chore: bump version to 0.8.16

docs: update landing page stats and branch naming convention (#2727 )
* docs: update landing page stats and branch naming convention - Update community extensions: 91 → 105 - Update extension authors: 50+ → 60+ - Update presets: 18 → 22 - Update GitHub stars: 96K+ → 106K+ - Add last-updated date to landing page - Clarify branch naming convention for PR-only changes * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
2026-07-03 20:36:23 +08:00 · 2026-05-27 21:34:55 +00:00 · 2026-05-27 16:33:33 -05:00 · 2026-05-27 13:00:58 -05:00 · 2026-05-27 12:49:54 -05:00 · 2026-05-27 09:52:57 -05:00
55 changed files with 2544 additions and 1120 deletions
--- a/.github/workflows/add-community-extension.lock.yml
+++ b/.github/workflows/add-community-extension.lock.yml
@@ -38,7 +38,7 @@
 #   - actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0 (source v9)
 #   - actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
 #   - actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
-#   - github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+#   - github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
 #
 # Container images used:
 #   - ghcr.io/github/gh-aw-firewall/agent:0.25.49
@@ -92,7 +92,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -370,7 +370,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1047,7 +1047,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1188,7 +1188,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1384,7 +1384,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1456,7 +1456,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
--- a/.github/workflows/add-community-preset.lock.yml
+++ b/.github/workflows/add-community-preset.lock.yml
@@ -38,7 +38,7 @@
 #   - actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0 (source v9)
 #   - actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
 #   - actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
-#   - github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+#   - github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
 #
 # Container images used:
 #   - ghcr.io/github/gh-aw-firewall/agent:0.25.49
@@ -92,7 +92,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -370,7 +370,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1047,7 +1047,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1188,7 +1188,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1384,7 +1384,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
@@ -1456,7 +1456,7 @@ jobs:
    steps:
      - name: Setup Scripts
        id: setup
-        uses: github/gh-aw-actions/setup@efa55847f72aadb03490d955263ff911bf758700 # v0.74.8
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
        with:
          destination: ${{ runner.temp }}/gh-aw/actions
          job-name: ${{ github.job }}
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -22,11 +22,11 @@ jobs:
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

      - name: Initialize CodeQL
-        uses: github/codeql-action/init@68bde559dea0fdcac2102bfdf6230c5f70eb485e # v4
+        uses: github/codeql-action/init@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4
        with:
          languages: ${{ matrix.language }}

      - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@68bde559dea0fdcac2102bfdf6230c5f70eb485e # v4
+        uses: github/codeql-action/analyze@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4
        with:
          category: "/language:${{ matrix.language }}"
--- a/.github/workflows/stale.yml
+++ b/.github/workflows/stale.yml
@@ -14,7 +14,7 @@ jobs:
  stale:
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # v10
        with:
          # Days of inactivity before an issue or PR becomes stale
          days-before-stale: 150
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -379,6 +379,33 @@ Implementation: Extends `YamlIntegration` (parallel to `TomlIntegration`):
 4. Uses `yaml.safe_dump()` for header fields to ensure proper escaping
 5. Sets `context_file = "AGENTS.md"` so the base setup manages the Spec Kit context section there

+## Branch Naming Convention
+
+Branches follow one of two patterns depending on whether an issue exists:
+
+```
+<type>/<number>-<short-slug>   # when an issue is created first
+<type>/<short-slug>            # when no issue exists (PR-only changes)
+```
+
+When an issue exists, include its number immediately after the prefix — this is what makes branches traceable. For small or self-contained changes that go straight to a PR without a tracking issue, omit the number.
+
+| Prefix | When to use | Example |
+|---|---|---|
+| `feat/` | New features | `feat/2342-workflow-cli-alignment` |
+| `fix/` | Bug fixes | `fix/2653-paths-only-validation` |
+| `docs/` | Documentation changes | `docs/2677-branch-naming-convention`, `docs/update-landing-stats` |
+| `community/` | Community catalog additions | `community/2492-add-mde-extension` |
+| `chore/` | Maintenance, tooling, CI | `chore/2366-editorconfig` |
+
+**Rules:**
+
+1. Include the issue number when one exists — this is what makes branches traceable
+2. Use kebab-case for the slug
+3. Keep the slug short — enough to identify the work without looking up the issue
+
+---
+
 ## Common Pitfalls

 1. **Using shorthand keys for CLI-based integrations**: For CLI-based integrations (`requires_cli: True`), the `key` must match the executable name (e.g., `"cursor-agent"` not `"cursor"`). `shutil.which(key)` is used for CLI tool checks — mismatches require special-case mappings. IDE-based integrations (`requires_cli: False`) are not subject to this constraint.
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,62 @@

 <!-- insert new changelog below this comment -->

+## [0.8.16] - 2026-05-27
+
+### Changed
+
+- docs: update landing page stats and branch naming convention (#2727)
+- feat(workflows): expose {{ context.run_id }} template variable (#2664)
+- fix: resolve __SPECKIT_COMMAND_*__ refs in preset skill rendering (#2717) (#2718)
+- Add Workflow Preset to community catalog (#2725)
+- fix: paths-only skips branch validation, setup-plan preserves existing plan (#2672)
+- docs: fix broken pipx homepage URLs to point to pipx.pypa.io (#2670)
+- Update Architecture Guard extension to v1.8.9 (#2723)
+- Re-validate spec quality checklist after clarify updates spec (#2715)
+- chore: release 0.8.15, begin 0.8.16.dev0 development (#2722)
+
+## [0.8.15] - 2026-05-27
+
+### Changed
+
+- Update Fiction Book Writing preset to v1.8.1 (#2714)
+- chore: update memorylint and superb to 1.4.0 (#2690)
+- fix: promote post-execution hook dispatch to H2 with directive language (#2713)
+- Add Token Budget extension to community catalog (#2712)
+- fix: create skills directory on demand during extension/preset install (#2711)
+- fix: PS 5.1 compat — replace non-ASCII chars in shipped PowerShell scripts (#2709)
+- docs: update security-governance preset to v0.3.0 (#2676)
+- Update README.md (#2675)
+- chore: release 0.8.14, begin 0.8.15.dev0 development (#2706)
+
+## [0.8.14] - 2026-05-26
+
+### Changed
+
+- Add util for windows sub-process (#2598)
+- refactor: create commands/ package and move init handler (PR-4/8) (#2615)
+- Add Product Spec Extension to community catalog (#2705)
+- fix init-options speckit version refresh (#2647)
+- chore(deps): bump github/gh-aw-actions from 0.74.8 to 0.74.9 (#2658)
+- docs: add branch naming convention to AGENTS.md and CONTRIBUTING.md (#2678)
+- chore(deps): bump actions/stale from 10.2.0 to 10.3.0 (#2657)
+- chore(deps): bump github/codeql-action from 4.35.4 to 4.35.5 (#2656)
+- chore: release 0.8.13, begin 0.8.14.dev0 development (#2669)
+
+## [0.8.13] - 2026-05-21
+
+### Changed
+
+- fix: while/do-while loop condition reads stale iteration-0 step output (#2662)
+- docs: fix directory hierarchy in README examples (#2639)
+- fix(catalogs): reject boolean priority in extension and preset catalog readers (#2589)
+- Update Agent Governance extension to v1.2.0 (#2659)
+- Add agentic workflows for community catalog submissions (#2655)
+- feat: add self-check tip to check output (#2574)
+- fix(cli): clarify exception diagnostics (#2602)
+- ci: add diff whitespace check (#2572)
+- chore: release 0.8.12, begin 0.8.13.dev0 development (#2648)
+
 ## [0.8.12] - 2026-05-20

 ### Changed
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -38,7 +38,7 @@ On [GitHub Codespaces](https://github.com/features/codespaces) it's even simpler
 1. Fork and clone the repository
 1. Configure and install the dependencies: `uv sync --extra test`
 1. Make sure the CLI works on your machine: `uv run specify --help`
-1. Create a new branch: `git checkout -b my-branch-name`
+1. Create a new branch: `git checkout -b <type>/<number>-<short-slug>` (see [Branch naming](#branch-naming) below)
 1. Make your change, add tests, and make sure everything still works
 1. Test the CLI functionality with a sample project if relevant
 1. Push to your fork and submit a pull request
@@ -55,6 +55,20 @@ Here are a few things you can do that will increase the likelihood of your pull
 - Write a [good commit message](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
 - Test your changes with the Spec-Driven Development workflow to ensure compatibility.

+### Branch naming
+
+We recommend naming branches as `<type>/<number>-<short-slug>`, where `<number>` is the issue or PR number (whichever comes first) and `<type>` is one of:
+
+| Prefix | When to use | Example |
+|---|---|---|
+| `feat/` | New features | `feat/2342-workflow-cli-alignment` |
+| `fix/` | Bug fixes | `fix/2653-paths-only-validation` |
+| `docs/` | Documentation changes | `docs/2677-branch-naming-convention` |
+| `community/` | Community catalog additions | `community/2492-add-mde-extension` |
+| `chore/` | Maintenance, tooling, CI | `chore/2366-editorconfig` |
+
+Including the issue or PR number makes branches traceable — especially useful since the project uses squash merges and `git branch --merged` won't detect merged branches. If you start with a PR (no issue), use the PR number once it's assigned.
+
 ## Development workflow

 When working on spec-kit:
--- a/README.md
+++ b/README.md
@@ -35,7 +35,7 @@
 - [🔧 Prerequisites](#-prerequisites)
 - [📖 Learn More](#-learn-more)
 - [📋 Detailed Process](#-detailed-process)
- [ Support](#-support)
+- [💬 Support](#-support)
 - [🙏 Acknowledgements](#-acknowledgements)
 - [📄 License](#-license)

@@ -281,7 +281,7 @@ Our research and experimentation focus on:

 - **Linux/macOS/Windows**
 - [Supported](#-supported-ai-coding-agent-integrations) AI coding agent.
- [uv](https://docs.astral.sh/uv/) for package management (recommended) or [pipx](https://pypa.github.io/pipx/) for persistent installation
+- [uv](https://docs.astral.sh/uv/) for package management (recommended) or [pipx](https://pipx.pypa.io/) for persistent installation
 - [Python 3.11+](https://www.python.org/downloads/)
 - [Git](https://git-scm.com/downloads)

@@ -581,7 +581,7 @@ Once the implementation is complete, test the application and resolve any runtim

 ---

-##  Support
+## 💬 Support

 For support, please open a [GitHub issue](https://github.com/github/spec-kit/issues/new). We welcome bug reports, feature requests, and questions about using Spec-Driven Development.

--- a/docs/community/extensions.md
+++ b/docs/community/extensions.md
@@ -27,7 +27,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | 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) |
 | API Evolve | Managed API contract evolution — breaking-change detection, semver enforcement, deprecation orchestration, and lifecycle gates across REST, GraphQL, and gRPC | `process` | Read+Write | [spec-kit-api-evolve](https://github.com/Quratulain-bilal/spec-kit-api-evolve) |
 | Architect Impact Previewer | Predicts architectural impact, complexity, and risks of proposed changes before implementation. | `visibility` | Read-only | [spec-kit-architect-preview](https://github.com/UmmeHabiba1312/spec-kit-architect-preview) |
-| Architecture Guard | Continuous architecture governance for AI-assisted development. Reviews specs, plans, and code for architecture drift, producing structured refactor tasks and evolution proposals. | `process` | Read+Write | [spec-kit-architecture-guard](https://github.com/DyanGalih/spec-kit-architecture-guard) |
+| Architecture Guard | Framework-agnostic architecture review extension for validating implementation against governance and architecture constitutions, detecting architectural drift, and generating non-blocking refactor tasks | `process` | Read+Write | [spec-kit-architecture-guard](https://github.com/DyanGalih/spec-kit-architecture-guard) |
 | Architecture Workflow | Generate or reverse project-level 4+1 architecture view artifacts and synthesis | `docs` | Read+Write | [spec-kit-arch](https://github.com/bigsmartben/spec-kit-arch) |
 | 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) |
@@ -78,6 +78,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
 | 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 from research to release — portfolio, lite mode, monorepo, optional V-Model | `process` | Read+Write | [speckit-product-forge](https://github.com/VaiYav/speckit-product-forge) |
+| Product Spec Extension | Generates PRFAQ, Lean PRD, stakeholder summaries, and technical designs from engineering specs | `docs` | Read+Write | [spec-kit-product](https://github.com/d0whc3r/spec-kit-product) |
 | 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) |
 | QA Testing Extension | Systematic QA testing with browser-driven or CLI-based validation of acceptance criteria from spec | `code` | Read-only | [spec-kit-qa](https://github.com/arunt14/spec-kit-qa) |
@@ -115,6 +116,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Team Assign | Assign tasks.md items to human engineers, split into subtasks, and generate a per-engineer workboard | `process` | Read+Write | [spec-kit-team-assign](https://github.com/tarunkumarbhati/spec-kit-team-assign) |
 | Time Machine | Retroactively apply the full SDD workflow to existing codebases — analyse, spec, and ship feature-by-feature | `process` | Read+Write | [spec-kit-time-machine](https://github.com/teeyo/spec-kit-time-machine) |
 | TinySpec | Lightweight single-file workflow for small tasks — skip the heavy multi-step SDD process | `process` | Read+Write | [spec-kit-tinyspec](https://github.com/Quratulain-bilal/spec-kit-tinyspec) |
+| Token Budget | Reduces LLM token consumption in Spec Kit workflows: compact artifacts in-place, scope per-phase reading, suppress prose padding, and report token usage | `process` | Read+Write | [spec-kit-token-budget](https://github.com/tinesoft/spec-kit-token-budget) |
 | Token Consumption Analyzer | Captures, analyzes, and compares token consumption across SDD workflows | `visibility` | Read-only | [spec-kit-token-analyzer](https://github.com/coderandhiker/spec-kit-token-analyzer) |
 | 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) |
--- a/docs/community/presets.md
+++ b/docs/community/presets.md
@@ -15,7 +15,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Claude AskUserQuestion | Upgrades `/speckit.clarify` and `/speckit.checklist` on Claude Code from Markdown-table prompts to the native AskUserQuestion picker, with a recommended option and reasoning on every question | 2 commands | — | [spec-kit-preset-claude-ask-questions](https://github.com/0xrafasec/spec-kit-preset-claude-ask-questions) |
 | Cross-Platform Governance | Adds Bash/PowerShell parity, dry-run/WhatIf parity, Unix man-page expectations, PowerShell comment-based help, and Verb-Noun Cmdlet discipline | 8 templates, 3 commands | — | [spec-kit-preset-cross-platform-governance](https://github.com/hindermath/spec-kit-preset-cross-platform-governance) |
 | Explicit Task Dependencies | Adds explicit `(depends on T###)` dependency declarations and an Execution Wave DAG to tasks.md for parallel scheduling | 1 template, 1 command | — | [spec-kit-preset-explicit-task-dependencies](https://github.com/Quratulain-bilal/spec-kit-preset-explicit-task-dependencies) |
-| Fiction Book Writing | It adapts the Spec-Driven Development workflow for storytelling to create books or audiobooks (with annotations) in 12 languages: features become story elements, specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports single and multi-POV, all major plot structure frameworks, and two style modes: an author voice sample or humanized AI prose. Supports interactive elements like brainstorming, interview, roleplay and extras like statistics, cover builder and bio command. Export with templates for KDP, D2D etc. | 22 templates, 27 commands, 2 scripts | — | [speckit-preset-fiction-book-writing](https://github.com/adaumann/speckit-preset-fiction-book-writing) |
+| Fiction Book Writing | It adapts the Spec-Driven Development workflow for storytelling to create books or audiobooks (with annotations) in 12 languages: features become story elements, specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports single and multi-POV, all major plot structure frameworks, and two style modes: an author voice sample or humanized AI prose principles. Supports interactive elements like brainstorming, interview, roleplay and extras like statistics, cover builder and bio command. Export with templates for KDP, D2D etc. | 25 templates, 33 commands, 2 scripts | — | [speckit-preset-fiction-book-writing](https://github.com/adaumann/speckit-preset-fiction-book-writing) |
 | Game Narrative Writing | Spec-Driven Development for interactive game narrative pre-production for video games. Authors write in a portable generic format, Twine/Sugarcube (.twee) or Ink (.ink). Covers choice-IF, visual novels, and branching dialogue. Supports Tier 1 mechanic hooks (flag, counter, inventory, timer, trust, currency, npc_state, ending_condition), multi-ending design, series carry-over variable registry, and NPC-focused character architecture. | 22 templates, 36 commands, 2 scripts | — | [speckit-preset-game-narrative-writing](https://github.com/adaumann/speckit-preset-game-narrative-writing) |
 | iSAQB Architecture Governance | Adds general iSAQB/CPSA-F and arc42 architecture governance: goals, context, building blocks, runtime and deployment views, quality scenarios, ADRs, risks, and technical debt | 13 templates, 3 commands | — | [spec-kit-preset-isaqb-architecture-governance](https://github.com/hindermath/spec-kit-preset-isaqb-architecture-governance) |
 | Jira Issue Tracking | Overrides `speckit.taskstoissues` to create Jira epics, stories, and tasks instead of GitHub Issues via Atlassian MCP tools | 1 command | — | [spec-kit-preset-jira](https://github.com/luno/spec-kit-preset-jira) |
@@ -23,9 +23,10 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Multi-Repo Branching | Coordinates feature branch creation across multiple git repositories (independent repos and submodules) during plan and tasks phases | 2 commands | — | [spec-kit-preset-multi-repo-branching](https://github.com/sakitA/spec-kit-preset-multi-repo-branching) |
 | 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) |
 | Screenwriting | Spec-Driven Development for screenwriting/scriptwriting/tutorials: feature films, television (pilot, episode, limited series), and stage plays. Adapts the Spec Kit workflow to screenplay craft — slug lines, action lines, act breaks, beat sheets, and industry-standard pitch documents. Supports three-act, Save the Cat, TV pilot, network episode, cable/streaming episode, and stage-play structural frameworks. Export to Fountain, FTX, PDF | 26 templates, 32 commands, 1 script | — | [speckit-preset-screenwriting](https://github.com/adaumann/speckit-preset-screenwriting) |
-| Security Governance | Adds secure development governance: memory-safe-language preference, secure code generation, NIST SSDF, CWE Top 25, OWASP ASVS, SBOM/VEX/SLSA, OpenSSF Scorecard, and EU CRA applicability | 12 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
+| Security Governance | Adds secure development governance: memory-safe-language preference, secure code generation, NIST SSDF, CWE Top 25, OWASP ASVS, SBOM/AI-SBOM, VEX/SLSA, OpenSSF Scorecard, G7/BSI AI-SBOM target evidence, and EU CRA applicability | 12 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
 | Spec2Cloud | Spec-driven workflow tuned for shipping to Azure: spec → plan → tasks → implement → deploy | 5 templates, 8 commands | — | [spec2cloud](https://github.com/Azure-Samples/Spec2Cloud) |
 | Table of Contents Navigation | Adds a navigable Table of Contents to generated spec.md, plan.md, and tasks.md documents | 3 templates, 3 commands | — | [spec-kit-preset-toc-navigation](https://github.com/Quratulain-bilal/spec-kit-preset-toc-navigation) |
 | VS Code Ask Questions | Enhances the clarify command to use `vscode/askQuestions` for batched interactive questioning. | 1 command | — | [spec-kit-presets](https://github.com/fdcastel/spec-kit-presets) |
+| Workflow Preset | Behavior-first specification, design artifacts, and agent-native handoff orchestration — adds requirement-phase behavior drafts, formal BDD/UIF/behavior contracts, optional design artifacts, and scoped implementation handoffs with Core Agent, Vertical Planner Agent, and Worker Agent modes | 23 templates, 7 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |

 To build and publish your own preset, see the [Presets Publishing Guide](https://github.com/github/spec-kit/blob/main/presets/PUBLISHING.md).
--- a/docs/index.md
+++ b/docs/index.md
@@ -43,7 +43,7 @@ Run `specify init` with your agent of choice and Spec Kit sets up the right comm

 ### Make it your own

-<span class="pillar-stat">91 community extensions</span> (50+ authors), <span class="pillar-stat">18 presets</span>, and growing. Tune the core process with presets, extend it with extensions, orchestrate it with workflows, or replace it entirely. Build and publish your own.
+<span class="pillar-stat">105 community extensions</span> (60+ authors), <span class="pillar-stat">22 presets</span>, and growing. Tune the core process with presets, extend it with extensions, orchestrate it with workflows, or replace it entirely. Build and publish your own.

 Including entirely different SDD processes:

@@ -82,7 +82,7 @@ Community extensions like CI Guard and Architecture Guard add compliance gates a

 <div class="stats-grid">
  <div class="stat-item">
-    <span class="stat-number">96K+</span>
+    <span class="stat-number">106K+</span>
    <span class="stat-label">GitHub stars</span>
  </div>
  <div class="stat-item">
@@ -94,11 +94,11 @@ Community extensions like CI Guard and Architecture Guard add compliance gates a
    <span class="stat-label">Integrations</span>
  </div>
  <div class="stat-item">
-    <span class="stat-number">91</span>
+    <span class="stat-number">105</span>
    <span class="stat-label">Extensions</span>
  </div>
  <div class="stat-item">
-    <span class="stat-number">18</span>
+    <span class="stat-number">22</span>
    <span class="stat-label">Presets</span>
  </div>
  <div class="stat-item">
@@ -150,3 +150,5 @@ specify init my-project --integration copilot
 Ready to start? Follow the [Quick Start Guide](quickstart.md).

