fix(changelog): correct 0.4.1 section ordering and version reference (#1954)

* Initial plan

* fix(changelog): correct 0.4.1 section ordering and version reference

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/98bc10bc-f444-4833-bd3a-ab8ea0f5e192

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>

.github/ISSUE_TEMPLATE/extension_submission.yml

@@ -12,7 +12,7 @@ body:
         - 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 <extension-name> --from <your-release-url>`
+        - Test installation: `specify extension add --from <your-release-url>`
 
   - type: input
     id: extension-id
@@ -229,7 +229,7 @@ body:
       placeholder: |
         ```bash
         # Install extension
-        specify extension add <extension-name> --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+        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

.github/workflows/docs.yml

@@ -64,5 +64,5 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v5
+        uses: actions/deploy-pages@v4
 

.github/workflows/lint.yml

@@ -15,7 +15,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Run markdownlint-cli2
-        uses: DavidAnson/markdownlint-cli2-action@v23
+        uses: DavidAnson/markdownlint-cli2-action@v19
         with:
           globs: |
             '**/*.md'

.github/workflows/release-trigger.yml

@@ -100,16 +100,18 @@ jobs:
               COMMITS="- Initial release"
             fi
 
-            # Create new changelog entry — insert after the marker comment
+            # Create new changelog entry
-            NEW_ENTRY=$(printf '%s\n' \
+            {
-              "" \
+              head -n 8 CHANGELOG.md
-              "## [${{ steps.version.outputs.version }}] - $DATE" \
+              echo ""
-              "" \
+              echo "## [${{ steps.version.outputs.version }}] - $DATE"
-              "### Changed" \
+              echo ""
-              "" \
+              echo "### Changes"
-              "$COMMITS")
+              echo ""
-
+              echo "$COMMITS"
-            awk -v entry="$NEW_ENTRY" '/<!-- insert new changelog below this comment -->/ { print; print entry; next } {print}' CHANGELOG.md > CHANGELOG.md.tmp
+              echo ""
+              tail -n +9 CHANGELOG.md
+            } > CHANGELOG.md.tmp
             mv CHANGELOG.md.tmp CHANGELOG.md
 
             echo "✅ Updated CHANGELOG.md with commits since $PREVIOUS_TAG"

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

@@ -202,7 +202,8 @@ agent: $basename
 }
 
 # Create skills in <skills_dir>\<name>\SKILL.md format.
-# Skills use hyphenated names (e.g. speckit-plan).
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
 #
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
@@ -462,7 +463,7 @@ function Build-Variant {
         'kimi' {
             $skillsDir = Join-Path $baseDir ".kimi/skills"
             New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
-            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi'
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi' -Separator '.'
         }
         'trae' {
             $rulesDir = Join-Path $baseDir ".trae/rules"
@@ -497,13 +498,13 @@ $AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode'
 $AllScripts = @('sh', 'ps')
 
 function Normalize-List {
-    param([string]$Value)
+    param([string]$Input)
 
-    if ([string]::IsNullOrEmpty($Value)) {
+    if ([string]::IsNullOrEmpty($Input)) {
         return @()
     }
 
-    $items = $Value -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
+    $items = $Input -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
     return $items
 }
 
@@ -526,7 +527,7 @@ function Validate-Subset {
 
 # Determine agent list
 if (-not [string]::IsNullOrEmpty($Agents)) {
-    $AgentList = Normalize-List -Value $Agents
+    $AgentList = Normalize-List -Input $Agents
     if (-not (Validate-Subset -Type 'agent' -Allowed $AllAgents -Items $AgentList)) {
         exit 1
     }
@@ -536,7 +537,7 @@ if (-not [string]::IsNullOrEmpty($Agents)) {
 
 # Determine script list
 if (-not [string]::IsNullOrEmpty($Scripts)) {
-    $ScriptList = Normalize-List -Value $Scripts
+    $ScriptList = Normalize-List -Input $Scripts
     if (-not (Validate-Subset -Type 'script' -Allowed $AllScripts -Items $ScriptList)) {
         exit 1
     }

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

@@ -140,7 +140,8 @@ EOF
 }
 
 # Create skills in <skills_dir>/<name>/SKILL.md format.
-# Skills use hyphenated names (e.g. speckit-plan).
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
 #
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
@@ -320,7 +321,7 @@ build_variant() {
       generate_commands vibe md "\$ARGUMENTS" "$base_dir/.vibe/prompts" "$script" ;;
     kimi)
       mkdir -p "$base_dir/.kimi/skills"
-      create_skills "$base_dir/.kimi/skills" "$script" "kimi" ;;
+      create_skills "$base_dir/.kimi/skills" "$script" "kimi" "." ;;
     trae)
       mkdir -p "$base_dir/.trae/rules"
       generate_commands trae md "\$ARGUMENTS" "$base_dir/.trae/rules" "$script" ;;

README.md

@@ -22,10 +22,7 @@
 - [🤔 What is Spec-Driven Development?](#-what-is-spec-driven-development)
 - [⚡ Get Started](#-get-started)
 - [📽️ Video Overview](#️-video-overview)
-- [🧩 Community Extensions](#-community-extensions)
-- [🎨 Community Presets](#-community-presets)
 - [🚶 Community Walkthroughs](#-community-walkthroughs)
-- [🛠️ Community Friends](#️-community-friends)
 - [🤖 Supported AI Agents](#-supported-ai-agents)
 - [🔧 Specify CLI Reference](#-specify-cli-reference)
 - [🧩 Making Spec Kit Your Own: Extensions & Presets](#-making-spec-kit-your-own-extensions--presets)
@@ -158,76 +155,6 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 
 [![Spec Kit video header](/media/spec-kit-video-header.jpg)](https://www.youtube.com/watch?v=a9eR1xsfvHg&pp=0gcJCckJAYcqIYzv)
 
-## 🧩 Community Extensions
-
-The following community-contributed extensions are available in [`catalog.community.json`](extensions/catalog.community.json):
-
-**Categories:**
-
-- `docs` — reads, validates, or generates spec artifacts
-- `code` — reviews, validates, or modifies source code
-- `process` — orchestrates workflow across phases
-- `integration` — syncs with external platforms
-- `visibility` — reports on project health or progress
-
-**Effect:**
-
-- `Read-only` — produces reports without modifying files
-- `Read+Write` — modifies files, creates artifacts, or updates specs
-
-| Extension | Purpose | Category | Effect | URL |
-|-----------|---------|----------|--------|-----|
-| AI-Driven Engineering (AIDE) | A structured 7-step workflow for building new projects from scratch with AI assistants — from vision through implementation | `process` | Read+Write | [aide](https://github.com/mnriem/spec-kit-extensions/tree/main/aide) |
-| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
-| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
-| Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
-| 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 | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
-| Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
-| Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
-| Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
-| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
-| Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
-| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
-| Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
-| MAQA — Multi-Agent & Quality Assurance | Coordinator → feature → QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins. Optional CI gate. | `process` | Read+Write | [spec-kit-maqa-ext](https://github.com/GenieRobot/spec-kit-maqa-ext) |
-| MAQA Azure DevOps Integration | Azure DevOps Boards integration for MAQA — syncs User Stories and Task children as features progress | `integration` | Read+Write | [spec-kit-maqa-azure-devops](https://github.com/GenieRobot/spec-kit-maqa-azure-devops) |
-| MAQA CI/CD Gate | Auto-detects GitHub Actions, CircleCI, GitLab CI, and Bitbucket Pipelines. Blocks QA handoff until pipeline is green. | `process` | Read+Write | [spec-kit-maqa-ci](https://github.com/GenieRobot/spec-kit-maqa-ci) |
-| MAQA GitHub Projects Integration | GitHub Projects v2 integration for MAQA — syncs draft issues and Status columns as features progress | `integration` | Read+Write | [spec-kit-maqa-github-projects](https://github.com/GenieRobot/spec-kit-maqa-github-projects) |
-| MAQA Jira Integration | Jira integration for MAQA — syncs Stories and Subtasks as features progress through the board | `integration` | Read+Write | [spec-kit-maqa-jira](https://github.com/GenieRobot/spec-kit-maqa-jira) |
-| MAQA Linear Integration | Linear integration for MAQA — syncs issues and sub-issues across workflow states as features progress | `integration` | Read+Write | [spec-kit-maqa-linear](https://github.com/GenieRobot/spec-kit-maqa-linear) |
-| MAQA Trello Integration | Trello board integration for MAQA — populates board from specs, moves cards, real-time checklist ticking | `integration` | Read+Write | [spec-kit-maqa-trello](https://github.com/GenieRobot/spec-kit-maqa-trello) |
-| Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
-| Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
-| Presetify | Create and validate presets and preset catalogs | `process` | Read+Write | [presetify](https://github.com/mnriem/spec-kit-extensions/tree/main/presetify) |
-| Product Forge | Full product lifecycle: research → product spec → SpecKit → implement → verify → test | `process` | Read+Write | [speckit-product-forge](https://github.com/VaiYav/speckit-product-forge) |
-| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
-| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
-| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
-| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
-| Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
-| Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
-| Superpowers Bridge | Orchestrates obra/superpowers skills within the spec-kit SDD workflow across the full lifecycle (clarification, TDD, review, verification, critique, debugging, branch completion) | `process` | Read+Write | [superpowers-bridge](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/superpowers-bridge) |
-| Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
-| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | `docs` | Read-only | [understanding](https://github.com/Testimonial/understanding) |
-| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
-| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
-| Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
-
-To submit your own extension, see the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md).
-
-## 🎨 Community Presets
-
-The following community-contributed presets customize how Spec Kit behaves — overriding templates, commands, and terminology without changing any tooling. Presets are available in [`catalog.community.json`](presets/catalog.community.json):
-
-| Preset | Purpose | Provides | Requires | URL |
-|--------|---------|----------|----------|-----|
-| AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
-| Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
-
-To build and publish your own preset, see the [Presets Publishing Guide](presets/PUBLISHING.md).
-
 ## 🚶 Community Walkthroughs
 
 See Spec-Driven Development in action across different scenarios with these community-contributed walkthroughs:
@@ -246,14 +173,6 @@ See Spec-Driven Development in action across different scenarios with these comm
 
 - **[Greenfield Spring Boot + React with a custom extension](https://github.com/mnriem/spec-kit-aide-extension-demo)** — Walks through the **AIDE extension**, a community extension that adds an alternative spec-driven workflow to spec-kit with high-level specs (vision) and low-level specs (work items) organized in a 7-step iterative lifecycle: vision → roadmap → progress tracking → work queue → work items → execution → feedback loops. Uses a family trading platform (Spring Boot 4, React 19, PostgreSQL, Docker Compose) as the scenario to illustrate how the extension mechanism lets you plug in a different style of spec-driven development without changing any core tooling — truly utilizing the "Kit" in Spec Kit.
 
-## 🛠️ Community Friends
-
-Community projects that extend, visualize, or build on Spec Kit:
-
-- **[cc-sdd](https://github.com/rhuss/cc-sdd)** - A Claude Code plugin that adds composable traits on top of Spec Kit with [Superpowers](https://github.com/obra/superpowers)-based quality gates, spec/code review, git worktree isolation, and parallel implementation via agent teams.
-
-- **[Spec Kit Assistant](https://marketplace.visualstudio.com/items?itemName=rfsales.speckit-assistant)** — A VS Code extension that provides a visual orchestrator for the full SDD workflow (constitution → specification → planning → tasks → implementation) with phase status visualization, an interactive task checklist, DAG visualization, and support for Claude, Gemini, GitHub Copilot, and OpenAI backends. Requires the `specify` CLI in your PATH.
-
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |
@@ -312,7 +231,7 @@ The `specify` command supports the following options:
 | `--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`). Extension commands are also auto-registered as skills when extensions are added later.                                                                                                                                                                                               |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                                                                                                                                                                                                                       |
 | `--branch-numbering`   | Option   | Branch numbering strategy: `sequential` (default — `001`, `002`, `003`) or `timestamp` (`YYYYMMDD-HHMMSS`). Timestamp mode is useful for distributed teams to avoid numbering conflicts                                                                                                                                                                                                  |
 
 ### Examples
@@ -463,7 +382,7 @@ specify extension add <extension-name>
 
 For example, extensions could add Jira integration, post-implementation code review, V-Model test traceability, or project health diagnostics.
 
-See the [Extensions README](./extensions/README.md) for the full guide and how to build and publish your own. Browse the [community extensions](#-community-extensions) above for what's available.
+See the [Extensions README](./extensions/README.md) for the full guide, the complete community catalog, and how to build and publish your own.
 
 ### Presets — Customize Existing Workflows
 

TESTING.md

@@ -1,79 +0,0 @@
-# Manual Testing Guide
-
-Any change that affects a slash command's behavior requires manually testing that command through an AI agent and submitting results with the PR.
-
-## Process
-
-1. **Identify affected commands** — use the [prompt below](#determining-which-tests-to-run) to have your agent analyze your changed files and determine which commands need testing.
-2. **Set up a test project** — scaffold from your local branch (see [Setup](#setup)).
-3. **Run each affected command** — invoke it in your agent, verify it completes successfully, and confirm it produces the expected output (files created, scripts executed, artifacts populated).
-4. **Run prerequisites first** — commands that depend on earlier commands (e.g., `/speckit.tasks` requires `/speckit.plan` which requires `/speckit.specify`) must be run in order.
-5. **Report results** — paste the [reporting template](#reporting-results) into your PR with pass/fail for each command tested.
-
-## Setup
-
-```bash
-# Install the CLI from your local branch
-cd <spec-kit-repo>
-uv venv .venv
-source .venv/bin/activate  # On Windows: .venv\Scripts\activate
-uv pip install -e .
-
-# Initialize a test project using your local changes
-specify init /tmp/speckit-test --ai <agent> --offline
-cd /tmp/speckit-test
-
-# Open in your agent
-```
-
-## Reporting results
-
-Paste this into your PR:
-
-~~~markdown
-## Manual test results
-
-**Agent**: [e.g., GitHub Copilot in VS Code]  |  **OS/Shell**: [e.g., macOS/zsh]
-
-| Command tested | Notes |
-|----------------|-------|
-| `/speckit.command` | |
-~~~
-
-## Determining which tests to run
-
-Copy this prompt into your agent. Include the agent's response (selected tests plus a brief explanation of the mapping) in your PR.
-
-~~~text
-Read TESTING.md, then run `git diff --name-only main` to get my changed files.
-For each changed file, determine which slash commands it affects by reading
-the command templates in templates/commands/ to understand what each command
-invokes. Use these mapping rules:
-
-- templates/commands/X.md → the command it defines
-- scripts/bash/Y.sh or scripts/powershell/Y.ps1 → every command that invokes that script (grep templates/commands/ for the script name). Also check transitive dependencies: if the changed script is sourced by other scripts (e.g., common.sh is sourced by create-new-feature.sh, check-prerequisites.sh, setup-plan.sh, update-agent-context.sh), then every command invoking those downstream scripts is also affected
-- templates/Z-template.md → every command that consumes that template during execution
-- src/specify_cli/*.py → CLI commands (`specify init`, `specify check`, `specify extension *`, `specify preset *`); test the affected CLI command and, for init/scaffolding changes, at minimum test /speckit.specify
-- extensions/X/commands/* → the extension command it defines
-- extensions/X/scripts/* → every extension command that invokes that script
-- extensions/X/extension.yml or config-template.yml → every command in that extension. Also check if the manifest defines hooks (look for `hooks:` entries like `before_specify`, `after_implement`, etc.) — if so, the core commands those hooks attach to are also affected
-- presets/*/* → test preset scaffolding via `specify init` with the preset
-- pyproject.toml → packaging/bundling; test `specify init` and verify bundled assets
-
-Include prerequisite tests (e.g., T5 requires T3 requires T1).
-
-Output in this format:
-
-### Test selection reasoning
-
-| Changed file | Affects | Test | Why |
-|---|---|---|---|
-| (path) | (command) | T# | (reason) |
-
-### Required tests
-
-Number each test sequentially (T1, T2, ...). List prerequisite tests first.
-
-- T1: /speckit.command — (reason)
-- T2: /speckit.command — (reason)
-~~~

extensions/EXTENSION-API-REFERENCE.md

@@ -44,7 +44,7 @@ provides:
     - 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, same pattern as name; namespace must match extension.id and must not shadow core or installed extension commands
+      aliases: [string]  # Optional, array of alternate names
 
   config:                # Optional, array of config files
     - name: string       # Config file name

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -41,7 +41,7 @@ provides:
     - name: "speckit.my-ext.hello"      # Must follow pattern: speckit.{ext-id}.{cmd}
       file: "commands/hello.md"
       description: "Say hello"
-      aliases: ["speckit.my-ext.hi"]    # Optional aliases, same pattern
+      aliases: ["speckit.hello"]        # Optional aliases
 
   config:                               # Optional: Config files
     - name: "my-ext-config.yml"
@@ -186,7 +186,7 @@ What the extension provides.
 - `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; each must match `speckit.{ext-id}.{command}`)
+- `aliases`: Alternative command names (optional, array)
 
 ### Optional Fields
 
@@ -514,7 +514,7 @@ zip -r spec-kit-my-ext-1.0.0.zip extension.yml commands/ scripts/ docs/
 Users install with:
 
 ```bash
-specify extension add <extension-name> --from https://github.com/.../spec-kit-my-ext-1.0.0.zip
+specify extension add --from https://github.com/.../spec-kit-my-ext-1.0.0.zip
 ```
 
 ### Option 3: Community Reference Catalog
@@ -523,7 +523,7 @@ Submit to the community catalog for public discovery:
 
 1. **Fork** spec-kit repository
 2. **Add entry** to `extensions/catalog.community.json`
-3. **Update** the Community Extensions table in `README.md` with your extension
+3. **Update** `extensions/README.md` with your extension
 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

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -122,7 +122,7 @@ Test that users can install from your release:
 specify extension add --dev /path/to/your-extension
 
 # Test from GitHub archive
-specify extension add <extension-name> --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+specify extension add --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
 ```
 
 ---
@@ -204,9 +204,9 @@ Edit `extensions/catalog.community.json` and add your extension:
 - Use current timestamp for `created_at` and `updated_at`
 - Update the top-level `updated_at` to current time
 
-### 3. Update Community Extensions Table
+### 3. Update Extensions README
 
-Add your extension to the Community Extensions table in the project root `README.md`:
+Add your extension to the Available Extensions table in `extensions/README.md`:
 
 ```markdown
 | Your Extension Name | Brief description of what it does | `<category>` | <effect> | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
@@ -234,7 +234,7 @@ Insert your extension in alphabetical order in the table.
 git checkout -b add-your-extension
 
 # Commit your changes
-git add extensions/catalog.community.json README.md
+git add extensions/catalog.community.json extensions/README.md
 git commit -m "Add your-extension to community catalog
 
 - Extension ID: your-extension
@@ -273,7 +273,7 @@ Brief description of what your extension does.
 - [x] All commands working
 - [x] No security vulnerabilities
 - [x] Added to extensions/catalog.community.json
-- [x] Added to Community Extensions table in README.md
+- [x] Added to extensions/README.md Available Extensions table
 
 ### Testing
 Tested on:

extensions/EXTENSION-USER-GUIDE.md

@@ -160,7 +160,7 @@ This will:
 
 ```bash
 # From GitHub release
-specify extension add <extension-name> --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
+specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
 ```
 
 ### Install from Local Directory (Development)
@@ -187,21 +187,6 @@ Provided commands:
    Check: .specify/extensions/jira/
 ```
 
-### Automatic Agent Skill Registration
-
-If your project was initialized with `--ai-skills`, extension commands are **automatically registered as agent skills** during installation. This ensures that extensions are discoverable by agents that use the [agentskills.io](https://agentskills.io) skill specification.
-
-```text
-✓ Extension installed successfully!
-
-Jira Integration (v1.0.0)
-  ...
-
-✓ 3 agent skill(s) auto-registered
-```
-
-When an extension is removed, its corresponding skills are also cleaned up automatically. Pre-existing skills that were manually customized are never overwritten.
-
 ---
 
 ## Using Extensions
@@ -214,8 +199,8 @@ Extensions add commands that appear in your AI agent (Claude Code):
 # In Claude Code
 > /speckit.jira.specstoissues
 
-# Or use a namespaced alias (if provided)
+# Or use short alias (if provided)
-> /speckit.jira.sync
+> /speckit.specstoissues
 ```
 
 ### Extension Configuration
@@ -737,7 +722,7 @@ You can still install extensions not in your catalog using `--from`:
 specify extension add jira
 
 # Direct URL (bypasses catalog)
-specify extension add <extension-name> --from https://github.com/someone/spec-kit-ext/archive/v1.0.0.zip
+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
@@ -807,7 +792,7 @@ specify extension add --dev /path/to/extension
 2. Install older version of extension:
 
    ```bash
-   specify extension add <extension-name> --from https://github.com/org/ext/archive/v1.0.0.zip
+   specify extension add --from https://github.com/org/ext/archive/v1.0.0.zip
    ```
 
 ### MCP Tool Not Available

extensions/README.md

@@ -59,7 +59,7 @@ Populate your `catalog.json` with approved extensions:
 Skip catalog curation - team members install directly using URLs:
 
 ```bash
-specify extension add <extension-name> --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
+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
@@ -68,9 +68,37 @@ specify extension add <extension-name> --from https://github.com/org/spec-kit-ex
 
 ## Available Community Extensions
 
-See the [Community Extensions](../README.md#-community-extensions) section in the main README for the full list of available community-contributed extensions.
+The following community-contributed extensions are available in [`catalog.community.json`](catalog.community.json):
 
-For the raw catalog data, see [`catalog.community.json`](catalog.community.json).
+**Categories:** `docs` — reads, validates, or generates spec artifacts · `code` — reviews, validates, or modifies source code · `process` — orchestrates workflow across phases · `integration` — syncs with external platforms · `visibility` — reports on project health or progress
+
+**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
+
+| Extension | Purpose | Category | Effect | URL |
+|-----------|---------|----------|--------|-----|
+| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
+| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
+| Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
+| 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 | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
+| Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
+| Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |
+| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
+| Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
+| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
+| Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
+| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
+| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
+| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
+| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
+| Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
+| Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
+| SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
+| Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
+| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | `docs` | Read-only | [understanding](https://github.com/Testimonial/understanding) |
+| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
+| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
+| Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
 
 
 ## Adding Your Extension
@@ -108,7 +136,7 @@ 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 <extension-name> --from https://github.com/<org>/<repo>/archive/refs/tags/<version>.zip
+specify extension add --from https://github.com/<org>/<repo>/archive/refs/tags/<version>.zip
 
 # List installed extensions
 specify extension list

extensions/RFC-EXTENSION-SYSTEM.md

@@ -223,7 +223,7 @@ provides:
     - name: "speckit.jira.specstoissues"
       file: "commands/specstoissues.md"
       description: "Create Jira hierarchy from spec and tasks"
-      aliases: ["speckit.jira.sync"]  # Alternate names
+      aliases: ["speckit.specstoissues"]  # Alternate names
 
     - name: "speckit.jira.discover-fields"
       file: "commands/discover-fields.md"
@@ -1517,7 +1517,7 @@ specify extension add github-projects
 /speckit.github.taskstoissues
 ```
 
-**Migration alias** (if needed):
+**Compatibility shim** (if needed):
 
 ```yaml
 # extension.yml
@@ -1525,10 +1525,10 @@ provides:
   commands:
     - name: "speckit.github.taskstoissues"
       file: "commands/taskstoissues.md"
-      aliases: ["speckit.github.sync-taskstoissues"]  # Alternate namespaced entry point
+      aliases: ["speckit.taskstoissues"]  # Backward compatibility
 ```
 
-AI agents register both names, so callers can migrate to the alternate alias without relying on deprecated global shortcuts like `/speckit.taskstoissues`.
+AI agent registers both names, so old scripts work.
 
