chore: bump version to 0.12.14

* Add Spec Kit Memory extension to community catalog

Add memory extension submitted by @zaytsevand to:
- extensions/catalog.community.json (alphabetical order)
- docs/community/extensions.md community extensions table

Closes #3446

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: resolve merge conflicts with main branch

- extensions/catalog.community.json: keep updated_at 2026-07-10 (more recent)
- docs/community/extensions.md: include both Spec Kit Figma (main) and
  Spec Kit Memory (this PR) in alphabetical order

Assisted-by: GitHub Copilot (model: claude-sonnet-4.5, autonomous)

* fix: add memsearch optional tool dependency to memory extension catalog entry

Assisted-by: GitHub Copilot (model: claude-sonnet-4.5, autonomous)

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

.github/CODEOWNERS

@@ -5,4 +5,3 @@
 /extensions/catalog.community.json @mnriem
 /integrations/catalog.community.json @mnriem
 /presets/catalog.community.json @mnriem
-

.github/ISSUE_TEMPLATE/agent_request.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for requesting a new agent! Before submitting, please check if the agent is already supported.
-        
+
         **Currently supported agents**: Amp, Antigravity, Auggie CLI, Claude Code, Cline, CodeBuddy, Codex CLI, Cursor, Devin for Terminal, Firebender, Forge, Gemini CLI, GitHub Copilot, Goose, Hermes Agent, IBM Bob, Junie, Kilo Code, Kimi Code, Kiro CLI, Lingma, Mistral Vibe, Oh My Pi, opencode, Pi Coding Agent, Qoder CLI, Qwen Code, RovoDev ACLI, SHAI, Tabnine CLI, Trae, ZCode, Zed
 
   - type: input

.github/ISSUE_TEMPLATE/extension_submission.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for contributing an extension! This template helps you submit your extension to the community catalog.
-        
+
         **Before submitting:**
         - Review the [Extension Publishing Guide](https://github.com/github/spec-kit/blob/main/extensions/EXTENSION-PUBLISHING-GUIDE.md)
         - Ensure your extension has a valid `extension.yml` manifest
@@ -209,9 +209,9 @@ body:
         **Tested on:**
         - macOS 14.0 with Spec Kit v0.1.0
         - Linux Ubuntu 22.04 with Spec Kit v0.1.0
-        
+
         **Test project:** [Link or description]
-        
+
         **Test scenarios:**
         1. Installed extension
         2. Configured settings
@@ -230,7 +230,7 @@ body:
         ```bash
         # Install extension
         specify extension add <extension-name> --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
-        
+
         # Use a command
         /speckit.your-extension.command-name arg1 arg2
         ```

.github/ISSUE_TEMPLATE/preset_submission.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for contributing a preset! This template helps you submit your preset to the community catalog.
-        
+
         **Before submitting:**
         - Review the [Preset Publishing Guide](https://github.com/github/spec-kit/blob/main/presets/PUBLISHING.md)
         - Ensure your preset has a valid `preset.yml` manifest

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,4 +19,3 @@
 - [ ] I **did** use AI assistance (describe below)
 
 <!-- If you used AI, briefly describe how (e.g., "Code generated by Copilot", "Consulted ChatGPT for approach"): -->
-

.github/workflows/lint.yml

@@ -37,7 +37,7 @@ jobs:
           fi
 
       - name: Run markdownlint-cli2
-        uses: DavidAnson/markdownlint-cli2-action@ded1f9488f68a970bc66ea5619e13e9b52e601cd # v23
+        uses: DavidAnson/markdownlint-cli2-action@8de2aa07cae85fd17c0b35642db70cf5495f1d25 # v24.0.0
         with:
           globs: |
             '**/*.md'

.github/workflows/publish-pypi.yml

@@ -32,7 +32,7 @@ jobs:
           ref: refs/tags/${{ inputs.tag }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -74,7 +74,7 @@ jobs:
           path: dist/
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Publish to PyPI
         run: uv publish

.github/workflows/stale.yml

@@ -20,24 +20,24 @@ jobs:
           days-before-stale: 150
           # Days of inactivity before a stale issue or PR is closed (after being marked stale)
           days-before-close: 30
-          
+
           # Stale issue settings
           stale-issue-message: 'This issue has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
           close-issue-message: 'This issue has been automatically closed due to inactivity (180 days total). If you believe this issue is still relevant, please reopen it or create a new issue.'
           stale-issue-label: 'stale'
-          
+
           # Stale PR settings
           stale-pr-message: 'This pull request has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
           close-pr-message: 'This pull request has been automatically closed due to inactivity (180 days total). If you believe this PR is still relevant, please reopen it or create a new PR.'
           stale-pr-label: 'stale'
-          
+
           # Exempt issues and PRs with these labels from being marked as stale
           exempt-issue-labels: 'pinned,security'
           exempt-pr-labels: 'pinned,security'
-          
+
           # Only issues or PRs with all of these labels are checked
           # Leave empty to check all issues and PRs
           any-of-labels: ''
-          
+
           # Operations per run (helps avoid rate limits)
           operations-per-run: 250

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -37,7 +37,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6

.markdownlint-cli2.jsonc

@@ -26,4 +26,4 @@
   "ignores": [
     ".genreleases/"
   ]
-}
+}

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-executables-have-shebangs
+      - id: check-yaml
+        exclude: \.lock\.yml$
+      - id: end-of-file-fixer
+        exclude: \.lock\.yml$
+      - id: trailing-whitespace
+        exclude: \.lock\.yml$

CHANGELOG.md

@@ -2,6 +2,112 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.12.14] - 2026-07-13
+
+### Changed
+
+- [extension] Add Spec Kit Memory extension to community catalog (#3455)
+- Add Test-First Governance preset to community catalog (#3504)
+- Add Autonomous Run Governance preset to community catalog (#3501)
+- fix(workflows): validate command step input/options are mappings (#3262)
+- fix(presets): resolve() honors manifest-declared file: for installed presets (#3351)
+- fix(init): don't block on confirmation for 'init --here' without a TTY (#3236)
+- [extension] Add Quality Gates (Enforcement Layer) extension to community catalog (#3431)
+- fix(integrations): exit cleanly on unbalanced quote in --integration-options (#3457) (#3466)
+- fix(integrations): declare kiro-cli multi-install safe (#3471) (#3485)
+- fix(workflows): fail fan-in step on non-list wait_for instead of crashing (#3482)
+- chore: release 0.12.13, begin 0.12.14.dev0 development (#3498)
+
+## [0.12.13] - 2026-07-13
+
+### Changed
+
+- fix(workflows): fail switch step on non-mapping cases instead of crashing (#3481)
+- Cleanup agent-file-template.md (#2579)
+- fix: mark Kiro integration as multi-install safe (#3472)
+- fix: rewrite extension-relative subdir paths in generated command bodies (#3444)
+- fix(templates): point constitution sync checklist at installed command files (#3418)
+- feat(workflows): make shell step timeout configurable (#3327) (#3328)
+- docs: clarify that release tags keep the leading v prefix (#3463)
+- fix(workflows): don't crash on membership test against a non-iterable (#3448)
+- fix(workflows): if-step validate accepts falsy non-list else (#3264)
+- chore: release 0.12.12, begin 0.12.13.dev0 development (#3490)
+
+## [0.12.12] - 2026-07-13
+
+### Changed
+
+- fix(extensions): set-priority repairs corrupted boolean priority (#3268)
+- fix(presets): set-priority repairs corrupted boolean priority (#3269)
+- fix(workflows): engine loop cap ignores bool max_iterations (#3270)
+- docs(bundles): document --integration on 'bundle update' (#3271)
+- fix(workflows): harden catalog.py against mis-shaped registry & non-string fields (#3375)
+- Add Verify Review Ship extension to community catalog (#3450)
+- fix(bundle): reject file:// / local download_url — catalog URLs are HTTPS-only (#3344)
+- fix(extensions): handle prefix-colliding env vars in _get_env_config (#3350)
+- docs: document copilot skills mode (--skills) and markdown deprecation (#3313)
+- chore: release 0.12.11, begin 0.12.12.dev0 development (#3460)
+
+## [0.12.11] - 2026-07-10
+
+### Changed
+
+- fix(agent-context): discover nested plan.md in scoped layouts (#3024) (#3301)
+- fix(auth): return no matches, not raw ValueError, for a malformed URL (#3437)
+- fix(catalogs): raise catalog error, not raw ValueError, on a malformed URL (#3435)
+- fix(bundler): raise BundlerError, not raw ValueError, on a malformed catalog URL (#3433)
+- chore: add pre-commit config and fix trailing whitespace/end-of-file (#3430)
+- Add EARS Requirements Syntax extension to community catalog (#3407)
+- Add Spec Kit Figma extension to community catalog (#3408)
+- fix(workflows): report validation errors instead of crashing on non-string workflow.yml scalars (#3421)
+- fix(templates): remove self-referencing path in plan-template.md note (#3417)
+- chore: release 0.12.10, begin 0.12.11.dev0 development (#3453)
+
+## [0.12.10] - 2026-07-10
+
+### Changed
+
+- chore(deps): bump astral-sh/setup-uv from 8.2.0 to 8.3.2 (#3439)
+- chore(deps): bump DavidAnson/markdownlint-cli2-action (#3438)
+- fix(templates): correct phase numbering in plan.md (#3416)
+- fix(git-ext): honor explicit -Number 0 in PowerShell branch creation (#3412)
+- docs: add 'spectatui' entry to friends.md (#3362)
+- test: pin interpreter probe so py-template render test passes on Windows (#3428)
+- feat(workflows): make shell step timeout configurable (#3404)
+- fix: find plans in nested spec directories (#3405)
+- feat(templates): add py: lines to command templates' scripts frontmatter (#3403)
+- chore: release 0.12.9, begin 0.12.10.dev0 development (#3426)
+
+## [0.12.9] - 2026-07-09
+
+### Changed
+
+- fix(integrations): skip Windows Store python3 alias stub in resolve_python_interpreter (#3385)
+- fix(integrations): escape control characters in SKILL.md frontmatter (#3399)
+- fix(workflows): apply chained expression filters left-to-right (#3339)
+- fix(scripts): resolve invoke_separator by parse success, not python3 availability (#3304) (#3320)
+- fix(shared-infra): refresh_shared_templates preserves recovered user files (#3378)
+- fix(agents): resolve skill placeholders in Goose (yaml) command output (#3374)
+- fix(bundler): enforce version pin on bundled preset/extension installs (#3377)
+- Update Golden Demo extension to v0.3.0 (#3394)
+- test: isolate integration test home (#3144)
+- chore: release 0.12.8, begin 0.12.9.dev0 development (#3410)
+
+## [0.12.8] - 2026-07-08
+
+### Changed
+
+- [extension] Add LLM Wiki extension to community catalog (#3361)
+- Docs: Document missing CLI flags and integrations (#3182)
+- Docs: Remove Cursor from CLI check list in README (#3184)
+- feat(extensions): port update-agent-context to Python (#3387)
+- fix(scripts): fall through to grep/sed when python3 is a broken stub in feature.json parser (#3312)
+- fix(toml): escape control characters so generated command files parse (#3341)
+- fix(cli): exit cleanly on malformed IPv6 URLs in `extension`/`preset`/`workflow add` (#3369)
+- fix(github-http): return None on malformed GHES port instead of raising (#3379)
+- fix(integrations): guard _sha256 against unreadable managed files (#3376)
+- chore: release 0.12.7, begin 0.12.8.dev0 development (#3398)
+
 ## [0.12.7] - 2026-07-07
 
 ### Changed

LICENSE

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.md

@@ -45,7 +45,7 @@ Spec-Driven Development **flips the script** on traditional software development
 
 ### 1. Install Specify CLI
 
-Requires **[uv](https://docs.astral.sh/uv/)** ([install uv](./docs/install/uv.md)). Replace `vX.Y.Z` with the latest tag from [Releases](https://github.com/github/spec-kit/releases):
+Requires **[uv](https://docs.astral.sh/uv/)** ([install uv](./docs/install/uv.md)). Replace `vX.Y.Z` with the latest release tag from [Releases](https://github.com/github/spec-kit/releases) — keep the leading `v` (for example, `v0.12.11`, not `0.12.11`):
 
 ```bash
 uv tool install specify-cli --from git+https://github.com/github/spec-kit.git@vX.Y.Z

docs/.gitignore

@@ -6,4 +6,3 @@ obj/
 # Temporary files
 *.tmp
 *.log
-

docs/community/extensions.md

@@ -52,13 +52,14 @@ The following community-contributed extensions are available in [`catalog.commun
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
 | DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| EARS Requirements Syntax | Author, lint, and convert requirements using EARS - the five industry-standard sentence patterns for unambiguous, testable requirements | `docs` | Read+Write | [spec-kit-ears](https://github.com/dhruv-15-03/spec-kit-ears) |
 | Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
 | Fix Findings | Automated analyze-fix-reanalyze loop that resolves spec findings until clean | `code` | Read+Write | [spec-kit-fix-findings](https://github.com/Quratulain-bilal/spec-kit-fix-findings) |
 | FixIt Extension | Spec-aware bug fixing — maps bugs to spec artifacts, proposes a plan, applies minimal changes | `code` | Read+Write | [spec-kit-fixit](https://github.com/speckit-community/spec-kit-fixit) |
 | Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
 | GitHub Issues Integration 1 | Generate spec artifacts from GitHub Issues - import issues, sync updates, and maintain bidirectional traceability | `integration` | Read+Write | [spec-kit-github-issues](https://github.com/Fatima367/spec-kit-github-issues) |
 | GitHub Issues Integration 2 | Creates and syncs local specs from an existing GitHub issue | `integration` | Read+Write | [spec-kit-issue](https://github.com/aaronrsun/spec-kit-issue) |
-| Golden Demo | Extracts acceptance criteria from specs, builds test vectors, and produces a behavioral drift report — complementary to Architecture Guard and CDD | `docs` | Read+Write | [spec-kit-golden-demo](https://github.com/jasstt/spec-kit-golden-demo) |
+| Golden Demo | Deterministic behavioral drift oracle. Extracts acceptance criteria, generates fuzz test vectors (seed=42), compares golden Python implementations against real code in any language. CI/CD gatekeeper with warn/strict modes. | `docs` | Read+Write | [spec-kit-golden-demo](https://github.com/jasstt/spec-kit-golden-demo) |
 | Improve Extension | Audits any codebase as a senior advisor and writes prioritized, self-contained spec prompts under specs/ that the spec-kit lifecycle can process | `process` | Read+Write | [spec-kit-improve](https://github.com/d0whc3r/spec-kit-improve) |
 | Intake | Normalize PRD, design, HTML SSOT, and test-case evidence into SDD-ready intake artifacts. | `docs` | Read+Write | [spec-kit-intake](https://github.com/bigsmartben/spec-kit-intake) |
 | Intelligent Agent Orchestrator | Cross-catalog agent discovery and intelligent prompt-to-command routing | `process` | Read+Write | [spec-kit-orchestrator](https://github.com/pragya247/spec-kit-orchestrator) |
@@ -97,6 +98,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | 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) |
+| Quality Gates (Enforcement Layer) | Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity). | `process` | Read+Write | [spec-gates](https://github.com/schwichtgit/spec-gates) |
 | RAG Azure Builder | Spec Kit extension for onboarding and operating an Azure RAG stack with guided workflows. | `process` | Read+Write | [spec-kit-extension-rag-azure-builder](https://github.com/Sertxito/spec-kit-extension-rag-azure-builder) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss-Projects/spec-kit-ralph) |
 | Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
@@ -117,6 +119,8 @@ The following community-contributed extensions are available in [`catalog.commun
 | Spec Critique Extension | Dual-lens critical review of spec and plan from product strategy and engineering risk perspectives | `docs` | Read-only | [spec-kit-critique](https://github.com/arunt14/spec-kit-critique) |
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
 | Spec Kit Discovery Extension | Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation | `process` | Read+Write | [spec-kit-discovery](https://github.com/bigsmartben/spec-kit-discovery) |
+| Spec Kit Figma | Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows. | `integration` | Read+Write | [spec-kit-figma](https://github.com/Fyloss/spec-kit-figma) |
+| Spec Kit Memory | Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows | `docs` | Read+Write | [spec-kit-memory](https://github.com/zaytsevand/spec-kit-memory) |
 | Spec Kit Preview | Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Spec Kit Schedule | Optimal multi-agent task scheduling via CP-SAT — DAG precedence, hallucination-aware caps, file-conflict avoidance, stochastic durations, replanning, and interactive HTML output | `process` | Read+Write | [spec-kit-schedule](https://github.com/jfranc38/spec-kit-schedule) |
 | Spec Kit TLDR | Render a feature's spec.md / plan.md into a review-oriented TLDR (self-contained HTML dashboard + PR-native Markdown) that surfaces risks for faster PR review. | `visibility` | Read+Write | [speckit-tldr](https://github.com/qurore/speckit-tldr) |
@@ -146,6 +150,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Token Economy | Token routing, measured savings, and context audit workflows | `process` | Read+Write | [spec-kit-token-economy](https://github.com/formin/spec-kit-token-economy) |
 | V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
 | Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
+| Verify Review Ship | Adds post-implementation verify, review, and ship readiness gates to Spec Kit workflows | `process` | Read-only | [spec-kit-verify-review-ship](https://github.com/cadugevaerd/spec-kit-verify-review-ship) |
 | Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
 | Version Guard | Verify tech stack versions against live npm registries before planning and implementation | `process` | Read-only | [spec-kit-version-guard](https://github.com/KevinBrown5280/spec-kit-version-guard) |
 | What-if Analysis | Preview the downstream impact (complexity, effort, tasks, risks) of requirement changes before committing to them | `visibility` | Read-only | [spec-kit-whatif](https://github.com/DevAbdullah90/spec-kit-whatif) |

docs/community/friends.md

@@ -14,3 +14,5 @@ Community projects that extend, visualize, or build on Spec Kit:
 - **[SpecKit Companion](https://marketplace.visualstudio.com/items?itemName=alfredoperez.speckit-companion)** — A VS Code extension that brings a visual GUI to Spec Kit. Browse specs in a rich markdown viewer with clickable file references, create specifications with image attachments, comment and refine each step inline (GitHub-style review), track your progress through the SDD workflow with a visual phase stepper, and manage steering documents like constitutions and templates.
 
 - **[cc-spec-kit](https://github.com/speckit-community/cc-spec-kit)** — Community-maintained plugin for Claude Code and GitHub Copilot CLI that installs Spec Kit skills via the plugin marketplace.
+
+- **[spectatui](https://github.com/tinesoft/spectatui)** — A terminal UI (TUI) dashboard for Spec Kit that lets you track features, manage specifications, integrations, presets, workflows, and extensions, and monitor AI agent workflows. Attach to existing AI sessions or launch new ones from your terminal. Keyboard and mouse support. Light/dark theme support. Customizable and performance-oriented. Requires the `specify` CLI in your PATH.

docs/community/presets.md

@@ -11,6 +11,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Agent Parity Governance | Adds shared-guidance parity, audit-ready Spec-Kit run evidence, and agent-neutral model-routing guidance across a project's declared AI-agent instruction surfaces so agent guidance does not drift. | 6 templates, 3 commands | — | [spec-kit-preset-agent-parity-governance](https://github.com/hindermath/spec-kit-preset-agent-parity-governance) |
 | AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Architecture Governance | Adds secure software architecture, STRIDE+CAPEC threat modeling, arc42 security cross-cutting concepts, S-ADRs, Zero Trust applicability, OWASP SAMM governance, BSI C3A cloud autonomy, BSI C5 cloud compliance assurance, and audit-ready Spec Kit run evidence | 13 templates, 3 commands | — | [spec-kit-preset-architecture-governance](https://github.com/hindermath/spec-kit-preset-architecture-governance) |
+| Autonomous Run Governance | Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning. | 10 templates, 2 commands | — | [spec-kit-preset-autonomous-run-governance](https://github.com/hindermath/spec-kit-preset-autonomous-run-governance) |
 | Canon Core | Adapts original Spec Kit workflow to work together with Canon extension | 2 templates, 8 commands | — | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon) |
 | 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) |
 | Command Density | Compacts the nine core Spec Kit command prompts while preserving scripts, handoffs, placeholders, hook output blocks, and rule structure | 9 commands | — | [spec-kit-preset-command-density](https://github.com/Xopoko/spec-kit-preset-command-density) |
@@ -28,6 +29,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | SicarioSpec Core | Baseline secure-by-default Spec Kit governance profile. | 5 templates | — | [sicario-spec](https://github.com/dfirs1car1o/sicario-spec) |
 | 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) |
+| Test-First Governance | Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates. | 10 templates, 8 commands | — | [spec-kit-preset-test-first-governance](https://github.com/ka-zo/spec-kit-preset-test-first-governance) |
 | 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 | 22 templates, 8 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |
 

docs/install/one-time.md

@@ -11,7 +11,8 @@ If you want to try Spec Kit without installing it permanently, use `uvx` to run
 # Create a new project (latest from main)
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
 
-# Or target a specific release (replace vX.Y.Z with a tag from Releases)
+# Or target a specific release (replace vX.Y.Z with a tag from Releases;
+# keep the leading v, e.g. v0.12.11 not 0.12.11)
 uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <PROJECT_NAME>
 
 # Initialize in the current directory

docs/install/pipx.md

@@ -7,7 +7,8 @@
 Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
 