 </div>
+
+<p class="text-end small text-body-secondary">Last updated: May 27, 2026</p>
--- a/docs/install/pipx.md
+++ b/docs/install/pipx.md
@@ -1,6 +1,6 @@
 # Installing with pipx

-[pipx](https://pypa.github.io/pipx/) is a tool for installing Python CLI applications in isolated environments. It does not require [uv](https://docs.astral.sh/uv/).
+[pipx](https://pipx.pypa.io/) is a tool for installing Python CLI applications in isolated environments. It does not require [uv](https://docs.astral.sh/uv/).

 ## Install Specify CLI

--- a/docs/installation.md
+++ b/docs/installation.md
@@ -4,7 +4,7 @@

 - **Linux/macOS** (or Windows; PowerShell scripts now supported without WSL)
 - AI coding agent: [Claude Code](https://www.anthropic.com/claude-code), [GitHub Copilot](https://code.visualstudio.com/), [Codebuddy CLI](https://www.codebuddy.ai/cli), [Gemini CLI](https://github.com/google-gemini/gemini-cli), or [Pi Coding Agent](https://pi.dev)
- [uv](https://docs.astral.sh/uv/) for package management (recommended) or [pipx](https://pypa.github.io/pipx/) for persistent installation
+- [uv](https://docs.astral.sh/uv/) for package management (recommended) or [pipx](https://pipx.pypa.io/) for persistent installation
 - [Python 3.11+](https://www.python.org/downloads/)
 - [Git](https://git-scm.com/downloads)

--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-05-21T00:00:00Z",
+  "updated_at": "2026-05-27T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
    "aide": {
@@ -240,10 +240,10 @@
    "architecture-guard": {
      "name": "Architecture Guard",
      "id": "architecture-guard",
-      "description": "Continuous architecture governance for AI-assisted development. Reviews specs, plans, and code for architecture drift, producing structured refactor tasks and evolution proposals.",
+      "description": "Framework-agnostic architecture review extension for validating implementation against governance and architecture constitutions, detecting architectural drift, and generating non-blocking refactor tasks.",
      "author": "DyanGalih",
-      "version": "1.8.4",
-      "download_url": "https://github.com/DyanGalih/spec-kit-architecture-guard/archive/refs/tags/v1.8.4.zip",
+      "version": "1.8.9",
+      "download_url": "https://github.com/DyanGalih/spec-kit-architecture-guard/archive/refs/tags/v1.8.9.zip",
      "repository": "https://github.com/DyanGalih/spec-kit-architecture-guard",
      "homepage": "https://github.com/DyanGalih/spec-kit-architecture-guard",
      "documentation": "https://github.com/DyanGalih/spec-kit-architecture-guard/blob/main/README.md",
@@ -258,17 +258,18 @@
      },
      "tags": [
        "architecture",
-        "governance",
-        "drift-detection",
+        "spec-kit",
+        "review",
        "refactor",
-        "monolithic",
-        "microservices"
+        "workflow",
+        "governance",
+        "guardrails"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-05-05T07:26:00Z",
-      "updated_at": "2026-05-11T14:58:00Z"
+      "updated_at": "2026-05-27T00:00:00Z"
    },
    "archive": {
      "name": "Archive Extension",
@@ -1646,8 +1647,8 @@
      "id": "memorylint",
      "description": "Agent memory governance tool: Automatically audits and fixes boundary conflicts between AGENTS.md and the constitution.",
      "author": "RbBtSn0w",
-      "version": "1.3.0",
-      "download_url": "https://github.com/RbBtSn0w/spec-kit-extensions/releases/download/memorylint-v1.3.0/memorylint.zip",
+      "version": "1.4.0",
+      "download_url": "https://github.com/RbBtSn0w/spec-kit-extensions/releases/download/memorylint-v1.4.0/memorylint.zip",
      "repository": "https://github.com/RbBtSn0w/spec-kit-extensions",
      "homepage": "https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/memorylint",
      "documentation": "https://github.com/RbBtSn0w/spec-kit-extensions/blob/main/memorylint/README.md",
@@ -1657,8 +1658,8 @@
        "speckit_version": ">=0.5.1"
      },
      "provides": {
-        "commands": 1,
-        "hooks": 1
+        "commands": 2,
+        "hooks": 3
      },
      "tags": [
        "memory",
@@ -1671,7 +1672,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-04-09T00:00:00Z",
-      "updated_at": "2026-04-16T13:10:26Z"
+      "updated_at": "2026-05-24T01:06:49Z"
    },
    "multi-model-review": {
      "name": "Multi-Model Review",
@@ -1945,6 +1946,38 @@
      "created_at": "2026-05-15T00:00:00Z",
      "updated_at": "2026-05-15T00:00:00Z"
    },
+    "product": {
+      "name": "Product Spec Extension",
+      "id": "product",
+      "description": "Generates PRFAQ, Lean PRD, stakeholder summaries, and technical designs from engineering specs.",
+      "author": "spec-kit-product contributors",
+      "version": "0.1.3",
+      "download_url": "https://github.com/d0whc3r/spec-kit-product/releases/download/v0.1.3/product-0.1.3.zip",
+      "repository": "https://github.com/d0whc3r/spec-kit-product",
+      "homepage": "https://github.com/d0whc3r/spec-kit-product",
+      "documentation": "https://github.com/d0whc3r/spec-kit-product/blob/main/README.md",
+      "changelog": "https://github.com/d0whc3r/spec-kit-product/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.2.0"
+      },
+      "provides": {
+        "commands": 4,
+        "hooks": 6
+      },
+      "tags": [
+        "product",
+        "spec",
+        "prd",
+        "design",
+        "documentation"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-05-26T00:00:00Z",
+      "updated_at": "2026-05-26T00:00:00Z"
+    },
    "product-forge": {
      "name": "Product Forge",
      "id": "product-forge",
@@ -2862,8 +2895,8 @@
      "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": "1.3.0",
-      "download_url": "https://github.com/RbBtSn0w/spec-kit-extensions/releases/download/superpowers-bridge-v1.3.0/superpowers-bridge.zip",
+      "version": "1.4.0",
+      "download_url": "https://github.com/RbBtSn0w/spec-kit-extensions/releases/download/superpowers-bridge-v1.4.0/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",
@@ -2881,7 +2914,7 @@
      },
      "provides": {
        "commands": 8,
-        "hooks": 4
+        "hooks": 3
      },
      "tags": [
        "methodology",
@@ -2898,7 +2931,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-30T00:00:00Z",
-      "updated_at": "2026-04-16T14:08:23Z"
+      "updated_at": "2026-05-24T01:07:34Z"
    },
    "superpowers-bridge": {
      "name": "Superpowers Bridge",
@@ -3128,6 +3161,48 @@
      "created_at": "2026-05-01T00:00:00Z",
      "updated_at": "2026-05-01T00:00:00Z"
    },
+    "token-budget": {
+      "name": "Token Budget",
+      "id": "token-budget",
+      "description": "Reduces LLM token consumption in Spec Kit workflows: compact artifacts in-place, scope per-phase reading, suppress prose padding, and report token usage.",
+      "author": "Tine Kondo",
+      "version": "1.0.1",
+      "download_url": "https://github.com/tinesoft/spec-kit-token-budget/archive/refs/tags/v1.0.1.zip",
+      "repository": "https://github.com/tinesoft/spec-kit-token-budget",
+      "homepage": "https://github.com/tinesoft/spec-kit-token-budget",
+      "documentation": "https://github.com/tinesoft/spec-kit-token-budget/blob/main/README.md",
+      "changelog": "https://github.com/tinesoft/spec-kit-token-budget/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "python3",
+            "required": false
+          },
+          {
+            "name": "rtk",
+            "required": false
+          }
+        ]
+      },
+      "provides": {
+        "commands": 4,
+        "hooks": 6
+      },
+      "tags": [
+        "tokens",
+        "budget",
+        "context",
+        "efficiency",
+        "cost-optimization"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-05-26T00:00:00Z",
+      "updated_at": "2026-05-26T00:00:00Z"
+    },
    "v-model": {
      "name": "V-Model Extension Pack",
      "id": "v-model",
--- a/extensions/git/commands/speckit.git.initialize.md
+++ b/extensions/git/commands/speckit.git.initialize.md
@@ -35,7 +35,7 @@ Replace the script to add project-specific Git initialization steps:
 ## Output

 On success:
- `✓ Git repository initialized`
+- `[OK] Git repository initialized`

 ## Graceful Degradation

--- a/extensions/git/scripts/powershell/auto-commit.ps1
+++ b/extensions/git/scripts/powershell/auto-commit.ps1
@@ -115,7 +115,7 @@ if (Test-Path $configFile) {
        }
    }
 } else {
-    # No config file — auto-commit disabled by default
+    # No config file -- auto-commit disabled by default
    exit 0
 }

--- a/extensions/git/scripts/powershell/git-common.ps1
+++ b/extensions/git/scripts/powershell/git-common.ps1
@@ -1,6 +1,6 @@
 #!/usr/bin/env pwsh
 # Git-specific common functions for the git extension.
-# Extracted from scripts/powershell/common.ps1 — contains only git-specific
+# Extracted from scripts/powershell/common.ps1 -- contains only git-specific
 # branch validation and detection logic.

 function Test-HasGit {
--- a/extensions/git/scripts/powershell/initialize-repo.ps1
+++ b/extensions/git/scripts/powershell/initialize-repo.ps1
@@ -1,7 +1,7 @@
 #!/usr/bin/env pwsh
 # Git extension: initialize-repo.ps1
 # Initialize a Git repository with an initial commit.
-# Customizable — replace this script to add .gitignore templates,
+# Customizable -- replace this script to add .gitignore templates,
 # default branch config, git-flow, LFS, signing, etc.
 $ErrorActionPreference = 'Stop'

@@ -66,4 +66,4 @@ try {
    exit 1
 }

-Write-Host "✓ Git repository initialized"
+Write-Host "[OK] Git repository initialized"
--- a/presets/catalog.community.json
+++ b/presets/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-05-05T10:00:00Z",
+  "updated_at": "2026-05-27T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
  "presets": {
    "a11y-governance": {
@@ -222,11 +222,11 @@
    "fiction-book-writing": {
      "name": "Fiction Book Writing",
      "id": "fiction-book-writing",
-      "version": "1.7.0",
-      "description": "Spec-Driven Development for novel and long-form fiction. 27 AI commands from idea to submission: story bible governance, 9 POV modes, all major plot structure frameworks, scene-by-scene drafting with quality gates, audiobook pipeline (SSML/ElevenLabs), cover design, sensitivity review, pacing and prose statistics, and pandoc-based export to DOCX/EPUB/LaTeX. Two style modes: author voice sample extraction or humanized-AI prose with 5 craft profiles. 12 languages supported. Support for offline semantic search.",
+      "version": "1.8.1",
+      "description": "Spec-Driven Development for novel and long-form fiction. 33 AI commands from idea to submission: story bible governance, 9 POV modes, all major plot structure frameworks, scene-by-scene drafting with quality gates, audiobook pipeline (SSML/ElevenLabs), cover design, sensitivity review, pacing and prose statistics, and pandoc-based export to DOCX/EPUB/LaTeX. Two style modes: author voice sample extraction or humanized-AI prose with 5 craft profiles. 12 languages supported. Support for offline semantic search.",
      "author": "Andreas Daumann",
      "repository": "https://github.com/adaumann/speckit-preset-fiction-book-writing",
-      "download_url": "https://github.com/adaumann/speckit-preset-fiction-book-writing/archive/refs/tags/v1.7.0.zip",
+      "download_url": "https://github.com/adaumann/speckit-preset-fiction-book-writing/archive/refs/tags/v1.8.1.zip",
      "homepage": "https://github.com/adaumann/speckit-preset-fiction-book-writing",
      "documentation": "https://github.com/adaumann/speckit-preset-fiction-book-writing/blob/main/fiction-book-writing/README.md",
      "license": "MIT",
@@ -234,8 +234,8 @@
        "speckit_version": ">=0.5.0"
      },
      "provides": {
-        "templates": 22,
-        "commands": 27,
+        "templates": 25,
+        "commands": 33,
        "scripts": 2
      },
      "tags": [
@@ -254,7 +254,7 @@
        "language-support"
      ],
      "created_at": "2026-04-09T08:00:00Z",
-      "updated_at": "2026-04-27T08:00:00Z"
+      "updated_at": "2026-05-24T08:00:00Z"
    },
    "game-narrative-writing": {
      "name": "Game Narrative Writing",
@@ -472,11 +472,11 @@
    "security-governance": {
      "name": "Security Governance",
      "id": "security-governance",
-      "version": "0.2.0",
-      "description": "Adds secure development governance, MSL preference, ASVS verification, supply-chain transparency, and EU CRA awareness.",
+      "version": "0.3.0",
+      "description": "Adds memory-safe-language preference, secure code generation, ASVS verification, SBOM/AI-SBOM supply-chain transparency, and EU Cyber Resilience Act awareness.",
      "author": "Thorsten Hindermann",
      "repository": "https://github.com/hindermath/spec-kit-preset-security-governance",
-      "download_url": "https://github.com/hindermath/spec-kit-preset-security-governance/archive/refs/tags/v0.2.0.zip",
+      "download_url": "https://github.com/hindermath/spec-kit-preset-security-governance/archive/refs/tags/v0.3.0.zip",
      "homepage": "https://github.com/hindermath/spec-kit-preset-security-governance",
      "documentation": "https://github.com/hindermath/spec-kit-preset-security-governance/blob/main/README.md",
      "license": "MIT",
@@ -491,11 +491,20 @@
        "security",
        "governance",
        "msl",
+        "ssdf",
        "asvs",
-        "supply-chain"
+        "supply-chain",
+        "sbom",
+        "ai-sbom",
+        "vex",
+        "slsa",
+        "cwe-top-25",
+        "g7",
+        "bsi",
+        "cra"
      ],
      "created_at": "2026-04-27T00:00:00Z",
-      "updated_at": "2026-04-27T00:00:00Z"
+      "updated_at": "2026-05-22T00:00:00Z"
    },
    "spec2cloud": {
      "name": "Spec2Cloud",
@@ -572,6 +581,34 @@
        "clarify",
        "interactive"
      ]
+    },
+    "workflow-preset": {
+      "name": "Workflow Preset",
+      "id": "workflow-preset",
+      "version": "1.2.0",
+      "description": "Behavior-first specification, design artifacts, and agent-native handoff orchestration.",
+      "author": "bigsmartben",
+      "repository": "https://github.com/bigsmartben/spec-kit-workflow-preset",
+      "download_url": "https://github.com/bigsmartben/spec-kit-workflow-preset/archive/refs/tags/v1.2.0.zip",
+      "homepage": "https://github.com/bigsmartben/spec-kit-workflow-preset",
+      "documentation": "https://github.com/bigsmartben/spec-kit-workflow-preset/blob/main/README.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.8.10.dev0"
+      },
+      "provides": {
+        "templates": 23,
+        "commands": 7
+      },
+      "tags": [
+        "behavior",
+        "bdd",
+        "planning",
+        "implementation",
+        "handoff"
+      ],
+      "created_at": "2026-05-27T00:00:00Z",
+      "updated_at": "2026-05-27T00:00:00Z"
    }
  }
 }
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.8.13.dev0"
+version = "0.8.16"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
--- a/scripts/bash/check-prerequisites.sh
+++ b/scripts/bash/check-prerequisites.sh
@@ -78,13 +78,12 @@ done
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"

-# Get feature paths and validate branch
+# Get feature paths
 _paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
 eval "$_paths_output"
 unset _paths_output
-check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1

-# If paths-only mode, output paths and exit (support JSON + paths-only combined)
+# If paths-only mode, output paths and exit (no validation)
 if $PATHS_ONLY; then
    if $JSON_MODE; then
        # Minimal JSON paths payload (no validation performed)
@@ -112,6 +111,9 @@ if $PATHS_ONLY; then
    exit 0
 fi

+# Validate branch name
+check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
+
 # Validate required directories and files
 if [[ ! -d "$FEATURE_DIR" ]]; then
    echo "ERROR: Feature directory not found: $FEATURE_DIR" >&2
--- a/scripts/bash/setup-plan.sh
+++ b/scripts/bash/setup-plan.sh
@@ -40,15 +40,31 @@ fi
 # Ensure the feature directory exists
 mkdir -p "$FEATURE_DIR"

-# Copy plan template if it exists
-TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
-if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
-    cp "$TEMPLATE" "$IMPL_PLAN"
-    echo "Copied plan template to $IMPL_PLAN"
+# Copy plan template if plan doesn't already exist
+if [[ -f "$IMPL_PLAN" ]]; then
+    if $JSON_MODE; then
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy" >&2
+    else
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy"
+    fi
 else
-    echo "Warning: Plan template not found"
-    # Create a basic plan file if template doesn't exist
-    touch "$IMPL_PLAN"
+    TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
+    if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
+        cp "$TEMPLATE" "$IMPL_PLAN"
+        if $JSON_MODE; then
+            echo "Copied plan template to $IMPL_PLAN" >&2
+        else
+            echo "Copied plan template to $IMPL_PLAN"
+        fi
+    else
+        if $JSON_MODE; then
+            echo "Warning: Plan template not found" >&2
+        else
+            echo "Warning: Plan template not found"
+        fi
+        # Create a basic plan file if template doesn't exist
+        touch "$IMPL_PLAN"
+    fi
 fi

 # Output results
--- a/scripts/powershell/check-prerequisites.ps1
+++ b/scripts/powershell/check-prerequisites.ps1
@@ -56,14 +56,10 @@ EXAMPLES:
 # Source common functions
 . "$PSScriptRoot/common.ps1"

-# Get feature paths and validate branch
+# Get feature paths
 $paths = Get-FeaturePathsEnv

-if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GIT)) { 
-    exit 1 
-}
-
-# If paths-only mode, output paths and exit (support combined -Json -PathsOnly)
+# If paths-only mode, output paths and exit (no validation)
 if ($PathsOnly) {
    if ($Json) {
        [PSCustomObject]@{
@@ -85,6 +81,11 @@ if ($PathsOnly) {
    exit 0
 }

+# Validate branch name
+if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GIT)) {
+    exit 1
+}
+
 # Validate required directories and files
 if (-not (Test-Path $paths.FEATURE_DIR -PathType Container)) {
    Write-Output "ERROR: Feature directory not found: $($paths.FEATURE_DIR)"
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -336,10 +336,10 @@ function Get-FeaturePathsEnv {
 function Test-FileExists {
    param([string]$Path, [string]$Description)
    if (Test-Path -Path $Path -PathType Leaf) {
-        Write-Output "  ✓ $Description"
+        Write-Output "  [OK] $Description"
        return $true
    } else {
-        Write-Output "  ✗ $Description"
+        Write-Output "  [FAIL] $Description"
        return $false
    }
 }
@@ -347,10 +347,10 @@ function Test-FileExists {
 function Test-DirHasFiles {
    param([string]$Path, [string]$Description)
    if ((Test-Path -Path $Path -PathType Container) -and (Get-ChildItem -Path $Path -ErrorAction SilentlyContinue | Where-Object { -not $_.PSIsContainer } | Select-Object -First 1)) {
-        Write-Output "  ✓ $Description"
+        Write-Output "  [OK] $Description"
        return $true
    } else {
-        Write-Output "  ✗ $Description"
+        Write-Output "  [FAIL] $Description"
        return $false
    }
 }
@@ -591,7 +591,7 @@ except Exception:

    if ($layerPaths.Count -eq 0) { return $null }

-    # If the top (highest-priority) layer is replace, it wins entirely —
+    # If the top (highest-priority) layer is replace, it wins entirely --
    # lower layers are irrelevant regardless of their strategies.
    if ($layerStrategies[0] -eq 'replace') {
        return (Get-Content $layerPaths[0] -Raw)
--- a/scripts/powershell/create-new-feature.ps1
+++ b/scripts/powershell/create-new-feature.ps1
@@ -312,7 +312,7 @@ if (-not $DryRun) {
                if ($AllowExistingBranch) {
                    # If we're already on the branch, continue without another checkout.
                    if ($currentBranch -eq $branchName) {
-                        # Already on the target branch — nothing to do
+                        # Already on the target branch -- nothing to do
                    } else {
                        # Otherwise switch to the existing branch instead of failing.
                        $switchBranchError = git checkout -q $branchName 2>&1 | Out-String
--- a/scripts/powershell/setup-plan.ps1
+++ b/scripts/powershell/setup-plan.ps1
@@ -33,17 +33,25 @@ if (-not (Test-FeatureJsonMatchesFeatureDir -RepoRoot $paths.REPO_ROOT -ActiveFe
 # Ensure the feature directory exists
 New-Item -ItemType Directory -Path $paths.FEATURE_DIR -Force | Out-Null

