2,18 +2,38 @@
 
 <!-- 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).
 
-## [0.1.4] - Unreleased
+## [0.1.6] - 2026-02-23
+
+### Fixed
+
+- **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
+
+## [0.1.5] - 2026-02-21
+
+### Fixed
+
+- **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
+
+## [0.1.4] - 2026-02-20
 
 ### 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] - Unreleased
+## [0.1.3] - 2026-02-20
 
 ### Added
 
@@ -60,7 +80,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [0.0.94] - 2026-02-11
 
 - Add stale workflow for 180-day inactive issues and PRs (#1594)
-
-## [0.0.93] - 2026-02-10
-
-- Add modular extension system (#1551)

docs/quickstart.md

@@ -81,6 +81,9 @@ Then, use the `/speckit.implement` slash command to execute the plan.
 /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:
@@ -135,7 +138,15 @@ Be specific about your tech stack and technical requirements:
 /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 6: Validate and Implement
+### Step 6: Define Tasks
+
+Generate an actionable task list using the `/speckit.tasks` command:
+
+```bash
+/speckit.tasks
+```
+
+### Step 7: Validate and Implement
 
 Have your AI agent audit the implementation plan using `/speckit.analyze`:
 
@@ -149,6 +160,9 @@ Finally, implement the solution:
 /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

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -456,18 +456,20 @@ Users install with:
 specify extension add --from https://github.com/.../spec-kit-my-ext-1.0.0.zip
 ```
 
-### Option 3: Extension Catalog (Future)
+### Option 3: Community Reference Catalog
 
-Submit to official catalog:
+Submit to the community catalog for public discovery:
 
 1. **Fork** spec-kit repository
-2. **Add entry** to `extensions/catalog.json`
+2. **Add entry** to `extensions/catalog.community.json`
-3. **Create PR**
+3. **Update** `extensions/README.md` with your extension
-4. **After merge**, users can install with:
+4. **Create PR** following the [Extension Publishing Guide](EXTENSION-PUBLISHING-GUIDE.md)
+5. **After merge**, your extension becomes available:
+   - Users can browse `catalog.community.json` to discover your extension
+   - Users copy the entry to their own `catalog.json`
+   - Users install with: `specify extension add my-ext` (from their catalog)
 
-   ```bash
+See the [Extension Publishing Guide](EXTENSION-PUBLISHING-GUIDE.md) for detailed submission instructions.
-   specify extension add my-ext  # No URL needed!
-   ```
 
 ---
 

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -129,26 +129,32 @@ specify extension add --from https://github.com/your-org/spec-kit-your-extension
 
 ## Submit to Catalog
 
+### Understanding the Catalogs
+
+Spec Kit uses a dual-catalog system. For details about how catalogs work, see the main [Extensions README](README.md#extension-catalogs).
+
+**For extension publishing**: All community extensions should be added to `catalog.community.json`. Users browse this catalog and copy extensions they trust into their own `catalog.json`.
+
 ### 1. Fork the spec-kit Repository
 
 ```bash
 # Fork on GitHub
-# https://github.com/statsperform/spec-kit/fork
+# https://github.com/github/spec-kit/fork
 
 # Clone your fork
 git clone https://github.com/YOUR-USERNAME/spec-kit.git
 cd spec-kit
 ```
 
-### 2. Add Extension to Catalog
+### 2. Add Extension to Community Catalog
 
-Edit `extensions/catalog.json` and add your extension:
+Edit `extensions/catalog.community.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",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "your-extension": {
       "name": "Your Extension Name",
@@ -198,15 +204,25 @@ Edit `extensions/catalog.json` and add your extension:
 - Use current timestamp for `created_at` and `updated_at`
 - Update the top-level `updated_at` to current time
 
-### 3. Submit Pull Request
+### 3. Update Extensions README
+
+Add your extension to the Available Extensions table in `extensions/README.md`:
+
+```markdown
+| Your Extension Name | Brief description of what it does | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
+```
+
+Insert your extension in alphabetical order in the table.
+
+### 4. Submit Pull Request
 
 ```bash
 # Create a branch
 git checkout -b add-your-extension
 
 # Commit your changes
-git add extensions/catalog.json
+git add extensions/catalog.community.json extensions/README.md
-git commit -m "Add your-extension to catalog
+git commit -m "Add your-extension to community catalog
 
 - Extension ID: your-extension
 - Version: 1.0.0
@@ -218,7 +234,7 @@ git commit -m "Add your-extension to catalog
 git push origin add-your-extension
 