 ```bash
-# Install a specific stable release (recommended — replace vX.Y.Z with the latest tag)
+# Install a specific stable release (recommended — replace vX.Y.Z with the
+# latest tag, keeping the leading v, e.g. v0.12.11 not 0.12.11)
 pipx install git+https://github.com/github/spec-kit.git@vX.Y.Z
 
 # Or install latest from main (may include unreleased changes)

docs/installation.md

@@ -15,7 +15,7 @@
 
 ### Persistent Installation (Recommended)
 
-Install once and use everywhere. Replace `vX.Y.Z` with a tag from [Releases](https://github.com/github/spec-kit/releases):
+Install once and use everywhere. Replace `vX.Y.Z` with a release tag from [Releases](https://github.com/github/spec-kit/releases) — keep the leading `v` (for example, `v0.12.11`, not `0.12.11`):
 
 > [!NOTE]
 > The command below requires **[uv](https://docs.astral.sh/uv/)**. If you see `command not found: uv`, [install uv first](./install/uv.md).

docs/reference/bundles.md

@@ -51,10 +51,11 @@ If the current directory is not yet a Spec Kit project, `install` initializes on
 specify bundle update [<bundle_id>]
 ```
 
-| Option       | Description                          |
-| ------------ | ------------------------------------ |
-| `--all`      | Update every installed bundle        |
-| `--offline`  | Do not access the network            |
+| Option           | Description                                                                                                            |
+| ---------------- | --------------------------------------------------------------------------------------------------------------------- |
+| `--all`          | Update every installed bundle                                                                                         |
+| `--integration`  | Override the integration used when refreshing components; applied only when the project's active integration can't be determined |
+| `--offline`      | Do not access the network                                                                                             |
 
 Re-resolves a bundle and **refreshes** its components through each primitive's update path, bringing already-installed components up to the bundle's newly pinned versions while preserving primitive-level overrides (such as preset priority). Provide a bundle id, or use `--all` to update everything installed.
 

docs/reference/integrations.md

@@ -18,7 +18,7 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Firebender](https://firebender.com/)                                                | `firebender`     | IDE-based agent for Android Studio / IntelliJ                                                                                             |
 | [Forge](https://forgecode.dev/)                                                      | `forge`          |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | `gemini`         |                                                                                                                                           |
-| [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        |                                                                                                                                           |
+| [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        | Defaults to legacy markdown mode: `.agent.md` command files under `.github/agents/`, companion `.prompt.md` files under `.github/prompts/`, and a `.vscode/settings.json` merge. Pass `--integration-options="--skills"` to scaffold skills as `speckit-<command>/SKILL.md` under `.github/skills/` instead. Legacy markdown mode is deprecated and will stop being the default in a future release. |
 | [Goose](https://goose-docs.ai/)                                                      | `goose`          | Uses YAML recipe format in `.goose/recipes/`                                                                                              |
 | [Hermes](https://github.com/NousResearch/hermes-agent)                               | `hermes`         | Skills-based integration; installs skills globally into `~/.hermes/skills/`                                                                |
 | [IBM Bob](https://www.ibm.com/products/bob)                                          | `bob`            | IDE-based agent                                                                                                                           |
@@ -219,6 +219,7 @@ Some integrations accept additional options via `--integration-options`:
 | ----------- | ------------------- | -------------------------------------------------------------- |
 | `generic`   | `--commands-dir`    | Required. Directory for command files                          |
 | `kimi`      | `--migrate-legacy`  | Migrate legacy `.kimi/skills/` installs to `.kimi-code/skills/` (including dotted→hyphenated skill naming, e.g. `speckit.xxx` → `speckit-xxx`) |
+| `copilot`   | `--skills`          | Scaffold commands as agent skills (`speckit-<command>/SKILL.md` under `.github/skills/`, invoked as `/speckit-<command>`) instead of the default legacy markdown mode (`.github/agents/*.agent.md` plus `.github/prompts/*.prompt.md` and a `.vscode/settings.json` merge). Without this flag, install warns that legacy markdown mode is deprecated. |
 
 Example:
 

extensions/agent-context/commands/speckit.agent-context.update.md

@@ -15,7 +15,7 @@ The script reads the agent-context extension config at
 - `context_files` — optional project-relative paths for multiple coding agent context files. When non-empty, the script updates each listed file and the list takes precedence over `context_file`.
 - `context_markers.start` / `.end` — the delimiters surrounding the managed section. Defaults to `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` when the field is missing.
 
-It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/<feature>/plan.md`).
+It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (any `plan.md` under `specs/`, including nested scoped layouts such as `specs/<scope>/<feature>/plan.md`).
 
 If `context_files` and `context_file` are empty, the command reports nothing to do and exits successfully. Context file paths must stay project-relative; absolute paths, Windows drive paths, backslash separators, and `..` path segments are rejected.
 
@@ -24,4 +24,4 @@ If `context_files` and `context_file` are empty, the command reports nothing to
 - **Bash**: `.specify/extensions/agent-context/scripts/bash/update-agent-context.sh [plan_path]`
 - **PowerShell**: `.specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1 [plan_path]`
 
-When `plan_path` is omitted, the script auto-detects the most recently modified `specs/*/plan.md`.
+When `plan_path` is omitted, the script auto-detects the most recently modified `specs/**/plan.md` (searched recursively, so nested scoped layouts are discovered).

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 set -euo pipefail
 
@@ -307,16 +307,28 @@ import sys
 from pathlib import Path
 root = Path(sys.argv[1]).resolve()
 specs = root / "specs"
-plans = sorted(
-    specs.glob("*/plan.md"),
-    key=lambda p: p.stat().st_mtime,
-    reverse=True,
-)
-if plans:
+
+def _resolved_rel(p):
+    # Resolve symlinks before checking containment: relative_to() is lexical
+    # and would otherwise accept a plan reached through a specs/ symlink that
+    # points outside the project, emitting an in-project-looking path for an
+    # out-of-project file (or picking it as "most recent").
     try:
-        print(plans[0].relative_to(root).as_posix())
-    except ValueError:
-        print("")
+        return p.resolve().relative_to(root)
+    except (OSError, ValueError):
+        return None
+
+# Recurse (rather than the old one-level specs/*/plan.md glob) so scoped layouts
+# created via SPECIFY_FEATURE_DIRECTORY, e.g. specs/<scope>/<feature>/plan.md,
+# are still discovered when feature.json is absent (#3024).
+candidates = []
+for p in specs.rglob("plan.md"):
+    rel = _resolved_rel(p)
+    if rel:
+        candidates.append((p, rel))
+candidates.sort(key=lambda pr: pr[0].stat().st_mtime, reverse=True)
+if candidates:
+    print(candidates[0][1].as_posix())
 else:
     print("")
 PY

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 [CmdletBinding()]
 param(
@@ -426,9 +426,11 @@ if (-not $PlanPath) {
     if (-not $PlanPath) {
         try {
             $specsDir = Join-Path $ProjectRoot 'specs'
-            $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
-                ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
-                Where-Object { $_ } |
+            # Recurse (rather than the old one-level specs/*/plan.md scan) so scoped
+            # layouts created via SPECIFY_FEATURE_DIRECTORY, e.g.
+            # specs/<scope>/<feature>/plan.md, are still discovered when
+            # feature.json is absent (#3024).
+            $candidate = Get-ChildItem -Path $specsDir -Filter 'plan.md' -File -Recurse -ErrorAction SilentlyContinue |
                 Sort-Object LastWriteTime -Descending |
                 Select-Object -First 1
             if ($candidate) {

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-07-06T00:00:00Z",
+  "updated_at": "2026-07-13T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -1180,6 +1180,39 @@
       "created_at": "2026-03-13T00:00:00Z",
       "updated_at": "2026-03-13T00:00:00Z"
     },
+    "ears": {
+      "name": "EARS Requirements Syntax",
+      "id": "ears",
+      "description": "Author, lint, and convert requirements using EARS (Easy Approach to Requirements Syntax) - the five industry-standard sentence patterns for unambiguous, testable requirements.",
+      "author": "dhruv-15-03",
+      "version": "1.0.0",
+      "download_url": "https://github.com/dhruv-15-03/spec-kit-ears/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/dhruv-15-03/spec-kit-ears",
+      "homepage": "https://github.com/dhruv-15-03/spec-kit-ears",
+      "documentation": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/README.md",
+      "changelog": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.9.0"
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 0
+      },
+      "tags": [
+        "ears",
+        "requirements",
+        "specification",
+        "quality"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-08T00:00:00Z",
+      "updated_at": "2026-07-08T00:00:00Z"
+    },
     "extensify": {
       "name": "Extensify",
       "id": "extensify",
@@ -1213,6 +1246,47 @@
       "created_at": "2026-03-18T00:00:00Z",
       "updated_at": "2026-04-23T00:00:00Z"
     },
+    "figma": {
+      "name": "Spec Kit Figma",
+      "id": "figma",
+      "description": "Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows.",
+      "author": "Fyloss",
+      "version": "1.6.0",
+      "download_url": "https://github.com/Fyloss/spec-kit-figma/archive/refs/tags/v1.6.0.zip",
+      "repository": "https://github.com/Fyloss/spec-kit-figma",
+      "homepage": "https://github.com/Fyloss/spec-kit-figma",
+      "documentation": "https://github.com/Fyloss/spec-kit-figma/blob/main/docs/INSTALL.md",
+      "changelog": "https://github.com/Fyloss/spec-kit-figma/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "integration",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          { "name": "git", "required": true },
+          { "name": "bash", "required": false },
+          { "name": "curl", "required": false },
+          { "name": "jq", "required": false },
+          { "name": "pwsh", "required": false }
+        ]
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 6
+      },
+      "tags": [
+        "figma",
+        "design",
+        "frontend",
+        "ui",
+        "design-system"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-08T00:00:00Z",
+      "updated_at": "2026-07-08T00:00:00Z"
+    },
     "fix-findings": {
       "name": "Fix Findings",
       "id": "fix-findings",
@@ -1353,6 +1427,57 @@
       "created_at": "2026-05-06T00:00:00Z",
       "updated_at": "2026-05-06T00:00:00Z"
     },
+    "gates": {
+      "name": "Quality Gates (Enforcement Layer)",
+      "id": "gates",
+      "description": "Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity).",
+      "author": "schwichtgit",
+      "version": "0.1.0",
+      "download_url": "https://github.com/schwichtgit/spec-gates/releases/download/v0.1.0/gates-0.1.0.zip",
+      "repository": "https://github.com/schwichtgit/spec-gates",
+      "homepage": "https://github.com/schwichtgit/spec-gates",
+      "documentation": "https://github.com/schwichtgit/spec-gates/blob/main/docs/how-it-works.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.12.0",
+        "tools": [
+          {
+            "name": "jq",
+            "required": true
+          },
+          {
+            "name": "git",
+            "required": true
+          },
+          {
+            "name": "node",
+            "required": false
+          },
+          {
+            "name": "shellcheck",
+            "required": false
+          }
+        ]
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 1
+      },
+      "tags": [
+        "quality",
+        "enforcement",
+        "hooks",
+        "ci",
+        "governance"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-09T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "github-issues": {
       "name": "GitHub Issues Integration 1",
       "id": "github-issues",
@@ -1398,10 +1523,10 @@
     "golden-demo": {
       "name": "Golden Demo",
       "id": "golden-demo",
-      "description": "Extracts acceptance criteria from specs, builds test vectors, and produces a behavioral drift report — complementary to Architecture Guard and CDD.",
+      "description": "Deterministic behavioral drift oracle. Extracts acceptance criteria, generates fuzz test vectors (seed=42), compares golden Python implementations against real code in any language. CI/CD gatekeeper with warn/strict modes.",
       "author": "jasstt",
-      "version": "0.1.1",
-      "download_url": "https://github.com/jasstt/spec-kit-golden-demo/archive/refs/tags/v0.1.1.zip",
+      "version": "0.3.0",
+      "download_url": "https://github.com/jasstt/spec-kit-golden-demo/archive/refs/tags/v0.3.0.zip",
       "repository": "https://github.com/jasstt/spec-kit-golden-demo",
       "homepage": "https://github.com/jasstt/spec-kit-golden-demo",
       "documentation": "https://github.com/jasstt/spec-kit-golden-demo",
@@ -1412,13 +1537,16 @@
         "speckit_version": ">=0.1.0"
       },
       "provides": {
-        "commands": 2,
+        "commands": 3,
         "hooks": 2
       },
       "tags": [
         "testing",
         "drift-detection",
         "behavioral-oracle",
+        "fuzzing",
+        "ci-cd",
+        "cross-language",
         "tdd",
         "quality"
       ],
@@ -1426,7 +1554,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-06-24T00:00:00Z",
-      "updated_at": "2026-06-24T00:00:00Z"
+      "updated_at": "2026-07-07T00:00:00Z"
     },
     "harness": {
       "name": "Research Harness",
@@ -2140,6 +2268,42 @@
       "created_at": "2026-05-08T00:00:00Z",
       "updated_at": "2026-05-08T00:00:00Z"
     },
+    "memory": {
+      "name": "Spec Kit Memory",
+      "id": "memory",
+      "description": "Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows.",
+      "author": "Andrey Zaytsev",
+      "version": "0.3.0",
+      "download_url": "https://github.com/zaytsevand/spec-kit-memory/archive/refs/tags/v0.3.0.zip",
+      "repository": "https://github.com/zaytsevand/spec-kit-memory",
+      "homepage": "https://github.com/zaytsevand/spec-kit-memory",
+      "documentation": "https://github.com/zaytsevand/spec-kit-memory/blob/main/README.md",
+      "changelog": "",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          { "name": "memsearch", "required": false }
+        ]
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 3
+      },
+      "tags": [
+        "memory",
+        "recall",
+        "research",
+        "memsearch"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-10T00:00:00Z",
+      "updated_at": "2026-07-10T00:00:00Z"
+    },
     "memory-loader": {
       "name": "Memory Loader",
       "id": "memory-loader",
@@ -4279,6 +4443,40 @@
       "created_at": "2026-03-03T00:00:00Z",
       "updated_at": "2026-04-09T00:00:00Z"
     },
+    "verify-review-ship": {
+      "name": "Verify Review Ship",
+      "id": "verify-review-ship",
+      "description": "Adds post-implementation verify, review, and ship readiness gates to Spec Kit workflows.",
+      "author": "Carlos Eduardo Gevaerd Araujo",
+      "version": "0.1.0",
+      "download_url": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/archive/refs/tags/v0.1.0.zip",
+      "repository": "https://github.com/cadugevaerd/spec-kit-verify-review-ship",
+      "homepage": "https://github.com/cadugevaerd/spec-kit-verify-review-ship",
+      "documentation": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/blob/main/README.md",
+      "changelog": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-only",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": [
+        "quality",
+        "review",
+        "shipping",
+        "workflow",
+        "testing"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-10T00:00:00Z",
+      "updated_at": "2026-07-10T00:00:00Z"
+    },
     "verify-tasks": {
       "name": "Verify Tasks Extension",
       "id": "verify-tasks",

extensions/catalog.json

@@ -48,4 +48,4 @@
       ]
     }
   }
-}
+}

extensions/git/scripts/powershell/create-new-feature-branch.ps1

@@ -446,7 +446,10 @@ if ($env:GIT_BRANCH_NAME) {
         $branchSuffix = Get-BranchName -Description $featureDesc
     }
 
-    if ($Timestamp -and $Number -ne 0) {
+    # Warn if -Number and -Timestamp are both specified. Use ContainsKey (not
+    # `-ne 0`) so an explicit `-Number 0` is also detected, matching the bash twin's
+    # `[ -n "$BRANCH_NUMBER" ]` check.
+    if ($Timestamp -and $PSBoundParameters.ContainsKey('Number')) {
         Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
         $Number = 0
     }
@@ -456,7 +459,10 @@ if ($env:GIT_BRANCH_NAME) {
         $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
     } else {
         $branchScopePrefix = Get-BranchScopePrefix -Template $branchTemplate -BranchSuffix $branchSuffix
-        if ($Number -eq 0) {
+        # Auto-detect the next number only when -Number was not supplied; an
+        # explicit value (including 0) is honored, matching the bash twin's
+        # `[ -z "$BRANCH_NUMBER" ]` check.
+        if (-not $PSBoundParameters.ContainsKey('Number')) {
             if ($DryRun -and $hasGit) {
                 $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch -ScopePrefix $branchScopePrefix
             } elseif ($DryRun) {

extensions/selftest/commands/selftest.md

@@ -48,7 +48,7 @@ cat .specify/extensions/.registry/$ARGUMENTS.json
 
 ### Step 4: Verification Report
 
-Analyze the standard output of the three steps. 
+Analyze the standard output of the three steps.
 Generate a terminal-style test output format detailing the results of discovery, installation, and registration. Return this directly to the user.
 
 Example output format:

newsletters/2026-March.md

@@ -76,5 +76,3 @@ Areas under discussion or in progress for future development:
 - **Continued agent expansion** -- seven new agents were added in March alone. The agent-agnostic design means support for emerging tools can be added by anyone. [\[byteiota.com\]](https://byteiota.com/spec-driven-development-kills-vibe-coding-march-2026/)
 - **Experience simplification** -- the preset system, custom workflows, and growing walkthrough library lower the learning curve, but extension discoverability will need a more robust solution as the catalog grows. [\[github.com\]](https://github.com/github/spec-kit/releases)
 - **Toward a stable release** -- nine releases in one month reflects pre-1.0 momentum. Reaching 1.0 will require stabilizing the extension and preset APIs and ensuring backward compatibility across the agent and extension surface area. [\[github.com\]](https://github.com/github/spec-kit/blob/main/newsletters/2026-February.md)
-
-

presets/ARCHITECTURE.md

@@ -158,8 +158,7 @@ presets/
         ├── plan-template.md
         ├── tasks-template.md
         ├── checklist-template.md
-        ├── constitution-template.md
-        └── agent-file-template.md
+        └── constitution-template.md
 ```
 