 ---
 

extensions/catalog.community.json

@@ -1,41 +1,8 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-30T00:00:00Z",
+  "updated_at": "2026-03-19T12:08:20Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
-    "aide": {
-      "name": "AI-Driven Engineering (AIDE)",
-      "id": "aide",
-      "description": "A structured 7-step workflow for building new projects from scratch with AI assistants — from vision through implementation.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/aide-v1.0.0/aide.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/aide/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/aide/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 7,
-        "hooks": 0
-      },
-      "tags": [
-        "workflow",
-        "project-management",
-        "ai-driven",
-        "new-project",
-        "planning",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
     "archive": {
       "name": "Archive Extension",
       "id": "archive",
@@ -242,7 +209,7 @@
       "updated_at": "2026-03-19T12:08:20Z"
     },
     "docguard": {
-      "name": "DocGuard — CDD Enforcement",
+      "name": "DocGuard \u2014 CDD Enforcement",
       "id": "docguard",
       "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies.",
       "author": "raccioly",
@@ -314,37 +281,6 @@
       "created_at": "2026-03-13T00:00:00Z",
       "updated_at": "2026-03-13T00:00:00Z"
     },
-    "extensify": {
-      "name": "Extensify",
-      "id": "extensify",
-      "description": "Create and validate extensions and extension catalogs.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/extensify-v1.0.0/extensify.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/extensify/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/extensify/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 4,
-        "hooks": 0
-      },
-      "tags": [
-        "extensions",
-        "workflow",
-        "validation",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
     "fleet": {
       "name": "Fleet Orchestrator",
       "id": "fleet",
@@ -437,390 +373,6 @@
       "created_at": "2026-03-05T00:00:00Z",
       "updated_at": "2026-03-05T00:00:00Z"
     },
-    "learn": {
-      "name": "Learning Extension",
-      "id": "learn",
-      "description": "Generate educational guides from implementations and enhance clarifications with mentoring context.",
-      "author": "Vianca Martinez",
-      "version": "1.0.0",
-      "download_url": "https://github.com/imviancagrace/spec-kit-learn/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/imviancagrace/spec-kit-learn",
-      "homepage": "https://github.com/imviancagrace/spec-kit-learn",
-      "documentation": "https://github.com/imviancagrace/spec-kit-learn/blob/main/README.md",
-      "changelog": "https://github.com/imviancagrace/spec-kit-learn/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 1
-      },
-      "tags": [
-        "learning",
-        "education",
-        "mentoring",
-        "knowledge-transfer"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-17T00:00:00Z",
-      "updated_at": "2026-03-17T00:00:00Z"
-    },
-    "maqa": {
-      "name": "MAQA — Multi-Agent & Quality Assurance",
-      "id": "maqa",
-      "description": "Coordinator → feature → QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins (Trello, Linear, GitHub Projects, Jira, Azure DevOps). Optional CI gate.",
-      "author": "GenieRobot",
-      "version": "0.1.3",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-ext/releases/download/maqa-v0.1.3/maqa.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-ext",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-ext",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-ext/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-ext/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 4,
-        "hooks": 1
-      },
-      "tags": [
-        "multi-agent",
-        "orchestration",
-        "quality-assurance",
-        "workflow",
-        "parallel",
-        "tdd"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-26T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-azure-devops": {
-      "name": "MAQA Azure DevOps Integration",
-      "id": "maqa-azure-devops",
-      "description": "Azure DevOps Boards integration for the MAQA extension. Populates work items from specs, moves User Stories across columns as features progress, real-time Task child ticking.",
-      "author": "GenieRobot",
-      "version": "0.1.0",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/releases/download/maqa-azure-devops-v0.1.0/maqa-azure-devops.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "azure-devops",
-        "project-management",
-        "multi-agent",
-        "maqa",
-        "kanban"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-ci": {
-      "name": "MAQA CI/CD Gate",
-      "id": "maqa-ci",
-      "description": "CI/CD pipeline gate for the MAQA extension. Auto-detects GitHub Actions, CircleCI, GitLab CI, and Bitbucket Pipelines. Blocks QA handoff until pipeline is green.",
-      "author": "GenieRobot",
-      "version": "0.1.0",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-ci/releases/download/maqa-ci-v0.1.0/maqa-ci.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-ci",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-ci",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-ci/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-ci/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "ci-cd",
-        "github-actions",
-        "circleci",
-        "gitlab-ci",
-        "quality-gate",
-        "maqa"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-github-projects": {
-      "name": "MAQA GitHub Projects Integration",
-      "id": "maqa-github-projects",
-      "description": "GitHub Projects v2 integration for the MAQA extension. Populates draft issues from specs, moves items across Status columns as features progress, real-time task list ticking.",
-      "author": "GenieRobot",
-      "version": "0.1.0",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/releases/download/maqa-github-projects-v0.1.0/maqa-github-projects.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-github-projects",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-github-projects",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "github-projects",
-        "project-management",
-        "multi-agent",
-        "maqa",
-        "kanban"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-jira": {
-      "name": "MAQA Jira Integration",
-      "id": "maqa-jira",
-      "description": "Jira integration for the MAQA extension. Populates Stories from specs, moves issues across board columns as features progress, real-time Subtask ticking.",
-      "author": "GenieRobot",
-      "version": "0.1.0",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-jira/releases/download/maqa-jira-v0.1.0/maqa-jira.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-jira",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-jira",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-jira/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-jira/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "jira",
-        "project-management",
-        "multi-agent",
-        "maqa",
-        "kanban"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-linear": {
-      "name": "MAQA Linear Integration",
-      "id": "maqa-linear",
-      "description": "Linear integration for the MAQA extension. Populates issues from specs, moves items across workflow states as features progress, real-time sub-issue ticking.",
-      "author": "GenieRobot",
-      "version": "0.1.0",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-linear/releases/download/maqa-linear-v0.1.0/maqa-linear.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-linear",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-linear",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-linear/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-linear/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "linear",
-        "project-management",
-        "multi-agent",
-        "maqa",
-        "kanban"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T00:00:00Z",
-      "updated_at": "2026-03-27T00:00:00Z"
-    },
-    "maqa-trello": {
-      "name": "MAQA Trello Integration",
-      "id": "maqa-trello",
-      "description": "Trello board integration for the MAQA extension. Populates board from specs, moves cards between lists as features progress, real-time checklist ticking.",
-      "author": "GenieRobot",
-      "version": "0.1.1",
-      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-trello/releases/download/maqa-trello-v0.1.1/maqa-trello.zip",
-      "repository": "https://github.com/GenieRobot/spec-kit-maqa-trello",
-      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-trello",
-      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-trello/blob/main/README.md",
-      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-trello/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.3.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 0
-      },
-      "tags": [
-        "trello",
-        "project-management",
-        "multi-agent",
-        "maqa",
-        "kanban"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-26T00:00:00Z",
-      "updated_at": "2026-03-26T00:00:00Z"
-    },
-    "onboard": {
-      "name": "Onboard",
-      "id": "onboard",
-      "description": "Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step.",
-      "author": "Rafael Sales",
-      "version": "2.1.0",
-      "download_url": "https://github.com/dmux/spec-kit-onboard/archive/refs/tags/v2.1.0.zip",
-      "repository": "https://github.com/dmux/spec-kit-onboard",
-      "homepage": "https://github.com/dmux/spec-kit-onboard",
-      "documentation": "https://github.com/dmux/spec-kit-onboard/blob/main/README.md",
-      "changelog": "https://github.com/dmux/spec-kit-onboard/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 7,
-        "hooks": 3
-      },
-      "tags": [
-        "onboarding",
-        "learning",
-        "mentoring",
-        "developer-experience",
-        "gamification",
-        "knowledge-transfer"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-26T00:00:00Z",
-      "updated_at": "2026-03-26T00:00:00Z"
-    },
-    "plan-review-gate": {
-      "name": "Plan Review Gate",
-      "id": "plan-review-gate",
-      "description": "Require spec.md and plan.md to be merged via MR/PR before allowing task generation",
-      "author": "luno",
-      "version": "1.0.0",
-      "download_url": "https://github.com/luno/spec-kit-plan-review-gate/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/luno/spec-kit-plan-review-gate",
-      "homepage": "https://github.com/luno/spec-kit-plan-review-gate",
-      "documentation": "https://github.com/luno/spec-kit-plan-review-gate/blob/main/README.md",
-      "changelog": "https://github.com/luno/spec-kit-plan-review-gate/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 1,
-        "hooks": 1
-      },
-      "tags": [
-        "review",
-        "quality",
-        "workflow",
-        "gate"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-27T08:22:30Z",
-      "updated_at": "2026-03-27T08:22:30Z"
-    },
-    "presetify": {
-      "name": "Presetify",
-      "id": "presetify",
-      "description": "Create and validate presets and preset catalogs.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/presetify-v1.0.0/presetify.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/presetify/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/presetify/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 4,
-        "hooks": 0
-      },
-      "tags": [
-        "presets",
-        "workflow",
-        "templates",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
-    "product-forge": {
-      "name": "Product Forge",
-      "id": "product-forge",
-      "description": "Full product lifecycle: research \u2192 product spec \u2192 SpecKit \u2192 implement \u2192 verify \u2192 test",
-      "author": "VaiYav",
-      "version": "1.1.1",
-      "download_url": "https://github.com/VaiYav/speckit-product-forge/archive/refs/tags/v1.1.1.zip",
-      "repository": "https://github.com/VaiYav/speckit-product-forge",
-      "homepage": "https://github.com/VaiYav/speckit-product-forge",
-      "documentation": "https://github.com/VaiYav/speckit-product-forge/blob/main/README.md",
-      "changelog": "https://github.com/VaiYav/speckit-product-forge/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 10,
-        "hooks": 0
-      },
-      "tags": [
-        "process",
-        "research",
-        "product-spec",
-        "lifecycle",
-        "testing"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-28T00:00:00Z",
-      "updated_at": "2026-03-28T00:00:00Z"
-    },
     "ralph": {
       "name": "Ralph Loop",
       "id": "ralph",
@@ -991,81 +543,6 @@
       "created_at": "2026-03-18T00:00:00Z",
       "updated_at": "2026-03-18T00:00:00Z"
     },
-    "status": {
-      "name": "Project Status",
-      "id": "status",
-      "description": "Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary.",
-      "author": "KhawarHabibKhan",
-      "version": "1.0.0",
-      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
-      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
-      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
-      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 1,
-        "hooks": 0
-      },
-      "tags": [
-        "status",
-        "workflow",
-        "progress",
-        "feature-tracking",
-        "task-progress"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-16T00:00:00Z",
-      "updated_at": "2026-03-16T00:00:00Z"
-    },
-    "superb": {
-      "name": "Superpowers Bridge",
-      "id": "superb",
-      "description": "Orchestrates obra/superpowers skills within the spec-kit SDD workflow. Thin bridge commands delegate to superpowers' authoritative SKILL.md files at runtime (with graceful fallback), while bridge-original commands provide spec-kit-native value. Eight commands cover the full lifecycle: intent clarification, TDD enforcement, task review, verification, critique, systematic debugging, branch completion, and review response. Hook-bound commands fire automatically; standalone commands are invoked when needed.",
-      "author": "rbbtsn0w",
-      "version": "1.0.0",
-      "download_url": "https://github.com/RbBtSn0w/spec-kit-extensions/releases/download/superpowers-bridge-v1.0.0/superpowers-bridge.zip",
-      "repository": "https://github.com/RbBtSn0w/spec-kit-extensions",
-      "homepage": "https://github.com/RbBtSn0w/spec-kit-extensions",
-      "documentation": "https://github.com/RbBtSn0w/spec-kit-extensions/blob/main/superpowers-bridge/README.md",
-      "changelog": "https://github.com/RbBtSn0w/spec-kit-extensions/blob/main/superpowers-bridge/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.4.3",
-        "tools": [
-          {
-            "name": "superpowers",
-            "version": ">=5.0.0",
-            "required": false
-          }
-        ]
-      },
-      "provides": {
-        "commands": 8,
-        "hooks": 4
-      },
-      "tags": [
-        "methodology",
-        "tdd",
-        "code-review",
-        "workflow",
-        "superpowers",
-        "brainstorming",
-        "verification",
-        "debugging",
-        "branch-management"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-30T00:00:00Z",
-      "updated_at": "2026-03-30T00:00:00Z"
-    },
     "sync": {
       "name": "Spec Sync",
       "id": "sync",
@@ -1101,7 +578,7 @@
     "understanding": {
       "name": "Understanding",
       "id": "understanding",
-      "description": "Automated requirements quality analysis — validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
+      "description": "Automated requirements quality analysis \u2014 validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
       "author": "Ladislav Bihari",
       "version": "3.4.0",
       "download_url": "https://github.com/Testimonial/understanding/archive/refs/tags/v3.4.0.zip",
@@ -1139,6 +616,38 @@
       "created_at": "2026-03-07T00:00:00Z",
       "updated_at": "2026-03-07T00:00:00Z"
     },
+    "status": {
+      "name": "Project Status",
+      "id": "status",
+      "description": "Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "status",
+        "workflow",
+        "progress",
+        "feature-tracking",
+        "task-progress"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-16T00:00:00Z"
+    },
     "v-model": {
       "name": "V-Model Extension Pack",
       "id": "v-model",
@@ -1171,6 +680,37 @@
       "created_at": "2026-02-20T00:00:00Z",
       "updated_at": "2026-02-22T00:00:00Z"
     },
+    "learn": {
+      "name": "Learning Extension",
+      "id": "learn",
+      "description": "Generate educational guides from implementations and enhance clarifications with mentoring context.",
+      "author": "Vianca Martinez",
+      "version": "1.0.0",
+      "download_url": "https://github.com/imviancagrace/spec-kit-learn/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/imviancagrace/spec-kit-learn",
+      "homepage": "https://github.com/imviancagrace/spec-kit-learn",
+      "documentation": "https://github.com/imviancagrace/spec-kit-learn/blob/main/README.md",
+      "changelog": "https://github.com/imviancagrace/spec-kit-learn/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 1
+      },
+      "tags": [
+        "learning",
+        "education",
+        "mentoring",
+        "knowledge-transfer"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-17T00:00:00Z",
+      "updated_at": "2026-03-17T00:00:00Z"
+    },
     "verify": {
       "name": "Verify Extension",
       "id": "verify",

extensions/template/extension.yml

@@ -47,8 +47,8 @@ provides:
     - name: "speckit.my-extension.example"
       file: "commands/example.md"
       description: "Example command that demonstrates functionality"
-      # Optional: Add aliases in the same namespaced format
+      # Optional: Add aliases for shorter command names
-      aliases: ["speckit.my-extension.example-short"]
+      aliases: ["speckit.example"]
 
     # ADD MORE COMMANDS: Copy this block for each command
     # - name: "speckit.my-extension.another-command"

presets/catalog.community.json

@@ -1,58 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-24T00:00:00Z",
+  "updated_at": "2026-03-09T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
-  "presets": {
+  "presets": {}
-    "aide-in-place": {
-      "name": "AIDE In-Place Migration",
-      "id": "aide-in-place",
-      "version": "1.0.0",
-      "description": "Adapts the AIDE workflow for in-place technology migrations (X → Y pattern). Overrides vision, roadmap, progress, and work item commands with migration-specific guidance.",
-      "author": "mnriem",
-      "repository": "https://github.com/mnriem/spec-kit-presets",
-      "download_url": "https://github.com/mnriem/spec-kit-presets/releases/download/aide-in-place-v1.0.0/aide-in-place.zip",
-      "homepage": "https://github.com/mnriem/spec-kit-presets",
-      "documentation": "https://github.com/mnriem/spec-kit-presets/blob/main/aide-in-place/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0",
-        "extensions": ["aide"]
-      },
-      "provides": {
-        "templates": 2,
-        "commands": 8
-      },
-      "tags": [
-        "migration",
-        "in-place",
-        "brownfield",
-        "aide"
-      ]
-    },
-    "pirate": {
-      "name": "Pirate Speak (Full)",
-      "id": "pirate",
-      "version": "1.0.0",
-      "description": "Arrr! Transforms all Spec Kit output into pirate speak. Specs, plans, and tasks be written fer scallywags.",
-      "author": "mnriem",
-      "repository": "https://github.com/mnriem/spec-kit-presets",
-      "download_url": "https://github.com/mnriem/spec-kit-presets/releases/download/pirate-v1.0.0/pirate.zip",
-      "homepage": "https://github.com/mnriem/spec-kit-presets",
-      "documentation": "https://github.com/mnriem/spec-kit-presets/blob/main/pirate/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "templates": 6,
-        "commands": 9
-      },
-      "tags": [
-        "pirate",
-        "theme",
-        "fun",
-        "experimental"
-      ]
-    }
-  }
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.4.3"
+version = "0.4.1"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

scripts/bash/create-new-feature.sh

@@ -3,7 +3,6 @@
 set -e
 
 JSON_MODE=false
-ALLOW_EXISTING=false
 SHORT_NAME=""
 BRANCH_NUMBER=""
 USE_TIMESTAMP=false
@@ -15,9 +14,6 @@ while [ $i -le $# ]; do
         --json)
             JSON_MODE=true
             ;;
-        --allow-existing-branch)
-            ALLOW_EXISTING=true
-            ;;
         --short-name)
             if [ $((i + 1)) -gt $# ]; then
                 echo 'Error: --short-name requires a value' >&2
@@ -49,11 +45,10 @@ while [ $i -le $# ]; do
             USE_TIMESTAMP=true
             ;;
         --help|-h)
-            echo "Usage: $0 [--json] [--allow-existing-branch] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
+            echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
-            echo "  --allow-existing-branch  Switch to branch if it already exists instead of failing"
             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 "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
@@ -74,7 +69,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--allow-existing-branch] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
     exit 1
 fi
 
@@ -94,9 +89,9 @@ get_highest_from_specs() {
         for dir in "$specs_dir"/*; do
             [ -d "$dir" ] || continue
             dirname=$(basename "$dir")
-            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
+            # Only match sequential prefixes (###-*), skip timestamp dirs
-            if echo "$dirname" | grep -Eq '^[0-9]{3,}-' && ! echo "$dirname" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$dirname" | grep -Eo '^[0-9]+')
+                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -120,9 +115,9 @@ get_highest_from_branches() {
             # Clean branch name: remove leading markers and remote prefixes
             clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
             
-            # Extract sequential feature number (>=3 digits), skip timestamp branches.
+            # Extract feature number if branch matches pattern ###-*
-            if echo "$clean_branch" | grep -Eq '^[0-9]{3,}-' && ! echo "$clean_branch" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$clean_branch" | grep -Eo '^[0-9]+' || echo "0")
+                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -292,19 +287,12 @@ if [ "$HAS_GIT" = true ]; then
     if ! git checkout -b "$BRANCH_NAME" 2>/dev/null; then
         # Check if branch already exists
         if git branch --list "$BRANCH_NAME" | grep -q .; then
-            if [ "$ALLOW_EXISTING" = true ]; then
+            if [ "$USE_TIMESTAMP" = true ]; then
-                # Switch to the existing branch instead of failing
-                if ! git checkout "$BRANCH_NAME" 2>/dev/null; then
-                    >&2 echo "Error: Failed to switch to existing branch '$BRANCH_NAME'. Please resolve any local changes or conflicts and try again."
-                    exit 1
-                fi
-            elif [ "$USE_TIMESTAMP" = true ]; then
                 >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Rerun to get a new timestamp or use a different --short-name."
-                exit 1
             else
                 >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
-                exit 1
             fi
+            exit 1
         else
             >&2 echo "Error: Failed to create git branch '$BRANCH_NAME'. Please check your git configuration and try again."
             exit 1
@@ -317,15 +305,13 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
+TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ ! -f "$SPEC_FILE" ]; then
+if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
-    TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
+    cp "$TEMPLATE" "$SPEC_FILE"
-    if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
+else
-        cp "$TEMPLATE" "$SPEC_FILE"
+    echo "Warning: Spec template not found; created empty spec file" >&2
-    else
+    touch "$SPEC_FILE"
-        echo "Warning: Spec template not found; created empty spec file" >&2
-        touch "$SPEC_FILE"
-    fi
 fi
 
 # Inform the user how to persist the feature variable in their own shell

scripts/bash/update-agent-context.sh

@@ -63,7 +63,7 @@ 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"

scripts/powershell/common.ps1

@@ -8,8 +8,7 @@ function Find-SpecifyRoot {
 
     # Normalize to absolute path to prevent issues with relative paths
     # Use -LiteralPath to handle paths with wildcard characters ([, ], *, ?)
-    $resolved = Resolve-Path -LiteralPath $StartDir -ErrorAction SilentlyContinue
+    $current = (Resolve-Path -LiteralPath $StartDir -ErrorAction SilentlyContinue)?.Path
-    $current = if ($resolved) { $resolved.Path } else { $null }
     if (-not $current) { return $null }
 
     while ($true) {

scripts/powershell/create-new-feature.ps1

@@ -3,10 +3,9 @@
 [CmdletBinding()]
 param(
     [switch]$Json,
-    [switch]$AllowExistingBranch,
     [string]$ShortName,
     [Parameter()]
-    [long]$Number = 0,
+    [int]$Number = 0,
     [switch]$Timestamp,
     [switch]$Help,
     [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
@@ -16,11 +15,10 @@ $ErrorActionPreference = 'Stop'
 
 # Show help if requested
 if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-AllowExistingBranch] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
+    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
-    Write-Host "  -AllowExistingBranch  Switch to branch if it already exists instead of failing"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
     Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
     Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
@@ -35,7 +33,7 @@ if ($Help) {
 
 # Check if feature description provided
 if (-not $FeatureDescription -or $FeatureDescription.Count -eq 0) {
-    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-AllowExistingBranch] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
+    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     exit 1
 }
 
@@ -50,15 +48,12 @@ if ([string]::IsNullOrWhiteSpace($featureDesc)) {
 function Get-HighestNumberFromSpecs {
     param([string]$SpecsDir)
     
-    [long]$highest = 0
+    $highest = 0
     if (Test-Path $SpecsDir) {
         Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
+            if ($_.Name -match '^(\d{3})-') {
-            if ($_.Name -match '^(\d{3,})-' -and $_.Name -notmatch '^\d{8}-\d{6}-') {
+                $num = [int]$matches[1]
-                [long]$num = 0
+                if ($num -gt $highest) { $highest = $num }
-                if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
-                    $highest = $num
-                }
             }
         }
     }
@@ -68,7 +63,7 @@ function Get-HighestNumberFromSpecs {
 function Get-HighestNumberFromBranches {
     param()
     
-    [long]$highest = 0
+    $highest = 0
     try {
         $branches = git branch -a 2>$null
         if ($LASTEXITCODE -eq 0) {
@@ -76,12 +71,10 @@ function Get-HighestNumberFromBranches {
                 # Clean branch name: remove leading markers and remote prefixes
                 $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
                 
-                # Extract sequential feature number (>=3 digits), skip timestamp branches.
+                # Extract feature number if branch matches pattern ###-*
-                if ($cleanBranch -match '^(\d{3,})-' -and $cleanBranch -notmatch '^\d{8}-\d{6}-') {
+                if ($cleanBranch -match '^(\d{3})-') {
-                    [long]$num = 0
+                    $num = [int]$matches[1]
-                    if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
+                    if ($num -gt $highest) { $highest = $num }
-                        $highest = $num
-                    }
                 }
             }
         }
@@ -253,20 +246,12 @@ if ($hasGit) {
         # Check if branch already exists
         $existingBranch = git branch --list $branchName 2>$null
         if ($existingBranch) {
-            if ($AllowExistingBranch) {
+            if ($Timestamp) {
-                # Switch to the existing branch instead of failing
-                git checkout -q $branchName 2>$null | Out-Null
-                if ($LASTEXITCODE -ne 0) {
-                    Write-Error "Error: Branch '$branchName' exists but could not be checked out. Resolve any uncommitted changes or conflicts and try again."
-                    exit 1
-                }
-            } elseif ($Timestamp) {
                 Write-Error "Error: Branch '$branchName' already exists. Rerun to get a new timestamp or use a different -ShortName."
-                exit 1
             } else {
                 Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
-                exit 1
             }
+            exit 1
         } else {
             Write-Error "Error: Failed to create git branch '$branchName'. Please check your git configuration and try again."
             exit 1
@@ -279,14 +264,12 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
 
+$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
 $specFile = Join-Path $featureDir 'spec.md'
-if (-not (Test-Path -PathType Leaf $specFile)) {
+if ($template -and (Test-Path $template)) { 
-    $template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
+    Copy-Item $template $specFile -Force 
-    if ($template -and (Test-Path $template)) {
+} else { 
-        Copy-Item $template $specFile -Force
+    New-Item -ItemType File -Path $specFile | Out-Null 
-    } else {
-        New-Item -ItemType File -Path $specFile | Out-Null
-    }
 }
 
 # Set the SPECIFY_FEATURE environment variable for the current session
@@ -307,3 +290,4 @@ if ($Json) {
     Write-Output "HAS_GIT: $hasGit"
     Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
 }
+

scripts/powershell/update-agent-context.ps1

@@ -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'

src/specify_cli/__init__.py

@@ -345,7 +345,6 @@ AI_ASSISTANT_HELP = _build_ai_assistant_help()
 SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
 
 CLAUDE_LOCAL_PATH = Path.home() / ".claude" / "local" / "claude"
-CLAUDE_NPM_LOCAL_PATH = Path.home() / ".claude" / "local" / "node_modules" / ".bin" / "claude"
 
 BANNER = """
 ███████╗██████╗ ███████╗ ██████╗██╗███████╗██╗   ██╗
@@ -606,15 +605,13 @@ def check_tool(tool: str, tracker: StepTracker = None) -> bool:
     Returns:
         True if tool is found, False otherwise
     """
-    # Special handling for Claude CLI local installs
+    # Special handling for Claude CLI after `claude migrate-installer`
     # See: https://github.com/github/spec-kit/issues/123
-    # See: https://github.com/github/spec-kit/issues/550
+    # The migrate-installer command REMOVES the original executable from PATH
-    # Claude Code can be installed in two local paths:
+    # and creates an alias at ~/.claude/local/claude instead
-    #   1. ~/.claude/local/claude          (after `claude migrate-installer`)
+    # This path should be prioritized over other claude executables in PATH
-    #   2. ~/.claude/local/node_modules/.bin/claude  (npm-local install, e.g. via nvm)
-    # Neither path may be on the system PATH, so we check them explicitly.
     if tool == "claude":
-        if CLAUDE_LOCAL_PATH.is_file() or CLAUDE_NPM_LOCAL_PATH.is_file():
+        if CLAUDE_LOCAL_PATH.exists() and CLAUDE_LOCAL_PATH.is_file():
             if tracker:
                 tracker.complete(tool, "available")
             return True
@@ -1493,6 +1490,12 @@ def load_init_options(project_path: Path) -> dict[str, Any]:
         return {}
 
 
+# Agent-specific skill directory overrides for agents whose skills directory
+# doesn't follow the standard <agent_folder>/skills/ pattern
+AGENT_SKILLS_DIR_OVERRIDES = {
+    "codex": ".agents/skills",  # Codex agent layout override
+}
+
 # Default skills directory for agents not in AGENT_CONFIG
 DEFAULT_SKILLS_DIR = ".agents/skills"
 
@@ -1525,9 +1528,13 @@ SKILL_DESCRIPTIONS = {
 def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
     """Resolve the agent-specific skills directory for the given AI assistant.
 