 # Create Pull Request on GitHub
-# https://github.com/statsperform/spec-kit/compare
+# https://github.com/github/spec-kit/compare
 ```
 
 **Pull Request Template**:
@@ -243,6 +259,8 @@ Brief description of what your extension does.
 - [x] Extension tested on real project
 - [x] All commands working
 - [x] No security vulnerabilities
+- [x] Added to extensions/catalog.community.json
+- [x] Added to extensions/README.md Available Extensions table
 
 ### Testing
 Tested on:

extensions/EXTENSION-USER-GUIDE.md

@@ -46,7 +46,7 @@ Extensions are modular packages that add new commands and functionality to Spec
 ### Check Your Version
 
 ```bash
-specify --version
+specify version
 # Should show 0.1.0 or higher
 ```
 
@@ -76,13 +76,15 @@ vim .specify/extensions/jira/jira-config.yml
 
 ## Finding Extensions
 
+**Note**: By default, `specify extension search` uses your organization's catalog (`catalog.json`). If the catalog is empty, you won't see any results. See [Extension Catalogs](#extension-catalogs) to learn how to populate your catalog from the community reference catalog.
+
 ### Browse All Extensions
 
 ```bash
 specify extension search
 ```
 
-Shows all available extensions in the catalog.
+Shows all extensions in your organization's catalog.
 
 ### Search by Keyword
 
@@ -415,11 +417,15 @@ export SPECKIT_CATALOG_URL="https://example.com/staging/catalog.json"
 
 ---
 
+## Extension Catalogs
+
+For information about how Spec Kit's dual-catalog system works (`catalog.json` vs `catalog.community.json`), see the main [Extensions README](README.md#extension-catalogs).
+
 ## Organization Catalog Customization
 
-### Why the Default Catalog is Empty
+### Why Customize Your Catalog
 
-The default spec-kit catalog ships empty by design. This allows organizations to:
+Organizations customize their `catalog.json` to:
 
 - **Control available extensions** - Curate which extensions your team can install
 - **Host private extensions** - Internal tools that shouldn't be public

extensions/README.md

@@ -0,0 +1,119 @@
+# Spec Kit Extensions
+
+Extension system for [Spec Kit](https://github.com/github/spec-kit) - add new functionality without bloating the core framework.
+
+## Extension Catalogs
+
+Spec Kit provides two catalog files with different purposes:
+
+### Your Catalog (`catalog.json`)
+
+- **Purpose**: Default upstream catalog of extensions used by the Spec Kit CLI
+- **Default State**: Empty by design in the upstream project - you or your organization populate a fork/copy with extensions you trust
+- **Location (upstream)**: `extensions/catalog.json` in the GitHub-hosted spec-kit repo
+- **CLI Default**: The `specify extension` commands use the upstream catalog URL by default, unless overridden
+- **Org Catalog**: Point `SPECKIT_CATALOG_URL` at your organization's fork or hosted catalog JSON to use it instead of the upstream default
+- **Customization**: Copy entries from the community catalog into your org catalog, or add your own extensions directly
+
+**Example override:**
+```bash
+# Override the default upstream catalog with your organization's catalog
+export SPECKIT_CATALOG_URL="https://your-org.com/spec-kit/catalog.json"
+specify extension search  # Now uses your organization's catalog instead of the upstream default
+```
+
+### Community Reference Catalog (`catalog.community.json`)
+
+- **Purpose**: Browse available community-contributed extensions
+- **Status**: Active - contains extensions submitted by the community
+- **Location**: `extensions/catalog.community.json`
+- **Usage**: Reference catalog for discovering available extensions
+- **Submission**: Open to community contributions via Pull Request
+
+**How It Works:**
+
+## Making Extensions Available
+
+You control which extensions your team can discover and install:
+
+### Option 1: Curated Catalog (Recommended for Organizations)
+
+Populate your `catalog.json` with approved extensions:
+
+1. **Discover** extensions from various sources:
+   - Browse `catalog.community.json` for community extensions
+   - Find private/internal extensions in your organization's repos
+   - Discover extensions from trusted third parties
+2. **Review** extensions and choose which ones you want to make available
+3. **Add** those extension entries to your own `catalog.json`
+4. **Team members** can now discover and install them:
+   - `specify extension search` shows your curated catalog
+   - `specify extension add <name>` installs from your catalog
+
+**Benefits**: Full control over available extensions, team consistency, organizational approval workflow
+
+**Example**: Copy an entry from `catalog.community.json` to your `catalog.json`, then your team can discover and install it by name.
+
+### Option 2: Direct URLs (For Ad-hoc Use)
+
+Skip catalog curation - team members install directly using URLs:
+
+```bash
+specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
+```
+
+**Benefits**: Quick for one-off testing or private extensions
+
+**Tradeoff**: Extensions installed this way won't appear in `specify extension search` for other team members unless you also add them to your `catalog.json`.
+
+## Available Community Extensions
+
+The following community-contributed extensions are available in [`catalog.community.json`](catalog.community.json):
+
+| 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
+
+### Submission Process
+
+To add your extension to the community catalog:
+
+1. **Prepare your extension** following the [Extension Development Guide](EXTENSION-DEVELOPMENT-GUIDE.md)
+2. **Create a GitHub release** for your extension
+3. **Submit a Pull Request** that:
+   - Adds your extension to `extensions/catalog.community.json`
+   - Updates this README with your extension in the Available Extensions table
+4. **Wait for review** - maintainers will review and merge if criteria are met
+
+See the [Extension Publishing Guide](EXTENSION-PUBLISHING-GUIDE.md) for detailed step-by-step instructions.
+
+### Submission Checklist
+
+Before submitting, ensure:
+
+- ✅ Valid `extension.yml` manifest
+- ✅ Complete README with installation and usage instructions
+- ✅ LICENSE file included
+- ✅ GitHub release created with semantic version (e.g., v1.0.0)
+- ✅ Extension tested on a real project
+- ✅ All commands working as documented
+
+## Installing Extensions
+Once extensions are available (either in your catalog or via direct URL), install them:
+
+```bash
+# From your curated catalog (by name)
+specify extension search                  # See what's in your catalog
+specify extension add <extension-name>    # Install by name
+
+# Direct from URL (bypasses catalog)
+specify extension add --from https://github.com/<org>/<repo>/archive/refs/tags/<version>.zip
+
+# List installed extensions
+specify extension list
+```
+
+For more information, see the [Extension User Guide](EXTENSION-USER-GUIDE.md).

extensions/RFC-EXTENSION-SYSTEM.md

@@ -858,11 +858,41 @@ def should_execute_hook(hook: dict, config: dict) -> bool:
 
 ## Extension Discovery & Catalog
 
-### Central Catalog
+### Dual Catalog System
+
+Spec Kit uses two catalog files with different purposes:
+
+#### User Catalog (`catalog.json`)
 
 **URL**: `https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.json`
 
-**Format**:
+- **Purpose**: Organization's curated catalog of approved extensions
+- **Default State**: Empty by design - users populate with extensions they trust
+- **Usage**: Default catalog used by `specify extension` CLI commands
+- **Control**: Organizations maintain their own fork/version for their teams
+
+#### Community Reference Catalog (`catalog.community.json`)
+
+**URL**: `https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json`
+
+- **Purpose**: Reference catalog of available community-contributed extensions
+- **Verification**: Community extensions may have `verified: false` initially
+- **Status**: Active - open for community contributions
+- **Submission**: Via Pull Request following the Extension Publishing Guide
+- **Usage**: Browse to discover extensions, then copy to your `catalog.json`
+
+**How It Works:**
+
+1. **Discover**: Browse `catalog.community.json` to find available extensions
+2. **Review**: Evaluate extensions for security, quality, and organizational fit
+3. **Curate**: Copy approved extension entries from community catalog to your `catalog.json`
+4. **Install**: Use `specify extension add <name>` (pulls from your curated catalog)
+
+This approach gives organizations full control over which extensions are available to their teams while maintaining a shared community resource for discovery.
+
+### Catalog Format
+
+**Format** (same for both catalogs):
 