 ## Module Structure

presets/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-30T00:00:00Z",
+  "updated_at": "2026-07-13T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
   "presets": {
     "a11y-governance": {
@@ -131,6 +131,34 @@
       "created_at": "2026-04-27T00:00:00Z",
       "updated_at": "2026-06-14T00:00:00Z"
     },
+    "autonomous-run-governance": {
+      "name": "Autonomous Run Governance",
+      "id": "autonomous-run-governance",
+      "version": "0.1.1",
+      "description": "Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning.",
+      "author": "Thorsten Hindermann",
+      "repository": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
+      "download_url": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/archive/refs/tags/v0.1.1.zip",
+      "homepage": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
+      "documentation": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/blob/main/README.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.8.3"
+      },
+      "provides": {
+        "templates": 10,
+        "commands": 2
+      },
+      "tags": [
+        "autonomous",
+        "governance",
+        "evidence",
+        "permissions",
+        "retrospective"
+      ],
+      "created_at": "2026-07-13T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "canon-core": {
       "name": "Canon Core",
       "id": "canon-core",
@@ -618,6 +646,34 @@
       "created_at": "2026-04-30T00:00:00Z",
       "updated_at": "2026-04-30T00:00:00Z"
     },
+    "test-first-governance": {
+      "name": "Test-First Governance",
+      "id": "test-first-governance",
+      "version": "1.3.0",
+      "description": "Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates.",
+      "author": "Zoltán Katona, PhD",
+      "repository": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
+      "download_url": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/archive/refs/tags/1.3.0.zip",
+      "homepage": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
+      "documentation": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/blob/main/README.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.12.11"
+      },
+      "provides": {
+        "templates": 10,
+        "commands": 8
+      },
+      "tags": [
+        "tdd",
+        "bdd",
+        "atdd",
+        "quality-gates",
+        "traceability"
+      ],
+      "created_at": "2026-07-13T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "toc-navigation": {
       "name": "Table of Contents Navigation",
       "id": "toc-navigation",

presets/self-test/preset.yml

@@ -44,12 +44,6 @@ provides:
       description: "Self-test constitution template"
       replaces: "constitution-template"
 
-    - type: "template"
-      name: "agent-file-template"
-      file: "templates/agent-file-template.md"
-      description: "Self-test agent file template"
-      replaces: "agent-file-template"
-
     - type: "command"
       name: "speckit.specify"
       file: "commands/speckit.specify.md"

presets/self-test/templates/agent-file-template.md

@@ -1,9 +0,0 @@
-# Agent File (Self-Test Preset)
-
-<!-- preset:self-test -->
-
-> This template is provided by the self-test preset.
-
-## Agent Instructions
-
-Follow these guidelines when working on this project.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.8.dev0"
+version = "0.12.14"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -83,4 +83,3 @@ extend-select = [
     "S604",  # call-with-shell-equals-true
     "S605",  # start-process-with-a-shell
 ]
-

scripts/bash/check-prerequisites.sh

@@ -57,13 +57,13 @@ OPTIONS:
 EXAMPLES:
   # Check task prerequisites (plan.md required)
   ./check-prerequisites.sh --json
-  
+
   # Check implementation prerequisites (plan.md + tasks.md required)
   ./check-prerequisites.sh --json --require-tasks --include-tasks
-  
+
   # Get feature paths only (no validation)
   ./check-prerequisites.sh --paths-only
-  
+
 EOF
             exit 0
             ;;
@@ -182,13 +182,13 @@ else
     # Text output
     echo "FEATURE_DIR:$FEATURE_DIR"
     echo "AVAILABLE_DOCS:"
-    
+
     # Show status of each potential document
     check_file "$RESEARCH" "research.md"
     check_file "$DATA_MODEL" "data-model.md"
     check_dir "$CONTRACTS_DIR" "contracts/"
     check_file "$QUICKSTART" "quickstart.md"
-    
+
     if $INCLUDE_TASKS; then
         check_file "$TASKS" "tasks.md"
     fi

scripts/bash/common.sh

@@ -244,21 +244,29 @@ get_invoke_separator() {
 
     local integration_json="$repo_root/.specify/integration.json"
     local separator="."
-    local parsed_with_jq=0
+    local parsed=0
 
     if [[ -f "$integration_json" ]]; then
+        # Try parsers in order (jq -> python3 -> awk), falling through on
+        # failure. Selection is by *parse success*, not mere availability: on
+        # Windows `python3` commonly resolves to the Microsoft Store App
+        # Execution Alias stub, which passes `command -v` but fails at runtime
+        # (exit 49). An availability-gated branch would pick python3, swallow
+        # its failure, and — because this function historically had no text
+        # fallback — silently return "." even for `-`-separator integrations
+        # (e.g. forge, cline), yielding wrong command hints (issue #3304).
         if command -v jq >/dev/null 2>&1; then
             local jq_separator
             if jq_separator=$(jq -r '(.default_integration // .integration // "") as $k | if $k == "" then "." else (.integration_settings[$k].invoke_separator // ".") end' "$integration_json" 2>/dev/null); then
-                parsed_with_jq=1
                 case "$jq_separator" in
-                    "."|"-") separator="$jq_separator" ;;
+                    "."|"-") separator="$jq_separator"; parsed=1 ;;
                 esac
             fi
         fi
 
-        if [[ "$parsed_with_jq" -eq 0 ]] && command -v python3 >/dev/null 2>&1; then
-            if separator=$(python3 - "$integration_json" <<'PY' 2>/dev/null
+        if [[ "$parsed" -eq 0 ]] && command -v python3 >/dev/null 2>&1; then
+            local py_separator
+            if py_separator=$(python3 - "$integration_json" <<'PY' 2>/dev/null
 import json
 import sys
 
@@ -274,17 +282,64 @@ try:
             separator = entry["invoke_separator"]
     print(separator)
 except Exception:
-    print(".")
+    sys.exit(1)
 PY
 ); then
-                case "$separator" in
-                    "."|"-") ;;
-                    *) separator="." ;;
+                case "$py_separator" in
+                    "."|"-") separator="$py_separator"; parsed=1 ;;
                 esac
-            else
-                separator="."
             fi
         fi
+
+        if [[ "$parsed" -eq 0 ]]; then
+            # Last-resort text fallback for environments with neither jq nor a
+            # working python3 (e.g. stock Windows + Git Bash). Reads the active
+            # integration key (default_integration, else integration) and its
+            # invoke_separator from within the integration_settings object.
+            # Handles both pretty-printed (the written form) and compact JSON.
+            # Accumulate all lines into one buffer in END rather than using
+            # gawk-only whole-file slurp (RS="^$"), so this stays portable to
+            # the BSD awk on macOS.
+            local awk_separator
+            awk_separator=$(awk '
+                function keyval(d, name,   v) {
+                    if (match(d, "\"" name "\"[ \t\r\n]*:[ \t\r\n]*\"[^\"]*\"")) {
+                        v=substr(d,RSTART,RLENGTH); sub(/^.*:[ \t\r\n]*"/,"",v); sub(/"$/,"",v); return v
+                    }
+                    return ""
+                }
+                { doc = doc $0 "\n" }
+                END {
+                    key=keyval(doc,"default_integration"); if (key=="") key=keyval(doc,"integration")
+                    sep="."
+                    if (key!="") {
+                        settings=doc
+                        if (match(doc, /"integration_settings"[ \t\r\n]*:[ \t\r\n]*[{]/)) {
+                            settings=substr(doc, RSTART+RLENGTH-1)
+                        }
+                        if (match(settings, "\"" key "\"[ \t\r\n]*:[ \t\r\n]*[{]")) {
+                            start=RSTART+RLENGTH-1
+                            depth=0
+                            obj=""
+                            for (i=start; i<=length(settings); i++) {
+                                c=substr(settings,i,1)
+                                obj=obj c
+                                if (c=="{") depth++
+                                else if (c=="}") { depth--; if (depth==0) break }
+                            }
+                            if (match(obj, /"invoke_separator"[ \t\r\n]*:[ \t\r\n]*"[-.]"/)) {
+                                tok=substr(obj,RSTART,RLENGTH); s=substr(tok,length(tok)-1,1)
+                                if (s=="." || s=="-") sep=s
+                            }
+                        }
+                    }
+                    print sep
+                }
+            ' "$integration_json" 2>/dev/null)
+            case "$awk_separator" in
+                "."|"-") separator="$awk_separator" ;;
+            esac
+        fi
     fi
 
     _SPECIFY_INVOKE_SEPARATOR_CACHE_REPO_ROOT="$repo_root"

scripts/bash/create-new-feature.sh

@@ -94,7 +94,7 @@ fi
 get_highest_from_specs() {
     local specs_dir="$1"
     local highest=0
-    
+
     if [ -d "$specs_dir" ]; then
         for dir in "$specs_dir"/*; do
             [ -d "$dir" ] || continue
@@ -109,7 +109,7 @@ get_highest_from_specs() {
             fi
         done
     fi
-    
+
     echo "$highest"
 }
 
@@ -135,19 +135,19 @@ fi
 # Function to generate branch name with stop word filtering and length filtering
 generate_branch_name() {
     local description="$1"
-    
+
     # Common stop words to filter out
     local stop_words="^(i|a|an|the|to|for|of|in|on|at|by|with|from|is|are|was|were|be|been|being|have|has|had|do|does|did|will|would|should|could|can|may|might|must|shall|this|that|these|those|my|your|our|their|want|need|add|get|set)$"
-    
+
     # Convert to lowercase and split into words
     local clean_name=$(printf '%s' "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/ /g')
-    
+
     # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
     local meaningful_words=()
     for word in $clean_name; do
         # Skip empty words
         [ -z "$word" ] && continue
-        
+
         # Keep words that are NOT stop words AND (length >= 3 OR are potential acronyms)
         if ! echo "$word" | grep -qiE "$stop_words"; then
             if [ ${#word} -ge 3 ]; then
@@ -160,12 +160,12 @@ generate_branch_name() {
             fi
         fi
     done
-    
+
     # If we have meaningful words, use first 3-4 of them
     if [ ${#meaningful_words[@]} -gt 0 ]; then
         local max_words=3
         if [ ${#meaningful_words[@]} -eq 4 ]; then max_words=4; fi
-        
+
         local result=""
         local count=0
         for word in "${meaningful_words[@]}"; do
@@ -221,15 +221,15 @@ if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
     # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
     PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
     MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
-    
+
     # Truncate suffix at word boundary if possible
     TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
     # Remove trailing hyphen if truncation created one
     TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
-    
+
     ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
     BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"
-    
+
     >&2 echo "[specify] Warning: Branch name exceeded GitHub's 244-byte limit"
     >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${#ORIGINAL_BRANCH_NAME} bytes)"
     >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"

scripts/bash/setup-plan.sh

@@ -8,17 +8,17 @@ ARGS=()
 
 for arg in "$@"; do
     case "$arg" in
-        --json) 
-            JSON_MODE=true 
+        --json)
+            JSON_MODE=true
             ;;
-        --help|-h) 
+        --help|-h)
             echo "Usage: $0 [--json]"
             echo "  --json    Output results in JSON format"
             echo "  --help    Show this help message"
-            exit 0 
+            exit 0
             ;;
-        *) 
-            ARGS+=("$arg") 
+        *)
+            ARGS+=("$arg")
             ;;
     esac
 done
@@ -77,8 +77,7 @@ if $JSON_MODE; then
     fi
 else
     echo "FEATURE_SPEC: $FEATURE_SPEC"
-    echo "IMPL_PLAN: $IMPL_PLAN" 
+    echo "IMPL_PLAN: $IMPL_PLAN"
     echo "SPECS_DIR: $FEATURE_DIR"
     echo "BRANCH: $CURRENT_BRANCH"
 fi
-

scripts/powershell/check-prerequisites.ps1

@@ -42,10 +42,10 @@ OPTIONS:
 EXAMPLES:
   # Check task prerequisites (plan.md required)
   .\check-prerequisites.ps1 -Json
-  
+
   # Check implementation prerequisites (plan.md + tasks.md required)
   .\check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  
+
   # Get feature paths only (no validation)
   .\check-prerequisites.ps1 -PathsOnly
 
@@ -118,35 +118,35 @@ if (Test-Path $paths.RESEARCH) { $docs += 'research.md' }
 if (Test-Path $paths.DATA_MODEL) { $docs += 'data-model.md' }
 
 # Check contracts directory (only if it exists and has files)
-if ((Test-Path $paths.CONTRACTS_DIR) -and (Get-ChildItem -Path $paths.CONTRACTS_DIR -ErrorAction SilentlyContinue | Select-Object -First 1)) { 
-    $docs += 'contracts/' 
+if ((Test-Path $paths.CONTRACTS_DIR) -and (Get-ChildItem -Path $paths.CONTRACTS_DIR -ErrorAction SilentlyContinue | Select-Object -First 1)) {
+    $docs += 'contracts/'
 }
 
 if (Test-Path $paths.QUICKSTART) { $docs += 'quickstart.md' }
 
 # Include tasks.md if requested and it exists
-if ($IncludeTasks -and (Test-Path $paths.TASKS)) { 
-    $docs += 'tasks.md' 
+if ($IncludeTasks -and (Test-Path $paths.TASKS)) {
+    $docs += 'tasks.md'
 }
 
 # Output results
 if ($Json) {
     # JSON output
-    [PSCustomObject]@{ 
+    [PSCustomObject]@{
         FEATURE_DIR = $paths.FEATURE_DIR
-        AVAILABLE_DOCS = $docs 
+        AVAILABLE_DOCS = $docs
     } | ConvertTo-Json -Compress
 } else {
     # Text output
     Write-Output "FEATURE_DIR:$($paths.FEATURE_DIR)"
     Write-Output "AVAILABLE_DOCS:"
-    
+
     # Show status of each potential document
     Test-FileExists -Path $paths.RESEARCH -Description 'research.md' | Out-Null
     Test-FileExists -Path $paths.DATA_MODEL -Description 'data-model.md' | Out-Null
     Test-DirHasFiles -Path $paths.CONTRACTS_DIR -Description 'contracts/' | Out-Null
     Test-FileExists -Path $paths.QUICKSTART -Description 'quickstart.md' | Out-Null
-    
+
     if ($IncludeTasks) {
         Test-FileExists -Path $paths.TASKS -Description 'tasks.md' | Out-Null
     }

scripts/powershell/common.ps1

@@ -191,7 +191,7 @@ function Get-FeaturePathsEnv {
         [Console]::Error.WriteLine("ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY or run the specify command to create .specify/feature.json.")
         exit 1
     }
-    
+
     # When no branch context exists (no SPECIFY_FEATURE, feature resolved via
     # SPECIFY_FEATURE_DIRECTORY or feature.json), fall back to the feature
     # directory basename so CURRENT_BRANCH is a usable identifier rather than

scripts/powershell/setup-plan.ps1

@@ -63,7 +63,7 @@ if (Test-Path $paths.IMPL_PLAN -PathType Leaf) {
 
 # Output results
 if ($Json) {
-    $result = [PSCustomObject]@{ 
+    $result = [PSCustomObject]@{
         FEATURE_SPEC = $paths.FEATURE_SPEC
         IMPL_PLAN = $paths.IMPL_PLAN
         SPECS_DIR = $paths.FEATURE_DIR

spec-kit.code-workspace

@@ -5,4 +5,4 @@
 		}
 	],
 	"settings": {}
-}
+}

src/specify_cli/__init__.py

@@ -141,8 +141,9 @@ def _install_shared_infra(
 
     Copies ``.specify/scripts/<variant>/`` and ``.specify/templates/`` from
     the bundled core_pack or source checkout, where ``<variant>`` is
-    ``bash`` when *script_type* is ``"sh"`` and ``powershell`` when it is
-    ``"ps"``.  Tracks all installed files in ``speckit.manifest.json``.
+    ``bash`` when *script_type* is ``"sh"``, ``python`` when it is ``"py"``,
+    and ``powershell`` when it is ``"ps"``.  Tracks all installed files in
+    ``speckit.manifest.json``.
 
     Shared scripts and page templates are processed to resolve
     ``__SPECKIT_COMMAND_<NAME>__`` placeholders using *invoke_separator*

src/specify_cli/agents.py

@@ -213,6 +213,52 @@ class CommandRegistrar:
             ".specify.specify/", ".specify/"
         )
 
+    @staticmethod
+    def rewrite_extension_paths(
+        text: str, extension_id: str, extension_dir: Path
+    ) -> str:
+        """Rewrite extension-relative paths to their installed locations.
+
+        Extension command bodies reference bundled files relative to the
+        extension root (e.g. ``agents/control/commander.md``). After install
+        those files live under ``.specify/extensions/<id>/``, so bare
+        references would resolve against the workspace root and never be
+        found (#2101).
+
+        Only directories that actually exist inside *extension_dir* are
+        rewritten, keeping the behaviour conservative and avoiding false
+        positives on prose. ``commands`` (slash-command sources), ``specs``
+        (user project artifacts) and dot-directories are never rewritten.
+        """
+        if not isinstance(text, str) or not text:
+            return text
+
+        skip = {"commands", ".git", "specs"}
+        try:
+            subdirs = [
+                entry.name
+                for entry in extension_dir.iterdir()
+                if entry.is_dir()
+                and entry.name not in skip
+                and not entry.name.startswith(".")
+            ]
+        except OSError:
+            return text
+
+        for subdir in subdirs:
+            # Only rewrite relative references (subdir/... or ./subdir/...);
+            # absolute paths like /subdir/... keep their meaning. Use a
+            # callable replacement: subdir/extension_id come from the
+            # filesystem and could contain backslashes or "\1"-like
+            # sequences, which would corrupt a string replacement template.
+            replacement = f".specify/extensions/{extension_id}/{subdir}/"
+            text = re.sub(
+                r'(^|[\s`"\'(])(?:\./)?' + re.escape(subdir) + "/",
+                lambda m: m.group(1) + replacement,
+                text,
+            )
+        return text
+
     def render_markdown_command(
         self, frontmatter: dict, body: str, source_id: str, context_note: str = None
     ) -> str:
@@ -639,6 +685,9 @@ class CommandRegistrar:
                         frontmatter[key] = core_frontmatter[key]
                 frontmatter.pop("strategy", None)
 
+            if extension_id:
+                body = self.rewrite_extension_paths(body, extension_id, source_root)
+
             frontmatter = self._adjust_script_paths(
                 frontmatter, extension_id=extension_id
             )
@@ -701,6 +750,12 @@ class CommandRegistrar:
                 )
                 output = self.render_toml_command(frontmatter, body, source_id)
             elif agent_config["format"] == "yaml":
+                body = self.resolve_skill_placeholders(
+                    agent_name, frontmatter, body, project_root
+                )
+                body = self._convert_argument_placeholder(
+                    body, "$ARGUMENTS", agent_config["args"]
+                )
                 output = self.render_yaml_command(
                     frontmatter, body, source_id, cmd_name
                 )

src/specify_cli/authentication/config.py

@@ -196,7 +196,15 @@ def find_entries_for_url(
     url: str, entries: list[AuthConfigEntry]
 ) -> list[AuthConfigEntry]:
     """Return entries whose ``hosts`` match the hostname of *url*."""
-    hostname = (urlparse(url).hostname or "").lower()
+    # A malformed authority (e.g. an unterminated IPv6 bracket "https://[::1")
+    # makes urlparse/hostname raise ValueError. Treat that the same as a
+    # host-less URL: no entry can match, so return no matches rather than
+    # leaking a raw ValueError out of the shared HTTP client (build_request /
+    # open_url call this before any URL validation).
+    try:
+        hostname = (urlparse(url).hostname or "").lower()
+    except ValueError:
+        return []
     if not hostname:
         return []
     return [

src/specify_cli/bundler/services/adapters.py

@@ -68,8 +68,18 @@ def _validate_remote_url(source_id: str, url: str) -> None:
     Mirrors ``specify_cli.catalogs`` URL validation to avoid MITM/downgrade
     issues before any network call.
     """
-    parsed = urlparse(url)
-    is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+    # A malformed authority (e.g. an unclosed IPv6 bracket ``https://[::1``)
+    # makes urlparse / hostname access raise ValueError. This function's
+    # contract is to raise BundlerError for a bad URL, so surface that as a
+    # clean error rather than leaking a raw ValueError to the caller.
+    try:
+        parsed = urlparse(url)
+        hostname = parsed.hostname
+    except ValueError:
+        raise BundlerError(
+            f"Catalog '{source_id}' URL is malformed: {url}"
+        ) from None
+    is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
     if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
         raise BundlerError(
             f"Catalog '{source_id}' URL must use HTTPS (got {parsed.scheme}://). "
@@ -79,7 +89,7 @@ def _validate_remote_url(source_id: str, url: str) -> None:
     # "https://:8080" or "https://user@...", so requiring netloc would let
     # those through even though they carry no host. hostname is None in those
     # cases. Mirrors the fix in ``specify_cli.catalogs`` (#3210).
-    if not parsed.hostname:
+    if not hostname:
         raise BundlerError(
             f"Catalog '{source_id}' URL must be a valid URL with a host: {url}"
         )

src/specify_cli/bundler/services/primitives.py

@@ -33,12 +33,13 @@ DEFAULT_PRIORITY = 10
 def _assert_pinned_version(
     kind: str, component_id: str, pinned: str | None, advertised: object
 ) -> None:
-    """Refuse to install when the catalog version differs from the manifest pin.
+    """Refuse to install when the resolved version differs from the manifest pin.
 