-# Copy plan template if it exists, otherwise note it or create empty file
-$template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
-if ($template -and (Test-Path $template)) { 
-    # Read the template content and write it to the implementation plan file with UTF-8 encoding without BOM
-    $content = [System.IO.File]::ReadAllText($template)
-    $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
-    [System.IO.File]::WriteAllText($paths.IMPL_PLAN, $content, $utf8NoBom)
+# Copy plan template if plan doesn't already exist
+if (Test-Path $paths.IMPL_PLAN -PathType Leaf) {
+    if ($Json) {
+        [Console]::Error.WriteLine("Plan already exists at $($paths.IMPL_PLAN), skipping template copy")
+    } else {
+        Write-Output "Plan already exists at $($paths.IMPL_PLAN), skipping template copy"
+    }
 } else {
-    Write-Warning "Plan template not found"
-    # Create a basic plan file if template doesn't exist
-    New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
+    $template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
+    if ($template -and (Test-Path $template)) {
+        # Read the template content and write it to the implementation plan file with UTF-8 encoding without BOM
+        $content = [System.IO.File]::ReadAllText($template)
+        $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
+        [System.IO.File]::WriteAllText($paths.IMPL_PLAN, $content, $utf8NoBom)
+    } else {
+        Write-Warning "Plan template not found"
+        # Create a basic plan file if template doesn't exist
+        New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
+    }
 }

 # Output results
--- a/src/specify_cli/init.py
+++ b/src/specify_cli/init.py
@@ -29,9 +29,7 @@ Or install globally:
 import os
 import sys
 import zipfile
-import shutil
 import json
-import shlex
 import yaml
 from pathlib import Path

@@ -39,7 +37,6 @@ from typing import Any, Optional

 import typer
 from rich.panel import Panel
-from rich.live import Live
 from rich.align import Align
 from rich.table import Table
 from .integration_runtime import (
@@ -70,13 +67,13 @@ from ._console import (
    StepTracker,
    console,
    get_key as get_key,
-    select_with_arrows,
+    select_with_arrows as select_with_arrows,
    show_banner,
 )
 from ._assets import (
    _locate_bundled_extension,
    _locate_bundled_preset,
-    _locate_bundled_workflow,
+    _locate_bundled_workflow as _locate_bundled_workflow,
    _locate_core_pack,
    _repo_root,
    get_speckit_version as get_speckit_version,
@@ -98,84 +95,13 @@ from ._version import (
    self_check as self_check,
    self_upgrade as self_upgrade,
 )
-
-def _build_agent_config() -> dict[str, dict[str, Any]]:
-    """Derive AGENT_CONFIG from INTEGRATION_REGISTRY."""
-    from .integrations import INTEGRATION_REGISTRY
-    config: dict[str, dict[str, Any]] = {}
-    for key, integration in INTEGRATION_REGISTRY.items():
-        if integration.config:
-            config[key] = dict(integration.config)
-    return config
-
-AGENT_CONFIG = _build_agent_config()
-DEFAULT_INIT_INTEGRATION = "copilot"
-
-AI_ASSISTANT_ALIASES = {
-    "kiro": "kiro-cli",
-}
-
-# Agents that use TOML command format (others use Markdown)
-_TOML_AGENTS = frozenset({"gemini", "tabnine"})
-
-def _build_ai_assistant_help() -> str:
-    """Build the --ai help text from AGENT_CONFIG so it stays in sync with runtime config."""
-
-    non_generic_agents = sorted(agent for agent in AGENT_CONFIG if agent != "generic")
-    base_help = (
-        f"AI assistant to use: {', '.join(non_generic_agents)}, "
-        "or generic (requires --ai-commands-dir)."
-    )
-
-    if not AI_ASSISTANT_ALIASES:
-        return base_help
-
-    alias_phrases = []
-    for alias, target in sorted(AI_ASSISTANT_ALIASES.items()):
-        alias_phrases.append(f"'{alias}' as an alias for '{target}'")
-
-    if len(alias_phrases) == 1:
-        aliases_text = alias_phrases[0]
-    else:
-        aliases_text = ', '.join(alias_phrases[:-1]) + ' and ' + alias_phrases[-1]
-
-    return base_help + " Use " + aliases_text + "."
-AI_ASSISTANT_HELP = _build_ai_assistant_help()
-
-
-def _build_integration_equivalent(
-    integration_key: str,
-    ai_commands_dir: str | None = None,
-) -> str:
-    """Build the modern --integration equivalent for legacy --ai usage."""
-
-    parts = [f"--integration {integration_key}"]
-    if integration_key == "generic" and ai_commands_dir:
-        parts.append(
-            f'--integration-options="--commands-dir {shlex.quote(ai_commands_dir)}"'
-        )
-    return " ".join(parts)
-
-
-def _build_ai_deprecation_warning(
-    integration_key: str,
-    ai_commands_dir: str | None = None,
-) -> str:
-    """Build the legacy --ai deprecation warning message."""
-
-    replacement = _build_integration_equivalent(
-        integration_key,
-        ai_commands_dir=ai_commands_dir,
-    )
-    return (
-        "[bold]--ai[/bold] is deprecated and will no longer be available in version 0.10.0 or later.\n\n"
-        f"Use [bold]{replacement}[/bold] instead."
-    )
-
-def _stdin_is_interactive() -> bool:
-    return sys.stdin.isatty()
-
-SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
+from ._agent_config import (
+    AGENT_CONFIG as AGENT_CONFIG,
+    AI_ASSISTANT_ALIASES as AI_ASSISTANT_ALIASES,
+    AI_ASSISTANT_HELP as AI_ASSISTANT_HELP,
+    DEFAULT_INIT_INTEGRATION as DEFAULT_INIT_INTEGRATION,
+    SCRIPT_TYPE_CHOICES as SCRIPT_TYPE_CHOICES,
+)

 app = typer.Typer(
    name="specify",
@@ -349,42 +275,6 @@ def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None =
            for f in failures:
                console.print(f"  - {f}")

-def ensure_constitution_from_template(project_path: Path, tracker: StepTracker | None = None) -> None:
-    """Copy constitution template to memory if it doesn't exist (preserves existing constitution on reinitialization)."""
-    memory_constitution = project_path / ".specify" / "memory" / "constitution.md"
-    template_constitution = project_path / ".specify" / "templates" / "constitution-template.md"
-
-    # If constitution already exists in memory, preserve it
-    if memory_constitution.exists():
-        if tracker:
-            tracker.add("constitution", "Constitution setup")
-            tracker.skip("constitution", "existing file preserved")
-        return
-
-    # If template doesn't exist, something went wrong with extraction
-    if not template_constitution.exists():
-        if tracker:
-            tracker.add("constitution", "Constitution setup")
-            tracker.error("constitution", "template not found")
-        return
-
-    # Copy template to memory directory
-    try:
-        memory_constitution.parent.mkdir(parents=True, exist_ok=True)
-        shutil.copy2(template_constitution, memory_constitution)
-        if tracker:
-            tracker.add("constitution", "Constitution setup")
-            tracker.complete("constitution", "copied from template")
-        else:
-            console.print("[cyan]Initialized constitution from template[/cyan]")
-    except Exception as e:
-        if tracker:
-            tracker.add("constitution", "Constitution setup")
-            tracker.error("constitution", str(e))
-        else:
-            console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")
-
-
 INIT_OPTIONS_FILE = ".specify/init-options.json"


@@ -427,6 +317,57 @@ def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
    return project_path / ".agents" / "skills"


+def resolve_active_skills_dir(project_root: Path) -> Path | None:
+    """Return the active skills directory, creating it on demand when enabled.
+
+    Reads ``.specify/init-options.json`` to determine whether skills are
+    enabled and which agent was selected.  When ``ai_skills`` is true the
+    directory is created safely (symlink/containment checks); when false
+    only Kimi's native-skills fallback is honoured (directory must already
+    exist).
+
+    Returns:
+        The skills directory ``Path``, or ``None`` if skills are not active.
+
+    Raises:
+        ValueError: If the resolved skills path escapes the project root,
+            a parent component is a symlink, or a path component exists
+            but is not a directory.
+        OSError: If the directory cannot be created (e.g. permission denied).
+    """
+    from .shared_infra import _ensure_safe_shared_directory
+
+    opts = load_init_options(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 = _get_skills_dir(project_root, agent)
+
+    if not ai_skills_enabled:
+        # Kimi native-skills fallback: use the directory only if it exists.
+        if not skills_dir.is_dir():
+            return None
+        _ensure_safe_shared_directory(
+            project_root, skills_dir,
+            create=False, context="agent skills directory",
+        )
+        return skills_dir
+
+    # ai_skills is explicitly enabled — create the directory safely.
+    _ensure_safe_shared_directory(
+        project_root, skills_dir, context="agent skills directory",
+    )
+    return skills_dir
+
+
 def _cli_error_detail(exc: BaseException) -> str:
    """Return a compact one-line exception detail for CLI output."""
    detail = str(exc).replace("\n", " ").strip()
@@ -471,690 +412,11 @@ SKILL_DESCRIPTIONS = {
 }


-@app.command()
-def init(
-    project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
-    ai_assistant: str = typer.Option(None, "--ai", help=AI_ASSISTANT_HELP),
-    ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
-    script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
-    ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for coding agent tools like Claude Code"),
-    no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
-    here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
-    force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
-    skip_tls: bool = typer.Option(False, "--skip-tls", help="Deprecated (no-op). Previously: skip SSL/TLS verification.", hidden=True),
-    debug: bool = typer.Option(False, "--debug", help="Deprecated (no-op). Previously: show verbose diagnostic output.", hidden=True),
-    github_token: str = typer.Option(None, "--github-token", help="Deprecated (no-op). Previously: GitHub token for API requests.", hidden=True),
-    ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
-    offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
-    preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
-    branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, …, 1000, … — expands past 999 automatically) or 'timestamp' (YYYYMMDD-HHMMSS)"),
-    integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
-    integration_options: str = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
-):
-    """
-    Initialize a new Specify project.
+# ===== init command =====
+# Moved to commands/init.py — registered here to preserve CLI surface.
+from .commands import init as _init_cmd  # noqa: E402
+_init_cmd.register(app)