 ```json
 {
@@ -931,25 +961,52 @@ specify extension info jira
 
 ### Custom Catalogs
 
-Organizations can host private catalogs:
+**⚠️ FUTURE FEATURE - NOT YET IMPLEMENTED**
+
+The following catalog management commands are proposed design concepts but are not yet available in the current implementation:
 
 ```bash
-# Add custom catalog
+# Add custom catalog (FUTURE - NOT AVAILABLE)
 specify extension add-catalog https://internal.company.com/spec-kit/catalog.json
 
-# Set as default
+# Set as default (FUTURE - NOT AVAILABLE)
 specify extension set-catalog --default https://internal.company.com/spec-kit/catalog.json
 
-# List catalogs
+# List catalogs (FUTURE - NOT AVAILABLE)
 specify extension catalogs
 ```
 
-**Catalog priority**:
+**Proposed catalog priority** (future design):
 
-1. Project-specific catalog (`.specify/extension-catalogs.yml`)
+1. Project-specific catalog (`.specify/extension-catalogs.yml`) - *not implemented*
-2. User-level catalog (`~/.specify/extension-catalogs.yml`)
+2. User-level catalog (`~/.specify/extension-catalogs.yml`) - *not implemented*
 3. Default GitHub catalog
 
+#### Current Implementation: SPECKIT_CATALOG_URL
+
+**The currently available method** for using custom catalogs is the `SPECKIT_CATALOG_URL` environment variable:
+
+```bash
+# Point to your organization's catalog
+export SPECKIT_CATALOG_URL="https://internal.company.com/spec-kit/catalog.json"
+
+# All extension commands now use your custom catalog
+specify extension search       # Uses custom catalog
+specify extension add jira     # Installs from custom catalog
+```
+
+**Requirements:**
+- URL must use HTTPS (HTTP only allowed for localhost testing)
+- Catalog must follow the standard catalog.json schema
+- Must be publicly accessible or accessible within your network
+
+**Example for testing:**
+```bash
+# Test with localhost during development
+export SPECKIT_CATALOG_URL="http://localhost:8000/catalog.json"
+specify extension search
+```
+
 ---
 
 ## CLI Commands

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.example.json

@@ -1,60 +0,0 @@
-{
-  "schema_version": "1.0",
-  "updated_at": "2026-02-03T00:00:00Z",
-  "catalog_url": "https://your-org.example.com/speckit/catalog.json",
-  "extensions": {
-    "jira": {
-      "name": "Jira Integration",
-      "id": "jira",
-      "description": "Create Jira Epics, Stories, and 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",
-      "homepage": "https://github.com/your-org/spec-kit-jira",
-      "documentation": "https://github.com/your-org/spec-kit-jira/blob/main/README.md",
-      "changelog": "https://github.com/your-org/spec-kit-jira/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0",
-        "tools": [
-          {
-            "name": "atlassian",
-            "version": ">=1.0.0",
-            "required": true
-          }
-        ]
-      },
-      "provides": {
-        "commands": 3,
-        "hooks": 1
-      },
-      "tags": ["jira", "atlassian", "issue-tracking"],
-      "verified": true,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-01-28T00:00:00Z",
-      "updated_at": "2026-02-03T00:00:00Z"
-    },
-    "linear": {
-      "name": "Linear Integration",
-      "id": "linear",
-      "description": "Sync specs and tasks with Linear issues",
-      "author": "Your Organization",
-      "version": "1.0.0",
-      "download_url": "https://github.com/your-org/spec-kit-linear/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/your-org/spec-kit-linear",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 2
-      },
-      "tags": ["linear", "issue-tracking"],
-      "verified": false,
-      "created_at": "2026-01-30T00:00:00Z",
-      "updated_at": "2026-01-30T00:00:00Z"
-    }
-  }
-}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.1.4"
+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 = [

src/specify_cli/__init__.py

@@ -123,119 +123,138 @@ def _format_rate_limit_error(status_code: int, headers: httpx.Headers, url: str)
     
     return "\n".join(lines)
 