     Bundle manifests pin component versions for reproducibility; installing
-    whatever the active catalog currently serves would silently violate the
-    pin. When the catalog advertises no version we cannot enforce the pin, so
-    installation proceeds (the catalog, not the bundler, owns that gap).
+    whatever the resolved source (catalog *or* bundled asset) provides would
+    silently violate the pin. When the source advertises no version we cannot
+    enforce the pin, so installation proceeds (the source, not the bundler,
+    owns that gap).
     """
     if not pinned or advertised is None:
         return
@@ -54,11 +55,35 @@ def _assert_pinned_version(
     if not matches:
         raise BundlerError(
             f"{kind} '{component_id}' is pinned to version {pinned} in the bundle "
-            f"manifest, but the active catalog serves {actual}. Update the bundle's "
-            "pinned version or the catalog before installing."
+            f"manifest, but the resolved version is {actual}. Update the bundle's "
+            "pinned version or the source before installing."
         )
 
 
+def _bundled_manifest_version(manifest_path: Path, root_key: str) -> str | None:
+    """Best-effort read of a bundled asset's declared version from its manifest.
+
+    Returns ``None`` when the manifest is missing/unreadable/invalid, which
+    ``_assert_pinned_version`` treats as "cannot enforce" (proceed) — matching
+    the catalog "advertises no version" escape hatch.
+    """
+    try:
+        import yaml
+
+        data = yaml.safe_load(manifest_path.read_text(encoding="utf-8"))
+        if isinstance(data, dict):
+            section = data.get(root_key)
+            if isinstance(section, dict):
+                version = section.get("version")
+                # Only a non-empty string is a usable version; anything else
+                # (missing / non-string / whitespace) means "cannot enforce".
+                if isinstance(version, str) and version.strip():
+                    return version
+    except Exception:  # noqa: BLE001 - unreadable/invalid manifest: skip pin
+        return None
+    return None
+
+
 class _KindManager(Protocol):
     def is_installed(self, component: ComponentRef) -> bool: ...
 
@@ -134,6 +159,15 @@ class _PresetKindManager:
 
         bundled = _locate_bundled_preset(component.id)
         if bundled is not None:
+            # Enforce the manifest pin against the bundled asset's own version,
+            # mirroring the catalog path below (the bundled path previously
+            # skipped the pin entirely).
+            _assert_pinned_version(
+                "Preset",
+                component.id,
+                component.version,
+                _bundled_manifest_version(bundled / "preset.yml", "preset"),
+            )
             self._manager.install_from_directory(bundled, speckit_version, priority)
             return
 
@@ -198,6 +232,15 @@ class _ExtensionKindManager:
 
         bundled = _locate_bundled_extension(component.id)
         if bundled is not None:
+            # Enforce the manifest pin against the bundled asset's own version,
+            # mirroring the catalog path below (the bundled path previously
+            # skipped the pin entirely).
+            _assert_pinned_version(
+                "Extension",
+                component.id,
+                component.version,
+                _bundled_manifest_version(bundled / "extension.yml", "extension"),
+            )
             self._manager.install_from_directory(
                 bundled, speckit_version, priority=priority
             )

src/specify_cli/catalogs.py

@@ -71,8 +71,12 @@ class CatalogStackBase:
         """Validate that a catalog URL uses HTTPS, except localhost HTTP."""
         from urllib.parse import urlparse
 
-        parsed = urlparse(url)
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        try:
+            parsed = urlparse(url)
+            hostname = parsed.hostname
+        except ValueError:
+            raise cls._error(f"Catalog URL is malformed: {url}") from None
+        is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
         if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
             raise cls._error(
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
@@ -81,7 +85,7 @@ class CatalogStackBase:
         # Check hostname, not netloc: netloc is truthy for host-less URLs like
         # "https://:8080" or "https://user@", so the host guarantee this error
         # promises would not actually hold. hostname is None in those cases (#3209).
-        if not parsed.hostname:
+        if not hostname:
             raise cls._error("Catalog URL must be a valid URL with a host.")
 
     def _load_catalog_config(self, config_path: Path) -> list[CatalogEntry] | None:

src/specify_cli/commands/bundle/__init__.py

@@ -746,11 +746,16 @@ def _resolve_manifest_path(path: Path | None) -> Path:
 def _download_manifest(resolved, *, offline: bool):
     """Resolve a bundle's manifest from its catalog ``download_url``.
 
-    Local/``file://`` URLs always work offline and may point at a ``.zip``
-    artifact, a bundle directory, or a ``bundle.yml`` (handled by
-    :func:`_local_manifest_source`). Remote ``https://`` URLs are fetched with
-    the shared authenticated, redirect-validated HTTP client, and only when not
-    ``--offline``.
+    Catalog ``download_url``s are HTTPS-only (``http`` allowed for localhost),
+    matching the extensions/presets/workflows catalog systems. Remote URLs are
+    fetched with the shared authenticated, redirect-validated HTTP client, and
+    only when not ``--offline``.
+
+    Local and ``file://`` sources are intentionally not resolved here: to
+    install a bundle from disk, pass the path positionally
+    (``specify bundle install ./path/to/bundle.yml`` — a bundle directory or a
+    ``.zip`` artifact also works), which :func:`_local_manifest_source` handles
+    before catalog resolution and which never touches ``download_url``.
     """
     from urllib.parse import urlparse
 
@@ -763,26 +768,35 @@ def _download_manifest(resolved, *, offline: bool):
     parsed = urlparse(url)
     scheme = parsed.scheme.lower()
 
-    # On Windows an absolute path like ``C:\bundle.yml`` parses with a
-    # single-letter ``scheme``; treat it as a local file, not a URL scheme.
+    # ``file://`` URLs and bare filesystem paths (including Windows drive paths
+    # like ``C:\bundle.yml``, which urlparse reads as a single-letter scheme)
+    # are not valid catalog download URLs. Catalog URLs are HTTPS-only across
+    # every catalog system; installing from disk is done by passing the path
+    # positionally, which never reaches URL resolution. Give an actionable
+    # error rather than accepting a scheme the rest of the codebase rejects.
     if scheme in ("", "file") or re.match(r"^[A-Za-z]:[\\/]", url):
-        local = Path(parsed.path if scheme == "file" else url)
-        manifest = _local_manifest_source(str(local))
-        if manifest is None:
-            raise BundlerError(f"Bundle manifest not found: {local}")
-        return manifest
+        raise BundlerError(
+            f"Catalog entry '{resolved.entry.id}' has a non-HTTP(S) download_url "
+            f"({url}); catalog download URLs must be HTTPS (http for localhost) — "
+            "a file:// URL, a local filesystem path, or a scheme-less value "
+            "(e.g. 'example.com/bundle.zip') is not accepted. "
+            "To install a bundle from disk, pass the path directly: "
+            "'specify bundle install <path-to-bundle.yml | bundle-dir | .zip>'."
+        )
 
-    if scheme in ("http", "https"):
-        if offline:
-            raise BundlerError(
-                f"Network access disabled; cannot download bundle '{resolved.entry.id}' "
-                f"from {url}."
-            )
-        return _download_remote_manifest(resolved.entry.id, url)
+    # Validate the scheme/host *before* the offline gate so an invalid or
+    # non-HTTPS download_url reports the real problem in every mode, rather
+    # than a misleading "Network access disabled" under --offline.
+    # (_download_remote_manifest re-checks this, but only once network access
+    # is permitted.) HTTPS-only, http allowed for localhost.
+    _require_https(f"bundle '{resolved.entry.id}'", url)
 
-    raise BundlerError(
-        f"Unsupported download_url scheme for bundle '{resolved.entry.id}': {url}"
-    )
+    if offline:
+        raise BundlerError(
+            f"Network access disabled; cannot download bundle '{resolved.entry.id}' "
+            f"from {url}."
+        )
+    return _download_remote_manifest(resolved.entry.id, url)
 
 
 def _require_https(label: str, url: str) -> None:

src/specify_cli/commands/init.py

@@ -220,16 +220,45 @@ def register(app: typer.Typer) -> None:
                 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:
+                    # Proceeding: the merge/overwrite warning is accurate here.
+                    console.print(
+                        "[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]"
+                    )
                     console.print(
                         "[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]"
                     )
                 else:
-                    response = typer.confirm("Do you want to continue?")
-                    if not response:
+                    # Fold the merge risk into the confirmation prompt rather than
+                    # printing it unconditionally first: on the EOF/no-input path
+                    # below the command exits without changing anything, so a
+                    # standalone "will be merged" line would mislead. Interactive
+                    # users still see the risk as part of the question.
+                    #
+                    # Call typer.confirm normally so piped y/n is honored — e.g.
+                    # `echo y | specify init --here` keeps reaching the
+                    # non-destructive preserve-merge path.
+                    try:
+                        proceed = typer.confirm(
+                            "Template files will be merged with existing content "
+                            "and may overwrite existing files. Do you want to continue?"
+                        )
+                    except (typer.Abort, EOFError):
+                        # typer.confirm raises Abort for BOTH an interactive Ctrl+C
+                        # and an EOF on closed/empty stdin. Distinguish them: a real
+                        # TTY cancellation is a normal exit (0, "cancelled"), while a
+                        # missing-input EOF (non-interactive) becomes an actionable
+                        # error pointing at --force.
+                        if _stdin_is_interactive():
+                            console.print("[yellow]Operation cancelled[/yellow]")
+                            raise typer.Exit(0) from None
+                        console.print(
+                            "[red]Error:[/red] Current directory is not empty and no "
+                            "confirmation input is available. Re-run with "
+                            "[bold]--force[/bold] to merge into it."
+                        )
+                        raise typer.Exit(1) from None
+                    if not proceed:
                         console.print("[yellow]Operation cancelled[/yellow]")
                         raise typer.Exit(0)
         else:

src/specify_cli/extensions/__init__.py

@@ -1078,6 +1078,11 @@ class ExtensionManager:
             frontmatter = registrar._adjust_script_paths(
                 frontmatter, extension_id=manifest.id
             )
+            # Mirror the register_commands() rewrite (#2101): resolve
+            # extension-relative subdir references (agents/, knowledge-base/,
+            # etc.) to their installed .specify/extensions/<id>/ location
+            # before the generic placeholder/path resolution below.
+            body = registrar.rewrite_extension_paths(body, manifest.id, extension_dir)
             body = registrar.resolve_skill_placeholders(
                 selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
             )
@@ -2755,18 +2760,32 @@ class ConfigManager:
             if not key.startswith(prefix):
                 continue
 
-            # Remove prefix and split into parts
-            config_path = key[len(prefix) :].lower().split("_")
+            # Remove prefix and split into parts. Drop empty components from a
+            # malformed name (e.g. ``SPECKIT_<EXT>_`` with no key, or
+            # consecutive underscores ``SPECKIT_X__Y``) so we never create an
+            # entry under an empty key.
+            config_path = [p for p in key[len(prefix) :].lower().split("_") if p]
+            if not config_path:
+                continue
 
-            # Build nested dict
+            # Build nested dict. Two env vars can collide on a prefix, e.g.
+            # SPECKIT_X_CONNECTION=a and SPECKIT_X_CONNECTION_URL=b. Guard the
+            # walk so a colliding scalar is replaced by a dict (deeper/more
+            # specific vars win) instead of being indexed into — which raised
+            # TypeError ('str' object does not support item assignment) — and
+            # guard the leaf so a scalar processed after the nested var does
+            # not clobber the nested dict. Order-independent: both insertion
+            # orders yield {'connection': {'url': ...}}. Nested-wins mirrors
+            # _merge_configs' dict-preserving semantics.
             current = env_config
             for part in config_path[:-1]:
-                if part not in current:
+                if not isinstance(current.get(part), dict):
                     current[part] = {}
                 current = current[part]
 
-            # Set the final value
-            current[config_path[-1]] = value
+            # Set the final value, unless a nested dict already occupies it.
+            if not isinstance(current.get(config_path[-1]), dict):
+                current[config_path[-1]] = value
 
         return env_config
 

src/specify_cli/extensions/_commands.py

@@ -1566,7 +1566,14 @@ def extension_set_priority(
     raw_priority = metadata.get("priority")
     # Only skip if the stored value is already a valid int equal to requested priority
     # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
+    # A bool is an int in Python (isinstance(True, int) is True), so exclude it explicitly —
+    # mirroring normalize_priority's bool guard — otherwise a corrupted True/False priority
+    # equals 1/0 here and is never repaired.
+    if (
+        isinstance(raw_priority, int)
+        and not isinstance(raw_priority, bool)
+        and raw_priority == priority
+    ):
         console.print(f"[yellow]Extension '{_escape_markup(str(display_name))}' already has priority {priority}[/yellow]")
         raise typer.Exit(0)
 

src/specify_cli/integrations/_helpers.py

@@ -190,7 +190,15 @@ def _parse_integration_options(integration: Any, raw_options: str) -> dict[str,
     """
     import shlex
     parsed: dict[str, Any] = {}
-    tokens = shlex.split(raw_options)
+    try:
+        tokens = shlex.split(raw_options)
+    except ValueError as exc:
+        # An unbalanced quote (e.g. --integration-options='--commands-dir "foo')
+        # makes shlex raise "No closing quotation". Translate it into the same
+        # clean exit-1 UX as every other bad-input path below rather than
+        # letting a raw traceback escape.
+        console.print(f"[red]Error:[/red] Could not parse integration options: {exc}.")
+        raise typer.Exit(1)
     declared_options = list(integration.options())
     declared = {opt.name.lstrip("-"): opt for opt in declared_options}
     allowed = ", ".join(sorted(opt.name for opt in declared_options))

src/specify_cli/integrations/base.py

@@ -17,6 +17,7 @@ import os
 import re
 import shlex
 import shutil
+import subprocess
 import sys
 from abc import ABC
 from dataclasses import dataclass
@@ -54,6 +55,18 @@ _CORE_COMMAND_TEMPLATE_RANK = {
 }
 
 
+def yaml_quote(value: str) -> str:
+    """Emit *value* as a double-quoted YAML scalar on a single line.
+
+    A hand-rolled quote cannot carry raw newlines (YAML folds them to
+    spaces) or control characters (the reader rejects them), so let the
+    YAML emitter produce the escapes.
+    """
+    return yaml.safe_dump(
+        str(value), default_style='"', allow_unicode=True, width=sys.maxsize
+    ).strip()
+
+
 # ---------------------------------------------------------------------------
 # IntegrationOption
 # ---------------------------------------------------------------------------
@@ -592,10 +605,42 @@ class IntegrationBase(ABC):
                 if candidate.exists():
                     return relative
         for name in ("python3", "python"):
-            if shutil.which(name):
-                return name
+            found = shutil.which(name)
+            if not found:
+                continue
+            # On Windows, python3/python on PATH may be the Microsoft
+            # Store App Execution Alias stub: it exists but only prints
+            # an installer hint and exits non-zero, so existence is not
+            # enough (see #3304 for the same defect in the sh scripts).
+            if sys.platform == "win32" and not IntegrationBase._interpreter_runs(
+                found
+            ):
+                continue
+            return name
         return sys.executable or "python3"
 
+    @staticmethod
+    def _interpreter_runs(path: str) -> bool:
+        """Return True when *path* executes as a Python interpreter.
+
+        Runs isolated (``-I``) without ``site`` (``-S``) and discards
+        I/O so the probe is a fast liveness check that cannot trigger
+        ``sitecustomize``/user startup hooks.
+        """
+        try:
+            return (
+                subprocess.run(
+                    [path, "-I", "-S", "-c", ""],
+                    stdin=subprocess.DEVNULL,
+                    stdout=subprocess.DEVNULL,
+                    stderr=subprocess.DEVNULL,
+                    timeout=15,
+                ).returncode
+                == 0
+            )
+        except (OSError, subprocess.SubprocessError):
+            return False
+
     @staticmethod
     def process_template(
         content: str,
@@ -1077,7 +1122,6 @@ class TomlIntegration(IntegrationBase):
 # YamlIntegration — YAML-format agents (Goose)
 # ---------------------------------------------------------------------------
 
-
 class YamlIntegration(IntegrationBase):
     """Concrete base for integrations that use YAML recipe format.
 