-    Uses ``AGENT_CONFIG[agent]["folder"] + "skills"`` and falls back to
+    Uses ``AGENT_SKILLS_DIR_OVERRIDES`` first, then falls back to
-    ``DEFAULT_SKILLS_DIR`` for unknown agents.
+    ``AGENT_CONFIG[agent]["folder"] + "skills"``, and finally to
+    ``DEFAULT_SKILLS_DIR``.
     """
+    if selected_ai in AGENT_SKILLS_DIR_OVERRIDES:
+        return project_path / AGENT_SKILLS_DIR_OVERRIDES[selected_ai]
+
     agent_config = AGENT_CONFIG.get(selected_ai, {})
     agent_folder = agent_config.get("folder", "")
     if agent_folder:
@@ -1641,7 +1648,10 @@ def install_ai_skills(
                 command_name = command_name[len("speckit."):]
             if command_name.endswith(".agent"):
                 command_name = command_name[:-len(".agent")]
-            skill_name = f"speckit-{command_name.replace('.', '-')}"
+            if selected_ai == "kimi":
+                skill_name = f"speckit.{command_name}"
+            else:
+                skill_name = f"speckit-{command_name}"
 
             # Create skill directory (additive — never removes existing content)
             skill_dir = skills_dir / skill_name
@@ -1720,64 +1730,8 @@ def _has_bundled_skills(project_path: Path, selected_ai: str) -> bool:
     if not skills_dir.is_dir():
         return False
 
-    return any(skills_dir.glob("speckit-*/SKILL.md"))
+    pattern = "speckit.*/SKILL.md" if selected_ai == "kimi" else "speckit-*/SKILL.md"
-
+    return any(skills_dir.glob(pattern))
-
-def _migrate_legacy_kimi_dotted_skills(skills_dir: Path) -> tuple[int, int]:
-    """Migrate legacy Kimi dotted skill dirs (speckit.xxx) to hyphenated format.
-
-    Temporary migration helper:
-    - Intended removal window: after 2026-06-25.
-    - Purpose: one-time cleanup for projects initialized before Kimi moved to
-      hyphenated skills (speckit-xxx).
-
-    Returns:
-        Tuple[migrated_count, removed_count]
-        - migrated_count: old dotted dir renamed to hyphenated dir
-        - removed_count: old dotted dir deleted when equivalent hyphenated dir existed
-    """
-    if not skills_dir.is_dir():
-        return (0, 0)
-
-    migrated_count = 0
-    removed_count = 0
-
-    for legacy_dir in sorted(skills_dir.glob("speckit.*")):
-        if not legacy_dir.is_dir():
-            continue
-        if not (legacy_dir / "SKILL.md").exists():
-            continue
-
-        suffix = legacy_dir.name[len("speckit."):]
-        if not suffix:
-            continue
-
-        target_dir = skills_dir / f"speckit-{suffix.replace('.', '-')}"
-
-        if not target_dir.exists():
-            shutil.move(str(legacy_dir), str(target_dir))
-            migrated_count += 1
-            continue
-
-        # If the new target already exists, avoid destructive cleanup unless
-        # both SKILL.md files are byte-identical.
-        target_skill = target_dir / "SKILL.md"
-        legacy_skill = legacy_dir / "SKILL.md"
-        if target_skill.is_file():
-            try:
-                if target_skill.read_bytes() == legacy_skill.read_bytes():
-                    # Preserve legacy directory when it contains extra user files.
-                    has_extra_entries = any(
-                        child.name != "SKILL.md" for child in legacy_dir.iterdir()
-                    )
-                    if not has_extra_entries:
-                        shutil.rmtree(legacy_dir)
-                        removed_count += 1
-            except OSError:
-                # Best-effort migration: preserve legacy dir on read failures.
-                pass
-
-    return (migrated_count, removed_count)
 
 
 AGENT_SKILLS_MIGRATIONS = {
@@ -2140,33 +2094,16 @@ def init(
 
             ensure_constitution_from_template(project_path, tracker=tracker)
 
-            # Determine skills directory and migrate any legacy Kimi dotted skills.
-            migrated_legacy_kimi_skills = 0
-            removed_legacy_kimi_skills = 0
-            skills_dir: Optional[Path] = None
-            if selected_ai in NATIVE_SKILLS_AGENTS:
-                skills_dir = _get_skills_dir(project_path, selected_ai)
-                if selected_ai == "kimi" and skills_dir.is_dir():
-                    (
-                        migrated_legacy_kimi_skills,
-                        removed_legacy_kimi_skills,
-                    ) = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
             if ai_skills:
                 if selected_ai in NATIVE_SKILLS_AGENTS:
+                    skills_dir = _get_skills_dir(project_path, selected_ai)
                     bundled_found = _has_bundled_skills(project_path, selected_ai)
                     if bundled_found:
-                        detail = f"bundled skills → {skills_dir.relative_to(project_path)}"
-                        if migrated_legacy_kimi_skills or removed_legacy_kimi_skills:
-                            detail += (
-                                f" (migrated {migrated_legacy_kimi_skills}, "
-                                f"removed {removed_legacy_kimi_skills} legacy Kimi dotted skills)"
-                            )
                         if tracker:
                             tracker.start("ai-skills")
-                            tracker.complete("ai-skills", detail)
+                            tracker.complete("ai-skills", f"bundled skills → {skills_dir.relative_to(project_path)}")
                         else:
-                            console.print(f"[green]✓[/green] Using {detail}")
+                            console.print(f"[green]✓[/green] Using bundled agent skills in {skills_dir.relative_to(project_path)}/")
                     else:
                         # Compatibility fallback: convert command templates to skills
                         # when an older template archive does not include native skills.
@@ -2351,7 +2288,7 @@ def init(
         if codex_skill_mode:
             return f"$speckit-{name}"
         if kimi_skill_mode:
-            return f"/skill:speckit-{name}"
+            return f"/skill:speckit.{name}"
         return f"/speckit.{name}"
 
     steps_lines.append(f"{step_num}. Start using {usage_label} with your AI agent:")
@@ -3657,15 +3594,6 @@ def extension_add(
         for cmd in manifest.commands:
             console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
 
-        # Report agent skills registration
-        reg_meta = manager.registry.get(manifest.id)
-        reg_skills = reg_meta.get("registered_skills", []) if reg_meta else []
-        # Normalize to guard against corrupted registry entries
-        if not isinstance(reg_skills, list):
-            reg_skills = []
-        if reg_skills:
-            console.print(f"\n[green]✓[/green] {len(reg_skills)} agent skill(s) auto-registered")
-
         console.print("\n[yellow]⚠[/yellow]  Configuration may be required")
         console.print(f"   Check: .specify/extensions/{manifest.id}/")
 
@@ -3704,19 +3632,14 @@ def extension_remove(
     installed = manager.list_installed()
     extension_id, display_name = _resolve_installed_extension(extension, installed, "remove")
 
-    # Get extension info for command and skill counts
+    # Get extension info for command count
     ext_manifest = manager.get_extension(extension_id)
     cmd_count = len(ext_manifest.commands) if ext_manifest else 0
-    reg_meta = manager.registry.get(extension_id)
-    raw_skills = reg_meta.get("registered_skills") if reg_meta else None
-    skill_count = len(raw_skills) if isinstance(raw_skills, list) else 0
 
     # Confirm removal
     if not force:
         console.print("\n[yellow]⚠  This will remove:[/yellow]")
         console.print(f"   • {cmd_count} commands from AI agent")
-        if skill_count:
-            console.print(f"   • {skill_count} agent skill(s)")
         console.print(f"   • Extension directory: .specify/extensions/{extension_id}/")
         if not keep_config:
             console.print("   • Config files (will be backed up)")

src/specify_cli/agents.py

@@ -10,8 +10,6 @@ from pathlib import Path
 from typing import Dict, List, Any
 
 import platform
-import re
-from copy import deepcopy
 import yaml
 
 
@@ -213,52 +211,24 @@ class CommandRegistrar:
         return f"---\n{yaml_str}---\n"
 
     def _adjust_script_paths(self, frontmatter: dict) -> dict:
-        """Normalize script paths in frontmatter to generated project locations.
+        """Adjust script paths from extension-relative to repo-relative.
-
-        Rewrites known repo-relative and top-level script paths under the
-        `scripts` and `agent_scripts` keys (for example `../../scripts/`,
-        `../../templates/`, `../../memory/`, `scripts/`, `templates/`, and
-        `memory/`) to the `.specify/...` paths used in generated projects.
 
         Args:
             frontmatter: Frontmatter dictionary
 
         Returns:
-            Modified frontmatter with normalized project paths
+            Modified frontmatter with adjusted paths
         """
-        frontmatter = deepcopy(frontmatter)
-
         for script_key in ("scripts", "agent_scripts"):
             scripts = frontmatter.get(script_key)
             if not isinstance(scripts, dict):
                 continue
 
             for key, script_path in scripts.items():
-                if isinstance(script_path, str):
+                if isinstance(script_path, str) and script_path.startswith("../../scripts/"):
-                    scripts[key] = self._rewrite_project_relative_paths(script_path)
+                    scripts[key] = f".specify/scripts/{script_path[14:]}"
         return frontmatter
 
-    @staticmethod
-    def _rewrite_project_relative_paths(text: str) -> str:
-        """Rewrite repo-relative paths to their generated project locations."""
-        if not isinstance(text, str) or not text:
-            return text
-
-        for old, new in (
-            ("../../memory/", ".specify/memory/"),
-            ("../../scripts/", ".specify/scripts/"),
-            ("../../templates/", ".specify/templates/"),
-        ):
-            text = text.replace(old, new)
-
-        # Only rewrite top-level style references so extension-local paths like
-        # ".specify/extensions/<ext>/scripts/..." remain intact.
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?scripts/', r"\1.specify/scripts/", text)
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text)
-
-        return text.replace(".specify/.specify/", ".specify/").replace(".specify.specify/", ".specify/")
-
     def render_markdown_command(
         self,
         frontmatter: dict,
@@ -307,25 +277,9 @@ class CommandRegistrar:
         toml_lines.append(f"# Source: {source_id}")
         toml_lines.append("")
 
-        # Keep TOML output valid even when body contains triple-quote delimiters.
+        toml_lines.append('prompt = """')
-        # Prefer multiline forms, then fall back to escaped basic string.
+        toml_lines.append(body)
-        if '"""' not in body:
+        toml_lines.append('"""')
-            toml_lines.append('prompt = """')
-            toml_lines.append(body)
-            toml_lines.append('"""')
-        elif "'''" not in body:
-            toml_lines.append("prompt = '''")
-            toml_lines.append(body)
-            toml_lines.append("'''")
-        else:
-            escaped_body = (
-                body.replace("\\", "\\\\")
-                .replace('"', '\\"')
-                .replace("\n", "\\n")
-                .replace("\r", "\\r")
-                .replace("\t", "\\t")
-            )
-            toml_lines.append(f'prompt = "{escaped_body}"')
 
         return "\n".join(toml_lines)
 
@@ -354,8 +308,8 @@ class CommandRegistrar:
         if not isinstance(frontmatter, dict):
             frontmatter = {}
 
-        if agent_name in {"codex", "kimi"}:
+        if agent_name == "codex":
-            body = self.resolve_skill_placeholders(agent_name, frontmatter, body, project_root)
+            body = self._resolve_codex_skill_placeholders(frontmatter, body, project_root)
 
         description = frontmatter.get("description", f"Spec-kit workflow command: {skill_name}")
         skill_frontmatter = {
@@ -370,8 +324,13 @@ class CommandRegistrar:
         return self.render_frontmatter(skill_frontmatter) + "\n" + body
 
     @staticmethod
-    def resolve_skill_placeholders(agent_name: str, frontmatter: dict, body: str, project_root: Path) -> str:
+    def _resolve_codex_skill_placeholders(frontmatter: dict, body: str, project_root: Path) -> str:
-        """Resolve script placeholders for skills-backed agents."""
+        """Resolve script placeholders for Codex skill overrides.
+
+        This intentionally scopes the fix to Codex, which is the newly
+        migrated runtime path in this PR. Existing Kimi behavior is left
+        unchanged for now.
+        """
         try:
             from . import load_init_options
         except ImportError:
@@ -387,11 +346,7 @@ class CommandRegistrar:
         if not isinstance(agent_scripts, dict):
             agent_scripts = {}
 
-        init_opts = load_init_options(project_root)
+        script_variant = load_init_options(project_root).get("script")
-        if not isinstance(init_opts, dict):
-            init_opts = {}
-
-        script_variant = init_opts.get("script")
         if script_variant not in {"sh", "ps"}:
             fallback_order = []
             default_variant = "ps" if platform.system().lower().startswith("win") else "sh"
@@ -421,8 +376,7 @@ class CommandRegistrar:
             agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
             body = body.replace("{AGENT_SCRIPT}", agent_script_command)
 
-        body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
+        return body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", "codex")
-        return CommandRegistrar._rewrite_project_relative_paths(body)
 
     def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
         """Convert argument placeholder format.
@@ -446,9 +400,8 @@ class CommandRegistrar:
         short_name = cmd_name
         if short_name.startswith("speckit."):
             short_name = short_name[len("speckit."):]
-        short_name = short_name.replace(".", "-")
 
-        return f"speckit-{short_name}"
+        return f"speckit.{short_name}" if agent_name == "kimi" else f"speckit-{short_name}"
 
     def register_commands(
         self,

src/specify_cli/extensions.py

@@ -25,49 +25,6 @@ import yaml
 from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
-_FALLBACK_CORE_COMMAND_NAMES = frozenset({
-    "analyze",
-    "checklist",
-    "clarify",
-    "constitution",
-    "implement",
-    "plan",
-    "specify",
-    "tasks",
-    "taskstoissues",
-})
-EXTENSION_COMMAND_NAME_PATTERN = re.compile(r"^speckit\.([a-z0-9-]+)\.([a-z0-9-]+)$")
-
-
-def _load_core_command_names() -> frozenset[str]:
-    """Discover bundled core command names from the packaged templates.
-
-    Prefer the wheel-time ``core_pack`` bundle when present, and fall back to
-    the source checkout when running from the repository. If neither is
-    available, use the baked-in fallback set so validation still works.
-    """
-    candidate_dirs = [
-        Path(__file__).parent / "core_pack" / "commands",
-        Path(__file__).resolve().parent.parent.parent / "templates" / "commands",
-    ]
-
-    for commands_dir in candidate_dirs:
-        if not commands_dir.is_dir():
-            continue
-
-        command_names = {
-            command_file.stem
-            for command_file in commands_dir.iterdir()
-            if command_file.is_file() and command_file.suffix == ".md"
-        }
-        if command_names:
-            return frozenset(command_names)
-
-    return _FALLBACK_CORE_COMMAND_NAMES
-
-
-CORE_COMMAND_NAMES = _load_core_command_names()
-
 
 class ExtensionError(Exception):
     """Base exception for extension-related errors."""
@@ -192,7 +149,7 @@ class ExtensionManifest:
                 raise ValidationError("Command missing 'name' or 'file'")
 
             # Validate command name format
-            if EXTENSION_COMMAND_NAME_PATTERN.match(cmd["name"]) is None:
+            if not re.match(r'^speckit\.[a-z0-9-]+\.[a-z0-9-]+$', cmd["name"]):
                 raise ValidationError(
                     f"Invalid command name '{cmd['name']}': "
                     "must follow pattern 'speckit.{extension}.{command}'"
@@ -489,126 +446,6 @@ class ExtensionManager:
         self.extensions_dir = project_root / ".specify" / "extensions"
         self.registry = ExtensionRegistry(self.extensions_dir)
 
-    @staticmethod
-    def _collect_manifest_command_names(manifest: ExtensionManifest) -> Dict[str, str]:
-        """Collect command and alias names declared by a manifest.
-
-        Performs install-time validation for extension-specific constraints:
-        - commands and aliases must use the canonical `speckit.{extension}.{command}` shape
-        - commands and aliases must use this extension's namespace
-        - command namespaces must not shadow core commands
-        - duplicate command/alias names inside one manifest are rejected
-
-        Args:
-            manifest: Parsed extension manifest
-
-        Returns:
-            Mapping of declared command/alias name -> kind ("command"/"alias")
-
-        Raises:
-            ValidationError: If any declared name is invalid
-        """
-        if manifest.id in CORE_COMMAND_NAMES:
-            raise ValidationError(
-                f"Extension ID '{manifest.id}' conflicts with core command namespace '{manifest.id}'"
-            )
-
-        declared_names: Dict[str, str] = {}
-
-        for cmd in manifest.commands:
-            primary_name = cmd["name"]
-            aliases = cmd.get("aliases", [])
-
-            if aliases is None:
-                aliases = []
-            if not isinstance(aliases, list):
-                raise ValidationError(
-                    f"Aliases for command '{primary_name}' must be a list"
-                )
-
-            for kind, name in [("command", primary_name)] + [
-                ("alias", alias) for alias in aliases
-            ]:
-                if not isinstance(name, str):
-                    raise ValidationError(
-                        f"{kind.capitalize()} for command '{primary_name}' must be a string"
-                    )
-
-                match = EXTENSION_COMMAND_NAME_PATTERN.match(name)
-                if match is None:
-                    raise ValidationError(
-                        f"Invalid {kind} '{name}': "
-                        "must follow pattern 'speckit.{extension}.{command}'"
-                    )
-
-                namespace = match.group(1)
-                if namespace != manifest.id:
-                    raise ValidationError(
-                        f"{kind.capitalize()} '{name}' must use extension namespace '{manifest.id}'"
-                    )
-
-                if namespace in CORE_COMMAND_NAMES:
-                    raise ValidationError(
-                        f"{kind.capitalize()} '{name}' conflicts with core command namespace '{namespace}'"
-                    )
-
-                if name in declared_names:
-                    raise ValidationError(
-                        f"Duplicate command or alias '{name}' in extension manifest"
-                    )
-
-                declared_names[name] = kind
-
-        return declared_names
-
-    def _get_installed_command_name_map(
-        self,
-        exclude_extension_id: Optional[str] = None,
-    ) -> Dict[str, str]:
-        """Return registered command and alias names for installed extensions."""
-        installed_names: Dict[str, str] = {}
-
-        for ext_id in self.registry.keys():
-            if ext_id == exclude_extension_id:
-                continue
-
-            manifest = self.get_extension(ext_id)
-            if manifest is None:
-                continue
-
-            for cmd in manifest.commands:
-                cmd_name = cmd.get("name")
-                if isinstance(cmd_name, str):
-                    installed_names.setdefault(cmd_name, ext_id)
-
-                aliases = cmd.get("aliases", [])
-                if not isinstance(aliases, list):
-                    continue
-
-                for alias in aliases:
-                    if isinstance(alias, str):
-                        installed_names.setdefault(alias, ext_id)
-
-        return installed_names
-
-    def _validate_install_conflicts(self, manifest: ExtensionManifest) -> None:
-        """Reject installs that would shadow core or installed extension commands."""
-        declared_names = self._collect_manifest_command_names(manifest)
-        installed_names = self._get_installed_command_name_map(
-            exclude_extension_id=manifest.id
-        )
-
-        collisions = [
-            f"{name} (already provided by extension '{installed_names[name]}')"
-            for name in sorted(declared_names)
-            if name in installed_names
-        ]
-        if collisions:
-            raise ValidationError(
-                "Extension commands conflict with installed extensions:\n- "
-                + "\n- ".join(collisions)
-            )
-
     @staticmethod
     def _load_extensionignore(source_dir: Path) -> Optional[Callable[[str, List[str]], Set[str]]]:
         """Load .extensionignore and return an ignore function for shutil.copytree.
@@ -673,283 +510,6 @@ class ExtensionManager:
 