-# Agent configuration with name, folder, install URL, and CLI tool requirement
+# Agent configuration with name, folder, install URL, CLI tool requirement, and commands subdirectory
 AGENT_CONFIG = {
     "copilot": {
         "name": "GitHub Copilot",
         "folder": ".github/",
+        "commands_subdir": "agents",  # Special: uses agents/ not commands/
         "install_url": None,  # IDE-based, no CLI check needed
         "requires_cli": False,
     },
     "claude": {
         "name": "Claude Code",
         "folder": ".claude/",
+        "commands_subdir": "commands",
         "install_url": "https://docs.anthropic.com/en/docs/claude-code/setup",
         "requires_cli": True,
     },
     "gemini": {
         "name": "Gemini CLI",
         "folder": ".gemini/",
+        "commands_subdir": "commands",
         "install_url": "https://github.com/google-gemini/gemini-cli",
         "requires_cli": True,
     },
     "cursor-agent": {
         "name": "Cursor",
         "folder": ".cursor/",
+        "commands_subdir": "commands",
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "qwen": {
         "name": "Qwen Code",
         "folder": ".qwen/",
+        "commands_subdir": "commands",
         "install_url": "https://github.com/QwenLM/qwen-code",
         "requires_cli": True,
     },
     "opencode": {
         "name": "opencode",
         "folder": ".opencode/",
+        "commands_subdir": "command",  # Special: singular 'command' not 'commands'
         "install_url": "https://opencode.ai",
         "requires_cli": True,
     },
     "codex": {
         "name": "Codex CLI",
         "folder": ".codex/",
+        "commands_subdir": "prompts",  # Special: uses prompts/ not commands/
         "install_url": "https://github.com/openai/codex",
         "requires_cli": True,
     },
     "windsurf": {
         "name": "Windsurf",
         "folder": ".windsurf/",
+        "commands_subdir": "workflows",  # Special: uses workflows/ not commands/
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "kilocode": {
         "name": "Kilo Code",
         "folder": ".kilocode/",
+        "commands_subdir": "workflows",  # Special: uses workflows/ not commands/
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "auggie": {
         "name": "Auggie CLI",
         "folder": ".augment/",
+        "commands_subdir": "commands",
         "install_url": "https://docs.augmentcode.com/cli/setup-auggie/install-auggie-cli",
         "requires_cli": True,
     },
     "codebuddy": {
         "name": "CodeBuddy",
         "folder": ".codebuddy/",
+        "commands_subdir": "commands",
         "install_url": "https://www.codebuddy.ai/cli",
         "requires_cli": True,
     },
     "qodercli": {
         "name": "Qoder CLI",
         "folder": ".qoder/",
+        "commands_subdir": "commands",
         "install_url": "https://qoder.com/cli",
         "requires_cli": True,
     },
     "roo": {
         "name": "Roo Code",
         "folder": ".roo/",
+        "commands_subdir": "commands",
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "q": {
         "name": "Amazon Q Developer CLI",
         "folder": ".amazonq/",
+        "commands_subdir": "prompts",  # Special: uses prompts/ not commands/
         "install_url": "https://aws.amazon.com/developer/learning/q-developer-cli/",
         "requires_cli": True,
     },
     "amp": {
         "name": "Amp",
         "folder": ".agents/",
+        "commands_subdir": "commands",
         "install_url": "https://ampcode.com/manual#install",
         "requires_cli": True,
     },
     "shai": {
         "name": "SHAI",
         "folder": ".shai/",
+        "commands_subdir": "commands",
         "install_url": "https://github.com/ovh/shai",
         "requires_cli": True,
     },
     "agy": {
         "name": "Antigravity",
         "folder": ".agent/",
+        "commands_subdir": "workflows",  # Special: uses workflows/ not commands/
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "bob": {
         "name": "IBM Bob",
         "folder": ".bob/",
+        "commands_subdir": "commands",
         "install_url": None,  # IDE-based
         "requires_cli": False,
     },
     "generic": {
         "name": "Generic (bring your own agent)",
         "folder": None,  # Set dynamically via --ai-commands-dir
+        "commands_subdir": "commands",
         "install_url": None,
         "requires_cli": False,
     },
@@ -1056,10 +1075,11 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
     # download_and_extract_template() already placed the .md files here.
     agent_config = AGENT_CONFIG.get(selected_ai, {})
     agent_folder = agent_config.get("folder", "")
+    commands_subdir = agent_config.get("commands_subdir", "commands")
     if agent_folder:
-        templates_dir = project_path / agent_folder.rstrip("/") / "commands"
+        templates_dir = project_path / agent_folder.rstrip("/") / commands_subdir
     else:
-        templates_dir = project_path / "commands"
+        templates_dir = project_path / commands_subdir
 
     if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
         # Fallback: try the repo-relative path (for running from source checkout)
@@ -1236,6 +1256,20 @@ def init(
 
     show_banner()
 
+    # Detect when option values are likely misinterpreted flags (parameter ordering issue)
+    if ai_assistant and ai_assistant.startswith("--"):
+        console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
+        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
+        console.print("[yellow]Example:[/yellow] specify init --ai claude --here")
+        console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
+        raise typer.Exit(1)
+    
+    if ai_commands_dir and ai_commands_dir.startswith("--"):
+        console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
+        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
+        console.print("[yellow]Example:[/yellow] specify init --ai generic --ai-commands-dir .myagent/commands/")
+        raise typer.Exit(1)
+
     if project_name == ".":
         here = True
         project_name = None  # Clear project_name to use existing validation logic

templates/commands/plan.md

@@ -75,10 +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:
+2. **Define interface contracts** (if project has external interfaces) → `/contracts/`:
-   - For each user action → endpoint
+   - Identify what interfaces the project exposes to users or other systems
-   - Use standard REST/GraphQL patterns
+   - Document the contract format appropriate for the project type
-   - Output OpenAPI/GraphQL schema to `/contracts/`
+   - 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

@@ -235,7 +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

@@ -28,14 +28,14 @@ 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
@@ -112,13 +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
+   - Map each interface contract → to the user story it serves
-   - If tests requested: Each contract → contract test task [P] before implementation in that story's phase
+   - 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/plan-template.md

@@ -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/test_ai_skills.py

@@ -630,3 +630,65 @@ class TestCliValidation:
         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