@@ -1480,21 +1524,17 @@ class SkillsIntegration(IntegrationBase):
             if not description:
                 description = f"Spec Kit: {command_name} workflow"
 
-            # Build SKILL.md with manually formatted frontmatter to match
-            # the release packaging script output exactly (double-quoted
-            # values, no yaml.safe_dump quoting differences).
-            def _quote(v: str) -> str:
-                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
-                return f'"{escaped}"'
-
+            # Build SKILL.md with manually formatted frontmatter (stable
+            # double-quoted values). yaml_quote escapes newlines and control
+            # characters that a plain quoted f-string cannot carry.
             skill_content = (
                 f"---\n"
-                f"name: {_quote(skill_name)}\n"
-                f"description: {_quote(description)}\n"
-                f"compatibility: {_quote('Requires spec-kit project structure with .specify/ directory')}\n"
+                f"name: {yaml_quote(skill_name)}\n"
+                f"description: {yaml_quote(description)}\n"
+                f"compatibility: {yaml_quote('Requires spec-kit project structure with .specify/ directory')}\n"
                 f"metadata:\n"
-                f"  author: {_quote('github-spec-kit')}\n"
-                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
+                f"  author: {yaml_quote('github-spec-kit')}\n"
+                f"  source: {yaml_quote('templates/commands/' + src_file.name)}\n"
                 f"---\n"
                 f"{processed_body}"
             )

src/specify_cli/integrations/devin/__init__.py

@@ -62,4 +62,4 @@ class DevinIntegration(SkillsIntegration):
                 default=True,
                 help="Install as agent skills (default for Devin)",
             ),
-        ]
+        ]

src/specify_cli/integrations/forge/__init__.py

@@ -18,13 +18,13 @@ from ..manifest import IntegrationManifest
 
 def format_forge_command_name(cmd_name: str) -> str:
     """Convert command name to Forge-compatible hyphenated format.
-    
+
     Forge requires command names to use hyphens instead of dots for
     compatibility with ZSH and other shells. This function converts
     dot-notation command names to hyphenated format.
-    
+
     The function is idempotent: already-formatted names are returned unchanged.
-    
+
     Examples:
         >>> format_forge_command_name("plan")
         'speckit-plan'
@@ -38,26 +38,26 @@ def format_forge_command_name(cmd_name: str) -> str:
         'speckit-my-extension-example'
         >>> format_forge_command_name("speckit.jira.sync-status")
         'speckit-jira-sync-status'
-    
+
     Args:
-        cmd_name: Command name in dot notation (speckit.foo.bar), 
+        cmd_name: Command name in dot notation (speckit.foo.bar),
                   hyphenated format (speckit-foo-bar), or plain name (foo)
-    
+
     Returns:
         Hyphenated command name with 'speckit-' prefix
     """
     # Already in hyphenated format - return as-is (idempotent)
     if cmd_name.startswith("speckit-"):
         return cmd_name
-    
+
     # Strip 'speckit.' prefix if present
     short_name = cmd_name
     if short_name.startswith("speckit."):
         short_name = short_name[len("speckit."):]
-    
+
     # Replace all dots with hyphens
     short_name = short_name.replace(".", "-")
-    
+
     # Return with 'speckit-' prefix
     return f"speckit-{short_name}"
 

src/specify_cli/integrations/hermes/__init__.py

@@ -18,7 +18,7 @@ from typing import Any
 
 import yaml
 
-from ..base import IntegrationOption, SkillsIntegration
+from ..base import IntegrationOption, SkillsIntegration, yaml_quote
 from ..manifest import IntegrationManifest
 
 
@@ -153,20 +153,18 @@ class HermesIntegration(SkillsIntegration):
             if not description:
                 description = f"Spec Kit: {command_name} workflow"
 
-            # Build SKILL.md with manually formatted frontmatter
-            def _quote(v: str) -> str:
-                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
-                return f'"{escaped}"'
-
+            # Build SKILL.md with manually formatted frontmatter. yaml_quote
+            # escapes newlines and control characters that a plain quoted
+            # f-string cannot carry.
             skill_content = (
                 f"---\n"
-                f"name: {_quote(skill_name)}\n"
-                f"description: {_quote(description)}\n"
+                f"name: {yaml_quote(skill_name)}\n"
+                f"description: {yaml_quote(description)}\n"
                 f"compatibility: "
-                f"{_quote('Requires spec-kit project structure with .specify/ directory')}\n"
+                f"{yaml_quote('Requires spec-kit project structure with .specify/ directory')}\n"
                 f"metadata:\n"
-                f"  author: {_quote('github-spec-kit')}\n"
-                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
+                f"  author: {yaml_quote('github-spec-kit')}\n"
+                f"  source: {yaml_quote('templates/commands/' + src_file.name)}\n"
                 f"---\n"
                 f"{processed_body}"
             )

src/specify_cli/integrations/kiro_cli/__init__.py

@@ -13,6 +13,7 @@ _KIRO_ARG_FALLBACK = "(the user will provide the argument in this conversation)"
 
 class KiroCliIntegration(MarkdownIntegration):
     key = "kiro-cli"
+    multi_install_safe = True
     config = {
         "name": "Kiro CLI",
         "folder": ".kiro/",
@@ -26,3 +27,10 @@ class KiroCliIntegration(MarkdownIntegration):
         "args": _KIRO_ARG_FALLBACK,
         "extension": ".md",
     }
+
+    # Kiro CLI keeps everything under a static, isolated agent root
+    # (``.kiro/`` with commands in ``.kiro/prompts``) that no other
+    # integration writes to, so it is safe to install alongside others
+    # (issue #3471). The registry's multi-install-safe contract tests
+    # enforce that isolation for every integration setting this flag.
+    multi_install_safe = True

src/specify_cli/presets/__init__.py

@@ -778,6 +778,7 @@ class PresetManager:
                                         matching_cmds, ext_id, ext_dir,
                                         self.project_root,
                                         context_note=f"\n<!-- Extension: {ext_id} -->\n<!-- Config: .specify/extensions/{ext_id}/ -->\n",
+                                        extension_id=ext_id,
                                     )
                                     registered = True
                             except Exception:
@@ -1199,6 +1200,8 @@ class PresetManager:
                     "command_name": cmd_name,
                     "source_file": source_file,
                     "source": f"extension:{manifest.id}",
+                    "extension_id": manifest.id,
+                    "extension_dir": ext_root,
                 }
                 modern_skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
                 restore_index.setdefault(modern_skill_name, restore_info)
@@ -1463,6 +1466,17 @@ class PresetManager:
             if extension_restore:
                 content = extension_restore["source_file"].read_text(encoding="utf-8")
                 frontmatter, body = registrar.parse_frontmatter(content)
+                # Mirror the register-time rewrite (#2101): resolve
+                # extension-relative subdir references (agents/,
+                # knowledge-base/, etc.) to their installed location before
+                # the generic placeholder resolution below, otherwise
+                # restoring after a preset override removal would leave
+                # bare, unresolvable paths in the skill body.
+                body = registrar.rewrite_extension_paths(
+                    body,
+                    extension_restore["extension_id"],
+                    extension_restore["extension_dir"],
+                )
                 if isinstance(selected_ai, str):
                     body = registrar.resolve_skill_placeholders(
                         selected_ai, frontmatter, body, self.project_root
@@ -2574,6 +2588,39 @@ class PresetResolver:
                 self._manifest_cache[key] = None
         return self._manifest_cache[key]
 
+    def _manifest_declared_template(
+        self, pack_dir: Path, template_name: str, template_type: str
+    ) -> tuple[dict | None, Path | None]:
+        """Resolve a preset's manifest-declared template entry and usable file.
+
+        Returns ``(entry, candidate)``:
+        - ``entry`` is the matching ``provides.templates`` mapping, or ``None`` if
+          the manifest is absent or does not list this ``(name, type)``.
+        - ``candidate`` is the declared ``file:`` resolved under ``pack_dir`` IFF
+          it is a regular file (``is_file()``); ``None`` otherwise — a missing,
+          empty, or non-file (e.g. directory) declaration yields ``(entry, None)``.
+
+        The manifest is authoritative: when it declares a template (``entry`` is
+        not ``None``) but the file is unusable (``candidate`` is ``None``),
+        callers must NOT fall back to the convention lookup — that would mask a
+        typo or pick up an undeclared file. Shared by ``resolve()`` and
+        ``collect_all_layers()`` so their manifest-first resolution cannot
+        silently diverge again (the divergence this fix addressed).
+        """
+        manifest = self._get_manifest(pack_dir)
+        if not manifest:
+            return None, None
+        for tmpl in manifest.templates:
+            if tmpl.get("name") == template_name and tmpl.get("type") == template_type:
+                file_path = tmpl.get("file")
+                if file_path:
+                    manifest_candidate = pack_dir / file_path
+                    return tmpl, (
+                        manifest_candidate if manifest_candidate.is_file() else None
+                    )
+                return tmpl, None
+        return None, None
+
     def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
         """Build unified list of registered and unregistered extensions sorted by priority.
 
@@ -2676,6 +2723,27 @@ class PresetResolver:
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
                 pack_dir = self.presets_dir / pack_id
+                # The preset manifest is authoritative: if it declares this
+                # template with an explicit ``file:``, resolve to that path —
+                # and do NOT fall back to convention when it's missing, to
+                # avoid masking typos or picking up an undeclared file. Only
+                # when the manifest is absent or doesn't list this template do
+                # we use the convention-based subdir lookup. Mirrors
+                # collect_all_layers()/resolve_content() so resolve() and
+                # resolve_with_source() agree with them instead of returning
+                # the core template (or a stray convention file).
+                entry, manifest_candidate = self._manifest_declared_template(
+                    pack_dir, template_name, template_type
+                )
+                if manifest_candidate is not None:
+                    return manifest_candidate
+                if entry is not None:
+                    # Manifest declares this template but the file is missing,
+                    # non-file (e.g. a directory), or an empty/falsey ``file``
+                    # value. The manifest is authoritative, so skip this pack's
+                    # convention fallback rather than mask a typo — mirrors
+                    # collect_all_layers().
+                    continue
                 for subdir in subdirs:
                     if subdir:
                         candidate = pack_dir / subdir / f"{template_name}{ext}"
@@ -2943,31 +3011,22 @@ class PresetResolver:
                 pack_dir = self.presets_dir / pack_id
                 # Read strategy and manifest file path from preset manifest
                 strategy = "replace"
-                manifest_file_path = None
                 manifest_has_strategy = False
-                manifest_found_entry = False
-                manifest = self._get_manifest(pack_dir)
-                if manifest:
-                    for tmpl in manifest.templates:
-                        if (tmpl.get("name") == template_name
-                                and tmpl.get("type") == template_type):
-                            strategy = tmpl.get("strategy", "replace")
-                            manifest_has_strategy = "strategy" in tmpl
-                            manifest_file_path = tmpl.get("file")
-                            manifest_found_entry = True
-                            break
-                # Use manifest file path if specified, otherwise convention-based
-                # lookup — but only when the manifest doesn't exist or doesn't
-                # list this template, so preset.yml stays authoritative.
+                entry, manifest_candidate = self._manifest_declared_template(
+                    pack_dir, template_name, template_type
+                )
+                if entry is not None:
+                    strategy = entry.get("strategy", "replace")
+                    manifest_has_strategy = "strategy" in entry
+                # Use the manifest's declared file when it's a usable regular file;
+                # only fall back to convention-based lookup when the manifest
+                # doesn't list this template at all, so preset.yml stays
+                # authoritative (a declared-but-unusable file skips convention —
+                # parity with resolve()).
                 candidate = None
-                if manifest_file_path:
-                    manifest_candidate = pack_dir / manifest_file_path
-                    if manifest_candidate.exists():
-                        candidate = manifest_candidate
-                    # Explicit file path that doesn't exist: skip convention
-                    # fallback to avoid masking typos or picking up unintended files.
-                elif not manifest_found_entry:
-                    # Manifest doesn't list this template — check convention paths
+                if manifest_candidate is not None:
+                    candidate = manifest_candidate
+                elif entry is None:
                     candidate = _find_in_subdirs(pack_dir)
                 if candidate:
                     # Legacy fallback: if manifest doesn't explicitly declare a
@@ -3038,6 +3097,8 @@ class PresetResolver:
                     "path": candidate,
                     "source": source,
                     "strategy": "replace",
+                    "extension_id": ext_id,
+                    "extension_dir": ext_dir,
                 })
 
         # Priority 4: Core templates (always "replace")
@@ -3157,10 +3218,32 @@ class PresetResolver:
         if not layers:
             return None
 
+        def _read_layer_content(layer: Dict[str, Any]) -> str:
+            """Read a layer's raw text, rewriting extension-relative subdir
+            references (agents/, knowledge-base/, etc.) to their installed
+            location when the layer is extension-provided (#2101).
+
+            Extension layers are always inserted with strategy "replace"
+            (see collect_all_layers), so a layer only ever needs this
+            rewrite when it wins outright above or serves as the
+            composition base below — never as a mid-stack composing
+            (append/prepend/wrap) layer.
+            """
+            text = layer["path"].read_text(encoding="utf-8")
+            extension_id = layer.get("extension_id")
+            extension_dir = layer.get("extension_dir")
+            if extension_id and extension_dir:
+                from ..agents import CommandRegistrar
+
+                text = CommandRegistrar.rewrite_extension_paths(
+                    text, extension_id, extension_dir
+                )
+            return text
+
         # If the top (highest-priority) layer is replace, it wins entirely —
         # lower layers are irrelevant regardless of their strategies.
         if layers[0]["strategy"] == "replace":
-            return layers[0]["path"].read_text(encoding="utf-8")
+            return _read_layer_content(layers[0])
 
         # Composition: build content bottom-up from the effective base.
         # The base is the nearest replace layer scanning from highest priority
@@ -3183,7 +3266,7 @@ class PresetResolver:
 
         # Convert to reversed_layers index
         base_reversed_idx = len(layers) - 1 - base_layer_idx
-        content = layers[base_layer_idx]["path"].read_text(encoding="utf-8")
+        content = _read_layer_content(layers[base_layer_idx])
         # Compose only the layers above the base (higher priority = lower index in layers,
         # higher index in reversed_layers). Process bottom-up from base+1.
         start_idx = base_reversed_idx + 1

src/specify_cli/presets/_commands.py

@@ -469,7 +469,14 @@ def preset_set_priority(
     raw_priority = metadata.get("priority")
     # Only skip if the stored value is already a valid int equal to requested priority
     # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
+    # A bool is an int in Python (isinstance(True, int) is True), so exclude it explicitly —
+    # mirroring normalize_priority's bool guard — otherwise a corrupted True/False priority
+    # equals 1/0 here and is never repaired.
+    if (
+        isinstance(raw_priority, int)
+        and not isinstance(raw_priority, bool)
+        and raw_priority == priority
+    ):
         console.print(f"[yellow]Preset '{preset_id}' already has priority {priority}[/yellow]")
         raise typer.Exit(0)
 

src/specify_cli/shared_infra.py

@@ -328,7 +328,10 @@ def refresh_shared_templates(
         _ensure_safe_shared_destination(project_path, dst)
         rel = dst.relative_to(project_path).as_posix()
         if dst.exists() and not force:
-            if rel not in tracked_files or rel in modified:
+            if rel not in tracked_files or rel in modified or manifest.is_recovered(rel):
+                # Never overwrite a recovered (pre-existing user) file without
+                # --force, matching install_shared_infra's is_recovered gate
+                # (#2918). Without this, refresh clobbers user content.
                 skipped_files.append(rel)
                 continue
 
@@ -344,7 +347,7 @@ def refresh_shared_templates(
 
     if skipped_files:
         console.print(
-            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified or untracked shared template file(s) were not updated:"
+            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified, untracked, or preserved (recovered) shared template file(s) were not updated:"
         )
         for rel in skipped_files:
             console.print(f"    {rel}")
@@ -400,7 +403,7 @@ def install_shared_infra(
     # manifest entries the core no longer ships (stale-script cleanup, #3076).
     seen_rels: set[str] = set()
     scripts_scanned = False
-    variant_dir = "bash" if script_type == "sh" else "powershell"
+    variant_dir = {"sh": "bash", "py": "python"}.get(script_type, "powershell")
 
     def _decide_overwrite(rel: str, dst: Path) -> tuple[bool, str | None]:
         """Return (write, bucket) where bucket is 'skip', 'preserved', or None."""
@@ -462,6 +465,10 @@ def install_shared_infra(
                     for src_path in variant_src.rglob("*"):
                         if not src_path.is_file():
                             continue
+                        # Python bytecode caches are local artifacts, not
+                        # workflow scripts — never install them.
+                        if "__pycache__" in src_path.parts:
+                            continue
                         # Mark scanned only once a real source file is seen. An
                         # empty (or symlink-skipped) variant keeps this False, so
                         # stale-cleanup is skipped — otherwise it would treat every

src/specify_cli/workflows/_commands.py

@@ -601,7 +601,15 @@ def workflow_add(
         except (ValueError, yaml.YAMLError) as exc:
             console.print(f"[red]Error:[/red] Invalid workflow YAML: {exc}")
             raise typer.Exit(1)
-        if not definition.id or not definition.id.strip():
+        # Non-string ids (e.g. unquoted ``id: 123`` or ``id: 0``) fall through
+        # to validate_workflow below, which reports a typed error instead of
+        # crashing on ``.strip()`` here. Only None/empty/whitespace-only ids
+        # are rejected as missing.
+        if (
+            definition.id is None
+            or definition.id == ""
+            or (isinstance(definition.id, str) and not definition.id.strip())
+        ):
             console.print("[red]Error:[/red] Workflow definition has an empty or missing 'id'")
             raise typer.Exit(1)
 

src/specify_cli/workflows/catalog.py

@@ -76,8 +76,16 @@ class WorkflowRegistry:
         if self.registry_path.exists():
             try:
                 with open(self.registry_path, encoding="utf-8") as f:
-                    return json.load(f)
-            except (json.JSONDecodeError, ValueError):
+                    data = json.load(f)
+                # Validate shape: must be a dict with a dict "workflows" field,
+                # otherwise every method that indexes data["workflows"] crashes.
+                # Mirrors StepRegistry._load.
+                if not isinstance(data, dict):
+                    return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
+                if not isinstance(data.get("workflows"), dict):
+                    data["workflows"] = {}
+                return data
+            except (json.JSONDecodeError, ValueError, OSError, UnicodeError):
                 # Corrupted registry file — reset to default
                 return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
         return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
@@ -438,9 +446,9 @@ class WorkflowCatalog:
                 q = query.lower()
                 searchable = " ".join(
                     [
-                        wf_data.get("name", ""),
-                        wf_data.get("description", ""),
-                        wf_data.get("id", ""),
+                        str(wf_data.get("name") or ""),
+                        str(wf_data.get("description") or ""),
+                        str(wf_data.get("id") or ""),
                     ]
                 ).lower()
                 if q not in searchable:

src/specify_cli/workflows/engine.py

@@ -129,26 +129,49 @@ def validate_workflow(definition: WorkflowDefinition) -> list[str]:
     errors: list[str] = []
 
     # -- Schema version ---------------------------------------------------
-    if definition.schema_version not in ("1.0", "1"):
+    # str() so an unquoted ``schema_version: 1.0`` (YAML float) is accepted —
+    # rejecting it would print "Unsupported schema_version 1.0. Expected '1.0'."
+    if str(definition.schema_version) != "1.0":
         errors.append(
             f"Unsupported schema_version {definition.schema_version!r}. "
             f"Expected '1.0'."
         )
 
     # -- Top-level fields -------------------------------------------------
-    if not definition.id:
+    # YAML parses unquoted scalars like ``id: 123`` or ``version: 1.0`` as
+    # int/float; check types before regex/string operations so authoring
+    # mistakes surface as validation errors instead of tracebacks. Only
+    # ``None``/empty-string count as missing so falsey non-strings
+    # (``id: 0``, ``name: false``) still get the typed error.
+    if definition.id is None or definition.id == "":
         errors.append("Workflow is missing 'workflow.id'.")
+    elif not isinstance(definition.id, str):
+        errors.append(
+            f"'workflow.id' must be a string, got "
+            f"{type(definition.id).__name__} ({definition.id!r})."
+        )
     elif not _ID_PATTERN.match(definition.id):
         errors.append(
             f"Workflow ID {definition.id!r} must be lowercase alphanumeric "
             f"with hyphens."
         )
 
-    if not definition.name:
+    if definition.name is None or definition.name == "":
         errors.append("Workflow is missing 'workflow.name'.")
+    elif not isinstance(definition.name, str):
+        errors.append(
+            f"'workflow.name' must be a string, got "
+            f"{type(definition.name).__name__} ({definition.name!r})."
+        )
 
-    if not definition.version:
+    if definition.version is None or definition.version == "":
         errors.append("Workflow is missing 'workflow.version'.")
+    elif not isinstance(definition.version, str):
+        errors.append(
+            f"'workflow.version' must be a string, got "
+            f"{type(definition.version).__name__} ({definition.version!r}) — "
+            f'quote it in YAML (version: "1.0.0").'
+        )
     elif not re.match(r"^\d+\.\d+\.\d+$", definition.version):
         errors.append(
             f"Workflow version {definition.version!r} is not valid "
@@ -256,9 +279,15 @@ def _validate_steps(
             continue
 
         step_id = step_config.get("id")
-        if not step_id:
+        if step_id is None or step_id == "":
             errors.append("Step is missing 'id' field.")
             continue
+        if not isinstance(step_id, str):
+            errors.append(
+                f"Step ID must be a string, got "
+                f"{type(step_id).__name__} ({step_id!r})."
+            )
+            continue
 
         if ":" in step_id:
             errors.append(
@@ -953,7 +982,16 @@ class WorkflowEngine:
                     from .expressions import evaluate_condition
 
                     max_iters = step_config.get("max_iterations")
-                    if not isinstance(max_iters, int) or max_iters < 1:
+                    # A bool is an int in Python (isinstance(True, int) is True
+                    # and True == 1), so a bool max_iterations would slip past
+                    # the int check and cap the loop at range(0)==1 iteration
+                    # instead of the default. Exclude bools, mirroring the
+                    # while/do-while validators and the continue_on_error guard.
+                    if (
+                        isinstance(max_iters, bool)
+                        or not isinstance(max_iters, int)
+                        or max_iters < 1
+                    ):
                         max_iters = 10
                     condition = step_config.get("condition", False)
                     for _loop_iter in range(max_iters - 1):

src/specify_cli/workflows/expressions.py

@@ -242,6 +242,26 @@ def _interpolate_expressions(template: str, namespace: dict[str, Any]) -> str:
     return "".join(out)
 
 
+def _split_top_level(text: str, sep: str) -> list[str]:
+    """Split *text* on each occurrence of *sep* that lies outside any quoted
+    string or nested brackets.
+
+    Used to break a filter chain (``a | map('x') | join(',')``) into its
+    individual filter segments without splitting on a ``|`` that appears inside
+    a quoted argument. Each returned segment is a slice at a top-level
+    boundary, so the quote/bracket scan restarts cleanly on the remainder.
+    """
+    parts: list[str] = []
+    start = 0
+    while True:
+        idx = _find_top_level(text[start:], sep)
+        if idx == -1:
+            parts.append(text[start:])
+            return parts
+        parts.append(text[start:start + idx])
+        start += idx + len(sep)
+
+
 def _split_top_level_commas(text: str) -> list[str]:
     """Split *text* on commas that are not inside quotes or nested brackets.
 