         return _ignore
 
-    def _get_skills_dir(self) -> Optional[Path]:
-        """Return the active skills directory for extension skill registration.
-
-        Reads ``.specify/init-options.json`` to determine whether skills
-        are enabled and which agent was selected, then delegates to
-        the module-level ``_get_skills_dir()`` helper for the concrete path.
-
-        Kimi is treated as a native-skills agent: if ``ai == "kimi"`` and
-        ``.kimi/skills`` exists, extension installs should still propagate
-        command skills even when ``ai_skills`` is false.
-
-        Returns:
-            The skills directory ``Path``, or ``None`` if skills were not
-            enabled and no native-skills fallback applies.
-        """
-        from . import load_init_options, _get_skills_dir as resolve_skills_dir
-
-        opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
-            opts = {}
-
-        agent = opts.get("ai")
-        if not isinstance(agent, str) or not agent:
-            return None
-
-        ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not ai_skills_enabled and agent != "kimi":
-            return None
-
-        skills_dir = resolve_skills_dir(self.project_root, agent)
-        if not skills_dir.is_dir():
-            return None
-
-        return skills_dir
-
-    def _register_extension_skills(
-        self,
-        manifest: ExtensionManifest,
-        extension_dir: Path,
-    ) -> List[str]:
-        """Generate SKILL.md files for extension commands as agent skills.
-
-        For every command in the extension manifest, creates a SKILL.md
-        file in the agent's skills directory following the agentskills.io
-        specification.  This is only done when ``--ai-skills`` was used
-        during project initialisation.
-
-        Args:
-            manifest: Extension manifest.
-            extension_dir: Installed extension directory.
-
-        Returns:
-            List of skill names that were created (for registry storage).
-        """
-        skills_dir = self._get_skills_dir()
-        if not skills_dir:
-            return []
-
-        from . import load_init_options
-        from .agents import CommandRegistrar
-        import yaml
-
-        written: List[str] = []
-        opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
-            opts = {}
-        selected_ai = opts.get("ai")
-        if not isinstance(selected_ai, str) or not selected_ai:
-            return []
-        registrar = CommandRegistrar()
-
-        for cmd_info in manifest.commands:
-            cmd_name = cmd_info["name"]
-            cmd_file_rel = cmd_info["file"]
-
-            # Guard against path traversal: reject absolute paths and ensure
-            # the resolved file stays within the extension directory.
-            cmd_path = Path(cmd_file_rel)
-            if cmd_path.is_absolute():
-                continue
-            try:
-                ext_root = extension_dir.resolve()
-                source_file = (ext_root / cmd_path).resolve()
-                source_file.relative_to(ext_root)  # raises ValueError if outside
-            except (OSError, ValueError):
-                continue
-
-            if not source_file.is_file():
-                continue
-
-            # Derive skill name from command name using the same hyphenated
-            # convention as hook rendering and preset skill registration.
-            short_name_raw = cmd_name
-            if short_name_raw.startswith("speckit."):
-                short_name_raw = short_name_raw[len("speckit."):]
-            skill_name = f"speckit-{short_name_raw.replace('.', '-')}"
-
-            # Check if skill already exists before creating the directory
-            skill_subdir = skills_dir / skill_name
-            skill_file = skill_subdir / "SKILL.md"
-            if skill_file.exists():
-                # Do not overwrite user-customized skills
-                continue
-
-            # Create skill directory; track whether we created it so we can clean
-            # up safely if reading the source file subsequently fails.
-            created_now = not skill_subdir.exists()
-            skill_subdir.mkdir(parents=True, exist_ok=True)
-
-            # Parse the command file — guard against IsADirectoryError / decode errors
-            try:
-                content = source_file.read_text(encoding="utf-8")
-            except (OSError, UnicodeDecodeError):
-                if created_now:
-                    try:
-                        skill_subdir.rmdir()  # undo the mkdir; dir is empty at this point
-                    except OSError:
-                        pass  # best-effort cleanup
-                continue
-            frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(frontmatter)
-            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
-            )
-
-            original_desc = frontmatter.get("description", "")
-            description = original_desc or f"Extension command: {cmd_name}"
-
-            frontmatter_data = {
-                "name": skill_name,
-                "description": description,
-                "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                "metadata": {
-                    "author": "github-spec-kit",
-                    "source": f"extension:{manifest.id}",
-                },
-            }
-            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-
-            # Derive a human-friendly title from the command name
-            short_name = cmd_name
-            if short_name.startswith("speckit."):
-                short_name = short_name[len("speckit."):]
-            title_name = short_name.replace(".", " ").replace("-", " ").title()
-
-            skill_content = (
-                f"---\n"
-                f"{frontmatter_text}\n"
-                f"---\n\n"
-                f"# {title_name} Skill\n\n"
-                f"{body}\n"
-            )
-
-            skill_file.write_text(skill_content, encoding="utf-8")
-            written.append(skill_name)
-
-        return written
-
-    def _unregister_extension_skills(self, skill_names: List[str], extension_id: str) -> None:
-        """Remove SKILL.md directories for extension skills.
-
-        Called during extension removal to clean up skill files that
-        were created by ``_register_extension_skills()``.
-
-        If ``_get_skills_dir()`` returns ``None`` (e.g. the user removed
-        init-options.json or toggled ai_skills after installation), we
-        fall back to scanning all known agent skills directories so that
-        orphaned skill directories are still cleaned up.  In that case
-        each candidate directory is verified against the SKILL.md
-        ``metadata.source`` field before removal to avoid accidentally
-        deleting user-created skills with the same name.
-
-        Args:
-            skill_names: List of skill names to remove.
-            extension_id: Extension ID used to verify ownership during
-                fallback candidate scanning.
-        """
-        if not skill_names:
-            return
-
-        skills_dir = self._get_skills_dir()
-
-        if skills_dir:
-            # Fast path: we know the exact skills directory
-            for skill_name in skill_names:
-                # Guard against path traversal from a corrupted registry entry:
-                # reject names that are absolute, contain path separators, or
-                # resolve to a path outside the skills directory.
-                sn_path = Path(skill_name)
-                if sn_path.is_absolute() or len(sn_path.parts) != 1:
-                    continue
-                try:
-                    skill_subdir = (skills_dir / skill_name).resolve()
-                    skill_subdir.relative_to(skills_dir.resolve())  # raises if outside
-                except (OSError, ValueError):
-                    continue
-                if not skill_subdir.is_dir():
-                    continue
-                # Safety check: only delete if SKILL.md exists and its
-                # metadata.source matches exactly this extension — mirroring
-                # the fallback branch — so a corrupted registry entry cannot
-                # delete an unrelated user skill.
-                skill_md = skill_subdir / "SKILL.md"
-                if not skill_md.is_file():
-                    continue
-                try:
-                    import yaml as _yaml
-                    raw = skill_md.read_text(encoding="utf-8")
-                    source = ""
-                    if raw.startswith("---"):
-                        parts = raw.split("---", 2)
-                        if len(parts) >= 3:
-                            fm = _yaml.safe_load(parts[1]) or {}
-                            source = (
-                                fm.get("metadata", {}).get("source", "")
-                                if isinstance(fm, dict)
-                                else ""
-                            )
-                    if source != f"extension:{extension_id}":
-                        continue
-                except (OSError, UnicodeDecodeError, Exception):
-                    continue
-                shutil.rmtree(skill_subdir)
-        else:
-            # Fallback: scan all possible agent skills directories
-            from . import AGENT_CONFIG, DEFAULT_SKILLS_DIR
-
-            candidate_dirs: set[Path] = set()
-            for cfg in AGENT_CONFIG.values():
-                folder = cfg.get("folder", "")
-                if folder:
-                    candidate_dirs.add(self.project_root / folder.rstrip("/") / "skills")
-            candidate_dirs.add(self.project_root / DEFAULT_SKILLS_DIR)
-
-            for skills_candidate in candidate_dirs:
-                if not skills_candidate.is_dir():
-                    continue
-                for skill_name in skill_names:
-                    # Same path-traversal guard as the fast path above
-                    sn_path = Path(skill_name)
-                    if sn_path.is_absolute() or len(sn_path.parts) != 1:
-                        continue
-                    try:
-                        skill_subdir = (skills_candidate / skill_name).resolve()
-                        skill_subdir.relative_to(skills_candidate.resolve())  # raises if outside
-                    except (OSError, ValueError):
-                        continue
-                    if not skill_subdir.is_dir():
-                        continue
-                    # Safety check: only delete if SKILL.md exists and its
-                    # metadata.source matches exactly this extension.  If the
-                    # file is missing or unreadable we skip to avoid deleting
-                    # unrelated user-created directories.
-                    skill_md = skill_subdir / "SKILL.md"
-                    if not skill_md.is_file():
-                        continue
-                    try:
-                        import yaml as _yaml
-                        raw = skill_md.read_text(encoding="utf-8")
-                        source = ""
-                        if raw.startswith("---"):
-                            parts = raw.split("---", 2)
-                            if len(parts) >= 3:
-                                fm = _yaml.safe_load(parts[1]) or {}
-                                source = (
-                                    fm.get("metadata", {}).get("source", "")
-                                    if isinstance(fm, dict)
-                                    else ""
-                                )
-                        # Only remove skills explicitly created by this extension
-                        if source != f"extension:{extension_id}":
-                            continue
-                    except (OSError, UnicodeDecodeError, Exception):
-                        # If we can't verify, skip to avoid accidental deletion
-                        continue
-                    shutil.rmtree(skill_subdir)
-
     def check_compatibility(
         self,
         manifest: ExtensionManifest,
@@ -1024,9 +584,6 @@ class ExtensionManager:
                 f"Use 'specify extension remove {manifest.id}' first."
             )
 
-        # Reject manifests that would shadow core commands or installed extensions.
-        self._validate_install_conflicts(manifest)
-
         # Install extension
         dest_dir = self.extensions_dir / manifest.id
         if dest_dir.exists():
@@ -1044,10 +601,6 @@ class ExtensionManager:
                 manifest, dest_dir, self.project_root
             )
 
-        # Auto-register extension commands as agent skills when --ai-skills
-        # was used during project initialisation (feature parity).
-        registered_skills = self._register_extension_skills(manifest, dest_dir)
-
         # Register hooks
         hook_executor = HookExecutor(self.project_root)
         hook_executor.register_hooks(manifest)
@@ -1059,8 +612,7 @@ class ExtensionManager:
             "manifest_hash": manifest.get_hash(),
             "enabled": True,
             "priority": priority,
-            "registered_commands": registered_commands,
+            "registered_commands": registered_commands
-            "registered_skills": registered_skills,
         })
 
         return manifest
@@ -1138,15 +690,9 @@ class ExtensionManager:
         if not self.registry.is_installed(extension_id):
             return False
 
-        # Get registered commands and skills before removal
+        # Get registered commands before removal
         metadata = self.registry.get(extension_id)
         registered_commands = metadata.get("registered_commands", {}) if metadata else {}
-        raw_skills = metadata.get("registered_skills", []) if metadata else []
-        # Normalize: must be a list of plain strings to avoid corrupted-registry errors
-        if isinstance(raw_skills, list):
-            registered_skills = [s for s in raw_skills if isinstance(s, str)]
-        else:
-            registered_skills = []
 
         extension_dir = self.extensions_dir / extension_id
 
@@ -1155,9 +701,6 @@ class ExtensionManager:
             registrar = CommandRegistrar()
             registrar.unregister_commands(registered_commands, self.project_root)
 
-        # Unregister agent skills
-        self._unregister_extension_skills(registered_skills, extension_id)
-
         if keep_config:
             # Preserve config files, only remove non-config files
             if extension_dir.exists():
@@ -2101,52 +1644,6 @@ class HookExecutor:
         self.project_root = project_root
         self.extensions_dir = project_root / ".specify" / "extensions"
         self.config_file = project_root / ".specify" / "extensions.yml"
-        self._init_options_cache: Optional[Dict[str, Any]] = None
-
-    def _load_init_options(self) -> Dict[str, Any]:
-        """Load persisted init options used to determine invocation style.
-
-        Uses the shared helper from specify_cli and caches values per executor
-        instance to avoid repeated filesystem reads during hook rendering.
-        """
-        if self._init_options_cache is None:
-            from . import load_init_options
-
-            payload = load_init_options(self.project_root)
-            self._init_options_cache = payload if isinstance(payload, dict) else {}
-        return self._init_options_cache
-
-    @staticmethod
-    def _skill_name_from_command(command: Any) -> str:
-        """Map a command id like speckit.plan to speckit-plan skill name."""
-        if not isinstance(command, str):
-            return ""
-        command_id = command.strip()
-        if not command_id.startswith("speckit."):
-            return ""
-        return f"speckit-{command_id[len('speckit.'):].replace('.', '-')}"
-
-    def _render_hook_invocation(self, command: Any) -> str:
-        """Render an agent-specific invocation string for a hook command."""
-        if not isinstance(command, str):
-            return ""
-
-        command_id = command.strip()
-        if not command_id:
-            return ""
-
-        init_options = self._load_init_options()
-        selected_ai = init_options.get("ai")
-        codex_skill_mode = selected_ai == "codex" and bool(init_options.get("ai_skills"))
-        kimi_skill_mode = selected_ai == "kimi"
-
-        skill_name = self._skill_name_from_command(command_id)
-        if codex_skill_mode and skill_name:
-            return f"${skill_name}"
-        if kimi_skill_mode and skill_name:
-            return f"/skill:{skill_name}"
-
-        return f"/{command_id}"
 
     def get_project_config(self) -> Dict[str, Any]:
         """Load project-level extension configuration.
@@ -2390,27 +1887,21 @@ class HookExecutor:
         for hook in hooks:
             extension = hook.get("extension")
             command = hook.get("command")
-            invocation = self._render_hook_invocation(command)
-            command_text = command if isinstance(command, str) and command.strip() else "<missing command>"
-            display_invocation = invocation or (
-                f"/{command_text}" if command_text != "<missing command>" else "/<missing command>"
-            )
             optional = hook.get("optional", True)
             prompt = hook.get("prompt", "")
             description = hook.get("description", "")
 
             if optional:
                 lines.append(f"\n**Optional Hook**: {extension}")
-                lines.append(f"Command: `{display_invocation}`")
+                lines.append(f"Command: `/{command}`")
                 if description:
                     lines.append(f"Description: {description}")
                 lines.append(f"\nPrompt: {prompt}")
-                lines.append(f"To execute: `{display_invocation}`")
+                lines.append(f"To execute: `/{command}`")
             else:
                 lines.append(f"\n**Automatic Hook**: {extension}")
-                lines.append(f"Executing: `{display_invocation}`")
+                lines.append(f"Executing: `/{command}`")
-                lines.append(f"EXECUTE_COMMAND: {command_text}")
+                lines.append(f"EXECUTE_COMMAND: {command}")
-                lines.append(f"EXECUTE_COMMAND_INVOCATION: {display_invocation}")
 
         return "\n".join(lines)
 
@@ -2474,7 +1965,6 @@ class HookExecutor:
         """
         return {
             "command": hook.get("command"),
-            "invocation": self._render_hook_invocation(hook.get("command")),
             "extension": hook.get("extension"),
             "optional": hook.get("optional", True),
             "description": hook.get("description", ""),
@@ -2518,3 +2008,4 @@ class HookExecutor:
                     hook["enabled"] = False
 
         self.save_project_config(config)
+

src/specify_cli/integrations/__init__.py

@@ -1,34 +0,0 @@
-"""Integration registry for AI coding assistants.
-
-Each integration is a self-contained subpackage that handles setup/teardown
-for a specific AI assistant (Copilot, Claude, Gemini, etc.).
-"""
-
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from .base import IntegrationBase
-
-# Maps integration key → IntegrationBase instance.
-# Populated by later stages as integrations are migrated.
-INTEGRATION_REGISTRY: dict[str, IntegrationBase] = {}
-
-
-def _register(integration: IntegrationBase) -> None:
-    """Register an integration instance in the global registry.
-
-    Raises ``ValueError`` for falsy keys and ``KeyError`` for duplicates.
-    """
-    key = integration.key
-    if not key:
-        raise ValueError("Cannot register integration with an empty key.")
-    if key in INTEGRATION_REGISTRY:
-        raise KeyError(f"Integration with key {key!r} is already registered.")
-    INTEGRATION_REGISTRY[key] = integration
-
-
-def get_integration(key: str) -> IntegrationBase | None:
-    """Return the integration for *key*, or ``None`` if not registered."""
-    return INTEGRATION_REGISTRY.get(key)

src/specify_cli/integrations/base.py

@@ -1,215 +0,0 @@
-"""Base classes for AI-assistant integrations.
-
-Provides:
-- ``IntegrationOption`` — declares a CLI option an integration accepts.
-- ``IntegrationBase`` — abstract base every integration must implement.
-- ``MarkdownIntegration`` — concrete base for standard Markdown-format
-  integrations (the common case — subclass, set three class attrs, done).
-"""
-
-from __future__ import annotations
-
-import shutil
-from abc import ABC
-from dataclasses import dataclass
-from pathlib import Path
-from typing import TYPE_CHECKING, Any
-
-if TYPE_CHECKING:
-    from .manifest import IntegrationManifest
-
-
-# ---------------------------------------------------------------------------
-# IntegrationOption
-# ---------------------------------------------------------------------------
-
-@dataclass(frozen=True)
-class IntegrationOption:
-    """Declares an option that an integration accepts via ``--integration-options``.
-
-    Attributes:
-        name:      The flag name (e.g. ``"--commands-dir"``).
-        is_flag:   ``True`` for boolean flags (``--skills``).
-        required:  ``True`` if the option must be supplied.
-        default:   Default value when not supplied (``None`` → no default).
-        help:      One-line description shown in ``specify integrate info``.
-    """
-
-    name: str
-    is_flag: bool = False
-    required: bool = False
-    default: Any = None
-    help: str = ""
-
-
-# ---------------------------------------------------------------------------
-# IntegrationBase — abstract base class
-# ---------------------------------------------------------------------------
-
-class IntegrationBase(ABC):
-    """Abstract base class every integration must implement.
-
-    Subclasses must set the following class-level attributes:
-
-    * ``key``              — unique identifier, matches actual CLI tool name
-    * ``config``           — dict compatible with ``AGENT_CONFIG`` entries
-    * ``registrar_config`` — dict compatible with ``CommandRegistrar.AGENT_CONFIGS``
-
-    And may optionally set:
-
-    * ``context_file``     — path (relative to project root) of the agent
-                             context/instructions file (e.g. ``"CLAUDE.md"``)
-    """
-
-    # -- Must be set by every subclass ------------------------------------
-
-    key: str = ""
-    """Unique integration key — should match the actual CLI tool name."""
-
-    config: dict[str, Any] | None = None
-    """Metadata dict matching the ``AGENT_CONFIG`` shape."""
-
-    registrar_config: dict[str, Any] | None = None
-    """Registration dict matching ``CommandRegistrar.AGENT_CONFIGS`` shape."""
-
-    # -- Optional ---------------------------------------------------------
-
-    context_file: str | None = None
-    """Relative path to the agent context file (e.g. ``CLAUDE.md``)."""
-
-    # -- Public API -------------------------------------------------------
-
-    @classmethod
-    def options(cls) -> list[IntegrationOption]:
-        """Return options this integration accepts. Default: none."""
-        return []
-
-    def templates_dir(self) -> Path:
-        """Return the path to this integration's bundled templates.
-
-        By convention, templates live in a ``templates/`` subdirectory
-        next to the file where the integration class is defined.
-        """
-        import inspect
-
-        module_file = inspect.getfile(type(self))
-        return Path(module_file).resolve().parent / "templates"
-
-    def setup(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        parsed_options: dict[str, Any] | None = None,
-        **opts: Any,
-    ) -> list[Path]:
-        """Install integration files into *project_root*.
-
-        Returns the list of files created.  The default implementation
-        copies every file from ``templates_dir()`` into the commands
-        directory derived from ``config``, recording each in *manifest*.
-        """
-        created: list[Path] = []
-        tpl_dir = self.templates_dir()
-        if not tpl_dir.is_dir():
-            return created
-
-        if not self.config:
-            raise ValueError(
-                f"{type(self).__name__}.config is not set; integration "
-                "subclasses must define a non-empty 'config' mapping."
-            )
-        folder = self.config.get("folder")
-        if not folder:
-            raise ValueError(
-                f"{type(self).__name__}.config is missing required 'folder' entry."
-            )
-
-        project_root_resolved = project_root.resolve()
-        if manifest.project_root != project_root_resolved:
-            raise ValueError(
-                f"manifest.project_root ({manifest.project_root}) does not match "
-                f"project_root ({project_root_resolved})"
-            )
-        subdir = self.config.get("commands_subdir", "commands")
-        dest = (project_root / folder / subdir).resolve()
-        # Ensure destination stays within the project root
-        try:
-            dest.relative_to(project_root_resolved)
-        except ValueError as exc:
-            raise ValueError(
-                f"Integration destination {dest} escapes "
-                f"project root {project_root_resolved}"
-            ) from exc
-
-        dest.mkdir(parents=True, exist_ok=True)
-
-        for src_file in sorted(tpl_dir.iterdir()):
-            if src_file.is_file():
-                dst_file = dest / src_file.name
-                dst_resolved = dst_file.resolve()
-                rel = dst_resolved.relative_to(project_root_resolved)
-                shutil.copy2(src_file, dst_file)
-                manifest.record_existing(rel)
-                created.append(dst_file)
-
-        return created
-
-    def teardown(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        *,
-        force: bool = False,
-    ) -> tuple[list[Path], list[Path]]:
-        """Uninstall integration files from *project_root*.
-
-        Delegates to ``manifest.uninstall()`` which only removes files
-        whose hash still matches the recorded value (unless *force*).
-
-        Returns ``(removed, skipped)`` file lists.
-        """
-        return manifest.uninstall(project_root, force=force)
-
-    # -- Convenience helpers for subclasses -------------------------------
-
-    def install(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        parsed_options: dict[str, Any] | None = None,
-        **opts: Any,
-    ) -> list[Path]:
-        """High-level install — calls ``setup()`` and returns created files."""
-        return self.setup(
-            project_root, manifest, parsed_options=parsed_options, **opts
-        )
-
-    def uninstall(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        *,
-        force: bool = False,
-    ) -> tuple[list[Path], list[Path]]:
-        """High-level uninstall — calls ``teardown()``."""
-        return self.teardown(project_root, manifest, force=force)
-
-
-# ---------------------------------------------------------------------------
-# MarkdownIntegration — covers ~20 standard agents
-# ---------------------------------------------------------------------------
-
-class MarkdownIntegration(IntegrationBase):
-    """Concrete base for integrations that use standard Markdown commands.
-
-    Subclasses only need to set ``key``, ``config``, ``registrar_config``
-    (and optionally ``context_file``).  Everything else is inherited.
-
-    The default ``setup()`` from ``IntegrationBase`` copies templates
-    into the agent's commands directory — which is correct for the
-    standard Markdown case.
-    """
-
-    # MarkdownIntegration inherits IntegrationBase.setup() as-is.
-    # Future stages may add markdown-specific path rewriting here.
-    pass