-    By default, project files are downloaded from the latest GitHub release.
-    Use --offline to scaffold from assets bundled inside the specify-cli
-    package instead (no internet access required, ideal for air-gapped or
-    enterprise environments).
-
-    NOTE: Starting with v0.6.0, bundled assets will be used by default and
-    the --offline flag will be removed. The GitHub download path will be
-    retired because bundled assets eliminate the need for network access,
-    avoid proxy/firewall issues, and guarantee that templates always match
-    the installed CLI version.
-
-    This command will:
-    1. Check that required tools are installed (git is optional)
-    2. Let you choose your coding agent integration, or default to Copilot
-       in non-interactive sessions
-    3. Download template from GitHub (or use bundled assets with --offline)
-    4. Initialize a fresh git repository (if not --no-git and no existing repo)
-    5. Optionally set up coding agent integration commands
-
-    Examples:
-        specify init my-project
-        specify init my-project --integration claude
-        specify init my-project --integration copilot --no-git
-        specify init --ignore-agent-tools my-project
-        specify init . --integration claude         # Initialize in current directory
-        specify init .                     # Initialize in current directory (interactive integration selection)
-        specify init --here --integration claude    # Alternative syntax for current directory
-        specify init --here --integration codex --integration-options="--skills"
-        specify init --here --integration codebuddy
-        specify init --here --integration vibe      # Initialize with Mistral Vibe support
-        specify init --here
-        specify init --here --force  # Skip confirmation when current directory not empty
-        specify init my-project --integration claude   # Claude installs skills by default
-        specify init --here --integration gemini
-        specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"  # Bring your own agent; requires --commands-dir
-        specify init my-project --integration claude --preset healthcare-compliance  # With preset
-    """
-
-    show_banner()
-    ai_deprecation_warning: str | None = None
-
-    # Detect when option values are likely misinterpreted flags (parameter ordering issue)
-    if ai_assistant and ai_assistant.startswith("--"):
-        console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
-        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
-        console.print("[yellow]Example:[/yellow] specify init --integration claude --here")
-        console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
-        raise typer.Exit(1)
-
-    if ai_commands_dir and ai_commands_dir.startswith("--"):
-        console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
-        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
-        console.print("[yellow]Example:[/yellow] specify init --integration generic --integration-options=\"--commands-dir .myagent/commands/\"")
-        raise typer.Exit(1)
-
-    if ai_assistant:
-        ai_assistant = AI_ASSISTANT_ALIASES.get(ai_assistant, ai_assistant)
-
-    # --integration and --ai are mutually exclusive
-    if integration and ai_assistant:
-        console.print("[red]Error:[/red] --integration and --ai are mutually exclusive")
-        raise typer.Exit(1)
-
-    # Resolve the integration — either from --integration or --ai
-    from .integrations import INTEGRATION_REGISTRY, get_integration
-    if integration:
-        resolved_integration = get_integration(integration)
-        if not resolved_integration:
-            console.print(f"[red]Error:[/red] Unknown integration: '{integration}'")
-            available = ", ".join(sorted(INTEGRATION_REGISTRY))
-            console.print(f"[yellow]Available integrations:[/yellow] {available}")
-            raise typer.Exit(1)
-        ai_assistant = integration
-    elif ai_assistant:
-        resolved_integration = get_integration(ai_assistant)
-        if not resolved_integration:
-            console.print(f"[red]Error:[/red] Unknown agent '{ai_assistant}'. Choose from: {', '.join(sorted(INTEGRATION_REGISTRY))}")
-            raise typer.Exit(1)
-        ai_deprecation_warning = _build_ai_deprecation_warning(
-            resolved_integration.key,
-            ai_commands_dir=ai_commands_dir,
-        )
-
-    # Deprecation warnings for --ai-skills and --ai-commands-dir (only when
-    # an integration has been resolved from --ai or --integration)
-    if ai_assistant or integration:
-        if ai_skills:
-            from .integrations.base import SkillsIntegration as _SkillsCheck
-            if isinstance(resolved_integration, _SkillsCheck):
-                console.print(
-                    "[dim]Note: --ai-skills is not needed; "
-                    "skills are the default for this integration.[/dim]"
-                )
-            else:
-                console.print(
-                    "[dim]Note: --ai-skills has no effect with "
-                    f"{resolved_integration.key}; this integration uses commands, not skills.[/dim]"
-                )
-        if ai_commands_dir and resolved_integration.key != "generic":
-            console.print(
-                "[dim]Note: --ai-commands-dir is deprecated; "
-                'use [bold]--integration generic --integration-options="--commands-dir <dir>"[/bold] instead.[/dim]'
-            )
-
-    if no_git:
-        console.print(
-            "[yellow]⚠️  --no-git is deprecated and will be removed in v0.10.0.[/yellow]\n"
-            "[yellow]The git extension will no longer be enabled by default "
-            "— use the [bold]specify extension[/bold] commands to install or enable the git extension if needed.[/yellow]"
-        )
-
-    if project_name == ".":
-        here = True
-        project_name = None  # Clear project_name to use existing validation logic
-
-    if here and project_name:
-        console.print("[red]Error:[/red] Cannot specify both project name and --here flag")
-        raise typer.Exit(1)
-
-    if not here and not project_name:
-        console.print("[red]Error:[/red] Must specify either a project name, use '.' for current directory, or use --here flag")
-        raise typer.Exit(1)
-
-    if ai_skills and not ai_assistant:
-        console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
-        console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
-        raise typer.Exit(1)
-
-    BRANCH_NUMBERING_CHOICES = {"sequential", "timestamp"}
-    if branch_numbering and branch_numbering not in BRANCH_NUMBERING_CHOICES:
-        console.print(f"[red]Error:[/red] Invalid --branch-numbering value '{branch_numbering}'. Choose from: {', '.join(sorted(BRANCH_NUMBERING_CHOICES))}")
-        raise typer.Exit(1)
-
-    dir_existed_before = False
-    if here:
-        project_name = Path.cwd().name
-        project_path = Path.cwd()
-        dir_existed_before = True
-
-        existing_items = list(project_path.iterdir())
-        if existing_items:
-            console.print(f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)")
-            console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
-            if force:
-                console.print("[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]")
-            else:
-                response = typer.confirm("Do you want to continue?")
-                if not response:
-                    console.print("[yellow]Operation cancelled[/yellow]")
-                    raise typer.Exit(0)
-    else:
-        project_path = Path(project_name).resolve()
-        dir_existed_before = project_path.exists()
-        if project_path.exists():
-            if not project_path.is_dir():
-                console.print(f"[red]Error:[/red] '{project_name}' exists but is not a directory.")
-                raise typer.Exit(1)
-            existing_items = list(project_path.iterdir())
-            if force:
-                if existing_items:
-                    console.print(f"[yellow]Warning:[/yellow] Directory '{project_name}' is not empty ({len(existing_items)} items)")
-                    console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
-                console.print(f"[cyan]--force supplied: merging into existing directory '[cyan]{project_name}[/cyan]'[/cyan]")
-            else:
-                error_panel = Panel(
-                    f"Directory already exists: '[cyan]{project_name}[/cyan]'\n"
-                    "Please choose a different project name or remove the existing directory.\n"
-                    "Use [bold]--force[/bold] to merge into the existing directory.",
-                    title="[red]Directory Conflict[/red]",
-                    border_style="red",
-                    padding=(1, 2)
-                )
-                console.print()
-                console.print(error_panel)
-                raise typer.Exit(1)
-
-    if ai_assistant:
-        if ai_assistant not in AGENT_CONFIG:
-            console.print(f"[red]Error:[/red] Invalid AI assistant '{ai_assistant}'. Choose from: {', '.join(AGENT_CONFIG.keys())}")
-            raise typer.Exit(1)
-        selected_ai = ai_assistant
-    elif not _stdin_is_interactive():
-        console.print(
-            f"[dim]Non-interactive session detected: defaulting to '{DEFAULT_INIT_INTEGRATION}'. "
-            "Use --integration to choose a different agent.[/dim]"
-        )
-        selected_ai = DEFAULT_INIT_INTEGRATION
-    else:
-        # Create options dict for selection (agent_key: display_name)
-        ai_choices = {key: config["name"] for key, config in AGENT_CONFIG.items()}
-        selected_ai = select_with_arrows(
-            ai_choices,
-            "Choose your coding agent integration:",
-            DEFAULT_INIT_INTEGRATION,
-        )
-
-    # Auto-promote interactively selected agents to the integration path
-    if not ai_assistant:
-        resolved_integration = get_integration(selected_ai)
-        if not resolved_integration:
-            console.print(f"[red]Error:[/red] Unknown agent '{selected_ai}'")
-            raise typer.Exit(1)
-
-    # Validate --ai-commands-dir usage.
-    # Skip validation when --integration-options is provided — the integration
-    # will validate its own options in setup().
-    if selected_ai == "generic" and not integration_options:
-        if not ai_commands_dir:
-            console.print("[red]Error:[/red] --ai-commands-dir is required when using --ai generic or --integration generic")
-            console.print('[dim]Example: specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"[/dim]')
-            raise typer.Exit(1)
-
-    current_dir = Path.cwd()
-
-    setup_lines = [
-        "[cyan]Specify Project Setup[/cyan]",
-        "",
-        f"{'Project':<15} [green]{project_path.name}[/green]",
-        f"{'Working Path':<15} [dim]{current_dir}[/dim]",
-    ]
-
-    if not here:
-        setup_lines.append(f"{'Target Path':<15} [dim]{project_path}[/dim]")
-
-    console.print(Panel("\n".join(setup_lines), border_style="cyan", padding=(1, 2)))
-
-    should_init_git = False
-    if not no_git:
-        should_init_git = check_tool("git")
-        if not should_init_git:
-            console.print("[yellow]Git not found - will skip repository initialization[/yellow]")
-
-    if not ignore_agent_tools:
-        agent_config = AGENT_CONFIG.get(selected_ai)
-        if agent_config and agent_config["requires_cli"]:
-            install_url = agent_config["install_url"]
-            if not check_tool(selected_ai):
-                error_panel = Panel(
-                    f"[cyan]{selected_ai}[/cyan] not found\n"
-                    f"Install from: [cyan]{install_url}[/cyan]\n"
-                    f"{agent_config['name']} is required to continue with this project type.\n\n"
-                    "Tip: Use [cyan]--ignore-agent-tools[/cyan] to skip this check",
-                    title="[red]Agent Detection Error[/red]",
-                    border_style="red",
-                    padding=(1, 2)
-                )
-                console.print()
-                console.print(error_panel)
-                raise typer.Exit(1)
-
-    if script_type:
-        if script_type not in SCRIPT_TYPE_CHOICES:
-            console.print(f"[red]Error:[/red] Invalid script type '{script_type}'. Choose from: {', '.join(SCRIPT_TYPE_CHOICES.keys())}")
-            raise typer.Exit(1)
-        selected_script = script_type
-    else:
-        default_script = "ps" if os.name == "nt" else "sh"
-
-        if _stdin_is_interactive():
-            selected_script = select_with_arrows(SCRIPT_TYPE_CHOICES, "Choose script type (or press Enter)", default_script)
-        else:
-            selected_script = default_script
-
-    console.print(f"[cyan]Selected coding agent integration:[/cyan] {selected_ai}")
-    console.print(f"[cyan]Selected script type:[/cyan] {selected_script}")
-
-    tracker = StepTracker("Initialize Specify Project")
-
-    sys._specify_tracker_active = True
-
-    tracker.add("precheck", "Check required tools")
-    tracker.complete("precheck", "ok")
-    tracker.add("ai-select", "Select coding agent integration")
-    tracker.complete("ai-select", f"{selected_ai}")
-    tracker.add("script-select", "Select script type")
-    tracker.complete("script-select", selected_script)
-
-    tracker.add("integration", "Install integration")
-    tracker.add("shared-infra", "Install shared infrastructure")
-
-    for key, label in [
-        ("chmod", "Ensure scripts executable"),
-        ("constitution", "Constitution setup"),
-        ("git", "Install git extension"),
-        ("workflow", "Install bundled workflow"),
-        ("final", "Finalize"),
-    ]:
-        tracker.add(key, label)
-
-    git_default_notice = False
-
-    with Live(tracker.render(), console=console, refresh_per_second=8, transient=True) as live:
-        tracker.attach_refresh(lambda: live.update(tracker.render()))
-        try:
-            # Integration-based scaffolding
-            from .integrations.manifest import IntegrationManifest
-            tracker.start("integration")
-            manifest = IntegrationManifest(
-                resolved_integration.key, project_path, version=get_speckit_version()
-            )
-
-            # Forward all legacy CLI flags to the integration as parsed_options.
-            # Integrations receive every option and decide what to use;
-            # irrelevant keys are simply ignored by the integration's setup().
-            integration_parsed_options: dict[str, Any] = {}
-            if ai_commands_dir:
-                integration_parsed_options["commands_dir"] = ai_commands_dir
-            if ai_skills:
-                integration_parsed_options["skills"] = True
-            # Parse --integration-options and merge into parsed_options so
-            # flags like --skills reach the integration's setup().
-            if integration_options:
-                extra = _parse_integration_options(resolved_integration, integration_options)
-                if extra:
-                    integration_parsed_options.update(extra)
-
-            resolved_integration.setup(
-                project_path, manifest,
-                parsed_options=integration_parsed_options or None,
-                script_type=selected_script,
-                raw_options=integration_options,
-            )
-            manifest.save()
-
-            integration_settings = _with_integration_setting(
-                {},
-                resolved_integration.key,
-                resolved_integration,
-                script_type=selected_script,
-                raw_options=integration_options,
-                parsed_options=integration_parsed_options or None,
-            )
-            _write_integration_json(
-                project_path,
-                resolved_integration.key,
-                [resolved_integration.key],
-                integration_settings,
-            )
-
-            tracker.complete("integration", resolved_integration.config.get("name", resolved_integration.key))
-
-            # Install shared infrastructure (scripts, templates)
-            tracker.start("shared-infra")
-            _install_shared_infra_or_exit(
-                project_path,
-                selected_script,
-                tracker=tracker,
-                force=force,
-                invoke_separator=resolved_integration.effective_invoke_separator(integration_parsed_options),
-            )
-            tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
-
-            ensure_constitution_from_template(project_path, tracker=tracker)
-
-            if not no_git:
-                tracker.start("git")
-                git_messages = []
-                git_has_error = False
-                # Step 1: Initialize git repo if needed
-                if is_git_repo(project_path):
-                    git_messages.append("existing repo detected")
-                elif should_init_git:
-                    success, error_msg = init_git_repo(project_path, quiet=True)
-                    if success:
-                        git_messages.append("initialized")
-                    else:
-                        git_has_error = True
-                        # Sanitize multi-line error_msg to single line for tracker
-                        if error_msg:
-                            sanitized = error_msg.replace('\n', ' ').strip()
-                            git_messages.append(f"init failed: {sanitized[:120]}")
-                        else:
-                            git_messages.append("init failed")
-                else:
-                    git_messages.append("git not available")
-                # Step 2: Install bundled git extension
-                try:
-                    from .extensions import ExtensionManager
-                    bundled_path = _locate_bundled_extension("git")
-                    if bundled_path:
-                        manager = ExtensionManager(project_path)
-                        if manager.registry.is_installed("git"):
-                            git_messages.append("extension already installed")
-                        else:
-                            manager.install_from_directory(
-                                bundled_path, get_speckit_version()
-                            )
-                            git_default_notice = True
-                            git_messages.append("extension installed")
-                    else:
-                        git_has_error = True
-                        git_messages.append("bundled extension not found")
-                except Exception as ext_err:
-                    git_has_error = True
-                    git_messages.append(
-                        f"extension install failed during optional git setup: {_cli_error_detail(ext_err)[:120]}"
-                    )
-                summary = "; ".join(git_messages)
-                if git_has_error:
-                    tracker.error("git", summary)
-                else:
-                    tracker.complete("git", summary)
-            else:
-                tracker.skip("git", "--no-git flag")
-
-            # Install bundled speckit workflow
-            try:
-                bundled_wf = _locate_bundled_workflow("speckit")
-                if bundled_wf:
-                    from .workflows.catalog import WorkflowRegistry
-                    from .workflows.engine import WorkflowDefinition
-                    wf_registry = WorkflowRegistry(project_path)
-                    if wf_registry.is_installed("speckit"):
-                        tracker.complete("workflow", "already installed")
-                    else:
-                        import shutil as _shutil
-                        dest_wf = project_path / ".specify" / "workflows" / "speckit"
-                        dest_wf.mkdir(parents=True, exist_ok=True)
-                        _shutil.copy2(
-                            bundled_wf / "workflow.yml",
-                            dest_wf / "workflow.yml",
-                        )
-                        definition = WorkflowDefinition.from_yaml(dest_wf / "workflow.yml")
-                        wf_registry.add("speckit", {
-                            "name": definition.name,
-                            "version": definition.version,
-                            "description": definition.description,
-                            "source": "bundled",
-                        })
-                        tracker.complete("workflow", "speckit installed")
-                else:
-                    tracker.skip("workflow", "bundled workflow not found")
-            except Exception as wf_err:
-                tracker.error(
-                    "workflow",
-                    f"install bundled workflow 'speckit' failed: {_cli_error_detail(wf_err)[:120]}",
-                )
-
-            # Fix permissions after all installs (scripts + extensions)
-            ensure_executable_scripts(project_path, tracker=tracker)
-
-            # Persist the CLI options so later operations (e.g. preset add)
-            # can adapt their behaviour without re-scanning the filesystem.
-            # Must be saved BEFORE preset install so _get_skills_dir() works.
-            init_opts = {
-                "ai": selected_ai,
-                "integration": resolved_integration.key,
-                "branch_numbering": branch_numbering or "sequential",
-                "context_file": resolved_integration.context_file,
-                "here": here,
-                "script": selected_script,
-                "speckit_version": get_speckit_version(),
-            }
-            # Ensure ai_skills is set for SkillsIntegration so downstream
-            # tools (extensions, presets) emit SKILL.md overrides correctly.
-            # Also set for integrations running in skills mode (e.g. Copilot
-            # with --skills).
-            from .integrations.base import SkillsIntegration as _SkillsPersist
-            if isinstance(resolved_integration, _SkillsPersist) or getattr(resolved_integration, "_skills_mode", False):
-                init_opts["ai_skills"] = True
-            save_init_options(project_path, init_opts)
-
-            # Install preset if specified
-            if preset:
-                try:
-                    from .presets import PresetManager, PresetCatalog, PresetError
-                    preset_manager = PresetManager(project_path)
-                    speckit_ver = get_speckit_version()
-
-                    # Try local directory first, then bundled, then catalog
-                    local_path = Path(preset).resolve()
-                    if local_path.is_dir() and (local_path / "preset.yml").exists():
-                        preset_manager.install_from_directory(local_path, speckit_ver)
-                    else:
-                        bundled_path = _locate_bundled_preset(preset)
-                        if bundled_path:
-                            preset_manager.install_from_directory(bundled_path, speckit_ver)
-                        else:
-                            preset_catalog = PresetCatalog(project_path)
-                            pack_info = preset_catalog.get_pack_info(preset)
-                            if not pack_info:
-                                console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
-                            elif pack_info.get("bundled") and not pack_info.get("download_url"):
-                                from .extensions import REINSTALL_COMMAND
-                                console.print(
-                                    f"[yellow]Warning:[/yellow] Preset '{preset}' is bundled with spec-kit "
-                                    f"but could not be found in the installed package."
-                                )
-                                console.print(
-                                    "This usually means the spec-kit installation is incomplete or corrupted."
-                                )
-                                console.print(f"Try reinstalling: {REINSTALL_COMMAND}")
-                            else:
-                                zip_path = None
-                                try:
-                                    zip_path = preset_catalog.download_pack(preset)
-                                    preset_manager.install_from_zip(zip_path, speckit_ver)
-                                except PresetError as preset_err:
-                                    _print_cli_warning(
-                                        "install",
-                                        "preset",
-                                        preset,
-                                        preset_err,
-                                        continuing="Continuing without the optional preset.",
-                                    )
-                                finally:
-                                    if zip_path is not None:
-                                        # Clean up downloaded ZIP to avoid cache accumulation
-                                        try:
-                                            zip_path.unlink(missing_ok=True)
-                                        except OSError:
-                                            # Best-effort cleanup; failure to delete is non-fatal
-                                            pass
-                except Exception as preset_err:
-                    # Optional preset install must not abort project initialization.
-                    _print_cli_warning(
-                        "install",
-                        "preset",
-                        preset,
-                        preset_err,
-                        continuing="Continuing without the optional preset.",
-                    )
-
-            tracker.complete("final", "project ready")
-        except (typer.Exit, SystemExit):
-            raise
-        except Exception as e:
-            tracker.error("final", str(e))
-            console.print(Panel(f"Initialization failed: {e}", title="Failure", border_style="red"))
-            if debug:
-                _env_pairs = [
-                    ("Python", sys.version.split()[0]),
-                    ("Platform", sys.platform),
-                    ("CWD", str(Path.cwd())),
-                ]
-                _label_width = max(len(k) for k, _ in _env_pairs)
-                env_lines = [f"{k.ljust(_label_width)} → [bright_black]{v}[/bright_black]" for k, v in _env_pairs]
-                console.print(Panel("\n".join(env_lines), title="Debug Environment", border_style="magenta"))
-            if not here and project_path.exists() and not dir_existed_before:
-                shutil.rmtree(project_path)
-            raise typer.Exit(1)
-        finally:
-            pass
-
-    console.print(tracker.render())
-    console.print("\n[bold green]Project ready.[/bold green]")
-
-    # Agent folder security notice
-    agent_config = AGENT_CONFIG.get(selected_ai)
-    if agent_config:
-        agent_folder = ai_commands_dir if selected_ai == "generic" else agent_config["folder"]
-        if agent_folder:
-            security_notice = Panel(
-                f"Some agents may store credentials, auth tokens, or other identifying and private artifacts in the agent folder within your project.\n"
-                f"Consider adding [cyan]{agent_folder}[/cyan] (or parts of it) to [cyan].gitignore[/cyan] to prevent accidental credential leakage.",
-                title="[yellow]Agent Folder Security[/yellow]",
-                border_style="yellow",
-                padding=(1, 2)
-            )
-            console.print()
-            console.print(security_notice)
-
-    if ai_deprecation_warning:
-        deprecation_notice = Panel(
-            ai_deprecation_warning,
-            title="[bold red]Deprecation Warning[/bold red]",
-            border_style="red",
-            padding=(1, 2),
-        )
-        console.print()
-        console.print(deprecation_notice)
-
-    if git_default_notice:
-        default_change_notice = Panel(
-            "The git extension is currently enabled by default during [bold]specify init[/bold].\n"
-            "Starting in [bold]v0.10.0[/bold], this will require explicit opt-in.\n"
-            "Use [bold]specify extension add git[/bold] after init when needed.",
-            title="[yellow]Notice: Git Default Changing[/yellow]",
-            border_style="yellow",
-            padding=(1, 2),
-        )
-        console.print()
-        console.print(default_change_notice)
-
-    steps_lines = []
-    if not here:
-        steps_lines.append(f"1. Go to the project folder: [cyan]cd {project_name}[/cyan]")
-        step_num = 2
-    else:
-        steps_lines.append("1. You're already in the project directory!")
-        step_num = 2
-
-    # Determine skill display mode for the next-steps panel.
-    # Skills integrations (codex, claude, kimi, agy, trae, cursor-agent, copilot, devin) should show skill invocation syntax.
-    from .integrations.base import SkillsIntegration as _SkillsInt
-    _is_skills_integration = isinstance(resolved_integration, _SkillsInt) or getattr(resolved_integration, "_skills_mode", False)
-
-    codex_skill_mode = selected_ai == "codex" and (ai_skills or _is_skills_integration)
-    claude_skill_mode = selected_ai == "claude" and (ai_skills or _is_skills_integration)
-    kimi_skill_mode = selected_ai == "kimi"
-    agy_skill_mode = selected_ai == "agy" and _is_skills_integration
-    trae_skill_mode = selected_ai == "trae"
-    cursor_agent_skill_mode = selected_ai == "cursor-agent" and (ai_skills or _is_skills_integration)
-    copilot_skill_mode = selected_ai == "copilot" and _is_skills_integration
-    devin_skill_mode = selected_ai == "devin"
-    native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode or trae_skill_mode or cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode
-
-    if codex_skill_mode and not ai_skills:
-        # Integration path installed skills; show the helpful notice
-        steps_lines.append(f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]")
-        step_num += 1
-    if claude_skill_mode and not ai_skills:
-        steps_lines.append(f"{step_num}. Start Claude in this project directory; spec-kit skills were installed to [cyan].claude/skills[/cyan]")
-        step_num += 1
-    if cursor_agent_skill_mode and not ai_skills:
-        steps_lines.append(f"{step_num}. Start Cursor Agent in this project directory; spec-kit skills were installed to [cyan].cursor/skills[/cyan]")
-        step_num += 1
-    if devin_skill_mode:
-        steps_lines.append(f"{step_num}. Start Devin in this project directory; spec-kit skills were installed to [cyan].devin/skills[/cyan]")
-        step_num += 1
-    usage_label = "skills" if native_skill_mode else "slash commands"
-
-    def _display_cmd(name: str) -> str:
-        if codex_skill_mode or agy_skill_mode or trae_skill_mode:
-            return f"$speckit-{name}"
-        if claude_skill_mode:
-            return f"/speckit-{name}"
-        if kimi_skill_mode:
-            return f"/skill:speckit-{name}"
-        if cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode:
-            return f"/speckit-{name}"
-        return f"/speckit.{name}"
-
-    steps_lines.append(f"{step_num}. Start using {usage_label} with your coding agent:")
-
-    steps_lines.append(f"   {step_num}.1 [cyan]{_display_cmd('constitution')}[/] - Establish project principles")
-    steps_lines.append(f"   {step_num}.2 [cyan]{_display_cmd('specify')}[/] - Create baseline specification")
-    steps_lines.append(f"   {step_num}.3 [cyan]{_display_cmd('plan')}[/] - Create implementation plan")
-    steps_lines.append(f"   {step_num}.4 [cyan]{_display_cmd('tasks')}[/] - Generate actionable tasks")
-    steps_lines.append(f"   {step_num}.5 [cyan]{_display_cmd('implement')}[/] - Execute implementation")
-
-    steps_panel = Panel("\n".join(steps_lines), title="Next Steps", border_style="cyan", padding=(1,2))
-    console.print()
-    console.print(steps_panel)
-
-    enhancement_intro = (
-        "Optional skills that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
-        if native_skill_mode
-        else "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
-    )
-    enhancement_lines = [
-        enhancement_intro,
-        "",
-        f"○ [cyan]{_display_cmd('clarify')}[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]{_display_cmd('plan')}[/] if used)",
-        f"○ [cyan]{_display_cmd('analyze')}[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]{_display_cmd('tasks')}[/], before [cyan]{_display_cmd('implement')}[/])",
-        f"○ [cyan]{_display_cmd('checklist')}[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]{_display_cmd('plan')}[/])"
-    ]
-    enhancements_title = "Enhancement Skills" if native_skill_mode else "Enhancement Commands"
-    enhancements_panel = Panel("\n".join(enhancement_lines), title=enhancements_title, border_style="cyan", padding=(1,2))
-    console.print()
-    console.print(enhancements_panel)

@app.command()
 def check():
@@ -1377,6 +639,15 @@ def _write_integration_json(
    )


+def _refresh_init_options_speckit_version(project_root: Path) -> None:
+    """Refresh only the Spec Kit version recorded in init-options.json."""
+    opts = load_init_options(project_root)
+    if not isinstance(opts, dict) or not opts:
+        return
+    opts["speckit_version"] = get_speckit_version()
+    save_init_options(project_root, opts)
+
+
 def _clear_init_options_for_integration(project_root: Path, integration_key: str) -> None:
    """Clear active integration keys from init-options.json when they match."""
    opts = load_init_options(project_root)
@@ -1737,6 +1008,8 @@ def integration_install(
        _write_integration_json(project_root, new_default, new_installed, settings)
        if new_default == integration.key:
            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)