@@ -305,6 +325,68 @@ def _find_top_level(text: str, token: str) -> int:
     return -1
 
 
+def _apply_filter(value: Any, filter_expr: str, namespace: dict[str, Any]) -> Any:
+    """Apply a single pipe filter segment to *value*.
+
+    *filter_expr* is one link of a filter chain — the text between two
+    top-level ``|`` separators, already stripped (e.g. ``map('name')``,
+    ``default('x')``, ``from_json``). Returns the filtered value so the caller
+    can feed it into the next link.
+
+    Raises ``ValueError`` on any mis-wired or unknown filter rather than
+    silently returning *value* unchanged: a passthrough would turn a mistyped
+    or unsupported filter into a wrong result with no signal.
+    """
+    # `from_json` is strict: it takes no arguments and tolerates no trailing
+    # tokens. Match on the leading filter name and require the whole filter to
+    # be exactly `from_json`, so every mis-wired form (`from_json()`,
+    # `from_json('x')`, `from_json)`, `from_json extra`) fails loudly instead of
+    # silently falling through to the unknown-filter path.
+    leading = re.match(r"\w+", filter_expr)
+    if leading and leading.group(0) == "from_json":
+        if filter_expr != "from_json":
+            raise ValueError(
+                "from_json: expected '| from_json' with no arguments or "
+                f"trailing tokens, got '| {filter_expr}'"
+            )
+        return _filter_from_json(value)
+
+    # Parse filter name and argument
+    filter_match = re.match(r"(\w+)\((.+)\)", filter_expr)
+    if filter_match:
+        fname = filter_match.group(1)
+        farg = _evaluate_simple_expression(filter_match.group(2).strip(), namespace)
+        if fname == "default":
+            return _filter_default(value, farg)
+        if fname == "join":
+            return _filter_join(value, farg)
+        if fname == "map":
+            return _filter_map(value, farg)
+        if fname == "contains":
+            return _filter_contains(value, farg)
+    # Filter without args
+    if filter_expr == "default":
+        return _filter_default(value)
+    # No recognized filter matched. Fail loudly rather than silently returning
+    # the unfiltered value. Distinguish a *registered* filter used in an
+    # unsupported form (e.g. `| join` or `| map` with no argument) from a
+    # genuinely unknown filter name, so the message names the real problem
+    # instead of calling a known filter "unknown".
+    name = leading.group(0) if leading else filter_expr
+    expected = (
+        "expected one of default or default('x'), join('sep'), "
+        "map('attr'), contains('s'), or from_json"
+    )
+    if name in _REGISTERED_FILTERS:
+        raise ValueError(
+            f"filter '{name}' used in an unsupported form (got "
+            f"'| {filter_expr}'): {expected}"
+        )
+    raise ValueError(
+        f"unknown filter '{name}': {expected} (got '| {filter_expr}')"
+    )
+
+
 def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     """Evaluate a simple expression against the namespace.
 
@@ -329,65 +411,17 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     # Handle pipe filters. Detect the pipe at the top level only, so a literal
     # '|' inside a quoted operand (e.g. `inputs.x == 'a|b'`) or nested brackets is
     # not mistaken for a filter separator — mirroring the operator parsing below.
+    # Filters chain left-to-right: `list | map('name') | join(', ')` feeds each
+    # filter's result into the next, so `map` (which yields a list) can be
+    # rendered by `join`. Splitting only at the first pipe would hand the whole
+    # tail to one filter and mangle any later `|`.
     pipe_idx = _find_top_level(expr, "|")
     if pipe_idx != -1:
-        value = _evaluate_simple_expression(expr[:pipe_idx].strip(), namespace)
-        filter_expr = expr[pipe_idx + 1:].strip()
-
-        # `from_json` is strict: it takes no arguments and tolerates no
-        # trailing tokens. Match on the leading filter name and require the
-        # whole filter to be exactly `from_json`, so every mis-wired form
-        # (`from_json()`, `from_json('x')`, `from_json)`, `from_json extra`)
-        # fails loudly instead of silently falling through to the
-        # unknown-filter path and returning the unparsed value. (filter_expr
-        # is already stripped above.)
-        leading = re.match(r"\w+", filter_expr)
-        if leading and leading.group(0) == "from_json":
-            if filter_expr != "from_json":
-                raise ValueError(
-                    "from_json: expected '| from_json' with no arguments or "
-                    f"trailing tokens, got '| {filter_expr}'"
-                )
-            return _filter_from_json(value)
-
-        # Parse filter name and argument
-        filter_match = re.match(r"(\w+)\((.+)\)", filter_expr)
-        if filter_match:
-            fname = filter_match.group(1)
-            farg = _evaluate_simple_expression(filter_match.group(2).strip(), namespace)
-            if fname == "default":
-                return _filter_default(value, farg)
-            if fname == "join":
-                return _filter_join(value, farg)
-            if fname == "map":
-                return _filter_map(value, farg)
-            if fname == "contains":
-                return _filter_contains(value, farg)
-        # Filter without args
-        filter_name = filter_expr.strip()
-        if filter_name == "default":
-            return _filter_default(value)
-        # No recognized filter matched. Fail loudly rather than silently
-        # returning the unfiltered value: a passthrough turns a mis-typed or
-        # unsupported filter into a wrong result with no signal. Mirrors the
-        # strict `from_json` handling above. Distinguish a *registered* filter
-        # used in an unsupported form (e.g. `| join` or `| map` with no
-        # argument) from a genuinely unknown filter name, so the message names
-        # the real problem instead of calling a known filter "unknown".
-        leading_name = re.match(r"\w+", filter_expr)
-        name = leading_name.group(0) if leading_name else filter_expr
-        expected = (
-            "expected one of default or default('x'), join('sep'), "
-            "map('attr'), contains('s'), or from_json"
-        )
-        if name in _REGISTERED_FILTERS:
-            raise ValueError(
-                f"filter '{name}' used in an unsupported form (got "
-                f"'| {filter_expr}'): {expected}"
-            )
-        raise ValueError(
-            f"unknown filter '{name}': {expected} (got '| {filter_expr}')"
-        )
+        segments = _split_top_level(expr, "|")
+        value = _evaluate_simple_expression(segments[0].strip(), namespace)
+        for segment in segments[1:]:
+            value = _apply_filter(value, segment.strip(), namespace)
+        return value
 
     # Boolean operators — parse 'or' first (lower precedence) so that
     # 'a or b and c' is evaluated as 'a or (b and c)'. Splits are quote/bracket
@@ -430,9 +464,9 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
             if op == "<=":
                 return _safe_compare(left, right, "<=")
             if op == " in ":
-                return left in right if right is not None else False
+                return _safe_membership(left, right, negate=False)
             if op == " not in ":
-                return left not in right if right is not None else True
+                return _safe_membership(left, right, negate=True)
 
     # Numeric literal
     try:
@@ -477,6 +511,26 @@ def _coerce_number(value: Any) -> Any:
     return value
 
 
+def _safe_membership(left: Any, right: Any, *, negate: bool) -> bool:
+    """Safely evaluate ``left in right`` (or ``not in``) without crashing.
+
+    ``left in right`` raises ``TypeError`` whenever the operands don't support
+    membership testing — most commonly a non-iterable right operand (``None``,
+    an int, a bool), but also cases like an unhashable ``left`` against a set.
+    In every such case the membership relation is undefined, so treat it as
+    ``False`` (``not in`` as ``True``) rather than leaking the error out of the
+    evaluator and crashing the whole workflow. Mirrors the graceful
+    ``TypeError`` handling in ``_safe_compare`` for the ordering operators, and
+    generalizes the previous ``right is not None`` guard to any operand pair
+    that can't be membership-tested.
+    """
+    try:
+        contained = left in right
+    except TypeError:
+        contained = False
+    return not contained if negate else contained
+
+
 def _safe_compare(left: Any, right: Any, op: str) -> bool:
     """Compare two values for ordering, coercing numeric strings when possible.
 

src/specify_cli/workflows/steps/command/__init__.py

@@ -31,6 +31,20 @@ class CommandStep(StepBase):
     def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
         command = config.get("command", "")
         input_data = config.get("input", {})
+        # validate() rejects a non-mapping input, but the engine does not
+        # auto-validate before execute(); a workflow that skipped validation can
+        # still reach here. Fail the step with the same contract error rather
+        # than silently coercing to {} and dispatching with empty args — that
+        # would change the command's meaning, hide the config error, and report
+        # COMPLETED, defeating the per-step FAILED / continue_on_error behavior.
+        if not isinstance(input_data, dict):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Command step {config.get('id', '?')!r}: 'input' must be a "
+                    f"mapping, got {type(input_data).__name__}."
+                ),
+            )
 
         # Resolve expressions in input
         resolved_input: dict[str, Any] = {}
@@ -50,8 +64,18 @@ class CommandStep(StepBase):
         # Merge options (workflow defaults ← step overrides)
         options = dict(context.default_options)
         step_options = config.get("options", {})
-        if step_options:
-            options.update(step_options)
+        # Same rationale as 'input': a malformed options fails the step rather
+        # than being silently ignored (which would let an invalid step run and
+        # apparently complete).
+        if not isinstance(step_options, dict):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Command step {config.get('id', '?')!r}: 'options' must be a "
+                    f"mapping, got {type(step_options).__name__}."
+                ),
+            )
+        options.update(step_options)
 
         # Attempt CLI dispatch
         args_str = str(resolved_input.get("args", ""))
@@ -155,4 +179,16 @@ class CommandStep(StepBase):
             errors.append(
                 f"Command step {config.get('id', '?')!r} is missing 'command' field."
             )
+        # execute() iterates input.items() and options.update(step_options); a
+        # non-mapping here would raise at run time. Validate the shape like the
+        # sibling steps (switch 'cases', fan-out 'step') so it is reported, not
+        # crashed on.
+        if "input" in config and not isinstance(config["input"], dict):
+            errors.append(
+                f"Command step {config.get('id', '?')!r}: 'input' must be a mapping."
+            )
+        if "options" in config and not isinstance(config["options"], dict):
+            errors.append(
+                f"Command step {config.get('id', '?')!r}: 'options' must be a mapping."
+            )
         return errors

src/specify_cli/workflows/steps/fan_in/__init__.py

@@ -24,6 +24,24 @@ class FanInStep(StepBase):
         if not isinstance(output_config, dict):
             output_config = {}
 
+        # The engine does not auto-validate step config, so an unvalidated run
+        # with a non-list ``wait_for`` reaches here raw. Iterating it then
+        # either crashes the whole run (a scalar like an int or None raises
+        # TypeError) or, worse, silently iterates a string's characters and
+        # yields a bogus join of empty results with a COMPLETED status — the
+        # exact "silent empty result + COMPLETED" wiring bug the engine's
+        # fan-in validation guards against. Fail this step loudly instead,
+        # mirroring the fan-out step's non-list ``items`` handling.
+        if not isinstance(wait_for, list):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Fan-in step {config.get('id', '?')!r}: 'wait_for' must be "
+                    f"a list of step IDs, got {type(wait_for).__name__}."
+                ),
+                output={"results": []},
+            )
+
         # Collect results from referenced steps
         results = []
         for step_id in wait_for:

src/specify_cli/workflows/steps/if_then/__init__.py

@@ -47,8 +47,8 @@ class IfThenStep(StepBase):
             errors.append(
                 f"If step {config.get('id', '?')!r}: 'then' must be a list of steps."
             )
-        else_branch = config.get("else", [])
-        if else_branch and not isinstance(else_branch, list):
+        else_branch = config.get("else")
+        if else_branch is not None and not isinstance(else_branch, list):
             errors.append(
                 f"If step {config.get('id', '?')!r}: 'else' must be a list of steps."
             )

src/specify_cli/workflows/steps/shell/__init__.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import json
+import math
 import subprocess
 from typing import Any
 
@@ -25,7 +26,20 @@ class ShellStep(StepBase):
         run_cmd = str(run_cmd)
 
         cwd = context.project_root or "."
-
+        # Per-step execution timeout in seconds; defaults to 300 for backward
+        # compatibility. The engine does not auto-validate step config, so
+        # validate here as well — a caller that skips WorkflowEngine.validate()
+        # must fail the step cleanly rather than crash subprocess.run() with a
+        # TypeError (or silently coerce ``timeout: true`` to a 1s duration,
+        # since bool is an int subclass).
+        timeout = config.get("timeout", 300)
+        timeout_error = self._timeout_error(config)
+        if timeout_error is not None:
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=timeout_error,
+                output={"exit_code": -1, "stdout": "", "stderr": "invalid timeout"},
+            )
         # NOTE: shell=True is required to support pipes, redirects, and
         # multi-command expressions in workflow YAML.  Workflow authors
         # control commands; catalog-installed workflows should be reviewed
@@ -37,7 +51,7 @@ class ShellStep(StepBase):
                 capture_output=True,
                 text=True,
                 cwd=cwd,
-                timeout=300,
+                timeout=timeout,
             )
             output = {
                 "exit_code": proc.returncode,
@@ -74,7 +88,7 @@ class ShellStep(StepBase):
         except subprocess.TimeoutExpired:
             return StepResult(
                 status=StepStatus.FAILED,
-                error="Shell command timed out after 300 seconds.",
+                error=f"Shell command timed out after {timeout} seconds.",
                 output={"exit_code": -1, "stdout": "", "stderr": "timeout"},
             )
         except OSError as exc:
@@ -84,6 +98,32 @@ class ShellStep(StepBase):
                 output={"exit_code": -1, "stdout": "", "stderr": str(exc)},
             )
 
+    @staticmethod
+    def _timeout_error(config: dict[str, Any]) -> str | None:
+        """Return an error message if ``config['timeout']`` is invalid, else None.
+
+        Shared by execute() and validate() so both paths reject the same
+        values with the same message. An absent ``timeout`` is valid (the
+        default is used). bool is a subclass of int, but ``timeout: true`` is a
+        config error rather than a duration, so it is rejected explicitly.
+        Non-finite floats (YAML ``.inf``/``.nan``) pass a plain ``> 0`` check
+        but would raise in subprocess.run(), so they are rejected too.
+        """
+        if "timeout" not in config:
+            return None
+        timeout = config["timeout"]
+        if (
+            isinstance(timeout, bool)
+            or not isinstance(timeout, (int, float))
+            or not math.isfinite(timeout)
+            or timeout <= 0
+        ):
+            return (
+                f"Shell step {config.get('id', '?')!r}: 'timeout' must be a "
+                f"positive number of seconds, got {timeout!r}."
+            )
+        return None
+
     def validate(self, config: dict[str, Any]) -> list[str]:
         errors = super().validate(config)
         if "run" not in config:
@@ -106,4 +146,7 @@ class ShellStep(StepBase):
                 f"Shell step {config.get('id', '?')!r}: 'output_format' must "
                 f"be 'json' when present, got {output_format!r}."
             )
+        timeout_error = self._timeout_error(config)
+        if timeout_error is not None:
+            errors.append(timeout_error)
         return errors

src/specify_cli/workflows/steps/switch/__init__.py

@@ -26,6 +26,20 @@ class SwitchStep(StepBase):
         str_value = str(value) if value is not None else ""
 
         cases = config.get("cases", {})
+        if not isinstance(cases, dict):
+            # The engine does not auto-validate step config, so an unvalidated
+            # run with a non-mapping ``cases`` (a list/scalar authoring mistake)
+            # would otherwise raise AttributeError from ``.items()`` below and
+            # crash the whole run. Fail this step loudly instead, mirroring the
+            # fan-out step's non-list ``items`` handling.
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Switch step {config.get('id', '?')!r}: 'cases' must be a "
+                    f"mapping, got {type(cases).__name__}."
+                ),
+                output={"matched_case": None, "expression_value": value},
+            )
         for case_key, case_steps in cases.items():
             if str(case_key) == str_value:
                 return StepResult(

templates/checklist-template.md

@@ -6,16 +6,16 @@
 
 **Note**: This checklist is generated by the `__SPECKIT_COMMAND_CHECKLIST__` command based on feature context and requirements.
 