src/specify_cli/integrations/manifest.py

@@ -1,265 +0,0 @@
-"""Hash-tracked installation manifest for integrations.
-
-Each installed integration records the files it created together with
-their SHA-256 hashes.  On uninstall only files whose hash still matches
-the recorded value are removed — modified files are left in place and
-reported to the caller.
-"""
-
-from __future__ import annotations
-
-import hashlib
-import json
-import os
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Any
-
-
-def _sha256(path: Path) -> str:
-    """Return the hex SHA-256 digest of *path*."""
-    h = hashlib.sha256()
-    with open(path, "rb") as fh:
-        for chunk in iter(lambda: fh.read(8192), b""):
-            h.update(chunk)
-    return h.hexdigest()
-
-
-def _validate_rel_path(rel: Path, root: Path) -> Path:
-    """Resolve *rel* against *root* and verify it stays within *root*.
-
-    Raises ``ValueError`` if *rel* is absolute, contains ``..`` segments
-    that escape *root*, or otherwise resolves outside the project root.
-    """
-    if rel.is_absolute():
-        raise ValueError(
-            f"Absolute paths are not allowed in manifests: {rel}"
-        )
-    resolved = (root / rel).resolve()
-    root_resolved = root.resolve()
-    try:
-        resolved.relative_to(root_resolved)
-    except ValueError:
-        raise ValueError(
-            f"Path {rel} resolves to {resolved} which is outside "
-            f"the project root {root_resolved}"
-        ) from None
-    return resolved
-
-
-class IntegrationManifest:
-    """Tracks files installed by a single integration.
-
-    Parameters:
-        key:          Integration identifier (e.g. ``"copilot"``).
-        project_root: Absolute path to the project directory.
-        version:      CLI version string recorded in the manifest.
-    """
-
-    def __init__(self, key: str, project_root: Path, version: str = "") -> None:
-        self.key = key
-        self.project_root = project_root.resolve()
-        self.version = version
-        self._files: dict[str, str] = {}  # rel_path → sha256 hex
-        self._installed_at: str = ""
-
-    # -- Manifest file location -------------------------------------------
-
-    @property
-    def manifest_path(self) -> Path:
-        """Path to the on-disk manifest JSON."""
-        return self.project_root / ".specify" / "integrations" / f"{self.key}.manifest.json"
-
-    # -- Recording files --------------------------------------------------
-
-    def record_file(self, rel_path: str | Path, content: bytes | str) -> Path:
-        """Write *content* to *rel_path* (relative to project root) and record its hash.
-
-        Creates parent directories as needed.  Returns the absolute path
-        of the written file.
-
-        Raises ``ValueError`` if *rel_path* resolves outside the project root.
-        """
-        rel = Path(rel_path)
-        abs_path = _validate_rel_path(rel, self.project_root)
-        abs_path.parent.mkdir(parents=True, exist_ok=True)
-
-        if isinstance(content, str):
-            content = content.encode("utf-8")
-        abs_path.write_bytes(content)
-
-        normalized = abs_path.relative_to(self.project_root).as_posix()
-        self._files[normalized] = hashlib.sha256(content).hexdigest()
-        return abs_path
-
-    def record_existing(self, rel_path: str | Path) -> None:
-        """Record the hash of an already-existing file at *rel_path*.
-
-        Raises ``ValueError`` if *rel_path* resolves outside the project root.
-        """
-        rel = Path(rel_path)
-        abs_path = _validate_rel_path(rel, self.project_root)
-        normalized = abs_path.relative_to(self.project_root).as_posix()
-        self._files[normalized] = _sha256(abs_path)
-
-    # -- Querying ---------------------------------------------------------
-
-    @property
-    def files(self) -> dict[str, str]:
-        """Return a copy of the ``{rel_path: sha256}`` mapping."""
-        return dict(self._files)
-
-    def check_modified(self) -> list[str]:
-        """Return relative paths of tracked files whose content changed on disk."""
-        modified: list[str] = []
-        for rel, expected_hash in self._files.items():
-            rel_path = Path(rel)
-            # Skip paths that are absolute or attempt to escape the project root
-            if rel_path.is_absolute() or ".." in rel_path.parts:
-                continue
-            abs_path = self.project_root / rel_path
-            if not abs_path.exists() and not abs_path.is_symlink():
-                continue
-            # Treat symlinks and non-regular-files as modified
-            if abs_path.is_symlink() or not abs_path.is_file():
-                modified.append(rel)
-                continue
-            if _sha256(abs_path) != expected_hash:
-                modified.append(rel)
-        return modified
-
-    # -- Uninstall --------------------------------------------------------
-
-    def uninstall(
-        self,
-        project_root: Path | None = None,
-        *,
-        force: bool = False,
-    ) -> tuple[list[Path], list[Path]]:
-        """Remove tracked files whose hash still matches.
-
-        Parameters:
-            project_root: Override for the project root.
-            force:        If ``True``, remove files even if modified.
-
-        Returns:
-            ``(removed, skipped)`` — absolute paths.
-        """
-        root = (project_root or self.project_root).resolve()
-        removed: list[Path] = []
-        skipped: list[Path] = []
-
-        for rel, expected_hash in self._files.items():
-            # Use non-resolved path for deletion so symlinks themselves
-            # are removed, not their targets.
-            path = root / rel
-            # Validate containment lexically (without following symlinks)
-            # by collapsing .. segments via Path resolution on the string parts.
-            try:
-                normed = Path(os.path.normpath(path))
-                normed.relative_to(root)
-            except (ValueError, OSError):
-                continue
-            if not path.exists() and not path.is_symlink():
-                continue
-            # Skip directories — manifest only tracks files
-            if not path.is_file() and not path.is_symlink():
-                skipped.append(path)
-                continue
-            # Never follow symlinks when comparing hashes. Only remove
-            # symlinks when forced, to avoid acting on tampered entries.
-            if path.is_symlink():
-                if not force:
-                    skipped.append(path)
-                    continue
-            else:
-                if not force and _sha256(path) != expected_hash:
-                    skipped.append(path)
-                    continue
-            try:
-                path.unlink()
-            except OSError:
-                skipped.append(path)
-                continue
-            removed.append(path)
-            # Clean up empty parent directories up to project root
-            parent = path.parent
-            while parent != root:
-                try:
-                    parent.rmdir()  # only succeeds if empty
-                except OSError:
-                    break
-                parent = parent.parent
-
-        # Remove the manifest file itself
-        manifest = root / ".specify" / "integrations" / f"{self.key}.manifest.json"
-        if manifest.exists():
-            manifest.unlink()
-            parent = manifest.parent
-            while parent != root:
-                try:
-                    parent.rmdir()
-                except OSError:
-                    break
-                parent = parent.parent
-
-        return removed, skipped
-
-    # -- Persistence ------------------------------------------------------
-
-    def save(self) -> Path:
-        """Write the manifest to disk.  Returns the manifest path."""
-        self._installed_at = self._installed_at or datetime.now(timezone.utc).isoformat()
-        data: dict[str, Any] = {
-            "integration": self.key,
-            "version": self.version,
-            "installed_at": self._installed_at,
-            "files": self._files,
-        }
-        path = self.manifest_path
-        path.parent.mkdir(parents=True, exist_ok=True)
-        path.write_text(json.dumps(data, indent=2) + "\n", encoding="utf-8")
-        return path
-
-    @classmethod
-    def load(cls, key: str, project_root: Path) -> IntegrationManifest:
-        """Load an existing manifest from disk.
-
-        Raises ``FileNotFoundError`` if the manifest does not exist.
-        """
-        inst = cls(key, project_root)
-        path = inst.manifest_path
-        try:
-            data = json.loads(path.read_text(encoding="utf-8"))
-        except json.JSONDecodeError as exc:
-            raise ValueError(
-                f"Integration manifest at {path} contains invalid JSON"
-            ) from exc
-
-        if not isinstance(data, dict):
-            raise ValueError(
-                f"Integration manifest at {path} must be a JSON object, "
-                f"got {type(data).__name__}"
-            )
-
-        files = data.get("files", {})
-        if not isinstance(files, dict) or not all(
-            isinstance(k, str) and isinstance(v, str) for k, v in files.items()
-        ):
-            raise ValueError(
-                f"Integration manifest 'files' at {path} must be a "
-                "mapping of string paths to string hashes"
-            )
-
-        inst.version = data.get("version", "")
-        inst._installed_at = data.get("installed_at", "")
-        inst._files = files
-
-        stored_key = data.get("integration", "")
-        if stored_key and stored_key != key:
-            raise ValueError(
-                f"Manifest at {path} belongs to integration {stored_key!r}, "
-                f"not {key!r}"
-            )
-
-        return inst

src/specify_cli/presets.py

@@ -556,31 +556,24 @@ class PresetManager:
         registrar.unregister_commands(registered_commands, self.project_root)
 
     def _get_skills_dir(self) -> Optional[Path]:
-        """Return the active skills directory for preset skill overrides.
+        """Return the skills directory if ``--ai-skills`` was used during init.
 
         Reads ``.specify/init-options.json`` to determine whether skills
         are enabled and which agent was selected, then delegates to
         the module-level ``_get_skills_dir()`` helper for the concrete path.
 
-        Kimi is treated as a native-skills agent: if ``ai == "kimi"`` and
-        ``.kimi/skills`` exists, presets should still propagate command
-        overrides to skills even when ``ai_skills`` is false.
-
         Returns:
             The skills directory ``Path``, or ``None`` if skills were not
-            enabled and no native-skills fallback applies.
+            enabled or the init-options file is missing.
         """
         from . import load_init_options, _get_skills_dir
 
         opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
+        if not opts.get("ai_skills"):
-            opts = {}
-        agent = opts.get("ai")
-        if not isinstance(agent, str) or not agent:
             return None
 
-        ai_skills_enabled = bool(opts.get("ai_skills"))
+        agent = opts.get("ai")
-        if not ai_skills_enabled and agent != "kimi":
+        if not agent:
             return None
 
         skills_dir = _get_skills_dir(self.project_root, agent)
@@ -589,76 +582,6 @@ class PresetManager:
 
         return skills_dir
 
-    @staticmethod
-    def _skill_names_for_command(cmd_name: str) -> tuple[str, str]:
-        """Return the modern and legacy skill directory names for a command."""
-        raw_short_name = cmd_name
-        if raw_short_name.startswith("speckit."):
-            raw_short_name = raw_short_name[len("speckit."):]
-
-        modern_skill_name = f"speckit-{raw_short_name.replace('.', '-')}"
-        legacy_skill_name = f"speckit.{raw_short_name}"
-        return modern_skill_name, legacy_skill_name
-
-    @staticmethod
-    def _skill_title_from_command(cmd_name: str) -> str:
-        """Return a human-friendly title for a skill command name."""
-        title_name = cmd_name
-        if title_name.startswith("speckit."):
-            title_name = title_name[len("speckit."):]
-        return title_name.replace(".", " ").replace("-", " ").title()
-
-    def _build_extension_skill_restore_index(self) -> Dict[str, Dict[str, Any]]:
-        """Index extension-backed skill restore data by skill directory name."""
-        from .extensions import ExtensionManifest, ValidationError
-
-        resolver = PresetResolver(self.project_root)
-        extensions_dir = self.project_root / ".specify" / "extensions"
-        restore_index: Dict[str, Dict[str, Any]] = {}
-
-        for _priority, ext_id, _metadata in resolver._get_all_extensions_by_priority():
-            ext_dir = extensions_dir / ext_id
-            manifest_path = ext_dir / "extension.yml"
-            if not manifest_path.is_file():
-                continue
-
-            try:
-                manifest = ExtensionManifest(manifest_path)
-            except ValidationError:
-                continue
-
-            ext_root = ext_dir.resolve()
-            for cmd_info in manifest.commands:
-                cmd_name = cmd_info.get("name")
-                cmd_file_rel = cmd_info.get("file")
-                if not isinstance(cmd_name, str) or not isinstance(cmd_file_rel, str):
-                    continue
-
-                cmd_path = Path(cmd_file_rel)
-                if cmd_path.is_absolute():
-                    continue
-
-                try:
-                    source_file = (ext_root / cmd_path).resolve()
-                    source_file.relative_to(ext_root)
-                except (OSError, ValueError):
-                    continue
-
-                if not source_file.is_file():
-                    continue
-
-                restore_info = {
-                    "command_name": cmd_name,
-                    "source_file": source_file,
-                    "source": f"extension:{manifest.id}",
-                }
-                modern_skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
-                restore_index.setdefault(modern_skill_name, restore_info)
-                if legacy_skill_name != modern_skill_name:
-                    restore_index.setdefault(legacy_skill_name, restore_info)
-
-        return restore_index
-
     def _register_skills(
         self,
         manifest: "PresetManifest",
@@ -706,15 +629,9 @@ class PresetManager:
             return []
 
         from . import SKILL_DESCRIPTIONS, load_init_options
-        from .agents import CommandRegistrar
 
-        init_opts = load_init_options(self.project_root)
+        opts = load_init_options(self.project_root)
-        if not isinstance(init_opts, dict):
+        selected_ai = opts.get("ai", "")
-            init_opts = {}
-        selected_ai = init_opts.get("ai")
-        if not isinstance(selected_ai, str):
-            return []
-        registrar = CommandRegistrar()
 
         written: List[str] = []
 
@@ -726,61 +643,62 @@ class PresetManager:
                 continue
 
             # Derive the short command name (e.g. "specify" from "speckit.specify")
-            raw_short_name = cmd_name
+            short_name = cmd_name
-            if raw_short_name.startswith("speckit."):
+            if short_name.startswith("speckit."):
-                raw_short_name = raw_short_name[len("speckit."):]
+                short_name = short_name[len("speckit."):]
-            short_name = raw_short_name.replace(".", "-")
+            if selected_ai == "kimi":
-            skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
+                skill_name = f"speckit.{short_name}"
-            skill_title = self._skill_title_from_command(cmd_name)
+            else:
+                skill_name = f"speckit-{short_name}"
 
-            # Only overwrite skills that already exist under skills_dir,
+            # Only overwrite if the skill already exists (i.e. --ai-skills was used)
-            # including Kimi native skills when ai_skills is false.
+            skill_subdir = skills_dir / skill_name
-            # If both modern and legacy directories exist, update both.
+            if not skill_subdir.exists():
-            target_skill_names: List[str] = []
-            if (skills_dir / skill_name).is_dir():
-                target_skill_names.append(skill_name)
-            if legacy_skill_name != skill_name and (skills_dir / legacy_skill_name).is_dir():
-                target_skill_names.append(legacy_skill_name)
-            if not target_skill_names:
                 continue
 
             # Parse the command file
             content = source_file.read_text(encoding="utf-8")
-            frontmatter, body = registrar.parse_frontmatter(content)
+            if content.startswith("---"):
+                parts = content.split("---", 2)
+                if len(parts) >= 3:
+                    frontmatter = yaml.safe_load(parts[1])
+                    if not isinstance(frontmatter, dict):
+                        frontmatter = {}
+                    body = parts[2].strip()
+                else:
+                    frontmatter = {}
+                    body = content
+            else:
+                frontmatter = {}
+                body = content
 
             original_desc = frontmatter.get("description", "")
             enhanced_desc = SKILL_DESCRIPTIONS.get(
                 short_name,
                 original_desc or f"Spec-kit workflow command: {short_name}",
             )
-            frontmatter = dict(frontmatter)
+
-            frontmatter["description"] = enhanced_desc
+            frontmatter_data = {
-            body = registrar.resolve_skill_placeholders(
+                "name": skill_name,
-                selected_ai, frontmatter, body, self.project_root
+                "description": enhanced_desc,
+                "compatibility": "Requires spec-kit project structure with .specify/ directory",
+                "metadata": {
+                    "author": "github-spec-kit",
+                    "source": f"preset:{manifest.id}",
+                },
+            }
+            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
+            skill_content = (
+                f"---\n"
+                f"{frontmatter_text}\n"
+                f"---\n\n"
+                f"# Speckit {short_name.title()} Skill\n\n"
+                f"{body}\n"
             )
 
-            for target_skill_name in target_skill_names:
+            skill_file = skill_subdir / "SKILL.md"
-                frontmatter_data = {
+            skill_file.write_text(skill_content, encoding="utf-8")
-                    "name": target_skill_name,
+            written.append(skill_name)
-                    "description": enhanced_desc,
-                    "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                    "metadata": {
-                        "author": "github-spec-kit",
-                        "source": f"preset:{manifest.id}",
-                    },
-                }
-                frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_content = (
-                    f"---\n"
-                    f"{frontmatter_text}\n"
-                    f"---\n\n"
-                    f"# Speckit {skill_title} Skill\n\n"
-                    f"{body}\n"
-                )
-
-                skill_file = skills_dir / target_skill_name / "SKILL.md"
-                skill_file.write_text(skill_content, encoding="utf-8")
-                written.append(target_skill_name)
 
         return written
 
@@ -802,17 +720,10 @@ class PresetManager:
         if not skills_dir:
             return
 
-        from . import SKILL_DESCRIPTIONS, load_init_options
+        from . import SKILL_DESCRIPTIONS
-        from .agents import CommandRegistrar
 
         # Locate core command templates from the project's installed templates
         core_templates_dir = self.project_root / ".specify" / "templates" / "commands"
-        init_opts = load_init_options(self.project_root)
-        if not isinstance(init_opts, dict):
-            init_opts = {}
-        selected_ai = init_opts.get("ai")
-        registrar = CommandRegistrar()
-        extension_restore_index = self._build_extension_skill_restore_index()
 
         for skill_name in skill_names:
             # Derive command name from skill name (speckit-specify -> specify)
@@ -824,10 +735,7 @@ class PresetManager:
 
             skill_subdir = skills_dir / skill_name
             skill_file = skill_subdir / "SKILL.md"
-            if not skill_subdir.is_dir():
+            if not skill_file.exists():
-                continue
-            if not skill_file.is_file():
-                # Only manage directories that contain the expected skill entrypoint.
                 continue
 
             # Try to find the core command template
@@ -838,11 +746,19 @@ class PresetManager:
             if core_file:
                 # Restore from core template
                 content = core_file.read_text(encoding="utf-8")
-                frontmatter, body = registrar.parse_frontmatter(content)
+                if content.startswith("---"):
-                if isinstance(selected_ai, str):
+                    parts = content.split("---", 2)
-                    body = registrar.resolve_skill_placeholders(
+                    if len(parts) >= 3:
-                        selected_ai, frontmatter, body, self.project_root
+                        frontmatter = yaml.safe_load(parts[1])
-                    )
+                        if not isinstance(frontmatter, dict):
+                            frontmatter = {}
+                        body = parts[2].strip()
+                    else:
+                        frontmatter = {}
+                        body = content
+                else:
+                    frontmatter = {}
+                    body = content
 
                 original_desc = frontmatter.get("description", "")
                 enhanced_desc = SKILL_DESCRIPTIONS.get(
@@ -860,49 +776,16 @@ class PresetManager:
                     },
                 }
                 frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_title = self._skill_title_from_command(short_name)
                 skill_content = (
                     f"---\n"
                     f"{frontmatter_text}\n"
                     f"---\n\n"
-                    f"# Speckit {skill_title} Skill\n\n"
+                    f"# Speckit {short_name.title()} Skill\n\n"
-                    f"{body}\n"
-                )
-                skill_file.write_text(skill_content, encoding="utf-8")
-                continue
-
-            extension_restore = extension_restore_index.get(skill_name)
-            if extension_restore:
-                content = extension_restore["source_file"].read_text(encoding="utf-8")
-                frontmatter, body = registrar.parse_frontmatter(content)
-                if isinstance(selected_ai, str):
-                    body = registrar.resolve_skill_placeholders(
-                        selected_ai, frontmatter, body, self.project_root
-                    )
-
-                command_name = extension_restore["command_name"]
-                title_name = self._skill_title_from_command(command_name)
-
-                frontmatter_data = {
-                    "name": skill_name,
-                    "description": frontmatter.get("description", f"Extension command: {command_name}"),
-                    "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                    "metadata": {
-                        "author": "github-spec-kit",
-                        "source": extension_restore["source"],
-                    },
-                }
-                frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_content = (
-                    f"---\n"
-                    f"{frontmatter_text}\n"
-                    f"---\n\n"
-                    f"# {title_name} Skill\n\n"
                     f"{body}\n"
                 )
                 skill_file.write_text(skill_content, encoding="utf-8")
             else:
-                # No core or extension template — remove the skill entirely
+                # No core template — remove the skill entirely
                 shutil.rmtree(skill_subdir)
 
     def install_from_directory(
@@ -1032,26 +915,17 @@ class PresetManager:
         if not self.registry.is_installed(pack_id):
             return False
 
+        # Unregister commands from AI agents
         metadata = self.registry.get(pack_id)
+        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
+        if registered_commands:
+            self._unregister_commands(registered_commands)
+
         # Restore original skills when preset is removed
         registered_skills = metadata.get("registered_skills", []) if metadata else []
-        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
         pack_dir = self.presets_dir / pack_id
         if registered_skills:
             self._unregister_skills(registered_skills, pack_dir)
-            try:
-                from . import NATIVE_SKILLS_AGENTS
-            except ImportError:
-                NATIVE_SKILLS_AGENTS = set()
-            registered_commands = {
-                agent_name: cmd_names
-                for agent_name, cmd_names in registered_commands.items()
-                if agent_name not in NATIVE_SKILLS_AGENTS
-            }
-
-        # Unregister non-skill command files from AI agents.
-        if registered_commands:
-            self._unregister_commands(registered_commands)
 
         if pack_dir.exists():
             shutil.rmtree(pack_dir)

templates/commands/analyze.md

@@ -44,7 +44,7 @@ Load only the minimal necessary context from each artifact:
 
 - Overview/Context
 - Functional Requirements
-- Success Criteria (measurable outcomes — e.g., performance, security, availability, user success, business impact)
+- Non-Functional Requirements
 - User Stories
 - Edge Cases (if present)
 
@@ -71,7 +71,7 @@ Load only the minimal necessary context from each artifact:
 
 Create internal representations (do not include raw artifacts in output):
 
-- **Requirements inventory**: For each Functional Requirement (FR-###) and Success Criterion (SC-###), record a stable key. Use the explicit FR-/SC- identifier as the primary key when present, and optionally also derive an imperative-phrase slug for readability (e.g., "User can upload file" → `user-can-upload-file`). Include only Success Criteria items that require buildable work (e.g., load-testing infrastructure, security audit tooling), and exclude post-launch outcome metrics and business KPIs (e.g., "Reduce support tickets by 50%").
+- **Requirements inventory**: Each functional + non-functional requirement with a stable key (derive slug based on imperative phrase; e.g., "User can upload file" → `user-can-upload-file`)
 - **User story/action inventory**: Discrete user actions with acceptance criteria
 - **Task coverage mapping**: Map each task to one or more requirements or stories (inference by keyword / explicit reference patterns like IDs or key phrases)
 - **Constitution rule set**: Extract principle names and MUST/SHOULD normative statements
@@ -105,7 +105,7 @@ Focus on high-signal findings. Limit to 50 findings total; aggregate remainder i
 
 - Requirements with zero associated tasks
 - Tasks with no mapped requirement/story
-- Success Criteria requiring buildable work (performance, security, availability) not reflected in tasks
+- Non-functional requirements not reflected in tasks (e.g., performance, security)
 
 #### F. Inconsistency
 

templates/commands/clarify.md

@@ -145,7 +145,7 @@ Execution steps:
        - Functional ambiguity → Update or add a bullet in Functional Requirements.
        - User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
        - Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
-       - Non-functional constraint → Add/modify measurable criteria in Success Criteria > Measurable Outcomes (convert vague adjective to metric or explicit target).
+       - Non-functional constraint → Add/modify measurable criteria in Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
        - Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
        - Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
     - If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.

tests/test_ai_skills.py

@@ -24,8 +24,8 @@ import specify_cli
 
 from specify_cli import (
     _get_skills_dir,
-    _migrate_legacy_kimi_dotted_skills,
     install_ai_skills,
+    AGENT_SKILLS_DIR_OVERRIDES,
     DEFAULT_SKILLS_DIR,
     SKILL_DESCRIPTIONS,
     AGENT_CONFIG,
@@ -169,8 +169,8 @@ class TestGetSkillsDir:
         result = _get_skills_dir(project_dir, "copilot")
         assert result == project_dir / ".github" / "skills"
 
-    def test_codex_skills_dir_from_agent_config(self, project_dir):
+    def test_codex_uses_override(self, project_dir):
-        """Codex should resolve skills directory from AGENT_CONFIG folder."""
+        """Codex should use the AGENT_SKILLS_DIR_OVERRIDES value."""
         result = _get_skills_dir(project_dir, "codex")
         assert result == project_dir / ".agents" / "skills"
 
@@ -203,71 +203,12 @@ class TestGetSkillsDir:
             # Should always end with "skills"
             assert result.name == "skills"
 
-class TestKimiLegacySkillMigration:
+    def test_override_takes_precedence_over_config(self, project_dir):
-    """Test temporary migration from Kimi dotted skill names to hyphenated names."""
+        """AGENT_SKILLS_DIR_OVERRIDES should take precedence over AGENT_CONFIG."""
-
+        for agent_key in AGENT_SKILLS_DIR_OVERRIDES:
-    def test_migrates_legacy_dotted_skill_directory(self, project_dir):
+            result = _get_skills_dir(project_dir, agent_key)
-        skills_dir = project_dir / ".kimi" / "skills"
+            expected = project_dir / AGENT_SKILLS_DIR_OVERRIDES[agent_key]
-        legacy_dir = skills_dir / "speckit.plan"
+            assert result == expected
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 1
-        assert removed == 0
-        assert not legacy_dir.exists()
-        assert (skills_dir / "speckit-plan" / "SKILL.md").exists()
-
-    def test_removes_legacy_dir_when_hyphenated_target_exists_with_same_content(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 1
-        assert not legacy_dir.exists()
-        assert (target_dir / "SKILL.md").read_text() == "legacy"
-
-    def test_keeps_legacy_dir_when_hyphenated_target_differs(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("new")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 0
-        assert legacy_dir.exists()
-        assert (legacy_dir / "SKILL.md").read_text() == "legacy"
-        assert (target_dir / "SKILL.md").read_text() == "new"
-
-    def test_keeps_legacy_dir_when_matching_target_but_extra_files_exist(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        (legacy_dir / "notes.txt").write_text("custom")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 0
-        assert legacy_dir.exists()
-        assert (legacy_dir / "notes.txt").read_text() == "custom"
 
 
 # ===== install_ai_skills Tests =====
@@ -532,7 +473,8 @@ class TestInstallAiSkills:
         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()]
-        expected_skill_name = "speckit-specify"
+        # Kimi uses dotted skill names; other agents use hyphen-separated names.
+        expected_skill_name = "speckit.specify" if agent_key == "kimi" else "speckit-specify"
         assert expected_skill_name in skill_dirs
         assert (skills_dir / expected_skill_name / "SKILL.md").exists()
 
@@ -831,32 +773,6 @@ class TestNewProjectCommandSkip:
         mock_skills.assert_called_once()
         assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
 
-    def test_kimi_legacy_migration_runs_without_ai_skills_flag(self, tmp_path):
-        """Kimi init should migrate dotted legacy skills even when --ai-skills is not set."""
-        from typer.testing import CliRunner
-
-        runner = CliRunner()
-        target = tmp_path / "kimi-legacy-no-ai-skills"
-
-        def fake_download(project_path, *args, **kwargs):
-            legacy_dir = project_path / ".kimi" / "skills" / "speckit.plan"
-            legacy_dir.mkdir(parents=True, exist_ok=True)
-            (legacy_dir / "SKILL.md").write_text("---\nname: speckit.plan\n---\n\nlegacy\n")
-
-        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.is_git_repo", return_value=False), \
-             patch("specify_cli.shutil.which", return_value="/usr/bin/kimi"):
-            result = runner.invoke(
-                app,
-                ["init", str(target), "--ai", "kimi", "--script", "sh", "--no-git"],
-            )
-
-        assert result.exit_code == 0
-        assert not (target / ".kimi" / "skills" / "speckit.plan").exists()
-        assert (target / ".kimi" / "skills" / "speckit-plan" / "SKILL.md").exists()
-
     def test_codex_ai_skills_here_mode_preserves_existing_codex_dir(self, tmp_path, monkeypatch):
         """Codex --here skills init should not delete a pre-existing .codex directory."""
         from typer.testing import CliRunner
@@ -1202,12 +1118,12 @@ class TestCliValidation:
             assert "Optional skills that you can use for your specs" in result.output
 
     def test_kimi_next_steps_show_skill_invocation(self, monkeypatch):
-        """Kimi next-steps guidance should display /skill:speckit-* usage."""
+        """Kimi next-steps guidance should display /skill:speckit.* usage."""
         from typer.testing import CliRunner
 
         def _fake_download(*args, **kwargs):
             project_path = Path(args[0])
-            skill_dir = project_path / ".kimi" / "skills" / "speckit-specify"
+            skill_dir = project_path / ".kimi" / "skills" / "speckit.specify"
             skill_dir.mkdir(parents=True, exist_ok=True)
             (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
 