    except Exception as exc:
        # Attempt rollback of any files written by setup
@@ -1829,6 +1102,7 @@ def _update_init_options_for_integration(
    opts["integration"] = integration.key
    opts["ai"] = integration.key
    opts["context_file"] = integration.context_file
+    opts["speckit_version"] = get_speckit_version()
    if script_type:
        opts["script"] = script_type
    if isinstance(integration, SkillsIntegration) or getattr(integration, "_skills_mode", False):
@@ -2408,6 +1682,8 @@ def integration_upgrade(
        _write_integration_json(project_root, installed_key, installed_keys, settings)
        if installed_key == key:
            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)
    except Exception as exc:
        # Don't teardown — setup overwrites in-place, so teardown would
        # delete files that were working before the upgrade.  Just report.
--- a/src/specify_cli/_agent_config.py
+++ b/src/specify_cli/_agent_config.py
@@ -0,0 +1,45 @@
+"""Agent configuration constants derived from the integration registry."""
+from __future__ import annotations
+
+from typing import Any
+
+
+def _build_agent_config() -> dict[str, dict[str, Any]]:
+    from .integrations import INTEGRATION_REGISTRY
+    config: dict[str, dict[str, Any]] = {}
+    for key, integration in INTEGRATION_REGISTRY.items():
+        if integration.config:
+            config[key] = dict(integration.config)
+    return config
+
+
+AGENT_CONFIG: dict[str, dict[str, Any]] = _build_agent_config()
+
+DEFAULT_INIT_INTEGRATION = "copilot"
+
+AI_ASSISTANT_ALIASES: dict[str, str] = {
+    "kiro": "kiro-cli",
+}
+
+
+def _build_ai_assistant_help() -> str:
+    non_generic_agents = sorted(agent for agent in AGENT_CONFIG if agent != "generic")
+    base_help = (
+        f"AI assistant to use: {', '.join(non_generic_agents)}, "
+        "or generic (requires --ai-commands-dir)."
+    )
+    if not AI_ASSISTANT_ALIASES:
+        return base_help
+    alias_phrases = []
+    for alias, target in sorted(AI_ASSISTANT_ALIASES.items()):
+        alias_phrases.append(f"'{alias}' as an alias for '{target}'")
+    if len(alias_phrases) == 1:
+        aliases_text = alias_phrases[0]
+    else:
+        aliases_text = ", ".join(alias_phrases[:-1]) + " and " + alias_phrases[-1]
+    return base_help + " Use " + aliases_text + "."
+
+
+AI_ASSISTANT_HELP: str = _build_ai_assistant_help()
+
+SCRIPT_TYPE_CHOICES: dict[str, str] = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
--- a/src/specify_cli/commands/init.py
+++ b/src/specify_cli/commands/init.py
@@ -0,0 +1,7 @@
+"""CLI command groups extracted from the main application.
+
+Implemented command modules expose a ``register(app)`` function. Placeholder
+modules are import-only anchors for command groups that still live in the main
+application module.
+"""
+from __future__ import annotations
--- a/src/specify_cli/commands/extension.py
+++ b/src/specify_cli/commands/extension.py
@@ -0,0 +1,2 @@
+"""specify extension * commands — placeholder for future extraction."""
+from __future__ import annotations
--- a/src/specify_cli/commands/init.py
+++ b/src/specify_cli/commands/init.py
@@ -0,0 +1,743 @@
+"""specify init command."""
+from __future__ import annotations
+
+import os
+import shlex
+import shutil
+import sys
+from pathlib import Path
+from typing import Any
+
+import typer
+from rich.live import Live
+from rich.panel import Panel
+
+from .._agent_config import (
+    AGENT_CONFIG,
+    AI_ASSISTANT_ALIASES,
+    AI_ASSISTANT_HELP,
+    DEFAULT_INIT_INTEGRATION,
+    SCRIPT_TYPE_CHOICES,
+)
+from .._assets import (
+    _locate_bundled_extension,
+    _locate_bundled_preset,
+    _locate_bundled_workflow,
+    get_speckit_version,
+)
+from .._console import StepTracker, console, select_with_arrows, show_banner
+from .._utils import check_tool, init_git_repo, is_git_repo
+
+def _build_integration_equivalent(
+    integration_key: str,
+    ai_commands_dir: str | None = None,
+) -> str:
+    parts = [f"--integration {integration_key}"]
+    if integration_key == "generic" and ai_commands_dir:
+        parts.append(
+            f'--integration-options="--commands-dir {shlex.quote(ai_commands_dir)}"'
+        )
+    return " ".join(parts)
+
+
+def _build_ai_deprecation_warning(
+    integration_key: str,
+    ai_commands_dir: str | None = None,
+) -> str:
+    replacement = _build_integration_equivalent(
+        integration_key,
+        ai_commands_dir=ai_commands_dir,
+    )
+    return (
+        "[bold]--ai[/bold] is deprecated and will no longer be available in version 0.10.0 or later.\n\n"
+        f"Use [bold]{replacement}[/bold] instead."
+    )
+
+
+def _stdin_is_interactive() -> bool:
+    return sys.stdin.isatty()
+
+
+def ensure_constitution_from_template(
+    project_path: Path, tracker: StepTracker | None = None
+) -> None:
+    """Copy constitution template to memory if it doesn't exist."""
+    memory_constitution = project_path / ".specify" / "memory" / "constitution.md"
+    template_constitution = project_path / ".specify" / "templates" / "constitution-template.md"
+
+    if memory_constitution.exists():
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.skip("constitution", "existing file preserved")
+        return
+
+    if not template_constitution.exists():
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.error("constitution", "template not found")
+        return
+
+    try:
+        memory_constitution.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copy2(template_constitution, memory_constitution)
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.complete("constitution", "copied from template")
+        else:
+            console.print("[cyan]Initialized constitution from template[/cyan]")
+    except Exception as e:
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.error("constitution", str(e))
+        else:
+            console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")
+
+
+def register(app: typer.Typer) -> None:
+    @app.command()
+    def init(
+        project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
+        ai_assistant: str = typer.Option(None, "--ai", help=AI_ASSISTANT_HELP),
+        ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
+        script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
+        ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for coding agent tools like Claude Code"),
+        no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
+        here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
+        force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
+        skip_tls: bool = typer.Option(False, "--skip-tls", help="Deprecated (no-op). Previously: skip SSL/TLS verification.", hidden=True),
+        debug: bool = typer.Option(False, "--debug", help="Deprecated. Previously: show verbose diagnostic output; currently only prints additional diagnostic details on failure.", hidden=True),
+        github_token: str = typer.Option(None, "--github-token", help="Deprecated (no-op). Previously: GitHub token for API requests.", hidden=True),
+        ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
+        offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
+        preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
+        branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, …, 1000, … — expands past 999 automatically) or 'timestamp' (YYYYMMDD-HHMMSS)"),
+        integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
+        integration_options: str = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
+    ):
+        """
+        Initialize a new Specify project.
+
+        Project files are scaffolded from assets bundled inside the specify-cli
+        package, so initialization does not need network access and templates
+        match the installed CLI version.
+
+        This command will:
+        1. Check that required tools are installed (git is optional)
+        2. Let you choose your coding agent integration, or default to Copilot
+           in non-interactive sessions
+        3. Install bundled Spec Kit templates, scripts, workflow, and shared
+           project infrastructure
+        4. Initialize a fresh git repository (if not --no-git and no existing repo)
+        5. Set up coding agent integration commands and optional presets
+
+        Examples:
+            specify init my-project
+            specify init my-project --integration claude
+            specify init my-project --integration copilot --no-git
+            specify init --ignore-agent-tools my-project
+            specify init . --integration claude         # Initialize in current directory
+            specify init .                     # Initialize in current directory (interactive integration selection)
+            specify init --here --integration claude    # Alternative syntax for current directory
+            specify init --here --integration codex --integration-options="--skills"
+            specify init --here --integration codebuddy
+            specify init --here --integration vibe      # Initialize with Mistral Vibe support
+            specify init --here
+            specify init --here --force  # Skip confirmation when current directory not empty
+            specify init my-project --integration claude   # Claude installs skills by default
+            specify init --here --integration gemini
+            specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"  # Bring your own agent; requires --commands-dir
+            specify init my-project --integration claude --preset healthcare-compliance  # With preset
+        """
+        # Lazy imports to avoid circular dependency — __init__.py imports this module
+        from .. import (
+            _install_shared_infra_or_exit,
+            _parse_integration_options,
+            _print_cli_warning,
+            _write_integration_json,
+            ensure_executable_scripts,
+            save_init_options,
+        )
+        from ..integration_runtime import with_integration_setting as _with_integration_setting
+
+        show_banner()
+        ai_deprecation_warning: str | None = None
+
+        if ai_assistant and ai_assistant.startswith("--"):
+            console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
+            console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
+            console.print("[yellow]Example:[/yellow] specify init --integration claude --here")
+            console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
+            raise typer.Exit(1)
+
+        if ai_commands_dir and ai_commands_dir.startswith("--"):
+            console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
+            console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
+            console.print("[yellow]Example:[/yellow] specify init --integration generic --integration-options=\"--commands-dir .myagent/commands/\"")
+            raise typer.Exit(1)
+
+        if ai_assistant:
+            ai_assistant = AI_ASSISTANT_ALIASES.get(ai_assistant, ai_assistant)
+
+        if integration and ai_assistant:
+            console.print("[red]Error:[/red] --integration and --ai are mutually exclusive")
+            raise typer.Exit(1)
+
+        from ..integrations import INTEGRATION_REGISTRY, get_integration
+        if integration:
+            resolved_integration = get_integration(integration)
+            if not resolved_integration:
+                console.print(f"[red]Error:[/red] Unknown integration: '{integration}'")
+                available = ", ".join(sorted(INTEGRATION_REGISTRY))
+                console.print(f"[yellow]Available integrations:[/yellow] {available}")
+                raise typer.Exit(1)
+            ai_assistant = integration
+        elif ai_assistant:
+            resolved_integration = get_integration(ai_assistant)
+            if not resolved_integration:
+                console.print(f"[red]Error:[/red] Unknown agent '{ai_assistant}'. Choose from: {', '.join(sorted(INTEGRATION_REGISTRY))}")
+                raise typer.Exit(1)
+            ai_deprecation_warning = _build_ai_deprecation_warning(
+                resolved_integration.key,
+                ai_commands_dir=ai_commands_dir,
+            )
+
+        if ai_assistant or integration:
+            if ai_skills:
+                from ..integrations.base import SkillsIntegration as _SkillsCheck
+                if isinstance(resolved_integration, _SkillsCheck):
+                    console.print(
+                        "[dim]Note: --ai-skills is not needed; "
+                        "skills are the default for this integration.[/dim]"
+                    )
+                else:
+                    console.print(
+                        "[dim]Note: --ai-skills has no effect with "
+                        f"{resolved_integration.key}; this integration uses commands, not skills.[/dim]"
+                    )
+            if ai_commands_dir and resolved_integration.key != "generic":
+                console.print(
+                    "[dim]Note: --ai-commands-dir is deprecated; "
+                    'use [bold]--integration generic --integration-options="--commands-dir <dir>"[/bold] instead.[/dim]'
+                )
+
+        if no_git:
+            console.print(
+                "[yellow]⚠️  --no-git is deprecated and will be removed in v0.10.0.[/yellow]\n"
+                "[yellow]The git extension will no longer be enabled by default "
+                "— use the [bold]specify extension[/bold] commands to install or enable the git extension if needed.[/yellow]"
+            )
+
+        if project_name == ".":
+            here = True
+            project_name = None
+
+        if here and project_name:
+            console.print("[red]Error:[/red] Cannot specify both project name and --here flag")
+            raise typer.Exit(1)
+
+        if not here and not project_name:
+            console.print("[red]Error:[/red] Must specify either a project name, use '.' for current directory, or use --here flag")
+            raise typer.Exit(1)
+
+        if ai_skills and not ai_assistant:
+            console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
+            console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
+            raise typer.Exit(1)
+
+        BRANCH_NUMBERING_CHOICES = {"sequential", "timestamp"}
+        if branch_numbering and branch_numbering not in BRANCH_NUMBERING_CHOICES:
+            console.print(f"[red]Error:[/red] Invalid --branch-numbering value '{branch_numbering}'. Choose from: {', '.join(sorted(BRANCH_NUMBERING_CHOICES))}")
+            raise typer.Exit(1)
+
+        dir_existed_before = False
+        if here:
+            project_name = Path.cwd().name
+            project_path = Path.cwd()
+            dir_existed_before = True
+
+            existing_items = list(project_path.iterdir())
+            if existing_items:
+                console.print(f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)")
+                console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
+                if force:
+                    console.print("[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]")
+                else:
+                    response = typer.confirm("Do you want to continue?")
+                    if not response:
+                        console.print("[yellow]Operation cancelled[/yellow]")
+                        raise typer.Exit(0)
+        else:
+            project_path = Path(project_name).resolve()
+            dir_existed_before = project_path.exists()
+            if project_path.exists():
+                if not project_path.is_dir():
+                    console.print(f"[red]Error:[/red] '{project_name}' exists but is not a directory.")
+                    raise typer.Exit(1)
+                existing_items = list(project_path.iterdir())
+                if force:
+                    if existing_items:
+                        console.print(f"[yellow]Warning:[/yellow] Directory '{project_name}' is not empty ({len(existing_items)} items)")
+                        console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
+                    console.print(f"[cyan]--force supplied: merging into existing directory '[cyan]{project_name}[/cyan]'[/cyan]")
+                else:
+                    error_panel = Panel(
+                        f"Directory already exists: '[cyan]{project_name}[/cyan]'\n"
+                        "Please choose a different project name or remove the existing directory.\n"
+                        "Use [bold]--force[/bold] to merge into the existing directory.",
+                        title="[red]Directory Conflict[/red]",
+                        border_style="red",
+                        padding=(1, 2)
+                    )
+                    console.print()
+                    console.print(error_panel)
+                    raise typer.Exit(1)
+
+        if ai_assistant:
+            if ai_assistant not in AGENT_CONFIG:
+                console.print(f"[red]Error:[/red] Invalid AI assistant '{ai_assistant}'. Choose from: {', '.join(AGENT_CONFIG.keys())}")
+                raise typer.Exit(1)
+            selected_ai = ai_assistant
+        elif not _stdin_is_interactive():
+            console.print(
+                f"[dim]Non-interactive session detected: defaulting to '{DEFAULT_INIT_INTEGRATION}'. "
+                "Use --integration to choose a different agent.[/dim]"
+            )
+            selected_ai = DEFAULT_INIT_INTEGRATION
+        else:
+            ai_choices = {key: config["name"] for key, config in AGENT_CONFIG.items()}
+            selected_ai = select_with_arrows(
+                ai_choices,
+                "Choose your coding agent integration:",
+                DEFAULT_INIT_INTEGRATION,
+            )
+
+        if not ai_assistant:
+            resolved_integration = get_integration(selected_ai)
+            if not resolved_integration:
+                console.print(f"[red]Error:[/red] Unknown agent '{selected_ai}'")
+                raise typer.Exit(1)
+
+        if selected_ai == "generic" and not integration_options:
+            if not ai_commands_dir:
+                console.print("[red]Error:[/red] --ai-commands-dir is required when using --ai generic or --integration generic")
+                console.print('[dim]Example: specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"[/dim]')
+                raise typer.Exit(1)
+
+        current_dir = Path.cwd()
+
+        setup_lines = [
+            "[cyan]Specify Project Setup[/cyan]",
+            "",
+            f"{'Project':<15} [green]{project_path.name}[/green]",
+            f"{'Working Path':<15} [dim]{current_dir}[/dim]",
+        ]
+
+        if not here:
+            setup_lines.append(f"{'Target Path':<15} [dim]{project_path}[/dim]")
+
+        console.print(Panel("\n".join(setup_lines), border_style="cyan", padding=(1, 2)))
+
+        should_init_git = False
+        if not no_git:
+            should_init_git = check_tool("git")
+            if not should_init_git:
+                console.print("[yellow]Git not found - will skip repository initialization[/yellow]")
+
+        if not ignore_agent_tools:
+            agent_config = AGENT_CONFIG.get(selected_ai)
+            if agent_config and agent_config["requires_cli"]:
+                install_url = agent_config["install_url"]
+                if not check_tool(selected_ai):
+                    error_panel = Panel(
+                        f"[cyan]{selected_ai}[/cyan] not found\n"
+                        f"Install from: [cyan]{install_url}[/cyan]\n"
+                        f"{agent_config['name']} is required to continue with this project type.\n\n"
+                        "Tip: Use [cyan]--ignore-agent-tools[/cyan] to skip this check",
+                        title="[red]Agent Detection Error[/red]",
+                        border_style="red",
+                        padding=(1, 2)
+                    )
+                    console.print()
+                    console.print(error_panel)
+                    raise typer.Exit(1)
+
+        if script_type:
+            if script_type not in SCRIPT_TYPE_CHOICES:
+                console.print(f"[red]Error:[/red] Invalid script type '{script_type}'. Choose from: {', '.join(SCRIPT_TYPE_CHOICES.keys())}")
+                raise typer.Exit(1)
+            selected_script = script_type
+        else:
+            default_script = "ps" if os.name == "nt" else "sh"
+
+            if _stdin_is_interactive():
+                selected_script = select_with_arrows(SCRIPT_TYPE_CHOICES, "Choose script type (or press Enter)", default_script)
+            else:
+                selected_script = default_script
+
+        console.print(f"[cyan]Selected coding agent integration:[/cyan] {selected_ai}")
+        console.print(f"[cyan]Selected script type:[/cyan] {selected_script}")
+
+        tracker = StepTracker("Initialize Specify Project")
+
+        tracker.add("precheck", "Check required tools")
+        tracker.complete("precheck", "ok")
+        tracker.add("ai-select", "Select coding agent integration")
+        tracker.complete("ai-select", f"{selected_ai}")
+        tracker.add("script-select", "Select script type")
+        tracker.complete("script-select", selected_script)
+
+        tracker.add("integration", "Install integration")
+        tracker.add("shared-infra", "Install shared infrastructure")
+
+        for key, label in [
+            ("chmod", "Ensure scripts executable"),
+            ("constitution", "Constitution setup"),
+            ("git", "Install git extension"),
+            ("workflow", "Install bundled workflow"),
+            ("final", "Finalize"),
+        ]:
+            tracker.add(key, label)
+
+        git_default_notice = False
+
+        with Live(tracker.render(), console=console, refresh_per_second=8, transient=True) as live:
+            tracker.attach_refresh(lambda: live.update(tracker.render()))
+            try:
+                from ..integrations.manifest import IntegrationManifest
+                tracker.start("integration")
+                manifest = IntegrationManifest(
+                    resolved_integration.key, project_path, version=get_speckit_version()
+                )
+
+                integration_parsed_options: dict[str, Any] = {}
+                if ai_commands_dir:
+                    integration_parsed_options["commands_dir"] = ai_commands_dir
+                if ai_skills:
+                    integration_parsed_options["skills"] = True
+                if integration_options:
+                    extra = _parse_integration_options(resolved_integration, integration_options)
+                    if extra:
+                        integration_parsed_options.update(extra)
+
+                resolved_integration.setup(
+                    project_path, manifest,
+                    parsed_options=integration_parsed_options or None,
+                    script_type=selected_script,
+                    raw_options=integration_options,
+                )
+                manifest.save()
+
+                integration_settings = _with_integration_setting(
+                    {},
+                    resolved_integration.key,
+                    resolved_integration,
+                    script_type=selected_script,
+                    raw_options=integration_options,
+                    parsed_options=integration_parsed_options or None,
+                )
+                _write_integration_json(
+                    project_path,
+                    resolved_integration.key,
+                    [resolved_integration.key],
+                    integration_settings,
+                )
+
+                tracker.complete("integration", resolved_integration.config.get("name", resolved_integration.key))
+
+                tracker.start("shared-infra")
+                _install_shared_infra_or_exit(
+                    project_path,
+                    selected_script,
+                    tracker=tracker,
+                    force=force,
+                    invoke_separator=resolved_integration.effective_invoke_separator(integration_parsed_options),
+                )
+                tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
+
+                ensure_constitution_from_template(project_path, tracker=tracker)
+
+                if not no_git:
+                    tracker.start("git")
+                    git_messages = []
+                    git_has_error = False
+                    if is_git_repo(project_path):
+                        git_messages.append("existing repo detected")
+                    elif should_init_git:
+                        success, error_msg = init_git_repo(project_path, quiet=True)
+                        if success:
+                            git_messages.append("initialized")
+                        else:
+                            git_has_error = True
+                            if error_msg:
+                                sanitized = error_msg.replace('\n', ' ').strip()
+                                git_messages.append(f"init failed: {sanitized[:120]}")
+                            else:
+                                git_messages.append("init failed")
+                    else:
+                        git_messages.append("git not available")
+                    try:
+                        from ..extensions import ExtensionManager
+                        bundled_path = _locate_bundled_extension("git")
+                        if bundled_path:
+                            manager = ExtensionManager(project_path)
+                            if manager.registry.is_installed("git"):
+                                git_messages.append("extension already installed")
+                            else:
+                                manager.install_from_directory(
+                                    bundled_path, get_speckit_version()
+                                )
+                                git_default_notice = True
+                                git_messages.append("extension installed")
+                        else:
+                            git_has_error = True
+                            git_messages.append("bundled extension not found")
+                    except Exception as ext_err:
+                        git_has_error = True
+                        sanitized_ext = str(ext_err).replace('\n', ' ').strip()
+                        git_messages.append(
+                            f"extension install failed: {sanitized_ext[:120]}"
+                        )
+                    summary = "; ".join(git_messages)
+                    if git_has_error:
+                        tracker.error("git", summary)
+                    else:
+                        tracker.complete("git", summary)
+                else:
+                    tracker.skip("git", "--no-git flag")
+
+                try:
+                    bundled_wf = _locate_bundled_workflow("speckit")
+                    if bundled_wf:
+                        from ..workflows.catalog import WorkflowRegistry
+                        from ..workflows.engine import WorkflowDefinition
+                        wf_registry = WorkflowRegistry(project_path)
+                        if wf_registry.is_installed("speckit"):
+                            tracker.complete("workflow", "already installed")
+                        else:
+                            import shutil as _shutil
+                            dest_wf = project_path / ".specify" / "workflows" / "speckit"
+                            dest_wf.mkdir(parents=True, exist_ok=True)
+                            _shutil.copy2(
+                                bundled_wf / "workflow.yml",
+                                dest_wf / "workflow.yml",
+                            )
+                            definition = WorkflowDefinition.from_yaml(dest_wf / "workflow.yml")
+                            wf_registry.add("speckit", {
+                                "name": definition.name,
+                                "version": definition.version,
+                                "description": definition.description,
+                                "source": "bundled",
+                            })
+                            tracker.complete("workflow", "speckit installed")
+                    else:
+                        tracker.skip("workflow", "bundled workflow not found")
+                except Exception as wf_err:
+                    sanitized_wf = str(wf_err).replace('\n', ' ').strip()
+                    tracker.error("workflow", f"install failed: {sanitized_wf[:120]}")
+
+                ensure_executable_scripts(project_path, tracker=tracker)
+
+                init_opts = {
+                    "ai": selected_ai,
+                    "integration": resolved_integration.key,
+                    "branch_numbering": branch_numbering or "sequential",
+                    "context_file": resolved_integration.context_file,
+                    "here": here,
+                    "script": selected_script,
+                    "speckit_version": get_speckit_version(),
+                }
+                from ..integrations.base import SkillsIntegration as _SkillsPersist
+                if isinstance(resolved_integration, _SkillsPersist) or getattr(resolved_integration, "_skills_mode", False):
+                    init_opts["ai_skills"] = True
+                save_init_options(project_path, init_opts)
+
+                if preset:
+                    try:
+                        from ..presets import PresetManager, PresetCatalog, PresetError
+                        preset_manager = PresetManager(project_path)
+                        speckit_ver = get_speckit_version()
+
+                        local_path = Path(preset).resolve()
+                        if local_path.is_dir() and (local_path / "preset.yml").exists():
+                            preset_manager.install_from_directory(local_path, speckit_ver)
+                        else:
+                            bundled_path = _locate_bundled_preset(preset)
+                            if bundled_path:
+                                preset_manager.install_from_directory(bundled_path, speckit_ver)
+                            else:
+                                preset_catalog = PresetCatalog(project_path)
+                                pack_info = preset_catalog.get_pack_info(preset)
+                                if not pack_info:
+                                    console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
+                                elif pack_info.get("bundled") and not pack_info.get("download_url"):
+                                    from ..extensions import REINSTALL_COMMAND
+                                    console.print(
+                                        f"[yellow]Warning:[/yellow] Preset '{preset}' is bundled with spec-kit "
+                                        f"but could not be found in the installed package."
+                                    )
+                                    console.print(
+                                        "This usually means the spec-kit installation is incomplete or corrupted."
+                                    )
+                                    console.print(f"Try reinstalling: {REINSTALL_COMMAND}")
+                                else:
+                                    zip_path = None
+                                    try:
+                                        zip_path = preset_catalog.download_pack(preset)
+                                        preset_manager.install_from_zip(zip_path, speckit_ver)
+                                    except PresetError as preset_err:
+                                        _print_cli_warning(
+                                            "install",
+                                            "preset",
+                                            preset,
+                                            preset_err,
+                                            continuing="Continuing without the optional preset.",
+                                        )
+                                    finally:
+                                        if zip_path is not None:
+                                            try:
+                                                zip_path.unlink(missing_ok=True)
+                                            except OSError:
+                                                pass
+                    except Exception as preset_err:
+                        _print_cli_warning(
+                            "install",
+                            "preset",
+                            preset,
+                            preset_err,
+                            continuing="Continuing without the optional preset.",
+                        )
+
+                tracker.complete("final", "project ready")
+            except (typer.Exit, SystemExit):
+                raise
+            except Exception as e:
+                tracker.error("final", str(e))
+                console.print(Panel(f"Initialization failed: {e}", title="Failure", border_style="red"))
+                if debug:
+                    _env_pairs = [
+                        ("Python", sys.version.split()[0]),
+                        ("Platform", sys.platform),
+                        ("CWD", str(Path.cwd())),
+                    ]
+                    _label_width = max(len(k) for k, _ in _env_pairs)
+                    env_lines = [f"{k.ljust(_label_width)} → [bright_black]{v}[/bright_black]" for k, v in _env_pairs]
+                    console.print(Panel("\n".join(env_lines), title="Debug Environment", border_style="magenta"))
+                if not here and project_path.exists() and not dir_existed_before:
+                    shutil.rmtree(project_path)
+                raise typer.Exit(1)
+            finally:
+                pass
+
+        console.print(tracker.render())
+        console.print("\n[bold green]Project ready.[/bold green]")
+
+        agent_config = AGENT_CONFIG.get(selected_ai)
+        if agent_config:
+            agent_folder = ai_commands_dir if selected_ai == "generic" else agent_config["folder"]
+            if agent_folder:
+                security_notice = Panel(
+                    f"Some agents may store credentials, auth tokens, or other identifying and private artifacts in the agent folder within your project.\n"
+                    f"Consider adding [cyan]{agent_folder}[/cyan] (or parts of it) to [cyan].gitignore[/cyan] to prevent accidental credential leakage.",
+                    title="[yellow]Agent Folder Security[/yellow]",
+                    border_style="yellow",
+                    padding=(1, 2)
+                )
+                console.print()
+                console.print(security_notice)
+
+        if ai_deprecation_warning:
+            deprecation_notice = Panel(
+                ai_deprecation_warning,
+                title="[bold red]Deprecation Warning[/bold red]",
+                border_style="red",
+                padding=(1, 2),
+            )
+            console.print()
+            console.print(deprecation_notice)
+
+        if git_default_notice:
+            default_change_notice = Panel(
+                "The git extension is currently enabled by default during [bold]specify init[/bold].\n"
+                "Starting in [bold]v0.10.0[/bold], this will require explicit opt-in.\n"
+                "Use [bold]specify extension add git[/bold] after init when needed.",
+                title="[yellow]Notice: Git Default Changing[/yellow]",
+                border_style="yellow",
+                padding=(1, 2),
+            )
+            console.print()
+            console.print(default_change_notice)
+
+        steps_lines = []
+        if not here:
+            steps_lines.append(f"1. Go to the project folder: [cyan]cd {project_name}[/cyan]")
+            step_num = 2
+        else:
+            steps_lines.append("1. You're already in the project directory!")
+            step_num = 2
+
+        from ..integrations.base import SkillsIntegration as _SkillsInt
+        _is_skills_integration = isinstance(resolved_integration, _SkillsInt) or getattr(resolved_integration, "_skills_mode", False)
+
+        codex_skill_mode = selected_ai == "codex" and (ai_skills or _is_skills_integration)
+        claude_skill_mode = selected_ai == "claude" and (ai_skills or _is_skills_integration)
+        kimi_skill_mode = selected_ai == "kimi"
+        agy_skill_mode = selected_ai == "agy" and _is_skills_integration
+        trae_skill_mode = selected_ai == "trae"
+        cursor_agent_skill_mode = selected_ai == "cursor-agent" and (ai_skills or _is_skills_integration)
+        copilot_skill_mode = selected_ai == "copilot" and _is_skills_integration
+        devin_skill_mode = selected_ai == "devin"
+        native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode or trae_skill_mode or cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode
+
+        if codex_skill_mode and not ai_skills:
+            steps_lines.append(f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]")
+            step_num += 1
+        if claude_skill_mode and not ai_skills:
+            steps_lines.append(f"{step_num}. Start Claude in this project directory; spec-kit skills were installed to [cyan].claude/skills[/cyan]")
+            step_num += 1
+        if cursor_agent_skill_mode and not ai_skills:
+            steps_lines.append(f"{step_num}. Start Cursor Agent in this project directory; spec-kit skills were installed to [cyan].cursor/skills[/cyan]")
+            step_num += 1
+        if devin_skill_mode:
+            steps_lines.append(f"{step_num}. Start Devin in this project directory; spec-kit skills were installed to [cyan].devin/skills[/cyan]")
+            step_num += 1
+        usage_label = "skills" if native_skill_mode else "slash commands"
+
+        def _display_cmd(name: str) -> str:
+            if codex_skill_mode or agy_skill_mode or trae_skill_mode:
+                return f"$speckit-{name}"
+            if claude_skill_mode:
+                return f"/speckit-{name}"
+            if kimi_skill_mode:
+                return f"/skill:speckit-{name}"
+            if cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode:
+                return f"/speckit-{name}"
+            return f"/speckit.{name}"
+
+        steps_lines.append(f"{step_num}. Start using {usage_label} with your coding agent:")
+
+        steps_lines.append(f"   {step_num}.1 [cyan]{_display_cmd('constitution')}[/] - Establish project principles")
+        steps_lines.append(f"   {step_num}.2 [cyan]{_display_cmd('specify')}[/] - Create baseline specification")
+        steps_lines.append(f"   {step_num}.3 [cyan]{_display_cmd('plan')}[/] - Create implementation plan")
+        steps_lines.append(f"   {step_num}.4 [cyan]{_display_cmd('tasks')}[/] - Generate actionable tasks")
+        steps_lines.append(f"   {step_num}.5 [cyan]{_display_cmd('implement')}[/] - Execute implementation")
+
+        steps_panel = Panel("\n".join(steps_lines), title="Next Steps", border_style="cyan", padding=(1, 2))
+        console.print()
+        console.print(steps_panel)
+
+        enhancement_intro = (
+            "Optional skills that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
+            if native_skill_mode
+            else "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
+        )
+        enhancement_lines = [
+            enhancement_intro,
+            "",
+            f"○ [cyan]{_display_cmd('clarify')}[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]{_display_cmd('plan')}[/] if used)",
+            f"○ [cyan]{_display_cmd('analyze')}[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]{_display_cmd('tasks')}[/], before [cyan]{_display_cmd('implement')}[/])",
+            f"○ [cyan]{_display_cmd('checklist')}[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]{_display_cmd('plan')}[/])"
+        ]
+        enhancements_title = "Enhancement Skills" if native_skill_mode else "Enhancement Commands"
+        enhancements_panel = Panel("\n".join(enhancement_lines), title=enhancements_title, border_style="cyan", padding=(1, 2))
+        console.print()
+        console.print(enhancements_panel)
--- a/src/specify_cli/commands/integration.py
+++ b/src/specify_cli/commands/integration.py
@@ -0,0 +1,2 @@
+"""specify integration * commands — placeholder for future extraction."""
+from __future__ import annotations
--- a/src/specify_cli/commands/preset.py
+++ b/src/specify_cli/commands/preset.py
@@ -0,0 +1,2 @@
+"""specify preset * commands — placeholder for future extraction."""
+from __future__ import annotations
--- a/src/specify_cli/commands/workflow.py
+++ b/src/specify_cli/commands/workflow.py
@@ -0,0 +1,2 @@
+"""specify workflow * commands — placeholder for future extraction."""
+from __future__ import annotations
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -801,38 +801,24 @@ class ExtensionManager:
    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.
+        Delegates to :func:`resolve_active_skills_dir` which reads
+        init-options, applies the Kimi native-skills fallback, and
+        safely creates the directory when ``ai_skills`` is enabled.