-<!-- 
+<!--
   ============================================================================
   IMPORTANT: The checklist items below are SAMPLE ITEMS for illustration only.
-  
+
   The __SPECKIT_COMMAND_CHECKLIST__ command MUST replace these with actual items based on:
   - User's specific checklist request
   - Feature requirements from spec.md
   - Technical context from plan.md
   - Implementation details from tasks.md
-  
+
   DO NOT keep these sample items in the generated checklist file.
   ============================================================================
 -->

templates/commands/analyze.md

@@ -3,6 +3,7 @@ description: Perform a non-destructive cross-artifact consistency and quality an
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/checklist.md

@@ -3,6 +3,7 @@ description: Generate a custom checklist for the current feature based on user r
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json
   ps: scripts/powershell/check-prerequisites.ps1 -Json
+  py: scripts/python/check_prerequisites.py --json
 ---
 
 ## Checklist Purpose: "Unit Tests for English"

templates/commands/clarify.md

@@ -1,12 +1,13 @@
 ---
 description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
-handoffs: 
+handoffs:
   - label: Build Technical Plan
     agent: speckit.plan
     prompt: Create a plan for the spec. I am building with...
 scripts:
    sh: scripts/bash/check-prerequisites.sh --json --paths-only
    ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly
+   py: scripts/python/check_prerequisites.py --json --paths-only
 ---
 
 ## User Input

templates/commands/constitution.md

@@ -1,6 +1,6 @@
 ---
 description: Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.
-handoffs: 
+handoffs:
   - label: Build Specification
     agent: speckit.specify
     prompt: Implement the feature specification based on the updated constitution. I want to build...
@@ -81,7 +81,7 @@ Follow this execution flow:
    - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
    - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
    - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
-   - Read each command file in `.specify/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
+   - Read each installed Spec Kit command file for your agent (including this one) — named `speckit.*` or `speckit-*` (dot or hyphen depending on the agent), or laid out as `speckit-<name>/SKILL.md` for skills-based integrations, e.g. in `.github/agents/`, `.github/skills/`, `.claude/skills/`, or your agent's equivalent commands directory — to verify no outdated references (CLAUDE-only or other agent-specific names) remain when generic guidance is required.
    - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
 
 5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):

templates/commands/converge.md

@@ -3,6 +3,7 @@ description: Assess the current codebase against the feature's spec, plan, and t
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/implement.md

@@ -3,6 +3,7 @@ description: Execute the implementation plan by processing and executing all tas
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input
@@ -42,7 +43,7 @@ You **MUST** consider the user input before proceeding (if not empty).
     **Automatic Pre-Hook**: {extension}
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
-    
+
     Wait for the result of the hook command before proceeding to the Outline.
     ```
     After emitting the block above you MUST actually invoke the hook and wait for it to finish before continuing. Run it the same way you would run the command yourself in this agent/session (the invocation may differ from the literal `{command}` id shown above, e.g. a skills-mode agent runs it as `/skill:speckit-...` or `$speckit-...`). Emitting the block alone does not run the hook.
@@ -144,7 +145,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 6. Execute implementation following the task plan:
    - **Phase-by-phase execution**: Complete each phase before moving to the next
-   - **Respect dependencies**: Run sequential tasks in order, parallel tasks [P] can run together  
+   - **Respect dependencies**: Run sequential tasks in order, parallel tasks [P] can run together
    - **Follow TDD approach**: Execute test tasks before their corresponding implementation tasks
    - **File-based coordination**: Tasks affecting the same files must run sequentially
    - **Validation checkpoints**: Verify each phase completion before proceeding

templates/commands/plan.md

@@ -1,6 +1,6 @@
 ---
 description: Execute the implementation planning workflow using the plan template to generate design artifacts.
-handoffs: 
+handoffs:
   - label: Create Tasks
     agent: speckit.tasks
     prompt: Break the plan into tasks
@@ -68,7 +68,6 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Evaluate gates (ERROR if violations unjustified)
    - Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
    - Phase 1: Generate data-model.md, contracts/, quickstart.md
-   - Phase 1: Update agent context by running the agent script
    - Re-evaluate Constitution Check post-design
 
 ## Mandatory Post-Execution Hooks
@@ -107,7 +106,7 @@ Check if `.specify/extensions.yml` exists in the project root.
 
 ## Completion Report
 
-Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
+Command ends after Phase 1 design. Report branch, IMPL_PLAN path, and generated artifacts.
 
 ## Phases
 

templates/commands/specify.md

@@ -1,6 +1,6 @@
 ---
 description: Create or update the feature specification from a natural language feature description.
-handoffs: 
+handoffs:
   - label: Build Technical Plan
     agent: speckit.plan
     prompt: Create a plan for the spec. I am building with...
@@ -147,20 +147,20 @@ Given that feature description, do this:
 
       ```markdown
       # Specification Quality Checklist: [FEATURE NAME]
-      
+
       **Purpose**: Validate specification completeness and quality before proceeding to planning
       **Created**: [DATE]
       **Feature**: [Link to spec.md]
-      
+
       ## Content Quality
-      
+
       - [ ] No implementation details (languages, frameworks, APIs)
       - [ ] Focused on user value and business needs
       - [ ] Written for non-technical stakeholders
       - [ ] All mandatory sections completed
-      
+
       ## Requirement Completeness
-      
+
       - [ ] No [NEEDS CLARIFICATION] markers remain
       - [ ] Requirements are testable and unambiguous
       - [ ] Success criteria are measurable
@@ -169,16 +169,16 @@ Given that feature description, do this:
       - [ ] Edge cases are identified
       - [ ] Scope is clearly bounded
       - [ ] Dependencies and assumptions identified
-      
+
       ## Feature Readiness
-      
+
       - [ ] All functional requirements have clear acceptance criteria
       - [ ] User scenarios cover primary flows
       - [ ] Feature meets measurable outcomes defined in Success Criteria
       - [ ] No implementation details leak into specification
-      
+
       ## Notes
-      
+
       - Items marked incomplete require spec updates before `__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`
       ```
 
@@ -203,20 +203,20 @@ Given that feature description, do this:
 
            ```markdown
            ## Question [N]: [Topic]
-           
+
            **Context**: [Quote relevant spec section]
-           
+
            **What we need to know**: [Specific question from NEEDS CLARIFICATION marker]
-           
+
            **Suggested Answers**:
-           
+
            | Option | Answer | Implications |
            |--------|--------|--------------|
            | A      | [First suggested answer] | [What this means for the feature] |
            | B      | [Second suggested answer] | [What this means for the feature] |
            | C      | [Third suggested answer] | [What this means for the feature] |
            | Custom | Provide your own answer | [Explain how to provide custom input] |
-           
+
            **Your choice**: _[Wait for user response]_
            ```
 

templates/commands/tasks.md

@@ -1,6 +1,6 @@
 ---
 description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
-handoffs: 
+handoffs:
   - label: Analyze For Consistency
     agent: speckit.analyze
     prompt: Run a project analysis for consistency
@@ -51,7 +51,7 @@ You **MUST** consider the user input before proceeding (if not empty).
     **Automatic Pre-Hook**: {extension}
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
-    
+
     Wait for the result of the hook command before proceeding to the Outline.
     ```
     After emitting the block above you MUST actually invoke the hook and wait for it to finish before continuing. Run it the same way you would run the command yourself in this agent/session (the invocation may differ from the literal `{command}` id shown above, e.g. a skills-mode agent runs it as `/skill:speckit-...` or `$speckit-...`). Emitting the block alone does not run the hook.
@@ -161,7 +161,7 @@ Every task MUST strictly follow this format:
 4. **[Story] label**: REQUIRED for user story phase tasks only
    - Format: [US1], [US2], [US3], etc. (maps to user stories from spec.md)
    - Setup phase: NO story label
-   - Foundational phase: NO story label  
+   - Foundational phase: NO story label
    - User Story phases: MUST have story label
    - Polish phase: NO story label
 5. **Description**: Clear action with exact file path

templates/commands/taskstoissues.md

@@ -4,6 +4,7 @@ tools: ['github/github-mcp-server/list_issues', 'github/github-mcp-server/issue_
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/plan-template.md

@@ -4,7 +4,7 @@
 
 **Input**: Feature specification from `/specs/[###-feature-name]/spec.md`
 
-**Note**: This template is filled in by the `__SPECKIT_COMMAND_PLAN__` command. See `.specify/templates/plan-template.md` for the execution workflow.
+**Note**: This template is filled in by the `__SPECKIT_COMMAND_PLAN__` command; its definition describes the execution workflow.
 
 ## Summary
 

templates/vscode-settings.json

@@ -11,4 +11,3 @@
         ".specify/scripts/powershell/": true
     }
 }
-

tests/contract/test_bundle_cli.py

@@ -175,7 +175,23 @@ def test_build_produces_artifact(project: Path):
     assert len(artifacts) == 1
 
 
-def test_info_expands_full_component_set(project: Path):
+def _mock_manifest_download(monkeypatch, source_path: Path) -> None:
+    """Mock the HTTPS manifest fetch to return a locally-authored manifest.
+
+    Catalog ``download_url``s are HTTPS-only, so ``info`` tests can no longer
+    point one at a local file. Patch ``_download_manifest`` to return the
+    manifest parsed from *source_path* (a bundle.yml or a .zip artifact),
+    exercising ``info``'s expansion without a network call.
+    """
+    from specify_cli.commands.bundle import _local_manifest_source
+
+    monkeypatch.setattr(
+        "specify_cli.commands.bundle._download_manifest",
+        lambda resolved, *, offline: _local_manifest_source(str(source_path)),
+    )
+
+
+def test_info_expands_full_component_set(project: Path, monkeypatch):
     bundle_dir = project / "src-bundle"
     bundle_dir.mkdir()
     (bundle_dir / "bundle.yml").write_text(
@@ -183,13 +199,14 @@ def test_info_expands_full_component_set(project: Path):
     )
     catalog = project / "local-catalog.json"
     entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
+        "demo-bundle", download_url="https://example.com/demo-bundle.zip"
     )
     write_catalog_file(catalog, {"demo-bundle": entry})
     added = runner.invoke(
         app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
     )
     assert added.exit_code == 0, added.output
+    _mock_manifest_download(monkeypatch, bundle_dir / "bundle.yml")
 
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
@@ -207,7 +224,7 @@ def test_info_expands_full_component_set(project: Path):
     assert "Trust" in text.output
 
 
-def test_info_expands_discovery_only_bundle(project: Path):
+def test_info_expands_discovery_only_bundle(project: Path, monkeypatch):
     # Discovery-only bundles must still be fully inspectable via `info`;
     # only `install` is refused for them.
     bundle_dir = project / "disc-bundle"
@@ -217,7 +234,7 @@ def test_info_expands_discovery_only_bundle(project: Path):
     )
     catalog = project / "disc-catalog.json"
     entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
+        "demo-bundle", download_url="https://example.com/demo-bundle.zip"
     )
     write_catalog_file(catalog, {"demo-bundle": entry})
     config = {
@@ -230,6 +247,7 @@ def test_info_expands_discovery_only_bundle(project: Path):
     (project / ".specify" / "bundle-catalogs.yml").write_text(
         yaml.safe_dump(config), encoding="utf-8"
     )
+    _mock_manifest_download(monkeypatch, bundle_dir / "bundle.yml")
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
     payload = json.loads(result.output)
@@ -237,8 +255,9 @@ def test_info_expands_discovery_only_bundle(project: Path):
     assert ("extensions", "ext-a") in components
 
 
-def test_info_resolves_local_zip_download_url(project: Path):
-    # A local .zip artifact as download_url is extracted to read bundle.yml.
+def test_info_expands_zip_sourced_bundle(project: Path, monkeypatch):
+    # A .zip artifact is extracted to read bundle.yml; info expands it. (The
+    # download itself is HTTPS-only now and mocked here — see contract note.)
     bundle_dir = project / "zip-src"
     bundle_dir.mkdir()
     (bundle_dir / "bundle.yml").write_text(
@@ -249,12 +268,15 @@ def test_info_resolves_local_zip_download_url(project: Path):
     catalog = project / "zip-catalog.json"
     write_catalog_file(
         catalog,
-        {"demo-bundle": catalog_entry_dict("demo-bundle", download_url=str(artifact))},
+        {"demo-bundle": catalog_entry_dict(
+            "demo-bundle", download_url="https://example.com/demo-bundle.zip"
+        )},
     )
     added = runner.invoke(
         app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
     )
     assert added.exit_code == 0, added.output
+    _mock_manifest_download(monkeypatch, artifact)
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
     payload = json.loads(result.output)

tests/extensions/git/test_git_extension.py

@@ -638,6 +638,21 @@ class TestCreateFeatureBash:
         assert result.returncode != 0
         assert "requires updated Spec Kit core scripts" in result.stderr
 
+    def test_explicit_number_zero_is_honored(self, tmp_path: Path):
+        """An explicit --number 0 is honored (yields 000), not treated as
+        'auto-detect'. Pins the canonical behavior the PowerShell twin must
+        mirror; the empty-string check (`[ -z "$BRANCH_NUMBER" ]`) already
+        distinguishes an unset flag from a supplied 0."""
+        project = _setup_project(tmp_path)
+        result = _run_bash(
+            "create-new-feature-branch.sh", project,
+            "--json", "--dry-run", "--number", "0", "--short-name", "zero", "Zero feature",
+        )
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "000-zero"
+        assert data["FEATURE_NUM"] == "000"
+
 
 @pytest.mark.skipif(not HAS_PWSH, reason="pwsh not available")
 class TestCreateFeaturePowerShell:
@@ -942,6 +957,23 @@ class TestCreateFeaturePowerShell:
         assert result.returncode != 0
         assert "requires updated Spec Kit core scripts" in result.stderr
 
+    def test_explicit_number_zero_is_honored(self, tmp_path: Path):
+        """An explicit -Number 0 is honored (yields 000), matching the bash twin's
+        --number 0. Regression guard: -Number defaults to 0, so a bare `-eq 0`
+        check cannot tell an unset flag from a supplied 0 and would silently
+        auto-detect instead. Uses PSBoundParameters.ContainsKey('Number')."""
+        project = _setup_project(tmp_path)
+        result = _run_pwsh(
+            "create-new-feature-branch.ps1", project,
+            "-Json", "-DryRun", "-Number", "0", "-ShortName", "zero", "Zero feature",
+        )
+        assert result.returncode == 0, result.stderr
+        json_line = [ln for ln in result.stdout.splitlines() if ln.strip().startswith("{")]
+        assert json_line, f"No JSON in output: {result.stdout}"
+        data = json.loads(json_line[-1])
+        assert data["BRANCH_NAME"] == "000-zero"
+        assert data["FEATURE_NUM"] == "000"
+
 
 # ── auto-commit.sh Tests ─────────────────────────────────────────────────────
 

tests/extensions/test_extension_agent_context.py

@@ -25,6 +25,14 @@ BASH = shutil.which("bash")
 POWERSHELL = (
     shutil.which("pwsh") or shutil.which("powershell.exe") or shutil.which("powershell")
 )
+# On Windows, prefer the built-in Windows PowerShell 5.1 (.NET Framework) when a
+# test needs to exercise a 5.1-specific code path; fall back to whatever
+# POWERSHELL resolves to elsewhere.
+WINDOWS_POWERSHELL = (
+    (shutil.which("powershell.exe") or shutil.which("powershell") or POWERSHELL)
+    if os.name == "nt"
+    else POWERSHELL
+)
 
 
 def _write_ext_config(project_root: Path, **overrides: object) -> None:
@@ -279,12 +287,14 @@ def shlex_quote(value: str) -> str:
     return "'" + value.replace("'", "'\"'\"'") + "'"
 
 
-def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
+def _run_powershell_agent_context_script(
+    project_root: Path, powershell: str | None = None
+) -> subprocess.CompletedProcess:
     script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
     env = _bundled_script_env(project_root)
     return subprocess.run(
         [
-            POWERSHELL,
+            powershell or POWERSHELL,
             "-NoProfile",
             "-ExecutionPolicy",
             "Bypass",
@@ -412,6 +422,29 @@ class TestBundledUpdaterPathValidation:
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @requires_bash
+    def test_bash_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024)."""
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        # The old one-level glob (specs/*/plan.md) would find nothing here, so no
+        # "at" line would be emitted. Normalize separators before matching: on
+        # MSYS bash the emitted path may be absolute with backslashes.
+        assert "specs/scope/001-feature/plan.md" in text.replace("\\", "/")
+
     @requires_bash
     def test_bash_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"
@@ -484,6 +517,33 @@ class TestBundledUpdaterPathValidation:
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @pytest.mark.skipif(WINDOWS_POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024).
+
+        The relative-path fix this covers is specific to Windows PowerShell 5.1
+        (.NET Framework), so prefer ``powershell.exe`` over ``pwsh`` here to
+        actually exercise that failure mode on Windows.
+        """
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_powershell_agent_context_script(
+            project, powershell=WINDOWS_POWERSHELL
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        assert "at specs/scope/001-feature/plan.md" in text
+
     @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
     def test_powershell_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"
@@ -688,6 +748,62 @@ class TestExtensionSelfSeed:
 _MDC_CONTEXT_FILE = ".cursor/rules/specify-rules.mdc"
 
 
+class TestPlanDiscovery:
+    """Mtime fallback must find plans in nested spec layouts (#3024).
+
+    Repos using SPECIFY_FEATURE_DIRECTORY place plans at
+    ``specs/<scope>/<feature>/plan.md``; a one-level ``specs/*/plan.md``
+    glob never matches those.
+    """
+
+    @staticmethod
+    def _make_plans(project: Path) -> Path:
+        # Older flat plan plus a newer nested plan: recursive discovery
+        # must pick the nested one by mtime.
+        flat = project / "specs" / "old-feature" / "plan.md"
+        flat.parent.mkdir(parents=True)
+        flat.write_text("flat plan\n", encoding="utf-8")
+        os.utime(flat, (1_000_000_000, 1_000_000_000))
+        nested = project / "specs" / "scope" / "new-feature" / "plan.md"
+        nested.parent.mkdir(parents=True)
+        nested.write_text("nested plan\n", encoding="utf-8")
+        return nested
+
+    @requires_bash
+    def test_bash_script_finds_nested_plan(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md"],
+        )
+        self._make_plans(project)
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        content = (project / "AGENTS.md").read_text(encoding="utf-8")
+        assert "specs/scope/new-feature/plan.md" in content
+
+    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_finds_nested_plan(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md"],
+        )
+        self._make_plans(project)
+
+        result = _run_powershell_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        content = (project / "AGENTS.md").read_text(encoding="utf-8")
+        assert "specs/scope/new-feature/plan.md" in content
+
+
 class TestMdcFrontmatter:
     """Cursor-style ``.mdc`` targets must carry ``alwaysApply: true`` frontmatter
     so the rule file is auto-loaded; non-``.mdc`` targets must not gain any."""

tests/hooks/.specify/extensions.yml

@@ -6,7 +6,7 @@ hooks:
       extension: "test-extension"
       command: "pre_implement_test"
       description: "Test before implement hook execution"
-      
+
   after_implement:
     - id: post_test
       enabled: true

tests/hooks/TESTING.md

@@ -7,7 +7,7 @@ This directory contains a mock project to verify that LLM agents correctly ident
 1. Open a chat with an LLM (like GitHub Copilot) in this project.
 2. Ask it to generate tasks for the current directory:
    > "Please follow `/speckit.tasks` for the `./tests/hooks` directory."
-3. **Expected Behavior**: 
+3. **Expected Behavior**:
    - Before doing any generation, the LLM should notice the `AUTOMATIC Pre-Hook` in `.specify/extensions.yml` under `before_tasks`.
    - It should state it is executing `EXECUTE_COMMAND: pre_tasks_test`.
    - It should then proceed to read the `.md` docs and produce a `tasks.md`.