@@ -1221,7 +1137,7 @@ class TestCliValidation:
             )
 
             assert result.exit_code == 0
-            assert "/skill:speckit-constitution" in result.output
+            assert "/skill:speckit.constitution" in result.output
             assert "/speckit.constitution" not in result.output
             assert "Optional skills that you can use for your specs" in result.output
 

tests/test_check_tool.py

@@ -1,96 +0,0 @@
-"""Tests for check_tool() — Claude Code CLI detection across install methods.
-
-Covers issue https://github.com/github/spec-kit/issues/550:
-  `specify check` reports "Claude Code CLI (not found)" even when claude is
-  installed via npm-local (the default `claude` installer path).
-"""
-
-from unittest.mock import patch, MagicMock
-
-from specify_cli import check_tool
-
-
-class TestCheckToolClaude:
-    """Claude CLI detection must work for all install methods."""
-
-    def test_detected_via_migrate_installer_path(self, tmp_path):
-        """claude migrate-installer puts binary at ~/.claude/local/claude."""
-        fake_claude = tmp_path / "claude"
-        fake_claude.touch()
-
-        # Ensure npm-local path is missing so we only exercise migrate-installer path
-        fake_missing = tmp_path / "nonexistent" / "claude"
-
-        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_claude), \
-             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
-             patch("shutil.which", return_value=None):
-            assert check_tool("claude") is True
-
-    def test_detected_via_npm_local_path(self, tmp_path):
-        """npm-local install puts binary at ~/.claude/local/node_modules/.bin/claude."""
-        fake_npm_claude = tmp_path / "node_modules" / ".bin" / "claude"
-        fake_npm_claude.parent.mkdir(parents=True)
-        fake_npm_claude.touch()
-
-        # Neither the migrate-installer path nor PATH has claude
-        fake_migrate = tmp_path / "nonexistent" / "claude"
-
-        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_migrate), \
-             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_npm_claude), \
-             patch("shutil.which", return_value=None):
-            assert check_tool("claude") is True
-
-    def test_detected_via_path(self, tmp_path):
-        """claude on PATH (global npm install) should still work."""
-        fake_missing = tmp_path / "nonexistent" / "claude"
-
-        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
-             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
-             patch("shutil.which", return_value="/usr/local/bin/claude"):
-            assert check_tool("claude") is True
-
-    def test_not_found_when_nowhere(self, tmp_path):
-        """Should return False when claude is genuinely not installed."""
-        fake_missing = tmp_path / "nonexistent" / "claude"
-
-        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
-             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
-             patch("shutil.which", return_value=None):
-            assert check_tool("claude") is False
-
-    def test_tracker_updated_on_npm_local_detection(self, tmp_path):
-        """StepTracker should be marked 'available' for npm-local installs."""
-        fake_npm_claude = tmp_path / "node_modules" / ".bin" / "claude"
-        fake_npm_claude.parent.mkdir(parents=True)
-        fake_npm_claude.touch()
-
-        fake_missing = tmp_path / "nonexistent" / "claude"
-        tracker = MagicMock()
-
-        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
-             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_npm_claude), \
-             patch("shutil.which", return_value=None):
-            result = check_tool("claude", tracker=tracker)
-
-        assert result is True
-        tracker.complete.assert_called_once_with("claude", "available")
-
-
-class TestCheckToolOther:
-    """Non-Claude tools should be unaffected by the fix."""
-
-    def test_git_detected_via_path(self):
-        with patch("shutil.which", return_value="/usr/bin/git"):
-            assert check_tool("git") is True
-
-    def test_missing_tool(self):
-        with patch("shutil.which", return_value=None):
-            assert check_tool("nonexistent-tool") is False
-
-    def test_kiro_fallback(self):
-        """kiro-cli detection should try both kiro-cli and kiro."""
-        def fake_which(name):
-            return "/usr/bin/kiro" if name == "kiro" else None
-
-        with patch("shutil.which", side_effect=fake_which):
-            assert check_tool("kiro-cli") is True

tests/test_core_pack_scaffold.py

@@ -142,7 +142,7 @@ def _expected_cmd_dir(project_path: Path, agent: str) -> Path:
 
 # Agents whose commands are laid out as <skills_dir>/<name>/SKILL.md.
 # Maps agent -> separator used in skill directory names.
-_SKILL_AGENTS: dict[str, str] = {"codex": "-", "kimi": "-"}
+_SKILL_AGENTS: dict[str, str] = {"codex": "-", "kimi": "."}
 
 
 def _expected_ext(agent: str) -> str:

tests/test_extension_skills.py

@@ -1,741 +0,0 @@
-"""
-Unit tests for extension skill auto-registration.
-
-Tests cover:
-- SKILL.md generation when --ai-skills was used during init
-- No skills created when ai_skills not active
-- SKILL.md content correctness
-- Existing user-modified skills not overwritten
-- Skill cleanup on extension removal
-- Registry metadata includes registered_skills
-"""
-
-import json
-import pytest
-import tempfile
-import shutil
-import yaml
-from pathlib import Path
-
-from specify_cli.extensions import (
-    ExtensionManifest,
-    ExtensionManager,
-    ExtensionError,
-)
-
-
-# ===== Helpers =====
-
-def _create_init_options(project_root: Path, ai: str = "claude", ai_skills: bool = True):
-    """Write a .specify/init-options.json file."""
-    opts_dir = project_root / ".specify"
-    opts_dir.mkdir(parents=True, exist_ok=True)
-    opts_file = opts_dir / "init-options.json"
-    opts_file.write_text(json.dumps({
-        "ai": ai,
-        "ai_skills": ai_skills,
-        "script": "sh",
-    }))
-
-
-def _create_skills_dir(project_root: Path, ai: str = "claude") -> Path:
-    """Create and return the expected skills directory for the given agent."""
-    # Match the logic in _get_skills_dir() from specify_cli
-    from specify_cli import AGENT_CONFIG, DEFAULT_SKILLS_DIR
-
-    agent_config = AGENT_CONFIG.get(ai, {})
-    agent_folder = agent_config.get("folder", "")
-    if agent_folder:
-        skills_dir = project_root / agent_folder.rstrip("/") / "skills"
-    else:
-        skills_dir = project_root / DEFAULT_SKILLS_DIR
-
-    skills_dir.mkdir(parents=True, exist_ok=True)
-    return skills_dir
-
-
-def _create_extension_dir(temp_dir: Path, ext_id: str = "test-ext") -> Path:
-    """Create a complete extension directory with manifest and command files."""
-    ext_dir = temp_dir / ext_id
-    ext_dir.mkdir()
-
-    manifest_data = {
-        "schema_version": "1.0",
-        "extension": {
-            "id": ext_id,
-            "name": "Test Extension",
-            "version": "1.0.0",
-            "description": "A test extension for skill registration",
-        },
-        "requires": {
-            "speckit_version": ">=0.1.0",
-        },
-        "provides": {
-            "commands": [
-                {
-                    "name": f"speckit.{ext_id}.hello",
-                    "file": "commands/hello.md",
-                    "description": "Test hello command",
-                },
-                {
-                    "name": f"speckit.{ext_id}.world",
-                    "file": "commands/world.md",
-                    "description": "Test world command",
-                },
-            ]
-        },
-    }
-
-    with open(ext_dir / "extension.yml", "w") as f:
-        yaml.dump(manifest_data, f)
-
-    commands_dir = ext_dir / "commands"
-    commands_dir.mkdir()
-
-    (commands_dir / "hello.md").write_text(
-        "---\n"
-        "description: \"Test hello command\"\n"
-        "---\n"
-        "\n"
-        "# Hello Command\n"
-        "\n"
-        "Run this to say hello.\n"
-        "$ARGUMENTS\n"
-    )
-
-    (commands_dir / "world.md").write_text(
-        "---\n"
-        "description: \"Test world command\"\n"
-        "---\n"
-        "\n"
-        "# World Command\n"
-        "\n"
-        "Run this to greet the world.\n"
-    )
-
-    return ext_dir
-
-
-# ===== 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 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
-
-
-@pytest.fixture
-def extension_dir(temp_dir):
-    """Create a complete extension directory."""
-    return _create_extension_dir(temp_dir)
-
-
-@pytest.fixture
-def skills_project(project_dir):
-    """Create a project with --ai-skills enabled and skills directory."""
-    _create_init_options(project_dir, ai="claude", ai_skills=True)
-    skills_dir = _create_skills_dir(project_dir, ai="claude")
-    return project_dir, skills_dir
-
-
-@pytest.fixture
-def no_skills_project(project_dir):
-    """Create a project without --ai-skills."""
-    _create_init_options(project_dir, ai="claude", ai_skills=False)
-    return project_dir
-
-
-# ===== ExtensionManager._get_skills_dir Tests =====
-
-class TestExtensionManagerGetSkillsDir:
-    """Test _get_skills_dir() on ExtensionManager."""
-
-    def test_returns_skills_dir_when_active(self, skills_project):
-        """Should return skills dir when ai_skills is true and dir exists."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result == skills_dir
-
-    def test_returns_none_when_no_ai_skills(self, no_skills_project):
-        """Should return None when ai_skills is false."""
-        manager = ExtensionManager(no_skills_project)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_none_when_no_init_options(self, project_dir):
-        """Should return None when init-options.json is missing."""
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_none_when_skills_dir_missing(self, project_dir):
-        """Should return None when skills dir doesn't exist on disk."""
-        _create_init_options(project_dir, ai="claude", ai_skills=True)
-        # Don't create the skills directory
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_kimi_skills_dir_when_ai_skills_disabled(self, project_dir):
-        """Kimi should still use its native skills dir when ai_skills is false."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = _create_skills_dir(project_dir, ai="kimi")
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result == skills_dir
-
-    def test_returns_none_for_non_dict_init_options(self, project_dir):
-        """Corrupted-but-parseable init-options should not crash skill-dir lookup."""
-        opts_file = project_dir / ".specify" / "init-options.json"
-        opts_file.parent.mkdir(parents=True, exist_ok=True)
-        opts_file.write_text("[]")
-        _create_skills_dir(project_dir, ai="claude")
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-
-# ===== Extension Skill Registration Tests =====
-
-class TestExtensionSkillRegistration:
-    """Test _register_extension_skills() on ExtensionManager."""
-
-    def test_skills_created_when_ai_skills_active(self, skills_project, extension_dir):
-        """Skills should be created when ai_skills is enabled."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Check that skill directories were created
-        skill_dirs = sorted([d.name for d in skills_dir.iterdir() if d.is_dir()])
-        assert "speckit-test-ext-hello" in skill_dirs
-        assert "speckit-test-ext-world" in skill_dirs
-
-    def test_skill_md_content_correct(self, skills_project, extension_dir):
-        """SKILL.md should have correct agentskills.io structure."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-
-        # Check structure
-        assert content.startswith("---\n")
-        assert "name: speckit-test-ext-hello" in content
-        assert "description:" in content
-        assert "Test hello command" in content
-        assert "source: extension:test-ext" in content
-        assert "author: github-spec-kit" in content
-        assert "compatibility:" in content
-        assert "Run this to say hello." in content
-
-    def test_skill_md_has_parseable_yaml(self, skills_project, extension_dir):
-        """Generated SKILL.md should contain valid, parseable YAML frontmatter."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        content = skill_file.read_text()
-
-        assert content.startswith("---\n")
-        parts = content.split("---", 2)
-        assert len(parts) >= 3
-        parsed = yaml.safe_load(parts[1])
-        assert isinstance(parsed, dict)
-        assert parsed["name"] == "speckit-test-ext-hello"
-        assert "description" in parsed
-
-    def test_no_skills_when_ai_skills_disabled(self, no_skills_project, extension_dir):
-        """No skills should be created when ai_skills is false."""
-        manager = ExtensionManager(no_skills_project)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify registry
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_no_skills_when_init_options_missing(self, project_dir, extension_dir):
-        """No skills should be created when init-options.json is absent."""
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_existing_skill_not_overwritten(self, skills_project, extension_dir):
-        """Pre-existing SKILL.md should not be overwritten."""
-        project_dir, skills_dir = skills_project
-
-        # Pre-create a custom skill
-        custom_dir = skills_dir / "speckit-test-ext-hello"
-        custom_dir.mkdir(parents=True)
-        custom_content = "# My Custom Hello Skill\nUser-modified content\n"
-        (custom_dir / "SKILL.md").write_text(custom_content)
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Custom skill should be untouched
-        assert (custom_dir / "SKILL.md").read_text() == custom_content
-
-        # But the other skill should still be created
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-        # The pre-existing one should NOT be in registered_skills (it was skipped)
-        assert "speckit-test-ext-hello" not in metadata["registered_skills"]
-
-    def test_registered_skills_in_registry(self, skills_project, extension_dir):
-        """Registry should contain registered_skills list."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "registered_skills" in metadata
-        assert len(metadata["registered_skills"]) == 2
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-
-    def test_kimi_uses_hyphenated_skill_names(self, project_dir, temp_dir):
-        """Kimi agent should use the same hyphenated skill names as hooks."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=True)
-        _create_skills_dir(project_dir, ai="kimi")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-
-    def test_kimi_creates_skills_when_ai_skills_disabled(self, project_dir, temp_dir):
-        """Kimi should still auto-register extension skills in native-skills mode."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = _create_skills_dir(project_dir, ai="kimi")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-    def test_skill_registration_resolves_script_placeholders(self, project_dir, temp_dir):
-        """Auto-registered extension skills should resolve script placeholders."""
-        _create_init_options(project_dir, ai="claude", ai_skills=True)
-        skills_dir = _create_skills_dir(project_dir, ai="claude")
-
-        ext_dir = temp_dir / "scripted-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "scripted-ext",
-                "name": "Scripted Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.scripted-ext.plan",
-                        "file": "commands/plan.md",
-                        "description": "Scripted plan command",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "plan.md").write_text(
-            "---\n"
-            "description: Scripted plan command\n"
-            "scripts:\n"
-            "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "agent_scripts:\n"
-            "  sh: ../../scripts/bash/update-agent-context.sh __AGENT__\n"
-            "---\n\n"
-            "Run {SCRIPT}\n"
-            "Then {AGENT_SCRIPT}\n"
-            "Review templates/checklist.md and memory/constitution.md for __AGENT__.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-        content = (skills_dir / "speckit-scripted-ext-plan" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
-        assert "{ARGS}" not in content
-        assert "__AGENT__" not in content
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh claude" in content
-        assert ".specify/templates/checklist.md" in content
-        assert ".specify/memory/constitution.md" in content
-
-    def test_missing_command_file_skipped(self, skills_project, temp_dir):
-        """Commands with missing source files should be skipped gracefully."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir = temp_dir / "missing-cmd-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "missing-cmd-ext",
-                "name": "Missing Cmd Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.missing-cmd-ext.exists",
-                        "file": "commands/exists.md",
-                        "description": "Exists",
-                    },
-                    {
-                        "name": "speckit.missing-cmd-ext.ghost",
-                        "file": "commands/ghost.md",
-                        "description": "Does not exist",
-                    },
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "exists.md").write_text(
-            "---\ndescription: Exists\n---\n\n# Exists\n\nBody.\n"
-        )
-        # Intentionally do NOT create ghost.md
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-missing-cmd-ext-exists" in metadata["registered_skills"]
-        assert "speckit-missing-cmd-ext-ghost" not in metadata["registered_skills"]
-
-
-# ===== Extension Skill Unregistration Tests =====
-
-class TestExtensionSkillUnregistration:
-    """Test _unregister_extension_skills() on ExtensionManager."""
-
-    def test_skills_removed_on_extension_remove(self, skills_project, extension_dir):
-        """Removing an extension should clean up its skill directories."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()
-
-        # Remove extension
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-        # Skills should be gone
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()
-
-    def test_other_skills_preserved_on_remove(self, skills_project, extension_dir):
-        """Non-extension skills should not be affected by extension removal."""
-        project_dir, skills_dir = skills_project
-
-        # Pre-create a custom skill
-        custom_dir = skills_dir / "my-custom-skill"
-        custom_dir.mkdir(parents=True)
-        (custom_dir / "SKILL.md").write_text("# My Custom Skill\n")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        manager.remove(manifest.id, keep_config=False)
-
-        # Custom skill should still exist
-        assert (custom_dir / "SKILL.md").exists()
-        assert (custom_dir / "SKILL.md").read_text() == "# My Custom Skill\n"
-
-    def test_remove_handles_already_deleted_skills(self, skills_project, extension_dir):
-        """Gracefully handle case where skill dirs were already deleted."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Manually delete skill dirs before calling remove
-        shutil.rmtree(skills_dir / "speckit-test-ext-hello")
-        shutil.rmtree(skills_dir / "speckit-test-ext-world")
-
-        # Should not raise
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-    def test_remove_no_skills_when_not_active(self, no_skills_project, extension_dir):
-        """Removal without active skills should not attempt skill cleanup."""
-        manager = ExtensionManager(no_skills_project)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Should not raise even though no skills exist
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-
-# ===== Command File Without Frontmatter =====
-
-class TestExtensionSkillEdgeCases:
-    """Test edge cases in extension skill registration."""
-
-    def test_install_with_non_dict_init_options_does_not_crash(self, project_dir, extension_dir):
-        """Corrupted init-options payloads should disable skill registration, not crash install."""
-        opts_file = project_dir / ".specify" / "init-options.json"
-        opts_file.parent.mkdir(parents=True, exist_ok=True)
-        opts_file.write_text("[]")
-        _create_skills_dir(project_dir, ai="claude")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_command_without_frontmatter(self, skills_project, temp_dir):
-        """Commands without YAML frontmatter should still produce valid skills."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir = temp_dir / "nofm-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "nofm-ext",
-                "name": "No Frontmatter Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.nofm-ext.plain",
-                        "file": "commands/plain.md",
-                        "description": "Plain command",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "plain.md").write_text(
-            "# Plain Command\n\nBody without frontmatter.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-nofm-ext-plain" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "name: speckit-nofm-ext-plain" in content
-        # Fallback description when no frontmatter description
-        assert "Extension command: speckit.nofm-ext.plain" in content
-        assert "Body without frontmatter." in content
-
-    def test_gemini_agent_skills(self, project_dir, temp_dir):
-        """Gemini agent should use .gemini/skills/ for skill directory."""
-        _create_init_options(project_dir, ai="gemini", ai_skills=True)
-        _create_skills_dir(project_dir, ai="gemini")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skills_dir = project_dir / ".gemini" / "skills"
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()
-
-    def test_multiple_extensions_independent_skills(self, skills_project, temp_dir):
-        """Installing and removing different extensions should be independent."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir_a = _create_extension_dir(temp_dir, ext_id="ext-a")
-        ext_dir_b = _create_extension_dir(temp_dir, ext_id="ext-b")
-
-        manager = ExtensionManager(project_dir)
-        manifest_a = manager.install_from_directory(
-            ext_dir_a, "0.1.0", register_commands=False
-        )
-        manifest_b = manager.install_from_directory(
-            ext_dir_b, "0.1.0", register_commands=False
-        )
-
-        # Both should have skills
-        assert (skills_dir / "speckit-ext-a-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()
-
-        # Remove ext-a
-        manager.remove("ext-a", keep_config=False)
-
-        # ext-a skills gone, ext-b skills preserved
-        assert not (skills_dir / "speckit-ext-a-hello").exists()
-        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()
-
-    def test_malformed_frontmatter_handled(self, skills_project, temp_dir):
-        """Commands with invalid YAML frontmatter should still produce valid skills."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir = temp_dir / "badfm-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "badfm-ext",
-                "name": "Bad Frontmatter Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.badfm-ext.broken",
-                        "file": "commands/broken.md",
-                        "description": "Broken frontmatter",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        # Malformed YAML: invalid key-value syntax
-        (ext_dir / "commands" / "broken.md").write_text(
-            "---\n"
-            "description: [invalid yaml\n"
-            "  unclosed: bracket\n"
-            "---\n"
-            "\n"
-            "# Broken Command\n"
-            "\n"
-            "This body should still be used.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        # Should not raise
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-badfm-ext-broken" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        # Fallback description since frontmatter was invalid
-        assert "Extension command: speckit.badfm-ext.broken" in content
-        assert "This body should still be used." in content
-
-    def test_remove_cleans_up_when_init_options_deleted(self, skills_project, extension_dir):
-        """Skills should be cleaned up even if init-options.json is deleted after install."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-        # Delete init-options.json to simulate user change
-        init_opts = project_dir / ".specify" / "init-options.json"
-        init_opts.unlink()
-
-        # Remove should still clean up via fallback scan
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()
-
-    def test_remove_cleans_up_when_ai_skills_toggled(self, skills_project, extension_dir):
-        """Skills should be cleaned up even if ai_skills is toggled to false after install."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-        # Toggle ai_skills to false
-        _create_init_options(project_dir, ai="claude", ai_skills=False)
-
-        # Remove should still clean up via fallback scan
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()

tests/test_extensions.py

@@ -18,12 +18,10 @@ from datetime import datetime, timezone
 
 from specify_cli.extensions import (
     CatalogEntry,
-    CORE_COMMAND_NAMES,
     ExtensionManifest,
     ExtensionRegistry,
     ExtensionManager,
     CommandRegistrar,
-    HookExecutor,
     ExtensionCatalog,
     ExtensionError,
     ValidationError,
@@ -64,7 +62,7 @@ def valid_manifest_data():
         "provides": {
             "commands": [
                 {
-                    "name": "speckit.test-ext.hello",
+                    "name": "speckit.test.hello",
                     "file": "commands/hello.md",
                     "description": "Test command",
                 }
@@ -72,7 +70,7 @@ def valid_manifest_data():
         },
         "hooks": {
             "after_tasks": {
-                "command": "speckit.test-ext.hello",
+                "command": "speckit.test.hello",
                 "optional": True,
                 "prompt": "Run test?",
             }
@@ -190,18 +188,7 @@ class TestExtensionManifest:
         assert manifest.version == "1.0.0"
         assert manifest.description == "A test extension"
         assert len(manifest.commands) == 1
-        assert manifest.commands[0]["name"] == "speckit.test-ext.hello"
+        assert manifest.commands[0]["name"] == "speckit.test.hello"
-
-    def test_core_command_names_match_bundled_templates(self):
-        """Core command reservations should stay aligned with bundled templates."""
-        commands_dir = Path(__file__).resolve().parent.parent / "templates" / "commands"
-        expected = {
-            command_file.stem
-            for command_file in commands_dir.iterdir()
-            if command_file.is_file() and command_file.suffix == ".md"
-        }
-
-        assert CORE_COMMAND_NAMES == expected
 
     def test_missing_required_field(self, temp_dir):
         """Test manifest missing required field."""
@@ -601,172 +588,6 @@ class TestExtensionManager:
         with pytest.raises(ExtensionError, match="already installed"):
             manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
 
-    def test_install_rejects_extension_id_in_core_namespace(self, temp_dir, project_dir):
-        """Install should reject extension IDs that shadow core commands."""
-        import yaml
-
-        ext_dir = temp_dir / "analyze-ext"
-        ext_dir.mkdir()
-        (ext_dir / "commands").mkdir()
-
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "analyze",
-                "name": "Analyze Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.analyze.extra",
-                        "file": "commands/cmd.md",
-                    }
-                ]
-            },
-        }
-
-        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
-        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
-
-        manager = ExtensionManager(project_dir)
-        with pytest.raises(ValidationError, match="conflicts with core command namespace"):
-            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-    def test_install_rejects_alias_without_extension_namespace(self, temp_dir, project_dir):
-        """Install should reject legacy short aliases that can shadow core commands."""
-        import yaml
-
-        ext_dir = temp_dir / "alias-shortcut"
-        ext_dir.mkdir()
-        (ext_dir / "commands").mkdir()
-
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "alias-shortcut",
-                "name": "Alias Shortcut",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.alias-shortcut.cmd",
-                        "file": "commands/cmd.md",
-                        "aliases": ["speckit.shortcut"],
-                    }
-                ]
-            },
-        }
-
-        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
-        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
-
-        manager = ExtensionManager(project_dir)
-        with pytest.raises(ValidationError, match="Invalid alias 'speckit.shortcut'"):
-            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-    def test_install_rejects_namespace_squatting(self, temp_dir, project_dir):
-        """Install should reject commands and aliases outside the extension namespace."""
-        import yaml
-
-        ext_dir = temp_dir / "squat-ext"
-        ext_dir.mkdir()
-        (ext_dir / "commands").mkdir()
-
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "squat-ext",
-                "name": "Squat Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.other-ext.cmd",
-                        "file": "commands/cmd.md",
-                        "aliases": ["speckit.squat-ext.ok"],
-                    }
-                ]
-            },
-        }
-
-        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
-        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
-
-        manager = ExtensionManager(project_dir)
-        with pytest.raises(ValidationError, match="must use extension namespace 'squat-ext'"):
-            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-    def test_install_rejects_command_collision_with_installed_extension(self, temp_dir, project_dir):
-        """Install should reject names already claimed by an installed legacy extension."""
-        import yaml
-
-        first_dir = temp_dir / "ext-one"
-        first_dir.mkdir()
-        (first_dir / "commands").mkdir()
-        first_manifest = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "ext-one",
-                "name": "Extension One",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.ext-one.sync",
-                        "file": "commands/cmd.md",
-                        "aliases": ["speckit.shared.sync"],
-                    }
-                ]
-            },
-        }
-        (first_dir / "extension.yml").write_text(yaml.dump(first_manifest))
-        (first_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
-        installed_ext_dir = project_dir / ".specify" / "extensions" / "ext-one"
-        installed_ext_dir.parent.mkdir(parents=True, exist_ok=True)
-        shutil.copytree(first_dir, installed_ext_dir)
-
-        second_dir = temp_dir / "ext-two"
-        second_dir.mkdir()
-        (second_dir / "commands").mkdir()
-        second_manifest = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "shared",
-                "name": "Shared Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.shared.sync",
-                        "file": "commands/cmd.md",
-                    }
-                ]
-            },
-        }
-        (second_dir / "extension.yml").write_text(yaml.dump(second_manifest))
-        (second_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
-
-        manager = ExtensionManager(project_dir)
-        manager.registry.add("ext-one", {"version": "1.0.0", "source": "local"})
-
-        with pytest.raises(ValidationError, match="already provided by extension 'ext-one'"):
-            manager.install_from_directory(second_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)
@@ -938,81 +759,6 @@ $ARGUMENTS
         assert "Prüfe Konformität" in output
         assert "\\u" not in output
 
-    def test_adjust_script_paths_does_not_mutate_input(self):
-        """Path adjustments should not mutate caller-owned frontmatter dicts."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        original = {
-            "scripts": {
-                "sh": "../../scripts/bash/setup-plan.sh {ARGS}",
-                "ps": "../../scripts/powershell/setup-plan.ps1 {ARGS}",
-            }
-        }
-        before = json.loads(json.dumps(original))
-
-        adjusted = registrar._adjust_script_paths(original)
-
-        assert original == before
-        assert adjusted["scripts"]["sh"] == ".specify/scripts/bash/setup-plan.sh {ARGS}"
-        assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"
-
-    def test_adjust_script_paths_preserves_extension_local_paths(self):
-        """Extension-local script paths should not be rewritten into .specify/.specify."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        original = {
-            "scripts": {
-                "sh": ".specify/extensions/test-ext/scripts/setup.sh {ARGS}",
-                "ps": "scripts/powershell/setup-plan.ps1 {ARGS}",
-            }
-        }
-
-        adjusted = registrar._adjust_script_paths(original)
-
-        assert adjusted["scripts"]["sh"] == ".specify/extensions/test-ext/scripts/setup.sh {ARGS}"
-        assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"
-
-    def test_rewrite_project_relative_paths_preserves_extension_local_body_paths(self):
-        """Body rewrites should preserve extension-local assets while fixing top-level refs."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-
-        body = (
-            "Read `.specify/extensions/test-ext/templates/spec.md`\n"
-            "Run scripts/bash/setup-plan.sh\n"
-        )
-
-        rewritten = AgentCommandRegistrar._rewrite_project_relative_paths(body)
-
-        assert ".specify/extensions/test-ext/templates/spec.md" in rewritten
-        assert ".specify/scripts/bash/setup-plan.sh" in rewritten
-
-    def test_render_toml_command_handles_embedded_triple_double_quotes(self):
-        """TOML renderer should stay valid when body includes triple double-quotes."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        output = registrar.render_toml_command(
-            {"description": "x"},
-            'line1\n"""danger"""\nline2',
-            "extension:test-ext",
-        )
-
-        assert "prompt = '''" in output
-        assert '"""danger"""' in output
-
-    def test_render_toml_command_escapes_when_both_triple_quote_styles_exist(self):
-        """If body has both triple quote styles, fall back to escaped basic string."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        output = registrar.render_toml_command(
-            {"description": "x"},
-            'a """ b\nc \'\'\' d',
-            "extension:test-ext",
-        )
-
-        assert 'prompt = "' in output
-        assert "\\n" in output
-        assert "\\\"\\\"\\\"" in output
-
     def test_register_commands_for_claude(self, extension_dir, project_dir):
         """Test registering commands for Claude agent."""
         # Create .claude directory
@@ -1030,10 +776,10 @@ $ARGUMENTS
         )
 
         assert len(registered) == 1
-        assert "speckit.test-ext.hello" in registered
+        assert "speckit.test.hello" in registered
 
         # Check command file was created
-        cmd_file = claude_dir / "speckit.test-ext.hello.md"
+        cmd_file = claude_dir / "speckit.test.hello.md"
         assert cmd_file.exists()
 
         content = cmd_file.read_text()
@@ -1063,9 +809,9 @@ $ARGUMENTS
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-alias.cmd",
+                        "name": "speckit.alias.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.ext-alias.shortcut"],
+                        "aliases": ["speckit.shortcut"],
                     }
                 ]
             },
@@ -1085,10 +831,10 @@ $ARGUMENTS
         registered = registrar.register_commands_for_claude(manifest, ext_dir, project_dir)
 
         assert len(registered) == 2
-        assert "speckit.ext-alias.cmd" in registered
+        assert "speckit.alias.cmd" in registered
-        assert "speckit.ext-alias.shortcut" in registered
+        assert "speckit.shortcut" in registered
-        assert (claude_dir / "speckit.ext-alias.cmd.md").exists()
+        assert (claude_dir / "speckit.alias.cmd.md").exists()
-        assert (claude_dir / "speckit.ext-alias.shortcut.md").exists()
+        assert (claude_dir / "speckit.shortcut.md").exists()
 
     def test_unregister_commands_for_codex_skills_uses_mapped_names(self, project_dir):
         """Codex skill cleanup should use the same mapped names as registration."""
@@ -1129,11 +875,11 @@ $ARGUMENTS
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, extension_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
+        skill_file = skills_dir / "speckit-test.hello" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
-        assert "name: speckit-test-ext-hello" in content
+        assert "name: speckit-test.hello" in content
         assert "description: Test hello command" in content
         assert "compatibility:" in content
         assert "metadata:" in content
@@ -1160,7 +906,7 @@ $ARGUMENTS
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-scripted.plan",
+                        "name": "speckit.test.plan",
                         "file": "commands/plan.md",
                         "description": "Scripted command",
                     }
@@ -1198,7 +944,7 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-ext-scripted-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-test.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1229,9 +975,9 @@ Agent __AGENT__
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-alias-skill.cmd",
+                        "name": "speckit.alias.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.ext-alias-skill.shortcut"],
+                        "aliases": ["speckit.shortcut"],
                     }
                 ]
             },
@@ -1248,13 +994,13 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        primary = skills_dir / "speckit-ext-alias-skill-cmd" / "SKILL.md"
+        primary = skills_dir / "speckit-alias.cmd" / "SKILL.md"
-        alias = skills_dir / "speckit-ext-alias-skill-shortcut" / "SKILL.md"
+        alias = skills_dir / "speckit-shortcut" / "SKILL.md"
 
         assert primary.exists()
         assert alias.exists()
-        assert "name: speckit-ext-alias-skill-cmd" in primary.read_text()
+        assert "name: speckit-alias.cmd" in primary.read_text()
-        assert "name: speckit-ext-alias-skill-shortcut" in alias.read_text()
+        assert "name: speckit-shortcut" in alias.read_text()
 
     def test_codex_skill_registration_uses_fallback_script_variant_without_init_options(
         self, project_dir, temp_dir
@@ -1278,7 +1024,7 @@ Agent __AGENT__
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-script-fallback.plan",
+                        "name": "speckit.fallback.plan",
                         "file": "commands/plan.md",
                     }
                 ]
@@ -1310,7 +1056,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-ext-script-fallback-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-fallback.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1319,62 +1065,6 @@ Then {AGENT_SCRIPT}
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
         assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
-    def test_codex_skill_registration_handles_non_dict_init_options(
-        self, project_dir, temp_dir
-    ):
-        """Non-dict init-options payloads should not crash skill placeholder resolution."""
-        import yaml
-
-        ext_dir = temp_dir / "ext-script-list-init"
-        ext_dir.mkdir()
-        (ext_dir / "commands").mkdir()
-
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "ext-script-list-init",
-                "name": "List init options",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.ext-script-list-init.plan",
-                        "file": "commands/plan.md",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands" / "plan.md").write_text(
-            """---
-description: "List init scripted command"
-scripts:
-  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
----
-
-Run {SCRIPT}
-"""
-        )
-
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        skills_dir = project_dir / ".agents" / "skills"
-        skills_dir.mkdir(parents=True)
-
-        manifest = ExtensionManifest(ext_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
-
-        content = (skills_dir / "speckit-ext-script-list-init-plan" / "SKILL.md").read_text()
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-
     def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
         self, project_dir, temp_dir, monkeypatch
     ):
@@ -1399,7 +1089,7 @@ Run {SCRIPT}
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-script-windows-fallback.plan",
+                        "name": "speckit.windows.plan",
                         "file": "commands/plan.md",
                     }
                 ]
@@ -1431,7 +1121,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-ext-script-windows-fallback-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-windows.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1453,14 +1143,14 @@ Then {AGENT_SCRIPT}
         )
 
         assert len(registered) == 1
-        assert "speckit.test-ext.hello" in registered
+        assert "speckit.test.hello" in registered
 
         # Verify command file uses .agent.md extension
-        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
+        cmd_file = agents_dir / "speckit.test.hello.agent.md"
         assert cmd_file.exists()
 
         # Verify NO plain .md file was created
-        plain_md_file = agents_dir / "speckit.test-ext.hello.md"
+        plain_md_file = agents_dir / "speckit.test.hello.md"
         assert not plain_md_file.exists()
 
         content = cmd_file.read_text()
@@ -1480,12 +1170,12 @@ Then {AGENT_SCRIPT}
         )
 
         # Verify companion .prompt.md file exists
-        prompt_file = project_dir / ".github" / "prompts" / "speckit.test-ext.hello.prompt.md"
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
         assert prompt_file.exists()
 
         # Verify content has correct agent frontmatter
         content = prompt_file.read_text()
-        assert content == "---\nagent: speckit.test-ext.hello\n---\n"
+        assert content == "---\nagent: speckit.test.hello\n---\n"
 
     def test_copilot_aliases_get_companion_prompts(self, project_dir, temp_dir):
         """Test that aliases also get companion .prompt.md files for Copilot."""
@@ -1506,9 +1196,9 @@ Then {AGENT_SCRIPT}
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.ext-alias-copilot.cmd",
+                        "name": "speckit.alias-copilot.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.ext-alias-copilot.shortcut"],
+                        "aliases": ["speckit.shortcut-copilot"],
                     }
                 ]
             },
@@ -1535,8 +1225,8 @@ Then {AGENT_SCRIPT}
 
         # Both primary and alias get companion .prompt.md
         prompts_dir = project_dir / ".github" / "prompts"
-        assert (prompts_dir / "speckit.ext-alias-copilot.cmd.prompt.md").exists()
+        assert (prompts_dir / "speckit.alias-copilot.cmd.prompt.md").exists()
-        assert (prompts_dir / "speckit.ext-alias-copilot.shortcut.prompt.md").exists()
+        assert (prompts_dir / "speckit.shortcut-copilot.prompt.md").exists()
 
     def test_non_copilot_agent_no_companion_file(self, extension_dir, project_dir):
         """Test that non-copilot agents do NOT create .prompt.md files."""
@@ -1609,7 +1299,7 @@ class TestIntegration:
         assert installed[0]["id"] == "test-ext"
 
         # Verify command registered
-        cmd_file = project_dir / ".claude" / "commands" / "speckit.test-ext.hello.md"
+        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)
@@ -1617,7 +1307,7 @@ class TestIntegration:
         registered_commands = metadata["registered_commands"]
         # Check that the command is registered for at least one agent
         assert any(
-            "speckit.test-ext.hello" in cmds
+            "speckit.test.hello" in cmds
             for cmds in registered_commands.values()
         )
 
@@ -1643,8 +1333,8 @@ class TestIntegration:
         assert "copilot" in metadata["registered_commands"]
 
         # Verify files exist before cleanup
-        agent_file = agents_dir / "speckit.test-ext.hello.agent.md"
+        agent_file = agents_dir / "speckit.test.hello.agent.md"
-        prompt_file = project_dir / ".github" / "prompts" / "speckit.test-ext.hello.prompt.md"
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
         assert agent_file.exists()
         assert prompt_file.exists()
 
@@ -2954,7 +2644,7 @@ class TestExtensionUpdateCLI:
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.test-ext.hello",
+                        "name": "speckit.test.hello",
                         "file": "commands/hello.md",
                         "description": "Test command",
                     }
@@ -2962,7 +2652,7 @@ class TestExtensionUpdateCLI:
             },
             "hooks": {
                 "after_tasks": {
-                    "command": "speckit.test-ext.hello",
+                    "command": "speckit.test.hello",
                     "optional": True,
                 }
             },
@@ -2991,7 +2681,7 @@ class TestExtensionUpdateCLI:
                 "description": "A test extension",
             },
             "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {"commands": [{"name": "speckit.test-ext.hello", "file": "commands/hello.md"}]},
+            "provides": {"commands": [{"name": "speckit.test.hello", "file": "commands/hello.md"}]},
         }
 
         with zipfile.ZipFile(zip_path, "w") as zf:
@@ -3541,128 +3231,3 @@ class TestExtensionPriorityBackwardsCompatibility:
         assert result[0][0] == "ext-with-priority"
         assert result[1][0] == "legacy-ext"
         assert result[2][0] == "ext-low-priority"
-
-
-class TestHookInvocationRendering:
-    """Test hook invocation formatting for different agent modes."""
-
-    def test_kimi_hooks_render_skill_invocation(self, project_dir):
-        """Kimi projects should render /skill:speckit-* invocations."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "before_plan",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "speckit.plan",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/skill:speckit-plan`" in message
-        assert "EXECUTE_COMMAND: speckit.plan" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-plan" in message
-
-    def test_codex_hooks_render_dollar_skill_invocation(self, project_dir):
-        """Codex projects with --ai-skills should render $speckit-* invocations."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "codex", "ai_skills": True}))
-
-        hook_executor = HookExecutor(project_dir)
-        execution = hook_executor.execute_hook(
-            {
-                "extension": "test-ext",
-                "command": "speckit.tasks",
-                "optional": False,
-            }
-        )
-
-        assert execution["command"] == "speckit.tasks"
-        assert execution["invocation"] == "$speckit-tasks"
-
-    def test_non_skill_command_keeps_slash_invocation(self, project_dir):
-        """Custom hook commands should keep slash invocation style."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "before_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "pre_tasks_test",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/pre_tasks_test`" in message
-        assert "EXECUTE_COMMAND: pre_tasks_test" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /pre_tasks_test" in message
-
-    def test_extension_command_uses_hyphenated_skill_invocation(self, project_dir):
-        """Multi-segment extension command ids should map to hyphenated skills."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "after_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "speckit.test-ext.hello",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/skill:speckit-test-ext-hello`" in message
-        assert "EXECUTE_COMMAND: speckit.test-ext.hello" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-test-ext-hello" in message
-
-    def test_hook_executor_caches_init_options_lookup(self, project_dir, monkeypatch):
-        """Init options should be loaded once per executor instance."""
-        calls = {"count": 0}
-
-        def fake_load_init_options(_project_root):
-            calls["count"] += 1
-            return {"ai": "kimi", "ai_skills": False}
-
-        monkeypatch.setattr("specify_cli.load_init_options", fake_load_init_options)
-
-        hook_executor = HookExecutor(project_dir)
-        assert hook_executor._render_hook_invocation("speckit.plan") == "/skill:speckit-plan"
-        assert hook_executor._render_hook_invocation("speckit.tasks") == "/skill:speckit-tasks"
-        assert calls["count"] == 1
-
-    def test_hook_message_falls_back_when_invocation_is_empty(self, project_dir):
-        """Hook messages should still render actionable command placeholders."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "after_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": None,
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/<missing command>`" in message
-        assert "EXECUTE_COMMAND: <missing command>" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /<missing command>" in message

tests/test_integrations.py

@@ -1,460 +0,0 @@
-"""Tests for the integrations foundation (Stage 1).
-
-Covers:
-- IntegrationOption dataclass
-- IntegrationBase ABC and MarkdownIntegration base class
-- IntegrationManifest — record, hash, save, load, uninstall, modified detection
-- INTEGRATION_REGISTRY basics
-"""
-
-import hashlib
-import json
-
-import pytest
-
-from specify_cli.integrations import (
-    INTEGRATION_REGISTRY,
-    _register,
-    get_integration,
-)
-from specify_cli.integrations.base import (
-    IntegrationBase,
-    IntegrationOption,
-    MarkdownIntegration,
-)
-from specify_cli.integrations.manifest import IntegrationManifest, _sha256
-
-
-# ── helpers ──────────────────────────────────────────────────────────────────
-
-
-class _StubIntegration(MarkdownIntegration):
-    """Minimal concrete integration for testing."""
-
-    key = "stub"
-    config = {
-        "name": "Stub Agent",
-        "folder": ".stub/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": False,
-    }
-    registrar_config = {
-        "dir": ".stub/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".md",
-    }
-    context_file = "STUB.md"
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationOption
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestIntegrationOption:
-    def test_defaults(self):
-        opt = IntegrationOption(name="--flag")
-        assert opt.name == "--flag"
-        assert opt.is_flag is False
-        assert opt.required is False
-        assert opt.default is None
-        assert opt.help == ""
-
-    def test_flag_option(self):
-        opt = IntegrationOption(name="--skills", is_flag=True, default=True, help="Enable skills")
-        assert opt.is_flag is True
-        assert opt.default is True
-        assert opt.help == "Enable skills"
-
-    def test_required_option(self):
-        opt = IntegrationOption(name="--commands-dir", required=True, help="Dir path")
-        assert opt.required is True
-
-    def test_frozen(self):
-        opt = IntegrationOption(name="--x")
-        with pytest.raises(AttributeError):
-            opt.name = "--y"  # type: ignore[misc]
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationBase / MarkdownIntegration
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestIntegrationBase:
-    def test_key_and_config(self):
-        i = _StubIntegration()
-        assert i.key == "stub"
-        assert i.config["name"] == "Stub Agent"
-        assert i.registrar_config["format"] == "markdown"
-        assert i.context_file == "STUB.md"
-
-    def test_options_default_empty(self):
-        assert _StubIntegration.options() == []
-
-    def test_templates_dir(self):
-        i = _StubIntegration()
-        td = i.templates_dir()
-        # Should point to a templates/ dir next to this test module.
-        # It won't exist, but the path should be well-formed.
-        assert td.name == "templates"
-
-    def test_setup_no_templates_returns_empty(self, tmp_path):
-        """setup() gracefully returns empty list when templates dir is missing."""
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        created = i.setup(tmp_path, manifest)
-        assert created == []
-
-    def test_setup_copies_templates(self, tmp_path, monkeypatch):
-        """setup() copies template files and records them in the manifest."""
-        # Create templates under tmp_path so we don't mutate the source tree
-        tpl = tmp_path / "_templates"
-        tpl.mkdir()
-        (tpl / "speckit.plan.md").write_text("plan content", encoding="utf-8")
-        (tpl / "speckit.specify.md").write_text("spec content", encoding="utf-8")
-
-        i = _StubIntegration()
-        monkeypatch.setattr(type(i), "templates_dir", lambda self: tpl)
-
-        project = tmp_path / "project"
-        project.mkdir()
-        created = i.setup(project, IntegrationManifest("stub", project))
-        assert len(created) == 2
-        assert (project / ".stub" / "commands" / "speckit.plan.md").exists()
-        assert (project / ".stub" / "commands" / "speckit.specify.md").exists()
-
-    def test_install_delegates_to_setup(self, tmp_path):
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        result = i.install(tmp_path, manifest)
-        assert result == []  # no templates dir → empty
-
-    def test_uninstall_delegates_to_teardown(self, tmp_path):
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        removed, skipped = i.uninstall(tmp_path, manifest)
-        assert removed == []
-        assert skipped == []
-
-
-class TestMarkdownIntegration:
-    def test_is_subclass_of_base(self):
-        assert issubclass(MarkdownIntegration, IntegrationBase)
-
-    def test_stub_is_markdown(self):
-        assert isinstance(_StubIntegration(), MarkdownIntegration)
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationManifest
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestManifestRecordFile:
-    def test_record_file_writes_and_hashes(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        content = "hello world"
-        abs_path = m.record_file("a/b.txt", content)
-
-        assert abs_path == tmp_path / "a" / "b.txt"
-        assert abs_path.read_text(encoding="utf-8") == content
-        expected_hash = hashlib.sha256(content.encode()).hexdigest()
-        assert m.files["a/b.txt"] == expected_hash
-
-    def test_record_file_bytes(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        data = b"\x00\x01\x02"
-        abs_path = m.record_file("bin.dat", data)
-        assert abs_path.read_bytes() == data
-        assert m.files["bin.dat"] == hashlib.sha256(data).hexdigest()
-
-    def test_record_existing(self, tmp_path):
-        f = tmp_path / "existing.txt"
-        f.write_text("content", encoding="utf-8")
-        m = IntegrationManifest("test", tmp_path)
-        m.record_existing("existing.txt")
-        assert m.files["existing.txt"] == _sha256(f)
-
-
-class TestManifestPathTraversal:
-    def test_record_file_rejects_parent_traversal(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        with pytest.raises(ValueError, match="outside"):
-            m.record_file("../escape.txt", "bad")
-
-    def test_record_file_rejects_absolute_path(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        with pytest.raises(ValueError, match="Absolute paths"):
-            m.record_file("/tmp/escape.txt", "bad")
-
-    def test_record_existing_rejects_parent_traversal(self, tmp_path):
-        # Create a file outside the project root
-        escape = tmp_path.parent / "escape.txt"
-        escape.write_text("evil", encoding="utf-8")
-        try:
-            m = IntegrationManifest("test", tmp_path)
-            with pytest.raises(ValueError, match="outside"):
-                m.record_existing("../escape.txt")
-        finally:
-            escape.unlink(missing_ok=True)
-
-    def test_uninstall_skips_traversal_paths(self, tmp_path):
-        """If a manifest is corrupted with traversal paths, uninstall ignores them."""
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("safe.txt", "good")
-        # Manually inject a traversal path into the manifest
-        m._files["../outside.txt"] = "fakehash"
-        m.save()
-
-        removed, skipped = m.uninstall()
-        # Only the safe file should have been removed
-        assert len(removed) == 1
-        assert removed[0].name == "safe.txt"
-
-
-class TestManifestCheckModified:
-    def test_unmodified_file(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        assert m.check_modified() == []
-
-    def test_modified_file(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        (tmp_path / "f.txt").write_text("changed", encoding="utf-8")
-        assert m.check_modified() == ["f.txt"]
-
-    def test_deleted_file_not_reported(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        (tmp_path / "f.txt").unlink()
-        assert m.check_modified() == []
-
-    def test_symlink_treated_as_modified(self, tmp_path):
-        """A tracked file replaced with a symlink is reported as modified."""
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        target = tmp_path / "target.txt"
-        target.write_text("target", encoding="utf-8")
-        (tmp_path / "f.txt").unlink()
-        (tmp_path / "f.txt").symlink_to(target)
-        assert m.check_modified() == ["f.txt"]
-
-
-class TestManifestUninstall:
-    def test_removes_unmodified(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("d/f.txt", "content")
-        m.save()
-
-        removed, skipped = m.uninstall()
-        assert len(removed) == 1
-        assert not (tmp_path / "d" / "f.txt").exists()
-        # Parent dir cleaned up because empty
-        assert not (tmp_path / "d").exists()
-        assert skipped == []
-
-    def test_skips_modified(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        m.save()
-        (tmp_path / "f.txt").write_text("modified", encoding="utf-8")
-
-        removed, skipped = m.uninstall()
-        assert removed == []
-        assert len(skipped) == 1
-        assert (tmp_path / "f.txt").exists()
-
-    def test_force_removes_modified(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        m.save()
-        (tmp_path / "f.txt").write_text("modified", encoding="utf-8")
-
-        removed, skipped = m.uninstall(force=True)
-        assert len(removed) == 1
-        assert skipped == []
-        assert not (tmp_path / "f.txt").exists()
-
-    def test_already_deleted_file(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "content")
-        m.save()
-        (tmp_path / "f.txt").unlink()
-
-        removed, skipped = m.uninstall()
-        assert removed == []
-        assert skipped == []
-
-    def test_removes_manifest_file(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path, version="1.0")
-        m.record_file("f.txt", "content")
-        m.save()
-        assert m.manifest_path.exists()
-
-        m.uninstall()
-        assert not m.manifest_path.exists()
-
-    def test_cleans_empty_parent_dirs(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("a/b/c/f.txt", "content")
-        m.save()
-
-        m.uninstall()
-        assert not (tmp_path / "a" / "b" / "c").exists()
-        assert not (tmp_path / "a" / "b").exists()
-        assert not (tmp_path / "a").exists()
-
-    def test_preserves_nonempty_parent_dirs(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("a/b/tracked.txt", "content")
-        # Create an untracked sibling
-        (tmp_path / "a" / "b" / "other.txt").write_text("keep", encoding="utf-8")
-        m.save()
-
-        m.uninstall()
-        assert not (tmp_path / "a" / "b" / "tracked.txt").exists()
-        assert (tmp_path / "a" / "b" / "other.txt").exists()
-        assert (tmp_path / "a" / "b").is_dir()
-
-    def test_symlink_skipped_without_force(self, tmp_path):
-        """A tracked file replaced with a symlink is skipped unless force."""
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        m.save()
-        target = tmp_path / "target.txt"
-        target.write_text("target", encoding="utf-8")
-        (tmp_path / "f.txt").unlink()
-        (tmp_path / "f.txt").symlink_to(target)
-
-        removed, skipped = m.uninstall()
-        assert removed == []
-        assert len(skipped) == 1
-        assert (tmp_path / "f.txt").is_symlink()  # still there
-
-    def test_symlink_removed_with_force(self, tmp_path):
-        """A tracked file replaced with a symlink is removed with force."""
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "original")
-        m.save()
-        target = tmp_path / "target.txt"
-        target.write_text("target", encoding="utf-8")
-        (tmp_path / "f.txt").unlink()
-        (tmp_path / "f.txt").symlink_to(target)
-
-        removed, skipped = m.uninstall(force=True)
-        assert len(removed) == 1
-        assert not (tmp_path / "f.txt").exists()
-        assert target.exists()  # target not deleted
-
-
-class TestManifestPersistence:
-    def test_save_and_load_roundtrip(self, tmp_path):
-        m = IntegrationManifest("myagent", tmp_path, version="2.0.1")
-        m.record_file("dir/file.md", "# Hello")
-        m.save()
-
-        loaded = IntegrationManifest.load("myagent", tmp_path)
-        assert loaded.key == "myagent"
-        assert loaded.version == "2.0.1"
-        assert loaded.files == m.files
-        assert loaded._installed_at == m._installed_at
-
-    def test_manifest_path(self, tmp_path):
-        m = IntegrationManifest("copilot", tmp_path)
-        assert m.manifest_path == tmp_path / ".specify" / "integrations" / "copilot.manifest.json"
-
-    def test_load_missing_raises(self, tmp_path):
-        with pytest.raises(FileNotFoundError):
-            IntegrationManifest.load("nonexistent", tmp_path)
-
-    def test_save_creates_directories(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "content")
-        path = m.save()
-        assert path.exists()
-        data = json.loads(path.read_text(encoding="utf-8"))
-        assert data["integration"] == "test"
-        assert "installed_at" in data
-        assert "f.txt" in data["files"]
-
-    def test_save_preserves_installed_at(self, tmp_path):
-        m = IntegrationManifest("test", tmp_path)
-        m.record_file("f.txt", "content")
-        m.save()
-        first_ts = m._installed_at
-
-        # Save again — timestamp should not change
-        m.save()
-        assert m._installed_at == first_ts
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# Registry
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestRegistry:
-    def test_registry_starts_empty(self):
-        # Registry may have been populated by other tests; at minimum
-        # it should be a dict.
-        assert isinstance(INTEGRATION_REGISTRY, dict)
-
-    def test_register_and_get(self):
-        stub = _StubIntegration()
-        _register(stub)
-        try:
-            assert get_integration("stub") is stub
-        finally:
-            INTEGRATION_REGISTRY.pop("stub", None)
-
-    def test_get_missing_returns_none(self):
-        assert get_integration("nonexistent-xyz") is None
-
-    def test_register_empty_key_raises(self):
-        class EmptyKey(MarkdownIntegration):
-            key = ""
-        with pytest.raises(ValueError, match="empty key"):
-            _register(EmptyKey())
-
-    def test_register_duplicate_raises(self):
-        stub = _StubIntegration()
-        _register(stub)
-        try:
-            with pytest.raises(KeyError, match="already registered"):
-                _register(_StubIntegration())
-        finally:
-            INTEGRATION_REGISTRY.pop("stub", None)
-
-
-class TestManifestLoadValidation:
-    def test_load_non_dict_raises(self, tmp_path):
-        path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
-        path.parent.mkdir(parents=True)
-        path.write_text('"just a string"', encoding="utf-8")
-        with pytest.raises(ValueError, match="JSON object"):
-            IntegrationManifest.load("bad", tmp_path)
-
-    def test_load_bad_files_type_raises(self, tmp_path):
-        path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
-        path.parent.mkdir(parents=True)
-        path.write_text(json.dumps({"files": ["not", "a", "dict"]}), encoding="utf-8")
-        with pytest.raises(ValueError, match="mapping"):
-            IntegrationManifest.load("bad", tmp_path)
-
-    def test_load_bad_files_values_raises(self, tmp_path):
-        path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
-        path.parent.mkdir(parents=True)
-        path.write_text(json.dumps({"files": {"a.txt": 123}}), encoding="utf-8")
-        with pytest.raises(ValueError, match="mapping"):
-            IntegrationManifest.load("bad", tmp_path)
-
-    def test_load_invalid_json_raises(self, tmp_path):
-        path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
-        path.parent.mkdir(parents=True)
-        path.write_text("{not valid json", encoding="utf-8")
-        with pytest.raises(ValueError, match="invalid JSON"):
-            IntegrationManifest.load("bad", tmp_path)

tests/test_presets.py

@@ -1170,12 +1170,8 @@ class TestPresetCatalog:
         assert not catalog.cache_file.exists()
         assert not catalog.cache_metadata_file.exists()
 
-    def test_search_with_cached_data(self, project_dir, monkeypatch):
+    def test_search_with_cached_data(self, project_dir):
         """Test search with cached catalog data."""
-        from unittest.mock import patch
-
-        # Only use the default catalog to prevent fetching the community catalog from the network
-        monkeypatch.setenv("SPECKIT_PRESET_CATALOG_URL", PresetCatalog.DEFAULT_CATALOG_URL)
         catalog = PresetCatalog(project_dir)
         catalog.cache_dir.mkdir(parents=True, exist_ok=True)
 
@@ -1204,26 +1200,23 @@ class TestPresetCatalog:
             "cached_at": datetime.now(timezone.utc).isoformat(),
         }))
 
-        # Isolate from community catalog so results are deterministic
+        # Search by query
-        default_only = [PresetCatalogEntry(url=catalog.DEFAULT_CATALOG_URL, name="default", priority=1, install_allowed=True)]
+        results = catalog.search(query="agile")
-        with patch.object(catalog, "get_active_catalogs", return_value=default_only):
+        assert len(results) == 1
-            # Search by query
+        assert results[0]["id"] == "safe-agile"
-            results = catalog.search(query="agile")
-            assert len(results) == 1
-            assert results[0]["id"] == "safe-agile"
 
-            # Search by tag
+        # Search by tag
-            results = catalog.search(tag="hipaa")
+        results = catalog.search(tag="hipaa")
-            assert len(results) == 1
+        assert len(results) == 1
-            assert results[0]["id"] == "healthcare"
+        assert results[0]["id"] == "healthcare"
 
-            # Search by author
+        # Search by author
-            results = catalog.search(author="agile-community")
+        results = catalog.search(author="agile-community")
-            assert len(results) == 1
+        assert len(results) == 1
 
-            # Search all
+        # Search all
-            results = catalog.search()
+        results = catalog.search()
-            assert len(results) == 2
+        assert len(results) == 2
 
     def test_get_pack_info(self, project_dir):
         """Test getting info for a specific pack."""
@@ -1942,10 +1935,10 @@ class TestInitOptions:
 class TestPresetSkills:
     """Tests for preset skill registration and unregistration."""
 
-    def _write_init_options(self, project_dir, ai="claude", ai_skills=True, script="sh"):
+    def _write_init_options(self, project_dir, ai="claude", ai_skills=True):
         from specify_cli import save_init_options
 
-        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills, "script": script})
+        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills})
 
     def _create_skill(self, skills_dir, skill_name, body="original body"):
         skill_dir = skills_dir / skill_name
@@ -1995,26 +1988,6 @@ class TestPresetSkills:
         content = skill_file.read_text()
         assert "untouched" in content, "Skill should not be modified when ai_skills=False"
 
-    def test_get_skills_dir_returns_none_for_non_string_ai(self, project_dir):
-        """Corrupted init-options ai values should not crash preset skill resolution."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text('{"ai":["codex"],"ai_skills":true,"script":"sh"}')
-
-        manager = PresetManager(project_dir)
-
-        assert manager._get_skills_dir() is None
-
-    def test_get_skills_dir_returns_none_for_non_dict_init_options(self, project_dir):
-        """Corrupted non-dict init-options payloads should fail closed."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        manager = PresetManager(project_dir)
-
-        assert manager._get_skills_dir() is None
-
     def test_skill_not_updated_without_init_options(self, project_dir, temp_dir):
         """When no init-options.json exists, preset install should not touch skills."""
         skills_dir = project_dir / ".claude" / "skills"
@@ -2060,52 +2033,6 @@ class TestPresetSkills:
         assert "preset:self-test" not in content, "Preset content should be gone"
         assert "templates/commands/specify.md" in content, "Should reference core template"
 
-    def test_skill_restored_on_remove_resolves_script_placeholders(self, project_dir):
-        """Core restore should resolve {SCRIPT}/{ARGS} placeholders like other skill paths."""
-        self._write_init_options(project_dir, ai="claude", ai_skills=True, script="sh")
-        skills_dir = project_dir / ".claude" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="old")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        core_cmds = project_dir / ".specify" / "templates" / "commands"
-        core_cmds.mkdir(parents=True, exist_ok=True)
-        (core_cmds / "specify.md").write_text(
-            "---\n"
-            "description: Core specify command\n"
-            "scripts:\n"
-            "  sh: .specify/scripts/bash/create-new-feature.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "Run:\n"
-            "{SCRIPT}\n"
-        )
-
-        manager = PresetManager(project_dir)
-        SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(SELF_TEST_DIR, "0.1.5")
-        manager.remove("self-test")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "{ARGS}" not in content
-        assert ".specify/scripts/bash/create-new-feature.sh --json \"$ARGUMENTS\"" in content
-
-    def test_skill_not_overridden_when_skill_path_is_file(self, project_dir):
-        """Preset install should skip non-directory skill targets."""
-        self._write_init_options(project_dir, ai="claude")
-        skills_dir = project_dir / ".claude" / "skills"
-        skills_dir.mkdir(parents=True, exist_ok=True)
-        (skills_dir / "speckit-specify").write_text("not-a-directory")
-
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(SELF_TEST_DIR, "0.1.5")
-
-        assert (skills_dir / "speckit-specify").is_file()
-        metadata = manager.registry.get("self-test")
-        assert "speckit-specify" not in metadata.get("registered_skills", [])
-
     def test_no_skills_registered_when_no_skill_dir_exists(self, project_dir, temp_dir):
         """Skills should not be created when no existing skill dir is found."""
         self._write_init_options(project_dir, ai="claude")
@@ -2120,304 +2047,6 @@ class TestPresetSkills:
         metadata = manager.registry.get("self-test")
         assert metadata.get("registered_skills", []) == []
 
-    def test_extension_skill_override_matches_hyphenated_multisegment_name(self, project_dir, temp_dir):
-        """Preset overrides for speckit.<ext>.<cmd> should target speckit-<ext>-<cmd> skills."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="untouched")
-        (project_dir / ".specify" / "extensions" / "fakeext").mkdir(parents=True, exist_ok=True)
-
-        preset_dir = temp_dir / "ext-skill-override"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-override\n"
-        )
-        manifest_data = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-override",
-                "name": "Ext Skill Override",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-fakeext-cmd" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:ext-skill-override" in content
-        assert "name: speckit-fakeext-cmd" in content
-        assert "# Speckit Fakeext Cmd Skill" in content
-
-        metadata = manager.registry.get("ext-skill-override")
-        assert "speckit-fakeext-cmd" in metadata.get("registered_skills", [])
-
-    def test_extension_skill_restored_on_preset_remove(self, project_dir, temp_dir):
-        """Preset removal should restore an extension-backed skill instead of deleting it."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="original extension skill")
-
-        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
-        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
-        (extension_dir / "commands" / "cmd.md").write_text(
-            "---\n"
-            "description: Extension fakeext cmd\n"
-            "scripts:\n"
-            "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "extension:fakeext\n"
-            "Run {SCRIPT}\n"
-        )
-        extension_manifest = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "fakeext",
-                "name": "Fake Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/cmd.md",
-                        "description": "Fake extension command",
-                    }
-                ]
-            },
-        }
-        with open(extension_dir / "extension.yml", "w") as f:
-            yaml.dump(extension_manifest, f)
-
-        preset_dir = temp_dir / "ext-skill-restore"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-restore\n"
-        )
-        preset_manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-restore",
-                "name": "Ext Skill Restore",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(preset_manifest, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-fakeext-cmd" / "SKILL.md"
-        assert "preset:ext-skill-restore" in skill_file.read_text()
-
-        manager.remove("ext-skill-restore")
-
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:ext-skill-restore" not in content
-        assert "source: extension:fakeext" in content
-        assert "extension:fakeext" in content
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert "# Fakeext Cmd Skill" in content
-
-    def test_preset_remove_skips_skill_dir_without_skill_file(self, project_dir, temp_dir):
-        """Preset removal should not delete arbitrary directories missing SKILL.md."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        stray_skill_dir = skills_dir / "speckit-fakeext-cmd"
-        stray_skill_dir.mkdir(parents=True, exist_ok=True)
-        note_file = stray_skill_dir / "notes.txt"
-        note_file.write_text("user content", encoding="utf-8")
-
-        preset_dir = temp_dir / "ext-skill-missing-file"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-missing-file\n"
-        )
-        preset_manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-missing-file",
-                "name": "Ext Skill Missing File",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(preset_manifest, f)
-
-        manager = PresetManager(project_dir)
-        installed_preset_dir = manager.presets_dir / "ext-skill-missing-file"
-        shutil.copytree(preset_dir, installed_preset_dir)
-        manager.registry.add(
-            "ext-skill-missing-file",
-            {
-                "version": "1.0.0",
-                "source": str(preset_dir),
-                "provides_templates": ["speckit.fakeext.cmd"],
-                "registered_skills": ["speckit-fakeext-cmd"],
-                "priority": 10,
-            },
-        )
-
-        manager.remove("ext-skill-missing-file")
-
-        assert stray_skill_dir.is_dir()
-        assert note_file.read_text(encoding="utf-8") == "user content"
-
-    def test_kimi_legacy_dotted_skill_override_still_applies(self, project_dir, temp_dir):
-        """Preset overrides should still target legacy dotted Kimi skill directories."""
-        self._write_init_options(project_dir, ai="kimi")
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit.specify", body="untouched")
-
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit.specify" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:self-test" in content
-        assert "name: speckit.specify" in content
-
-        metadata = manager.registry.get("self-test")
-        assert "speckit.specify" in metadata.get("registered_skills", [])
-
-    def test_kimi_skill_updated_even_when_ai_skills_disabled(self, project_dir, temp_dir):
-        """Kimi presets should still propagate command overrides to existing skills."""
-        self._write_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:self-test" in content
-        assert "name: speckit-specify" in content
-
-        metadata = manager.registry.get("self-test")
-        assert "speckit-specify" in metadata.get("registered_skills", [])
-
-    def test_kimi_preset_skill_override_resolves_script_placeholders(self, project_dir, temp_dir):
-        """Kimi preset skill overrides should resolve placeholders and rewrite project paths."""
-        self._write_init_options(project_dir, ai="kimi", ai_skills=False, script="sh")
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        preset_dir = temp_dir / "kimi-placeholder-override"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.specify.md").write_text(
-            "---\n"
-            "description: Kimi placeholder override\n"
-            "scripts:\n"
-            "  sh: scripts/bash/create-new-feature.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "Execute `{SCRIPT}` for __AGENT__\n"
-            "Review templates/checklist.md and memory/constitution.md\n"
-        )
-        manifest_data = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "kimi-placeholder-override",
-                "name": "Kimi Placeholder Override",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.specify",
-                        "file": "commands/speckit.specify.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "__AGENT__" not in content
-        assert ".specify/scripts/bash/create-new-feature.sh --json \"$ARGUMENTS\"" in content
-        assert ".specify/templates/checklist.md" in content
-        assert ".specify/memory/constitution.md" in content
-        assert "for kimi" in content
-
-    def test_preset_skill_registration_handles_non_dict_init_options(self, project_dir, temp_dir):
-        """Non-dict init-options payloads should not crash preset install/remove flows."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        skills_dir = project_dir / ".claude" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "untouched" in content
-
 
 class TestPresetSetPriority:
     """Test preset set-priority CLI command."""

tests/test_timestamp_branches.py

@@ -14,7 +14,6 @@ import pytest
 
 PROJECT_ROOT = Path(__file__).resolve().parent.parent
 CREATE_FEATURE = PROJECT_ROOT / "scripts" / "bash" / "create-new-feature.sh"
-CREATE_FEATURE_PS = PROJECT_ROOT / "scripts" / "powershell" / "create-new-feature.ps1"
 COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
 
 
@@ -148,24 +147,6 @@ class TestSequentialBranch:
                 branch = line.split(":", 1)[1].strip()
         assert branch == "003-next-feat", f"expected 003-next-feat, got: {branch}"
 
-    def test_sequential_supports_four_digit_prefixes(self, git_repo: Path):
-        """Sequential numbering should continue past 999 without truncation."""
-        (git_repo / "specs" / "999-last-3digit").mkdir(parents=True)
-        (git_repo / "specs" / "1000-first-4digit").mkdir(parents=True)
-        result = run_script(git_repo, "--short-name", "next-feat", "Next feature")
-        assert result.returncode == 0, result.stderr
-        branch = None
-        for line in result.stdout.splitlines():
-            if line.startswith("BRANCH_NAME:"):
-                branch = line.split(":", 1)[1].strip()
-        assert branch == "1001-next-feat", f"expected 1001-next-feat, got: {branch}"
-
-    def test_powershell_scanner_uses_long_tryparse_for_large_prefixes(self):
-        """PowerShell scanner should parse large prefixes without [int] casts."""
-        content = CREATE_FEATURE_PS.read_text(encoding="utf-8")
-        assert "[long]::TryParse($matches[1], [ref]$num)" in content
-        assert "$num = [int]$matches[1]" not in content
-
 
 # ── check_feature_branch Tests ───────────────────────────────────────────────
 
@@ -269,146 +250,3 @@ class TestE2EFlow:
         assert (git_repo / "specs" / branch).is_dir()
         val = source_and_call(f'check_feature_branch "{branch}" "true"')
         assert val.returncode == 0
-
-
-# ── Allow Existing Branch Tests ──────────────────────────────────────────────
-
-
-class TestAllowExistingBranch:
-    def test_allow_existing_switches_to_branch(self, git_repo: Path):
-        """T006: Pre-create branch, verify script switches to it."""
-        subprocess.run(
-            ["git", "checkout", "-b", "004-pre-exist"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        subprocess.run(
-            ["git", "checkout", "-"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--short-name", "pre-exist",
-            "--number", "4", "Pre-existing feature",
-        )
-        assert result.returncode == 0, result.stderr
-        current = subprocess.run(
-            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
-            cwd=git_repo, capture_output=True, text=True,
-        ).stdout.strip()
-        assert current == "004-pre-exist", f"expected 004-pre-exist, got {current}"
-
-    def test_allow_existing_already_on_branch(self, git_repo: Path):
-        """T007: Verify success when already on the target branch."""
-        subprocess.run(
-            ["git", "checkout", "-b", "005-already-on"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--short-name", "already-on",
-            "--number", "5", "Already on branch",
-        )
-        assert result.returncode == 0, result.stderr
-
-    def test_allow_existing_creates_spec_dir(self, git_repo: Path):
-        """T008: Verify spec directory created on existing branch."""
-        subprocess.run(
-            ["git", "checkout", "-b", "006-spec-dir"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        subprocess.run(
-            ["git", "checkout", "-"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--short-name", "spec-dir",
-            "--number", "6", "Spec dir feature",
-        )
-        assert result.returncode == 0, result.stderr
-        assert (git_repo / "specs" / "006-spec-dir").is_dir()
-        assert (git_repo / "specs" / "006-spec-dir" / "spec.md").exists()
-
-    def test_without_flag_still_errors(self, git_repo: Path):
-        """T009: Verify backwards compatibility (error without flag)."""
-        subprocess.run(
-            ["git", "checkout", "-b", "007-no-flag"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        subprocess.run(
-            ["git", "checkout", "-"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--short-name", "no-flag", "--number", "7", "No flag feature",
-        )
-        assert result.returncode != 0, "should fail without --allow-existing-branch"
-        assert "already exists" in result.stderr
-
-    def test_allow_existing_no_overwrite_spec(self, git_repo: Path):
-        """T010: Pre-create spec.md with content, verify it is preserved."""
-        subprocess.run(
-            ["git", "checkout", "-b", "008-no-overwrite"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        spec_dir = git_repo / "specs" / "008-no-overwrite"
-        spec_dir.mkdir(parents=True)
-        spec_file = spec_dir / "spec.md"
-        spec_file.write_text("# My custom spec content\n")
-        subprocess.run(
-            ["git", "checkout", "-"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--short-name", "no-overwrite",
-            "--number", "8", "No overwrite feature",
-        )
-        assert result.returncode == 0, result.stderr
-        assert spec_file.read_text() == "# My custom spec content\n"
-
-    def test_allow_existing_creates_branch_if_not_exists(self, git_repo: Path):
-        """T011: Verify normal creation when branch doesn't exist."""
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--short-name", "new-branch",
-            "New branch feature",
-        )
-        assert result.returncode == 0, result.stderr
-        current = subprocess.run(
-            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
-            cwd=git_repo, capture_output=True, text=True,
-        ).stdout.strip()
-        assert "new-branch" in current
-
-    def test_allow_existing_with_json(self, git_repo: Path):
-        """T012: Verify JSON output is correct."""
-        import json
-
-        subprocess.run(
-            ["git", "checkout", "-b", "009-json-test"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        subprocess.run(
-            ["git", "checkout", "-"],
-            cwd=git_repo, check=True, capture_output=True,
-        )
-        result = run_script(
-            git_repo, "--allow-existing-branch", "--json", "--short-name", "json-test",
-            "--number", "9", "JSON test",
-        )
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "009-json-test"
-
-    def test_allow_existing_no_git(self, no_git_dir: Path):
-        """T013: Verify flag is silently ignored in non-git repos."""
-        result = run_script(
-            no_git_dir, "--allow-existing-branch", "--short-name", "no-git",
-            "No git feature",
-        )
-        assert result.returncode == 0, result.stderr
-
-
-class TestAllowExistingBranchPowerShell:
-    def test_powershell_supports_allow_existing_branch_flag(self):
-        """Static guard: PS script exposes and uses -AllowExistingBranch."""
-        contents = CREATE_FEATURE_PS.read_text(encoding="utf-8")
-        assert "-AllowExistingBranch" in contents
-        # Ensure the flag is referenced in script logic, not just declared
-        assert "AllowExistingBranch" in contents.replace("-AllowExistingBranch", "")