-        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.
+        Returns ``None`` (instead of raising) when the directory cannot
+        be created due to symlink, containment, or permission issues so
+        that callers can fall back gracefully.
        """
-        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:
+        from . import resolve_active_skills_dir, _print_cli_warning
+        try:
+            return resolve_active_skills_dir(self.project_root)
+        except (ValueError, OSError) as exc:
+            _print_cli_warning(
+                "resolve", "skills directory", None, exc,
+                continuing="Continuing without skill registration.",
+            )
            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,
--- a/src/specify_cli/integrations/copilot/init.py
+++ b/src/specify_cli/integrations/copilot/init.py
@@ -24,6 +24,16 @@ from ..base import IntegrationBase, IntegrationOption, SkillsIntegration
 from ..manifest import IntegrationManifest


+def _copilot_executable() -> str:
+    """Return the executable name for Copilot CLI on this platform.
+
+    On Windows, subprocess invocation is reliable with `copilot.cmd`.
+    """
+    if os.name == "nt":
+        return "copilot.cmd"
+    return "copilot"
+
+
 def _allow_all() -> bool:
    """Return True if the Copilot CLI should run with full permissions.

@@ -138,7 +148,7 @@ class CopilotIntegration(IntegrationBase):
        # Controlled by SPECKIT_COPILOT_ALLOW_ALL_TOOLS env var
        # (default: enabled).  The deprecated SPECKIT_ALLOW_ALL_TOOLS
        # is also honoured as a fallback.
-        args = ["copilot", "-p", prompt]
+        args = [_copilot_executable(), "-p", prompt]
        if _allow_all():
            args.append("--yolo")
        if model:
@@ -206,7 +216,7 @@ class CopilotIntegration(IntegrationBase):
            agent_name = f"speckit.{stem}"
            prompt = args or ""

-        cli_args = ["copilot", "-p", prompt]
+        cli_args = [_copilot_executable(), "-p", prompt]
        if not skills_mode:
            cli_args.extend(["--agent", agent_name])
        if _allow_all():
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -28,6 +28,7 @@ from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier

 from .extensions import REINSTALL_COMMAND, ExtensionRegistry, normalize_priority
+from .integrations.base import IntegrationBase


 def _substitute_core_template(
@@ -1058,6 +1059,9 @@ class PresetManager:
                        body = registrar.resolve_skill_placeholders(
                            selected_ai, fm, body, self.project_root
                        )
+                        body = self._resolve_skill_command_refs(
+                            body, registrar, selected_ai
+                        )
                    fm_data = registrar.build_skill_frontmatter(
                        selected_ai if isinstance(selected_ai, str) else "",
                        skill_name, desc,
@@ -1097,37 +1101,24 @@ class PresetManager:
    def _get_skills_dir(self) -> Optional[Path]:
        """Return the active skills directory for preset skill overrides.

-        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.
+        Delegates to :func:`resolve_active_skills_dir` which reads
+        init-options, applies the Kimi native-skills fallback, and
+        safely creates the directory when ``ai_skills`` is enabled.

-        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.
+        Returns ``None`` (instead of raising) when the directory cannot
+        be created due to symlink, containment, or permission issues so
+        that callers can fall back gracefully.
        """
-        from . import load_init_options, _get_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:
+        from . import resolve_active_skills_dir, _print_cli_warning
+        try:
+            return resolve_active_skills_dir(self.project_root)
+        except (ValueError, OSError) as exc:
+            _print_cli_warning(
+                "resolve", "skills directory", None, exc,
+                continuing="Continuing without skill registration.",
+            )
            return None

-        ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not ai_skills_enabled and agent != "kimi":
-            return None
-
-        skills_dir = _get_skills_dir(self.project_root, agent)
-        if not skills_dir.is_dir():
-            return None
-
-        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."""
@@ -1147,6 +1138,23 @@ class PresetManager:
            title_name = title_name[len("speckit."):]
        return title_name.replace(".", " ").replace("-", " ").title()

+    @staticmethod
+    def _resolve_skill_command_refs(
+        body: str, registrar: "CommandRegistrar", selected_ai: str
+    ) -> str:
+        """Render ``__SPECKIT_COMMAND_*__`` tokens in a skill body as invocations.
+
+        Looks up the agent's invoke separator and rewrites each
+        ``__SPECKIT_COMMAND_<NAME>__`` placeholder into the matching
+        slash-command invocation — ``/speckit-<cmd>`` for a ``-`` separator,
+        ``/speckit.<cmd>`` for ``.`` — the same rendering the command layer
+        applies via ``CommandRegistrar.register_commands()``.
+        """
+        separator = registrar.AGENT_CONFIGS.get(selected_ai, {}).get(
+            "invoke_separator", "."
+        )
+        return IntegrationBase.resolve_command_refs(body, separator)
+
    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
@@ -1323,6 +1331,7 @@ class PresetManager:
            body = registrar.resolve_skill_placeholders(
                selected_ai, frontmatter, body, self.project_root
            )
+            body = self._resolve_skill_command_refs(body, registrar, selected_ai)

            for target_skill_name in target_skill_names:
                skill_subdir = skills_dir / target_skill_name
@@ -1415,6 +1424,9 @@ class PresetManager:
                    body = registrar.resolve_skill_placeholders(
                        selected_ai, frontmatter, body, self.project_root
                    )
+                    body = self._resolve_skill_command_refs(
+                        body, registrar, selected_ai
+                    )

                original_desc = frontmatter.get("description", "")
                enhanced_desc = original_desc or SKILL_DESCRIPTIONS.get(
@@ -1452,6 +1464,9 @@ class PresetManager:
                    body = registrar.resolve_skill_placeholders(
                        selected_ai, frontmatter, body, self.project_root
                    )
+                    body = self._resolve_skill_command_refs(
+                        body, registrar, selected_ai
+                    )

                command_name = extension_restore["command_name"]
                title_name = self._skill_title_from_command(command_name)
--- a/src/specify_cli/shared_infra.py
+++ b/src/specify_cli/shared_infra.py
@@ -88,7 +88,13 @@ def _shared_relative_path(project_path: Path, dest: Path) -> Path:
    return rel


-def _ensure_safe_shared_directory(project_path: Path, directory: Path, *, create: bool = True) -> None:
+def _ensure_safe_shared_directory(
+    project_path: Path,
+    directory: Path,
+    *,
+    create: bool = True,
+    context: str = "shared infrastructure directory",
+) -> None:
    """Create a shared infra directory without following symlinked parents."""
    root = project_path.resolve()
    rel = _shared_relative_path(project_path, directory)
@@ -98,24 +104,24 @@ def _ensure_safe_shared_directory(project_path: Path, directory: Path, *, create
        current = current / part
        label = _shared_destination_label(project_path, current)
        if current.is_symlink():
-            raise SymlinkedSharedPathError(f"Refusing to use symlinked shared infrastructure directory: {label}")
+            raise SymlinkedSharedPathError(f"Refusing to use symlinked {context}: {label}")
        if current.exists():
            if not current.is_dir():
-                raise ValueError(f"Shared infrastructure directory path is not a directory: {label}")
+                raise ValueError(f"{context.capitalize()} path is not a directory: {label}")
            try:
                current.resolve().relative_to(root)
            except (OSError, ValueError):
-                raise ValueError(f"Shared infrastructure directory escapes project root: {label}") from None
+                raise ValueError(f"{context.capitalize()} escapes project root: {label}") from None
            continue
        if not create:
-            raise ValueError(f"Shared infrastructure directory does not exist: {label}")
+            raise ValueError(f"{context.capitalize()} does not exist: {label}")
        current.mkdir()
        if current.is_symlink():
-            raise SymlinkedSharedPathError(f"Refusing to use symlinked shared infrastructure directory: {label}")
+            raise SymlinkedSharedPathError(f"Refusing to use symlinked {context}: {label}")
        try:
            current.resolve().relative_to(root)
        except (OSError, ValueError):
-            raise ValueError(f"Shared infrastructure directory escapes project root: {label}") from None
+            raise ValueError(f"{context.capitalize()} escapes project root: {label}") from None


 def _validate_safe_shared_directory(project_path: Path, directory: Path) -> None:
--- a/src/specify_cli/workflows/expressions.py
+++ b/src/specify_cli/workflows/expressions.py
@@ -102,6 +102,15 @@ def _build_namespace(context: Any) -> dict[str, Any]:
        ns["item"] = context.item
    if hasattr(context, "fan_in"):
        ns["fan_in"] = context.fan_in or {}
+    # Engine-managed runtime metadata. Always present (even outside a
+    # run) so templates referencing it never error: `run_id` falls back
+    # to an empty string when no run is active (dry-run, validation,
+    # ad-hoc evaluator usage). The value is the same one Spec Kit
+    # prints as `Run ID:` at the end of `workflow run` — auto-generated
+    # runs use an 8-character uuid4 hex; operator-supplied ids may be
+    # any alphanumeric string with hyphens or underscores.
+    run_id = getattr(context, "run_id", None) or ""
+    ns["context"] = {"run_id": run_id}
    return ns


--- a/templates/commands/clarify.md
+++ b/templates/commands/clarify.md
@@ -197,13 +197,24 @@ Execution steps:

 7. Write the updated spec back to `FEATURE_SPEC`.

-8. Report completion (after questioning loop ends or early termination):
-   - Number of questions asked & answered.
-   - Path to updated spec.
-   - Sections touched (list names).
-   - Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
-   - If any Outstanding or Deferred remain, recommend whether to proceed to `__SPECKIT_COMMAND_PLAN__` or run `__SPECKIT_COMMAND_CLARIFY__` again later post-plan.
-   - Suggested next command.
+8. **Re-validate Spec Quality Checklist** (if it exists):
+   - Check if `FEATURE_DIR/checklists/requirements.md` exists.
+   - If it does NOT exist, skip this step silently.
+   - If it exists:
+     1. Read the checklist file.
+     2. Identify all GitHub task-list checkbox lines — lines matching `- [ ]`, `- [x]`, or `- [X]` (case-insensitive, tolerant of leading whitespace for nested items) outside of code fences. Ignore all other content (headings, notes, non-checkbox bullets, metadata).
+     3. For each checkbox line, record its current marker state (checked or unchecked) and item text into a before-snapshot list.
+     4. Re-evaluate each checkbox item against the **updated** spec (the version just saved in step 7).
+     5. For each checkbox item, update only if the checked/unchecked state actually changes:
+        - If the item now passes and was unchecked: change `[ ]` to `[x]`.
+        - If the item now fails and was checked: change `[x]`/`[X]` to `[ ]`.
+        - If the state is unchanged: leave the marker as-is (preserve existing case to avoid cosmetic diffs).
+     6. Save the updated checklist file. **Only toggle the `[ ]`/`[x]` marker portion of checkbox lines whose state changed.** All other file content — headings, metadata, notes, line ordering, whitespace — must remain unchanged to avoid noisy diffs.
+     7. Compare the before-snapshot with the current state to compute three lists for the Completion Report:
+        - **Newly passing**: items that changed from unchecked to checked.
+        - **Regressions**: items that changed from checked to unchecked.
+        - **Still unchecked**: items that remain unchecked.
+     8. Record the before/after pass counts as checked/total checkbox items (e.g., "12/16 → 15/16 items passing").