tests/integration/test_bundler_local_install.py

@@ -112,3 +112,62 @@ def test_install_bundled_extension_from_zip_offline(tmp_path: Path):
         assert not ExtensionManager(project).registry.is_installed("agent-context")
     finally:
         os.chdir(previous)
+
+
+def test_download_manifest_rejects_file_url(tmp_path: Path):
+    """A catalog ``file://`` download_url is rejected — catalog URLs are
+    HTTPS-only, matching extensions/presets/workflows. Disk installs go through
+    the positional path (see the local-source tests above), not download_url.
+    """
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    manifest_path = write_manifest(tmp_path / "my bundles")
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(id="demo-bundle", download_url=manifest_path.as_uri())
+    )
+
+    with pytest.raises(BundlerError, match="bundle install"):
+        _download_manifest(resolved, offline=True)
+
+
+def test_download_manifest_rejects_bare_path(tmp_path: Path):
+    """A bare filesystem path download_url is likewise rejected."""
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    manifest_path = write_manifest(tmp_path / "plain")
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(id="demo-bundle", download_url=str(manifest_path))
+    )
+
+    with pytest.raises(BundlerError, match="bundle install"):
+        _download_manifest(resolved, offline=True)
+
+
+def test_local_install_still_resolves_via_positional_path(tmp_path: Path):
+    """The supported local route — a positional path, not a download_url —
+    still resolves the manifest via _local_manifest_source."""
+    manifest_path = write_manifest(tmp_path / "my bundles")
+    manifest = _local_manifest_source(str(manifest_path))
+    assert manifest is not None
+    assert manifest.bundle.id == "demo-bundle"
+
+
+def test_download_manifest_rejects_non_https_url_even_offline(tmp_path: Path):
+    """A non-HTTPS download_url must report the HTTPS problem, not a misleading
+    'Network access disabled', even under --offline (scheme is validated before
+    the offline gate)."""
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(
+            id="demo-bundle", download_url="http://example.com/bundle.zip"
+        )
+    )
+    with pytest.raises(BundlerError, match="HTTPS"):
+        _download_manifest(resolved, offline=True)

tests/integrations/conftest.py

@@ -5,10 +5,8 @@ import pytest
 from specify_cli.integrations.base import MarkdownIntegration
 
 
-@pytest.fixture(autouse=True)
-def _isolate_integration_home(monkeypatch: pytest.MonkeyPatch, tmp_path):
-    """Keep integration tests from reading or writing the real user home."""
-    home = tmp_path / "home"
+def _redirect_home(monkeypatch: pytest.MonkeyPatch, home) -> None:
+    """Point HOME/USERPROFILE/XDG env vars at an isolated *home* directory."""
     for path in (home, home / ".cache", home / ".config", home / ".local" / "share"):
         path.mkdir(parents=True, exist_ok=True)
 
@@ -19,6 +17,28 @@ def _isolate_integration_home(monkeypatch: pytest.MonkeyPatch, tmp_path):
     monkeypatch.setenv("XDG_DATA_HOME", str(home / ".local" / "share"))
 
 
+@pytest.fixture(scope="session", autouse=True)
+def _isolate_integration_home_session(tmp_path_factory):
+    """Isolate the user home for setup that runs outside a test function.
+
+    The per-test fixture below re-points HOME for each test, but function-scoped
+    fixtures do not apply to module-/session-scoped fixtures. Some of those (e.g.
+    the ``status_*_template`` fixtures in ``test_integration_subcommand.py``) run
+    ``specify init`` during setup, before any per-test isolation takes effect.
+    A standalone ``MonkeyPatch`` gives them an isolated home too.
+    """
+    monkeypatch = pytest.MonkeyPatch()
+    _redirect_home(monkeypatch, tmp_path_factory.mktemp("session-home"))
+    yield
+    monkeypatch.undo()
+
+
+@pytest.fixture(autouse=True)
+def _isolate_integration_home(monkeypatch: pytest.MonkeyPatch, tmp_path):
+    """Keep integration tests from reading or writing the real user home."""
+    _redirect_home(monkeypatch, tmp_path / "home")
+
+
 class StubIntegration(MarkdownIntegration):
     """Minimal concrete integration for testing."""
 

tests/integrations/test_base.py

@@ -306,9 +306,12 @@ class TestResolveCommandRefs:
 class TestResolvePythonInterpreter:
     def test_returns_python_on_path(self, monkeypatch):
         # Positive: when python3 is on PATH it is preferred over python.
+        # Pin a POSIX platform so the Windows stub probe (tested separately
+        # below) does not reject the fake PATH entries on Windows CI.
         def fake_which(name):
             return f"/usr/bin/{name}" if name in ("python3", "python") else None
 
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "linux")
         monkeypatch.setattr(
             "specify_cli.integrations.base.shutil.which", fake_which
         )
@@ -318,6 +321,7 @@ class TestResolvePythonInterpreter:
         def fake_which(name):
             return "/usr/bin/python" if name == "python" else None
 
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "linux")
         monkeypatch.setattr(
             "specify_cli.integrations.base.shutil.which", fake_which
         )
@@ -369,12 +373,79 @@ class TestResolvePythonInterpreter:
 
     def test_ignores_missing_venv(self, monkeypatch, tmp_path):
         # Negative: no venv directory -> PATH resolution is used instead.
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "linux")
         monkeypatch.setattr(
             "specify_cli.integrations.base.shutil.which",
             lambda name: "/usr/bin/python3" if name == "python3" else None,
         )
         assert IntegrationBase.resolve_python_interpreter(tmp_path) == "python3"
 
+    def test_windows_skips_store_alias_stub(self, monkeypatch):
+        # On Windows, python3 on PATH may be the Microsoft Store App
+        # Execution Alias stub: it exists but only prints an installer
+        # hint and exits non-zero. Existence is not enough; the
+        # interpreter must actually run (mirrors #3304 for the CLI).
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "win32")
+        monkeypatch.setattr(
+            "specify_cli.integrations.base.shutil.which",
+            lambda name: f"C:\\WindowsApps\\{name}.exe"
+            if name in ("python3", "python")
+            else None,
+        )
+        monkeypatch.setattr(
+            IntegrationBase, "_interpreter_runs", staticmethod(lambda path: False)
+        )
+        monkeypatch.setattr(
+            "specify_cli.integrations.base.sys.executable", "C:\\Python\\python.exe"
+        )
+        result = IntegrationBase.resolve_python_interpreter()
+        assert result == "C:\\Python\\python.exe"
+
+    def test_windows_keeps_working_interpreter(self, monkeypatch):
+        # Positive: a real python3 on Windows PATH passes the run check.
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "win32")
+        monkeypatch.setattr(
+            "specify_cli.integrations.base.shutil.which",
+            lambda name: f"C:\\Python\\{name}.exe" if name == "python3" else None,
+        )
+        monkeypatch.setattr(
+            IntegrationBase, "_interpreter_runs", staticmethod(lambda path: True)
+        )
+        assert IntegrationBase.resolve_python_interpreter() == "python3"
+
+    def test_windows_stub_python3_falls_through_to_working_python(self, monkeypatch):
+        # python3 is the stub but python is a real install: pick python.
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "win32")
+        monkeypatch.setattr(
+            "specify_cli.integrations.base.shutil.which",
+            lambda name: f"C:\\somewhere\\{name}.exe"
+            if name in ("python3", "python")
+            else None,
+        )
+        monkeypatch.setattr(
+            IntegrationBase,
+            "_interpreter_runs",
+            staticmethod(lambda path: path.endswith("python.exe")),
+        )
+        assert IntegrationBase.resolve_python_interpreter() == "python"
+
+    def test_posix_does_not_spawn_run_check(self, monkeypatch):
+        # Non-Windows platforms have no App Execution Alias; existence
+        # on PATH stays sufficient and no subprocess is spawned.
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "linux")
+        monkeypatch.setattr(
+            "specify_cli.integrations.base.shutil.which",
+            lambda name: "/usr/bin/python3" if name == "python3" else None,
+        )
+
+        def boom(path):
+            raise AssertionError("run check must not execute on POSIX")
+
+        monkeypatch.setattr(
+            IntegrationBase, "_interpreter_runs", staticmethod(boom)
+        )
+        assert IntegrationBase.resolve_python_interpreter() == "python3"
+
 
 class TestProcessTemplatePyScriptType:
     CONTENT = (
@@ -390,6 +461,7 @@ class TestProcessTemplatePyScriptType:
     def test_py_prefixes_interpreter(self, monkeypatch):
         # Positive: py script type prefixes a resolved interpreter and the
         # script path is rewritten to the .specify location.
+        monkeypatch.setattr("specify_cli.integrations.base.sys.platform", "linux")
         monkeypatch.setattr(
             "specify_cli.integrations.base.shutil.which",
             lambda name: "/usr/bin/python3" if name == "python3" else None,

tests/integrations/test_cli.py

@@ -115,6 +115,63 @@ class TestInitIntegrationFlag:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == specify_cli.DEFAULT_INIT_INTEGRATION
 
+    def test_init_here_nonempty_noninteractive_errors_with_force_guidance(self, tmp_path):
+        """`init --here` on a non-empty directory with no confirmation input (empty
+        stdin) must fail fast with guidance to use --force, instead of the bare
+        'Aborted.' from an EOF on typer.confirm. CliRunner with no `input=` provides
+        empty stdin, so typer.confirm raises Abort, which the command converts to the
+        actionable error."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "nonempty-here"
+        project.mkdir()
+        (project / "existing.txt").write_text("keep me", encoding="utf-8")
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 1, result.output
+        assert "--force" in result.output
+        # Aborted before scaffolding: the pre-existing file is untouched.
+        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
+
+    def test_init_here_interactive_cancel_exits_zero(self, tmp_path, monkeypatch):
+        """An interactive Ctrl+C at the merge confirmation (typer.Abort on a TTY)
+        is a normal cancellation — exit 0, "cancelled" — NOT the missing-input
+        --force error, which is reserved for non-interactive EOF. Guards the
+        regression where Abort was caught unconditionally and every cancel became
+        an exit-1 --force error."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        import specify_cli.commands.init as init_mod
+
+        # Simulate an interactive terminal so the Abort is treated as a cancel.
+        monkeypatch.setattr(init_mod, "_stdin_is_interactive", lambda: True)
+
+        project = tmp_path / "cancel-here"
+        project.mkdir()
+        (project / "existing.txt").write_text("keep me", encoding="utf-8")
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            # No input → typer.confirm raises Abort (stands in for Ctrl+C).
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, result.output
+        assert "cancelled" in result.output.lower()
+        assert "--force" not in result.output  # not the missing-input error
+        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
+
     def test_integration_copilot_auto_promotes(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app
@@ -835,7 +892,8 @@ class TestInitIntegrationFlag:
         assert (scripts_dir / "common.sh").read_text(encoding="utf-8") != custom_content
 
     def test_init_here_without_force_preserves_shared_infra(self, tmp_path):
-        """E2E: specify init --here (no --force) preserves existing shared infra files."""
+        """E2E: confirming the merge with piped "y" (no --force) preserves
+        existing shared infra files (unlike --force, which overwrites them)."""
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -2073,3 +2131,44 @@ class TestIntegrationCatalogDiscoveryCLI:
         assert listing.exit_code == 0, listing.output
         assert "default" in listing.output
         assert "community" in listing.output
+
+
+def test_refresh_shared_templates_preserves_recovered_user_file(tmp_path):
+    """refresh_shared_templates must not overwrite a recovered (pre-existing
+    user) template without --force, matching install_shared_infra's gate (#2918).
+    """
+    from specify_cli.shared_infra import (
+        load_speckit_manifest,
+        refresh_shared_templates,
+    )
+
+    project = tmp_path / "proj"
+    templates_dir = project / ".specify" / "templates"
+    templates_dir.mkdir(parents=True)
+    user_file = templates_dir / "spec-template.md"
+    user_file.write_text("# USER CUSTOM CONTENT\n", encoding="utf-8")
+
+    # Record the pre-existing file as recovered (its hash was adopted, not written).
+    manifest = load_speckit_manifest(project, version="test", console=_NoopConsole())
+    rel = ".specify/templates/spec-template.md"
+    manifest.record_existing(rel, recovered=True)
+    manifest.save()
+
+    # Bundled source ships a different body for the same template.
+    core_pack = tmp_path / "core-pack"
+    src = core_pack / "templates"
+    src.mkdir(parents=True)
+    (src / "spec-template.md").write_text("# BUNDLED CONTENT v2\n", encoding="utf-8")
+
+    refresh_shared_templates(
+        project,
+        version="test",
+        core_pack=core_pack,
+        repo_root=tmp_path / "unused",
+        console=_NoopConsole(),
+        invoke_separator=".",
+        force=False,
+    )
+
+    # Recovered user content must survive (fail-before: replaced by bundled body).
+    assert user_file.read_text(encoding="utf-8") == "# USER CUSTOM CONTENT\n"

tests/integrations/test_home_isolation.py

@@ -15,6 +15,10 @@ def test_integration_tests_use_tmp_home(tmp_path: Path) -> None:
     assert Path(os.environ["XDG_CONFIG_HOME"]) == home / ".config"
     assert Path(os.environ["XDG_DATA_HOME"]) == home / ".local" / "share"
 
+    # Most integrations resolve the user home via Path.home() (e.g. Hermes,
+    # catalog), so the isolation has to reach that API, not just the env vars.
+    assert Path.home() == home
+
     assert home.is_dir()
     assert (home / ".cache").is_dir()
     assert (home / ".config").is_dir()

tests/integrations/test_integration_catalog.py

@@ -84,6 +84,20 @@ class TestCatalogURLValidation:
         with pytest.raises(IntegrationCatalogError, match="valid URL"):
             IntegrationCatalog._validate_catalog_url(url)
 
+    @pytest.mark.parametrize(
+        "url",
+        [
+            "https://[::1",                 # unclosed ipv6 bracket
+            "https://[not-an-ip]/c.json",   # bracketed non-ip host
+        ],
+    )
+    def test_malformed_url_rejected_cleanly(self, url):
+        # A malformed authority makes urlparse/hostname raise ValueError. The
+        # validator must turn that into its normal catalog error, not leak a
+        # raw ValueError to the caller.
+        with pytest.raises(IntegrationCatalogError, match="malformed"):
+            IntegrationCatalog._validate_catalog_url(url)
+
 
 # ---------------------------------------------------------------------------
 # IntegrationCatalog — active catalogs

tests/integrations/test_integration_cursor_agent.py

@@ -231,4 +231,3 @@ class TestCursorAgentCliDispatch:
 
         argv = mock_run.call_args[0][0]
         assert argv[0] == "cursor-agent"
-

tests/integrations/test_integration_devin.py

@@ -71,4 +71,4 @@ class TestDevinInitFlow:
         )
 
         assert result.exit_code == 0, f"init --integration devin failed: {result.output}"
-        assert (target / ".devin" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        assert (target / ".devin" / "skills" / "speckit-plan" / "SKILL.md").exists()

tests/integrations/test_integration_forge.py

@@ -288,13 +288,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_formats_extension_command_names_for_forge(self, tmp_path):
         """Verify CommandRegistrar converts dot notation to hyphens for Forge."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         # Create a test command with dot notation name
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
@@ -304,7 +304,7 @@ class TestForgeCommandRegistrar:
             "Test content with $ARGUMENTS\n",
             encoding="utf-8"
         )
-        
+
         # Register with Forge
         registrar = CommandRegistrar()
         commands = [
@@ -313,7 +313,7 @@ class TestForgeCommandRegistrar:
                 "file": "commands/example.md"
             }
         ]
-        
+
         registered = registrar.register_commands(
             "forge",
             commands,
@@ -321,14 +321,14 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Verify registration succeeded
         assert "speckit.my-extension.example" in registered
-        
+
         # Check the generated file has hyphenated name in frontmatter
         forge_cmd = tmp_path / ".forge" / "commands" / "speckit-my-extension-example.md"
         assert forge_cmd.exists()
-        
+
         content = forge_cmd.read_text(encoding="utf-8")
         # Parse frontmatter to validate name field precisely
         frontmatter, _ = registrar.parse_frontmatter(content)
@@ -339,13 +339,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_formats_alias_names_for_forge(self, tmp_path):
         """Verify CommandRegistrar converts alias names to hyphens for Forge."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
             "---\n"
@@ -354,7 +354,7 @@ class TestForgeCommandRegistrar:
             "Test content\n",
             encoding="utf-8"
         )
-        
+
         # Register with Forge including an alias
         registrar = CommandRegistrar()
         commands = [
@@ -364,7 +364,7 @@ class TestForgeCommandRegistrar:
                 "aliases": ["speckit.my-extension.ex"]
             }
         ]
-        
+
         registrar.register_commands(
             "forge",
             commands,
@@ -372,11 +372,11 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Check the alias file has hyphenated name in frontmatter
         alias_file = tmp_path / ".forge" / "commands" / "speckit-my-extension-ex.md"
         assert alias_file.exists()
-        
+
         content = alias_file.read_text(encoding="utf-8")
         # Parse frontmatter to validate alias name field precisely
         frontmatter, _ = registrar.parse_frontmatter(content)
@@ -387,13 +387,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_does_not_affect_other_agents(self, tmp_path):
         """Verify format_name callback is Forge-specific and doesn't affect other agents."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
             "---\n"
@@ -402,7 +402,7 @@ class TestForgeCommandRegistrar:
             "Test content with $ARGUMENTS\n",
             encoding="utf-8"
         )
-        
+
         # Register with Kilo Code (standard markdown agent without inject_name)
         registrar = CommandRegistrar()
         commands = [
@@ -411,7 +411,7 @@ class TestForgeCommandRegistrar:
                 "file": "commands/example.md"
             }
         ]
-        
+
         registrar.register_commands(
             "kilocode",
             commands,
@@ -419,12 +419,12 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Kilo Code uses standard markdown format without name injection.
         # The format_name callback should not be invoked for non-Forge agents.
         kilocode_cmd = tmp_path / ".kilocode" / "workflows" / "speckit.my-extension.example.md"
         assert kilocode_cmd.exists()
-        
+
         content = kilocode_cmd.read_text(encoding="utf-8")
         # Kilo Code should NOT have a name field injected
         assert "name:" not in content, (

tests/integrations/test_integration_goose.py

@@ -36,3 +36,50 @@ class TestGooseIntegration(YamlIntegrationTests):
                 param.get("key") == "args"
                 for param in data.get("parameters", [])
             ), f"{recipe_file} uses {{{{args}}}} but does not declare args"
+
+
+class TestGooseCommandPlaceholderResolution:
+    """register_commands must resolve skill placeholders for the yaml branch.
+
+    The yaml (Goose recipe) branch previously skipped
+    resolve_skill_placeholders / _convert_argument_placeholder that the
+    markdown and toml branches apply, so extension/preset command bodies
+    kept literal {SCRIPT} / __AGENT__ / repo-relative paths.
+    """
+
+    def test_register_commands_resolves_placeholders_in_recipe(self, tmp_path):
+        from specify_cli.agents import CommandRegistrar
+
+        ext_dir = tmp_path / "extension"
+        cmd_dir = ext_dir / "commands"
+        cmd_dir.mkdir(parents=True)
+        cmd_file = cmd_dir / "example.md"
+        cmd_file.write_text(
+            "---\n"
+            "description: Placeholder command\n"
+            "scripts:\n"
+            "  sh: scripts/bash/do.sh\n"
+            "  ps: scripts/powershell/do.ps1\n"
+            "---\n\n"
+            "Run {SCRIPT} for agent __AGENT__ with $ARGUMENTS.\n",
+            encoding="utf-8",
+        )
+
+        registrar = CommandRegistrar()
+        commands = [{"name": "speckit.example", "file": "commands/example.md"}]
+        registrar.register_commands("goose", commands, "test-ext", ext_dir, tmp_path)
+
+        recipe = tmp_path / ".goose" / "recipes" / "speckit.example.yaml"
+        assert recipe.exists(), "goose recipe should be generated"
+        # Parse the recipe and assert the prompt actually got the correct
+        # replacements — not merely that the literal tokens are absent (which
+        # a wrong-but-token-free output could also satisfy).
+        data = yaml.safe_load(recipe.read_text(encoding="utf-8"))
+        prompt = data["prompt"]
+        assert ".specify/scripts/" in prompt  # {SCRIPT} -> resolved script path
+        assert "agent goose" in prompt  # __AGENT__ -> agent name
+        assert "{{args}}" in prompt  # $ARGUMENTS -> goose args token
+        # And the raw placeholders must not survive.
+        assert "{SCRIPT}" not in prompt
+        assert "__AGENT__" not in prompt
+        assert "$ARGUMENTS" not in prompt