 Behavior rules:

@@ -217,17 +228,27 @@ Behavior rules:

 Context for prioritization: {ARGS}

-## Post-Execution Checks
+## Mandatory Post-Execution Hooks
+
+**You MUST complete this section before reporting completion to the user.**

-**Check for extension hooks (after clarification)**:
 Check if `.specify/extensions.yml` exists in the project root.
- If it exists, read it and look for entries under the `hooks.after_clarify` key
- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
+- If it does not exist, or no hooks are registered under `hooks.after_clarify`, skip to the Completion Report.
+- If it exists, read it and look for entries under the `hooks.after_clarify` key.
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
 - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
 - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
 - For each executable hook, output the following based on its `optional` flag:
+  - **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
+    ```
+    ## Extension Hooks
+
+    **Automatic Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+    ```
  - **Optional hook** (`optional: true`):
    ```
    ## Extension Hooks
@@ -239,12 +260,21 @@ Check if `.specify/extensions.yml` exists in the project root.
    Prompt: {prompt}
    To execute: `/{command}`
    ```
-  - **Mandatory hook** (`optional: false`):
-    ```
-    ## Extension Hooks

-    **Automatic Hook**: {extension}
-    Executing: `/{command}`
-    EXECUTE_COMMAND: {command}
-    ```
- If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+## Completion Report
+
+Report completion (after questioning loop ends or early termination):
+- Number of questions asked & answered.
+- Path to updated spec.
+- Sections touched (list names).
+- Spec quality checklist status (if `FEATURE_DIR/checklists/requirements.md` was re-validated): show before/after pass counts (e.g., "Spec Quality Checklist: 12/16 → 15/16 items passing") and list any items that changed state — both newly checked (unchecked → checked) and any regressions (checked → unchecked). If any items remain unchecked, list them as areas needing attention.
+- Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
+- If any Outstanding or Deferred remain, recommend whether to proceed to `__SPECKIT_COMMAND_PLAN__` or run `__SPECKIT_COMMAND_CLARIFY__` again later post-plan.
+- Suggested next command.
+
+## Done When
+
+- [ ] Spec ambiguities identified and clarifications integrated into spec file
+- [ ] Spec quality checklist re-validated against updated spec (if `FEATURE_DIR/checklists/requirements.md` exists)
+- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
+- [ ] Completion reported to user with questions answered, sections touched, checklist status, and coverage summary
--- a/templates/commands/implement.md
+++ b/templates/commands/implement.md
@@ -168,35 +168,49 @@ You **MUST** consider the user input before proceeding (if not empty).
   - Check that implemented features match the original specification
   - Validate that tests pass and coverage meets requirements
   - Confirm the implementation follows the technical plan
-   - Report final status with summary of completed work

 Note: This command assumes a complete task breakdown exists in tasks.md. If tasks are incomplete or missing, suggest running `__SPECKIT_COMMAND_TASKS__` first to regenerate the task list.

-10. **Check for extension hooks**: After completion validation, check if `.specify/extensions.yml` exists in the project root.
-    - If it exists, read it and look for entries under the `hooks.after_implement` key
-    - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-    - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
-    - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
-      - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
-      - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
-    - For each executable hook, output the following based on its `optional` flag:
-      - **Optional hook** (`optional: true`):
-        ```
-        ## Extension Hooks
+## Mandatory Post-Execution Hooks

-        **Optional Hook**: {extension}
-        Command: `/{command}`
-        Description: {description}
+**You MUST complete this section before reporting completion to the user.**

-        Prompt: {prompt}
-        To execute: `/{command}`
-        ```
-      - **Mandatory hook** (`optional: false`):
-        ```
-        ## Extension Hooks
+Check if `.specify/extensions.yml` exists in the project root.
+- If it does not exist, or no hooks are registered under `hooks.after_implement`, skip to the Completion Report.
+- If it exists, read it and look for entries under the `hooks.after_implement` key.
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
+- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+- For each executable hook, output the following based on its `optional` flag:
+  - **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
+    ```
+    ## Extension Hooks

-        **Automatic Hook**: {extension}
-        Executing: `/{command}`
-        EXECUTE_COMMAND: {command}
-        ```
-    - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+    **Automatic Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+    ```
+  - **Optional hook** (`optional: true`):
+    ```
+    ## Extension Hooks
+
+    **Optional Hook**: {extension}
+    Command: `/{command}`
+    Description: {description}
+
+    Prompt: {prompt}
+    To execute: `/{command}`
+    ```
+
+## Completion Report
+
+Report final status with summary of completed work.
+
+## Done When
+
+- [ ] All tasks in tasks.md completed and marked `[X]`
+- [ ] Implementation validated against specification, plan, and test coverage
+- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
+- [ ] Completion reported to user with summary of completed work
--- a/templates/commands/plan.md
+++ b/templates/commands/plan.md
@@ -70,36 +70,42 @@ You **MUST** consider the user input before proceeding (if not empty).
   - Phase 1: Update agent context by running the agent script
   - Re-evaluate Constitution Check post-design

-4. **Stop and report**: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
+## Mandatory Post-Execution Hooks

-5. **Check for extension hooks**: After reporting, check if `.specify/extensions.yml` exists in the project root.
-   - If it exists, read it and look for entries under the `hooks.after_plan` key
-   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
-   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
-     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
-     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
-   - For each executable hook, output the following based on its `optional` flag:
-     - **Optional hook** (`optional: true`):
-       ```
-       ## Extension Hooks
+**You MUST complete this section before reporting completion to the user.**

-       **Optional Hook**: {extension}
-       Command: `/{command}`
-       Description: {description}
+Check if `.specify/extensions.yml` exists in the project root.
+- If it does not exist, or no hooks are registered under `hooks.after_plan`, skip to the Completion Report.
+- If it exists, read it and look for entries under the `hooks.after_plan` key.
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
+- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+- For each executable hook, output the following based on its `optional` flag:
+  - **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
+    ```
+    ## Extension Hooks

-       Prompt: {prompt}
-       To execute: `/{command}`
-       ```
-     - **Mandatory hook** (`optional: false`):
-       ```
-       ## Extension Hooks
+    **Automatic Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+    ```
+  - **Optional hook** (`optional: true`):
+    ```
+    ## Extension Hooks

-       **Automatic Hook**: {extension}
-       Executing: `/{command}`
-       EXECUTE_COMMAND: {command}
-       ```
-   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+    **Optional Hook**: {extension}
+    Command: `/{command}`
+    Description: {description}
+
+    Prompt: {prompt}
+    To execute: `/{command}`
+    ```
+
+## Completion Report
+
+Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.

 ## Phases

@@ -150,3 +156,9 @@ You **MUST** consider the user input before proceeding (if not empty).

 - Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
 - ERROR on gate failures or unresolved clarifications
+
+## Done When
+
+- [ ] Plan workflow executed and design artifacts generated
+- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
+- [ ] Completion reported to user with branch, plan path, and generated artifacts
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -183,7 +183,7 @@ Given that feature description, do this:

   c. **Handle Validation Results**:

-      - **If all items pass**: Mark checklist complete and proceed to step 8
+      - **If all items pass**: Mark checklist complete and proceed to the Mandatory Post-Execution Hooks section

      - **If items fail (excluding [NEEDS CLARIFICATION])**:
        1. List the failing items and specific issues
@@ -228,40 +228,46 @@ Given that feature description, do this:

   d. **Update Checklist**: After each validation iteration, update the checklist file with current pass/fail status

-8. **Report completion** to the user with:
-   - `SPECIFY_FEATURE_DIRECTORY` — the feature directory path
-   - `SPEC_FILE` — the spec file path
-   - Checklist results summary
-   - Readiness for the next phase (`__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`)
+## Mandatory Post-Execution Hooks

-9. **Check for extension hooks**: After reporting completion, check if `.specify/extensions.yml` exists in the project root.
-   - If it exists, read it and look for entries under the `hooks.after_specify` key
-   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
-   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
-     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
-     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
-   - For each executable hook, output the following based on its `optional` flag:
-     - **Optional hook** (`optional: true`):
-       ```
-       ## Extension Hooks
+**You MUST complete this section before reporting completion to the user.**

-       **Optional Hook**: {extension}
-       Command: `/{command}`
-       Description: {description}
+Check if `.specify/extensions.yml` exists in the project root.
+- If it does not exist, or no hooks are registered under `hooks.after_specify`, skip to the Completion Report.
+- If it exists, read it and look for entries under the `hooks.after_specify` key.
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
+- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+- For each executable hook, output the following based on its `optional` flag:
+  - **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
+    ```
+    ## Extension Hooks

-       Prompt: {prompt}
-       To execute: `/{command}`
-       ```
-     - **Mandatory hook** (`optional: false`):
-       ```
-       ## Extension Hooks
+    **Automatic Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+    ```
+  - **Optional hook** (`optional: true`):
+    ```
+    ## Extension Hooks

-       **Automatic Hook**: {extension}
-       Executing: `/{command}`
-       EXECUTE_COMMAND: {command}
-       ```
-   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+    **Optional Hook**: {extension}
+    Command: `/{command}`
+    Description: {description}
+
+    Prompt: {prompt}
+    To execute: `/{command}`
+    ```
+
+## Completion Report
+
+Report completion to the user with:
+- `SPECIFY_FEATURE_DIRECTORY` — the feature directory path
+- `SPEC_FILE` — the spec file path
+- Checklist results summary
+- Readiness for the next phase (`__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`)

 **NOTE:** Branch creation is handled by the `before_specify` hook (git extension). Spec directory and file creation are always handled by this core command.

@@ -325,3 +331,9 @@ Success criteria must be:
 - "Database can handle 1000 TPS" (implementation detail, use user-facing metric)
 - "React components render efficiently" (framework-specific)
 - "Redis cache hit rate above 80%" (technology-specific)
+
+## Done When
+
+- [ ] Specification written to `SPEC_FILE` and validated against quality checklist
+- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
+- [ ] Completion reported to user with feature directory, spec file path, and checklist results
--- a/templates/commands/tasks.md
+++ b/templates/commands/tasks.md
@@ -89,42 +89,48 @@ You **MUST** consider the user input before proceeding (if not empty).
   - Parallel execution examples per story
   - Implementation strategy section (MVP first, incremental delivery)

-5. **Report**: Output path to generated tasks.md and summary:
-   - Total task count
-   - Task count per user story
-   - Parallel opportunities identified
-   - Independent test criteria for each story
-   - Suggested MVP scope (typically just User Story 1)
-   - Format validation: Confirm ALL tasks follow the checklist format (checkbox, ID, labels, file paths)
+## Mandatory Post-Execution Hooks

-6. **Check for extension hooks**: After tasks.md is generated, check if `.specify/extensions.yml` exists in the project root.
-   - If it exists, read it and look for entries under the `hooks.after_tasks` key
-   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
-   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
-     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
-     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
-   - For each executable hook, output the following based on its `optional` flag:
-     - **Optional hook** (`optional: true`):
-       ```
-       ## Extension Hooks
+**You MUST complete this section before reporting completion to the user.**

-       **Optional Hook**: {extension}
-       Command: `/{command}`
-       Description: {description}
+Check if `.specify/extensions.yml` exists in the project root.
+- If it does not exist, or no hooks are registered under `hooks.after_tasks`, skip to the Completion Report.
+- If it exists, read it and look for entries under the `hooks.after_tasks` key.
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue to the Completion Report.
+- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+- For each executable hook, output the following based on its `optional` flag:
+  - **Mandatory hook** (`optional: false`) — **You MUST emit `EXECUTE_COMMAND:` for each mandatory hook**:
+    ```
+    ## Extension Hooks

-       Prompt: {prompt}
-       To execute: `/{command}`
-       ```
-     - **Mandatory hook** (`optional: false`):
-       ```
-       ## Extension Hooks
+    **Automatic Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+    ```
+  - **Optional hook** (`optional: true`):
+    ```
+    ## Extension Hooks

-       **Automatic Hook**: {extension}
-       Executing: `/{command}`
-       EXECUTE_COMMAND: {command}
-       ```
-   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+    **Optional Hook**: {extension}
+    Command: `/{command}`
+    Description: {description}
+
+    Prompt: {prompt}
+    To execute: `/{command}`
+    ```
+
+## Completion Report
+
+Output path to generated tasks.md and summary:
+- Total task count
+- Task count per user story
+- Parallel opportunities identified
+- Independent test criteria for each story
+- Suggested MVP scope (typically just User Story 1)
+- Format validation: Confirm ALL tasks follow the checklist format (checkbox, ID, labels, file paths)

 Context for task generation: {ARGS}

@@ -201,3 +207,9 @@ Every task MUST strictly follow this format:
  - Within each story: Tests (if requested) → Models → Services → Endpoints → Integration
  - Each phase should be a complete, independently testable increment
 - **Final Phase**: Polish & Cross-Cutting Concerns
+
+## Done When
+
+- [ ] tasks.md generated with all phases, task IDs, and file paths
+- [ ] Extension hooks dispatched or skipped according to the rules in Mandatory Post-Execution Hooks above
+- [ ] Completion reported to user with task count, story breakdown, and MVP scope
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -335,10 +335,11 @@ class TestInitIntegrationFlag:
        _install_shared_infra(project, "sh", force=False)

        captured = capsys.readouterr()
-        assert "already exist and were not updated" in captured.out
-        assert "specify init --here --force" in captured.out
+        plain = strip_ansi(captured.out)
+        assert "already exist and were not updated" in plain
+        assert "specify init --here --force" in plain
        # Rich may wrap long lines; normalize whitespace for the second command
-        normalized = " ".join(captured.out.split())
+        normalized = " ".join(plain.split())
        assert "specify integration upgrade --force" in normalized

    def test_shared_infra_warns_when_manifest_cannot_be_loaded(self, tmp_path, capsys):
--- a/tests/integrations/test_integration_claude.py
+++ b/tests/integrations/test_integration_claude.py
@@ -197,8 +197,8 @@ class TestClaudeIntegration:
            os.chdir(project)
            runner = CliRunner()
            with (
-                patch("specify_cli._stdin_is_interactive", return_value=True),
-                patch("specify_cli.select_with_arrows", return_value="claude"),
+                patch("specify_cli.commands.init._stdin_is_interactive", return_value=True),
+                patch("specify_cli.commands.init.select_with_arrows", return_value="claude"),
            ):
                result = runner.invoke(
                    app,
--- a/tests/integrations/test_integration_subcommand.py
+++ b/tests/integrations/test_integration_subcommand.py
@@ -7,6 +7,7 @@ import pytest
 from typer.testing import CliRunner

 from specify_cli import app
+from tests.conftest import strip_ansi


 runner = CliRunner()
@@ -49,7 +50,8 @@ def _write_invalid_manifest(project, key):


 def _integration_list_row_cells(output: str, key: str) -> list[str]:
-    row = next(line for line in output.splitlines() if line.startswith(f"│ {key}"))
+    plain = strip_ansi(output)
+    row = next(line for line in plain.splitlines() if line.startswith(f"│ {key}"))
    return [cell.strip() for cell in row.split("│")[1:-1]]


@@ -160,8 +162,9 @@ class TestIntegrationInstall:
        finally:
            os.chdir(old_cwd)
        assert result.exit_code == 0
-        assert "already installed" in result.output
-        normalized = " ".join(result.output.split())
+        plain = strip_ansi(result.output)
+        assert "already installed" in plain
+        normalized = " ".join(plain.split())
        assert "specify integration upgrade copilot" in normalized
        assert "already the default integration" in normalized
        assert "No files were changed" in normalized
@@ -197,9 +200,10 @@ class TestIntegrationInstall:
        finally:
            os.chdir(old_cwd)
        assert result.exit_code != 0
-        assert "Installed integrations: copilot" in result.output
-        assert "Default integration: copilot" in result.output
-        normalized = " ".join(result.output.split())
+        plain = strip_ansi(result.output)
+        assert "Installed integrations: copilot" in plain
+        assert "Default integration: copilot" in plain
+        normalized = " ".join(plain.split())
        assert "To replace the default integration" in normalized
        assert "specify integration switch claude" in normalized
        assert "To install 'claude' alongside" in normalized
@@ -230,6 +234,29 @@ class TestIntegrationInstall:
        assert (project / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
        assert (project / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()

+    def test_install_non_default_refreshes_init_options_version_only(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "claude")
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "install", "codex",
+            "--script", "sh",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+        assert updated["integration"] == "claude"
+        assert updated["ai"] == "claude"
+        assert updated["context_file"] == "CLAUDE.md"
+
    def test_install_additional_preserves_shared_manifest(self, tmp_path):
        project = _init_project(tmp_path, "claude")
        shared_manifest = project / ".specify" / "integrations" / "speckit.manifest.json"
@@ -286,9 +313,10 @@ class TestIntegrationInstall:
        finally:
            os.chdir(old_cwd)
        assert result.exit_code != 0
-        assert "Installed integrations: copilot" in result.output
-        assert "multi-install safe" in result.output
-        normalized = " ".join(result.output.split())
+        plain = strip_ansi(result.output)
+        assert "Installed integrations: copilot" in plain
+        assert "multi-install safe" in plain
+        normalized = " ".join(plain.split())
        assert "To replace the default integration" in normalized
        assert "specify integration switch claude" in normalized
        assert "To install 'claude' alongside" in normalized
@@ -1144,6 +1172,56 @@ class TestIntegrationUpgrade:
        assert "manifest" in result.output
        assert "unreadable" in result.output

+    def test_upgrade_refreshes_init_options_speckit_version(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "claude")
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "claude",
+            "--force",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+
+    def test_upgrade_non_default_refreshes_init_options_version_only(self, tmp_path, monkeypatch):
+        project = _init_project(tmp_path, "gemini")
+        install = _run_in_project(project, [
+            "integration", "install", "claude",
+            "--script", "sh",
+        ])
+        assert install.exit_code == 0, install.output
+
+        init_options = project / ".specify" / "init-options.json"
+        opts = json.loads(init_options.read_text(encoding="utf-8"))
+        opts["speckit_version"] = "0.6.1"
+        init_options.write_text(json.dumps(opts), encoding="utf-8")
+
+        import specify_cli
+
+        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "claude",
+            "--script", "sh",
+            "--force",
+        ])
+
+        assert result.exit_code == 0, result.output
+        updated = json.loads(init_options.read_text(encoding="utf-8"))
+        assert updated["speckit_version"] == "0.8.11"
+        assert updated["integration"] == "gemini"
+        assert updated["ai"] == "gemini"
+        assert updated["context_file"] == "GEMINI.md"
+
    def test_upgrade_does_not_persist_state_when_template_refresh_fails(self, tmp_path, monkeypatch):
        project = _init_project(tmp_path, "claude")
        int_json = project / ".specify" / "integration.json"
--- a/tests/test_check_prerequisites_paths_only.py
+++ b/tests/test_check_prerequisites_paths_only.py
@@ -0,0 +1,205 @@
+"""Tests for check-prerequisites --paths-only skipping branch validation (#2653)."""
+
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+from tests.conftest import requires_bash
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+CHECK_PREREQS_SH = PROJECT_ROOT / "scripts" / "bash" / "check-prerequisites.sh"
+COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+CHECK_PREREQS_PS = PROJECT_ROOT / "scripts" / "powershell" / "check-prerequisites.ps1"
+
+HAS_PWSH = shutil.which("pwsh") is not None
+_POWERSHELL = shutil.which("powershell.exe") or shutil.which("powershell")
+
+
+def _install_bash_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "bash"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_SH, d / "common.sh")
+    shutil.copy(CHECK_PREREQS_SH, d / "check-prerequisites.sh")
+
+
+def _install_ps_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "powershell"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PS, d / "common.ps1")
+    shutil.copy(CHECK_PREREQS_PS, d / "check-prerequisites.ps1")
+
+
+def _clean_env() -> dict[str, str]:
+    env = os.environ.copy()
+    for key in list(env):
+        if key.startswith("SPECIFY_"):
+            env.pop(key)
+    return env
+
+
+def _git_init(repo: Path) -> None:
+    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
+    )
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
+    )
+
+
+@pytest.fixture
+def prereq_repo(tmp_path: Path) -> Path:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    (repo / ".specify").mkdir()
+    _install_bash_scripts(repo)
+    _install_ps_scripts(repo)
+    return repo
+
+
+# ── Bash tests ────────────────────────────────────────────────────────────
+
+
+@requires_bash
+def test_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only must return paths without branch validation (main branch)."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "REPO_ROOT" in data
+    assert "BRANCH" in data
+    assert "FEATURE_DIR" in data
+
+
+@requires_bash
+def test_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only must also work on a properly named spec branch."""
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=prereq_repo,
+        check=True,
+    )
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "FEATURE_DIR" in data
+    assert "001-my-feature" in data.get("BRANCH", "")
+
+
+@requires_bash
+def test_paths_only_text_mode_on_non_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only without --json must return text paths on a non-spec branch."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    assert "REPO_ROOT:" in result.stdout
+    assert "FEATURE_DIR:" in result.stdout
+
+
+@requires_bash
+def test_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
+    """Without --paths-only, branch validation must still fail on main."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode != 0
+    assert "Not on a feature branch" in result.stderr
+
+
+# ── PowerShell tests ──────────────────────────────────────────────────────
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
+    """-PathsOnly must return paths without branch validation (main branch)."""
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "REPO_ROOT" in data
+    assert "BRANCH" in data
+    assert "FEATURE_DIR" in data
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
+    """-PathsOnly must also work on a properly named spec branch."""
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=prereq_repo,
+        check=True,
+    )
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "FEATURE_DIR" in data
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
+    """Without -PathsOnly, branch validation must still fail on main."""
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode != 0
+    assert "Not on a feature branch" in result.stderr
--- a/tests/test_commands_package.py
+++ b/tests/test_commands_package.py
@@ -0,0 +1,48 @@
+"""Tests for the commands/ package structure."""
+import importlib
+
+
+def test_commands_package_importable():
+    mod = importlib.import_module("specify_cli.commands")
+    assert mod is not None
+
+
+def test_commands_init_importable():
+    mod = importlib.import_module("specify_cli.commands.init")
+    assert hasattr(mod, "register")
+    assert callable(mod.register)
+
+
+def test_commands_stubs_importable():
+    for name in ("integration", "preset", "extension", "workflow"):
+        mod = importlib.import_module(f"specify_cli.commands.{name}")
+        assert mod is not None
+
+
+def test_agent_config_importable():
+    from specify_cli._agent_config import (
+        AGENT_CONFIG,
+        AI_ASSISTANT_ALIASES,
+        AI_ASSISTANT_HELP,
+        DEFAULT_INIT_INTEGRATION,
+        SCRIPT_TYPE_CHOICES,
+    )
+    assert isinstance(AGENT_CONFIG, dict)
+    assert isinstance(AI_ASSISTANT_ALIASES, dict)
+    assert isinstance(AI_ASSISTANT_HELP, str)
+    assert DEFAULT_INIT_INTEGRATION == "copilot"
+    assert "sh" in SCRIPT_TYPE_CHOICES
+
+
+def test_agent_config_re_exported_from_init():
+    from specify_cli import AGENT_CONFIG, AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP, SCRIPT_TYPE_CHOICES
+    assert isinstance(AGENT_CONFIG, dict)
+    assert "sh" in SCRIPT_TYPE_CHOICES
+
+
+def test_init_command_registered():
+    from specify_cli import app
+    callback_names = [
+        cmd.callback.__name__ for cmd in app.registered_commands if cmd.callback
+    ]
+    assert "init" in callback_names
--- a/tests/test_extension_skills.py
+++ b/tests/test_extension_skills.py
@@ -173,24 +173,32 @@ class TestExtensionManagerGetSkillsDir:
        assert result == skills_dir

    def test_returns_none_when_no_ai_skills(self, no_skills_project):
-        """Should return None when ai_skills is false."""
+        """Should return None when ai_skills is false and not create the dir."""
        manager = ExtensionManager(no_skills_project)
        result = manager._get_skills_dir()
        assert result is None
+        # Ensure the directory was NOT created on disk
+        from specify_cli import _get_skills_dir as resolve_skills_dir
+        skills_path = resolve_skills_dir(no_skills_project, "claude")
+        assert not skills_path.exists()

    def test_returns_none_when_no_init_options(self, project_dir):
-        """Should return None when init-options.json is missing."""
+        """Should return None when init-options.json is missing and not create any dir."""
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
        assert result is None
+        # No agent skills directory should have been created
+        assert not (project_dir / ".claude" / "skills").exists()
+        assert not (project_dir / ".agents" / "skills").exists()

-    def test_returns_none_when_skills_dir_missing(self, project_dir):
-        """Should return None when skills dir doesn't exist on disk."""
+    def test_creates_skills_dir_on_demand(self, project_dir):
+        """Should create skills dir when ai_skills is enabled but dir is missing."""
        _create_init_options(project_dir, ai="claude", ai_skills=True)
-        # Don't create the skills directory
+        # Don't create the skills directory — _get_skills_dir should do it
        manager = ExtensionManager(project_dir)
        result = manager._get_skills_dir()
-        assert result is None
+        assert result is not None
+        assert result.is_dir()

    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."""
@@ -460,6 +468,38 @@ class TestExtensionSkillRegistration:
        assert "speckit-missing-cmd-ext-exists" in metadata["registered_skills"]
        assert "speckit-missing-cmd-ext-ghost" not in metadata["registered_skills"]

+    @pytest.mark.parametrize("ai", ["claude", "codex"])
+    def test_skills_registered_when_dir_missing(self, project_dir, temp_dir, ai):
+        """Extension add should create skills dir on demand and register skills.
+
+        Regression test for https://github.com/github/spec-kit/issues/2682:
+        when an extension is installed before the agent skills directory exists,
+        skills must still be materialized (the directory is created on demand).
+        """
+        _create_init_options(project_dir, ai=ai, ai_skills=True)
+        # Deliberately do NOT create the skills directory
+        ext_dir = _create_extension_dir(temp_dir, ext_id="early-ext")
+
+        manager = ExtensionManager(project_dir)
+        manifest = manager.install_from_directory(
+            ext_dir, "0.1.0", register_commands=False
+        )
+
+        # Skills dir should have been created automatically
+        from specify_cli import _get_skills_dir as resolve_skills_dir
+        skills_dir = resolve_skills_dir(project_dir, ai)
+        assert skills_dir.is_dir()
+
+        # SKILL.md files should exist
+        assert (skills_dir / "speckit-early-ext-hello" / "SKILL.md").exists()
+        assert (skills_dir / "speckit-early-ext-world" / "SKILL.md").exists()
+
+        # Registry should record them
+        metadata = manager.registry.get(manifest.id)
+        assert len(metadata["registered_skills"]) == 2
+        assert "speckit-early-ext-hello" in metadata["registered_skills"]
+        assert "speckit-early-ext-world" in metadata["registered_skills"]
+

 # ===== Extension Skill Unregistration Tests =====

--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -2346,6 +2346,154 @@ class TestPresetSkills:
        metadata = manager.registry.get("self-test")
        assert "speckit-specify" in metadata.get("registered_skills", [])

+    def test_register_skills_resolves_command_refs(self, project_dir, temp_dir):
+        """Preset skill overrides must resolve __SPECKIT_COMMAND_*__ tokens (issue #2717).
+
+        ``_register_skills()`` previously ran only ``resolve_skill_placeholders()``,
+        so command cross-references leaked into SKILL.md as raw placeholders
+        instead of rendering as ``/speckit-<cmd>`` like the command layer.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-install",
+            "speckit.specify",
+            "Override specify",
+            "Run `__SPECKIT_COMMAND_SPECIFY__` then `__SPECKIT_COMMAND_PLAN__`.\n",
+        )
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked into SKILL.md"
+        # Claude's invoke_separator is "-", so tokens render as /speckit-<cmd>.
+        assert "/speckit-specify" in content
+        assert "/speckit-plan" in content
+
+    def test_restore_skill_resolves_command_refs(self, project_dir, temp_dir):
+        """Skill restore on preset removal must also resolve command tokens (issue #2717)."""
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        core_cmds = project_dir / ".specify" / "templates" / "commands"
+        core_cmds.mkdir(parents=True, exist_ok=True)
+        (core_cmds / "specify.md").write_text(
+            "---\ndescription: Core specify\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\n"
+        )
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-restore",
+            "speckit.specify",
+            "Override specify",
+            "Override body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-restore")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on restore"
+        assert "/speckit-plan" in content
+
+    def test_reconcile_override_skill_resolves_command_refs(self, project_dir, temp_dir):
+        """Reconcile's project-override restore must resolve command tokens (issue #2717).
+
+        When a preset that overrode a command is removed and a project override
+        becomes the winning layer, ``_reconcile_skills`` rewrites the skill from
+        the override body — which must also render ``__SPECKIT_COMMAND_*__`` tokens.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        # Project override wins once the preset is removed; its body carries a
+        # command cross-reference token. No core template exists for "specify",
+        # so the skill is restored exclusively via the reconcile override branch.
+        overrides_dir = project_dir / ".specify" / "templates" / "overrides"
+        overrides_dir.mkdir(parents=True, exist_ok=True)
+        (overrides_dir / "speckit.specify.md").write_text(
+            "---\ndescription: Override specify\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\n"
+        )
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-reconcile",
+            "speckit.specify",
+            "Preset specify",
+            "Preset body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-reconcile")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "override:speckit.specify" in content, "skill should be restored from the project override"
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on reconcile"
+        assert "/speckit-plan" in content
+
+    def test_extension_restore_resolves_command_refs(self, project_dir, temp_dir):
+        """Extension-backed skill restore must resolve command tokens (issue #2717).
+
+        When a preset override is removed and the skill is restored from an
+        extension command body, ``__SPECKIT_COMMAND_*__`` tokens in that body
+        must render as slash-command invocations like the core-template path.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "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(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\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 = self._create_command_preset(
+            temp_dir,
+            "cmdref-ext-restore",
+            "speckit.fakeext.cmd",
+            "Override fakeext cmd",
+            "Override body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-ext-restore")
+
+        content = (skills_dir / "speckit-fakeext-cmd" / "SKILL.md").read_text()
+        assert "source: extension:fakeext" in content, "skill should be restored from the extension"
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on extension restore"
+        assert "/speckit-plan" in content
+
    def test_core_command_override_skill_uses_preset_command_description(self, project_dir, temp_dir):
        """Preset skill overrides for core commands should keep preset frontmatter descriptions."""
        self._write_init_options(project_dir, ai="claude")
--- a/tests/test_ps1_encoding.py
+++ b/tests/test_ps1_encoding.py
@@ -0,0 +1,54 @@
+"""Regression tests for PowerShell 5.1 compatibility (GitHub issue #2680).
+
+PowerShell 5.1 (built-in on Windows) defaults to the system's legacy encoding
+when reading .ps1 files.  Non-ASCII characters in UTF-8-encoded scripts cause
+parse errors because multi-byte sequences are misinterpreted as individual bytes.
+
+These tests ensure that all shipped .ps1 files remain ASCII-only so they work
+on both PowerShell 5.1 and 7+.
+"""
+
+from pathlib import Path
+
+import pytest
+
+REPO_ROOT = Path(__file__).resolve().parent.parent
+
+# All directories that contain shipped PowerShell scripts.
+_PS1_DIRS = [
+    REPO_ROOT / "scripts" / "powershell",
+    REPO_ROOT / "extensions" / "git" / "scripts" / "powershell",
+]
+
+
+def _collect_ps1_files():
+    """Yield all .ps1 files under the known script directories."""
+    for d in _PS1_DIRS:
+        if d.is_dir():
+            yield from sorted(d.rglob("*.ps1"))
+
+
+_PS1_FILES = list(_collect_ps1_files())
+
+
+@pytest.mark.parametrize("ps1_file", _PS1_FILES, ids=lambda p: str(p.relative_to(REPO_ROOT)))
+def test_ps1_file_is_ascii_only(ps1_file: Path):
+    """Every .ps1 file must contain only ASCII characters (PS 5.1 compat)."""
+    content = ps1_file.read_bytes()
+    non_ascii = [
+        (i + 1, byte)
+        for i, byte in enumerate(content)
+        if byte > 127
+    ]
+    assert not non_ascii, (
+        f"{ps1_file.relative_to(REPO_ROOT)} contains non-ASCII bytes "
+        f"(PowerShell 5.1 incompatible): "
+        f"first at byte offset {non_ascii[0][0]} (0x{non_ascii[0][1]:02x})"
+    )
+
+
+def test_ps1_files_discovered():
+    """Sanity check: at least the known script files are found."""
+    names = {p.name for p in _PS1_FILES}
+    assert "common.ps1" in names
+    assert "initialize-repo.ps1" in names
--- a/tests/test_setup_plan_no_overwrite.py
+++ b/tests/test_setup_plan_no_overwrite.py
@@ -0,0 +1,216 @@
+"""Tests for setup-plan preserving existing plan.md (#2653)."""
+
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+from tests.conftest import requires_bash
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+SETUP_PLAN_SH = PROJECT_ROOT / "scripts" / "bash" / "setup-plan.sh"
+COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+SETUP_PLAN_PS = PROJECT_ROOT / "scripts" / "powershell" / "setup-plan.ps1"
+PLAN_TEMPLATE = PROJECT_ROOT / "templates" / "plan-template.md"
+
+HAS_PWSH = shutil.which("pwsh") is not None
+_POWERSHELL = shutil.which("powershell.exe") or shutil.which("powershell")
+
+
+def _install_bash_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "bash"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_SH, d / "common.sh")
+    shutil.copy(SETUP_PLAN_SH, d / "setup-plan.sh")
+
+
+def _install_ps_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "powershell"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PS, d / "common.ps1")
+    shutil.copy(SETUP_PLAN_PS, d / "setup-plan.ps1")
+
+
+def _minimal_templates(repo: Path) -> None:
+    tdir = repo / ".specify" / "templates"
+    tdir.mkdir(parents=True, exist_ok=True)
+    shutil.copy(PLAN_TEMPLATE, tdir / "plan-template.md")
+
+
+def _clean_env() -> dict[str, str]:
+    env = os.environ.copy()
+    for key in list(env):
+        if key.startswith("SPECIFY_"):
+            env.pop(key)
+    return env
+
+
+def _git_init(repo: Path) -> None:
+    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
+    )
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
+    )
+
+
+@pytest.fixture
+def plan_repo(tmp_path: Path) -> Path:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=repo,
+        check=True,
+    )
+    (repo / ".specify").mkdir()
+    _minimal_templates(repo)
+    _install_bash_scripts(repo)
+    _install_ps_scripts(repo)
+    return repo
+
+
+# ── Bash tests ────────────────────────────────────────────────────────────
+
+
+@requires_bash
+def test_setup_plan_creates_plan_when_missing(plan_repo: Path) -> None:
+    """First run must create plan.md from the template."""
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    plan_path = Path(data["IMPL_PLAN"])
+    assert plan_path.is_file()
+    # Template content should be present
+    content = plan_path.read_text(encoding="utf-8")
+    assert len(content) > 0
+
+
+@requires_bash
+def test_setup_plan_preserves_existing_plan(plan_repo: Path) -> None:
+    """Rerun must not overwrite an existing plan.md."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    existing_content = "# My carefully authored plan\n\nDo not overwrite me.\n"
+    (feat / "plan.md").write_text(existing_content, encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    # Plan must be unchanged
+    assert (feat / "plan.md").read_text(encoding="utf-8") == existing_content
+
+
+@requires_bash
+def test_setup_plan_skip_message_on_stderr_in_json_mode(plan_repo: Path) -> None:
+    """In --json mode, status messages must go to stderr, not stdout."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# existing\n", encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    # stdout must be valid JSON (no status messages mixed in)
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    # The skip message should be on stderr
+    assert "already exists" in result.stderr
+
+
+@requires_bash
+def test_setup_plan_json_parseable_on_first_run(plan_repo: Path) -> None:
+    """In --json mode, first-run stdout must be parseable JSON (no status on stdout)."""
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    assert "Copied plan template" in result.stderr
+
+
+# ── PowerShell tests ──────────────────────────────────────────────────────
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_setup_plan_creates_plan_when_missing(plan_repo: Path) -> None:
+    """First run must create plan.md from the template."""
+    script = plan_repo / ".specify" / "scripts" / "powershell" / "setup-plan.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    plan_path = Path(data["IMPL_PLAN"])
+    assert plan_path.is_file()
+    content = plan_path.read_text(encoding="utf-8")
+    assert len(content) > 0
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_setup_plan_preserves_existing_plan(plan_repo: Path) -> None:
+    """Rerun must not overwrite an existing plan.md."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    existing_content = "# My carefully authored plan\n\nDo not overwrite me.\n"
+    (feat / "plan.md").write_text(existing_content, encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "powershell" / "setup-plan.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    assert (feat / "plan.md").read_text(encoding="utf-8") == existing_content
+    # stdout must be valid JSON (no status messages mixed in)
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    # The skip message should be on stderr
+    assert "already exists" in result.stderr
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -13,6 +13,7 @@ Covers:
 from __future__ import annotations

 import json
+import os
 import shutil
 import tempfile
 from pathlib import Path
@@ -332,6 +333,44 @@ class TestExpressions:
        result = evaluate_expression("{{ steps.tasks.output.task_list[0].file }}", ctx)
        assert result == "a.md"

+    def test_context_run_id_resolves(self):
+        """``{{ context.run_id }}`` resolves to ``StepContext.run_id``.
+
+        Locks the contract from issue #2590: workflow templates can
+        reference the engine-assigned run id for telemetry, artifact
+        metadata, or per-run scratch isolation.
+        """
+        from specify_cli.workflows.expressions import evaluate_expression
+        from specify_cli.workflows.base import StepContext
+
+        ctx = StepContext(run_id="a1b2c3d4")
+        assert evaluate_expression("{{ context.run_id }}", ctx) == "a1b2c3d4"
+
+    def test_context_run_id_defaults_to_empty_when_unset(self):
+        """``{{ context.run_id }}`` resolves to ``""`` when no run is
+        active (dry-run, validation, ad-hoc evaluator usage) rather
+        than raising — workflows referencing the variable never error
+        outside a run context.
+        """
+        from specify_cli.workflows.expressions import evaluate_expression
+        from specify_cli.workflows.base import StepContext
+
+        # No run_id set on the context.
+        ctx = StepContext()
+        assert evaluate_expression("{{ context.run_id }}", ctx) == ""
+
+    def test_context_run_id_string_interpolation(self):
+        """Run id interpolates inside a larger template string — the
+        common pattern for stamping shell commands and artifact paths
+        with the run id.
+        """
+        from specify_cli.workflows.expressions import evaluate_expression
+        from specify_cli.workflows.base import StepContext
+
+        ctx = StepContext(run_id="deadbeef")
+        result = evaluate_expression("RUN_ID={{ context.run_id }}", ctx)
+        assert result == "RUN_ID=deadbeef"
+

 # ===== Integration Dispatch Tests =====

@@ -373,7 +412,8 @@ class TestBuildExecArgs:
        from specify_cli.integrations.copilot import CopilotIntegration
        impl = CopilotIntegration()
        args = impl.build_exec_args("do stuff", model="claude-sonnet-4-20250514")
-        assert args[0] == "copilot"
+        expected_exec = "copilot.cmd" if os.name == "nt" else "copilot"
+        assert args[0] == expected_exec
        assert "-p" in args
        assert "--yolo" in args
        assert "--model" in args
@@ -2152,6 +2192,147 @@ steps:
        assert "retry-loop:step-b:2" in state.step_results


+# ===== context.run_id Tests =====
+#
+# End-to-end coverage for the `{{ context.run_id }}` template
+# variable introduced in issue #2590. Locks resolution inside the
+# three step types the acceptance criteria called out — shell `run:`,
+# command `input.args:`, and switch `expression:` — plus the
+# "workflow doesn't reference it" backward-compat path.
+
+
+class TestContextRunId:
+    """End-to-end tests for `{{ context.run_id }}` in workflow YAML."""
+
+    def test_shell_run_resolves_run_id(self, project_dir):
+        """`run: "echo {{ context.run_id }}"` substitutes the
+        engine-assigned run id into the spawned shell, and the
+        same value appears on `state.run_id`.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "stamp-run-id"
+  name: "Stamp Run Id"
+  version: "1.0.0"
+steps:
+  - id: stamp
+    type: shell
+    run: "echo RUN_ID={{ context.run_id }}"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition, run_id="abc12345")
+
+        assert state.run_id == "abc12345"
+        stdout = state.step_results["stamp"]["output"]["stdout"]
+        assert stdout.strip() == "RUN_ID=abc12345"
+
+    def test_command_input_args_resolves_run_id(self, project_dir):
+        """`input.args: "{{ context.run_id }}"` is resolved by
+        `CommandStep` and recorded in step output, even when CLI
+        dispatch is unavailable (no integration installed). Covers
+        the artifact-metadata use case from the issue.
+        """
+        from unittest.mock import patch
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "command-stamp"
+  name: "Command Stamp"
+  version: "1.0.0"
+  integration: claude
+steps:
+  - id: tag-artifact
+    command: speckit.specify
+    input:
+      args: "{{ context.run_id }}"
+""")
+        engine = WorkflowEngine(project_dir)
+        with patch(
+            "specify_cli.workflows.steps.command.shutil.which",
+            return_value=None,
+        ):
+            state = engine.execute(definition, run_id="cafef00d")
+
+        # Even when dispatch fails (no CLI), the resolved input is
+        # recorded so downstream observers see the run id in artifact
+        # metadata.
+        assert state.step_results["tag-artifact"]["output"]["input"]["args"] == "cafef00d"
+
+    def test_switch_expression_matches_on_run_id(self, project_dir):
+        """`switch` over `{{ context.run_id }}` matches against case
+        keys, and the nested branch can ALSO reference
+        `{{ context.run_id }}`. Demonstrates the run id is a
+        first-class value in the expression engine (not just a
+        string-interpolation token) AND that it propagates into
+        nested step execution via the recursive `_execute_steps`
+        traversal.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "switch-on-run-id"
+  name: "Switch On Run Id"
+  version: "1.0.0"
+steps:
+  - id: route
+    type: switch
+    expression: "{{ context.run_id }}"
+    cases:
+      target-run:
+        - id: matched-branch
+          type: shell
+          run: "echo nested-run-id={{ context.run_id }}"
+    default:
+      - id: default-branch
+        type: shell
+        run: "echo defaulted"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition, run_id="target-run")
+
+        assert state.status == RunStatus.COMPLETED
+        assert state.step_results["route"]["output"]["matched_case"] == "target-run"
+        assert "matched-branch" in state.step_results
+        assert "default-branch" not in state.step_results
+        # The nested branch sees the same run id — propagation through
+        # recursive `_execute_steps` is intact.
+        nested_stdout = state.step_results["matched-branch"]["output"]["stdout"]
+        assert nested_stdout.strip() == "nested-run-id=target-run"
+
+    def test_workflow_without_context_reference_unchanged(self, project_dir):
+        """Workflows that do not reference `{{ context.run_id }}`
+        continue to run exactly as before. Locks the byte-equivalent
+        default required by the issue's acceptance criteria.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "no-context-ref"
+  name: "No Context Ref"
+  version: "1.0.0"
+steps:
+  - id: only-step
+    type: shell
+    run: "echo hello"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.COMPLETED
+        assert state.step_results["only-step"]["output"]["stdout"].strip() == "hello"
+
+
 # ===== State Persistence Tests =====

 class TestRunState:
--- a/workflows/README.md
+++ b/workflows/README.md
@@ -239,6 +239,33 @@ message: "{{ status | default('pending') }}"

 Supported filters: `default`, `join`, `contains`, `map`.

+### Runtime Context
+
+`{{ context.* }}` exposes engine-managed runtime metadata for the
+current run:
+
+| Variable | Description |
+|----------|-------------|
+| `context.run_id` | The current workflow run id (the same value Spec Kit prints as `Run ID:` at the end of `workflow run`). Auto-generated runs are 8-character hex from `uuid4`; operator-supplied ids may be any alphanumeric string with hyphens or underscores. Empty string outside a run context. |
+
+```yaml
+# Stamp telemetry events with the run id for cross-system join.
+- id: emit-event
+  type: shell
+  run: 'echo "{\"run_id\":\"{{ context.run_id }}\",\"event\":\"started\"}" >> events.jsonl'
+
+# Per-run scratch directory.
+- id: prep-scratch
+  type: shell
+  run: 'mkdir -p /tmp/run-{{ context.run_id }}'
+
+# Pass run id into a command for artifact metadata.
+- id: tag-artifact
+  command: speckit.specify
+  input:
+    args: "{{ context.run_id }}"
+```
+
 ## Input Types

 Workflow inputs are type-checked and coerced from CLI string values: