chore: bump version to 0.3.1

docs: add greenfield Spring Boot pirate-speak preset demo to README (#1878 )
fix(ai-skills): exclude non-speckit copilot agent markdown from skill… (#1867 )
2026-03-17 19:03:08 +00:00 · 2026-03-17 16:30:05 +00:00 · 2026-03-17 11:05:37 -05:00 · 2026-03-17 10:25:18 -05:00 · 2026-03-17 10:03:54 -05:00 · 2026-03-17 09:51:13 -05:00
47 changed files with 7640 additions and 646 deletions
--- a/.github/workflows/scripts/create-github-release.sh
+++ b/.github/workflows/scripts/create-github-release.sh
@@ -58,6 +58,8 @@ gh release create "$VERSION" \
  .genreleases/spec-kit-template-vibe-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-kimi-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-kimi-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-trae-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-trae-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-generic-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-generic-ps-"$VERSION".zip \
  --title "Spec Kit Templates - $VERSION_NO_V" \
--- a/.github/workflows/scripts/create-release-packages.ps1
+++ b/.github/workflows/scripts/create-release-packages.ps1
@@ -14,7 +14,7 @@

 .PARAMETER Agents
    Comma or space separated subset of agents to build (default: all)
-    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, generic
+    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, trae, generic

 .PARAMETER Scripts
    Comma or space separated subset of script types to build (default: both)
@@ -454,6 +454,11 @@ function Build-Variant {
            New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
            New-KimiSkills -SkillsDir $skillsDir -ScriptVariant $Script
        }
+        'trae' {
+            $rulesDir = Join-Path $baseDir ".trae/rules"
+            New-Item -ItemType Directory -Force -Path $rulesDir | Out-Null
+            Generate-Commands -Agent 'trae' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $rulesDir -ScriptVariant $Script
+        }
        'generic' {
            $cmdDir = Join-Path $baseDir ".speckit/commands"
            Generate-Commands -Agent 'generic' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
@@ -470,7 +475,7 @@ function Build-Variant {
 }

 # Define all agents and scripts
-$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'generic')
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'trae', 'generic')
 $AllScripts = @('sh', 'ps')

 function Normalize-List {
--- a/.github/workflows/scripts/create-release-packages.sh
+++ b/.github/workflows/scripts/create-release-packages.sh
@@ -6,7 +6,7 @@ set -euo pipefail
 # Usage: .github/workflows/scripts/create-release-packages.sh <version>
 #   Version argument should include leading 'v'.
 #   Optionally set AGENTS and/or SCRIPTS env vars to limit what gets built.
-#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi generic (default: all)
+#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae generic (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -291,6 +291,9 @@ build_variant() {
    kimi)
      mkdir -p "$base_dir/.kimi/skills"
      create_kimi_skills "$base_dir/.kimi/skills" "$script" ;;
+    trae)
+      mkdir -p "$base_dir/.trae/rules"
+      generate_commands trae md "\$ARGUMENTS" "$base_dir/.trae/rules" "$script" ;;
    generic)
      mkdir -p "$base_dir/.speckit/commands"
      generate_commands generic md "\$ARGUMENTS" "$base_dir/.speckit/commands" "$script" ;;
@@ -300,7 +303,7 @@ build_variant() {
 }

 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi generic)
+ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae generic)
 ALL_SCRIPTS=(sh ps)

 norm_list() {
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -10,10 +10,6 @@ The toolkit supports multiple AI coding assistants, allowing teams to use their

 ---

-## General practices
-
- Any changes to `__init__.py` for the Specify CLI require a version rev in `pyproject.toml` and addition of entries to `CHANGELOG.md`.
-
 ## Adding New Agent Support

 This section explains how to add support for new AI agents/assistants to the Specify CLI. Use this guide as a reference when integrating new AI tools into the Spec-Driven Development workflow.
@@ -50,6 +46,7 @@ Specify supports multiple AI agents by generating agent-specific command files a
 | **Tabnine CLI**            | `.tabnine/agent/commands/` | TOML | `tabnine`       | Tabnine CLI                 |
 | **Kimi Code**              | `.kimi/skills/`        | Markdown | `kimi`          | Kimi Code CLI (Moonshot AI) |
 | **IBM Bob**                | `.bob/commands/`       | Markdown | N/A (IDE-based) | IBM Bob IDE                 |
+| **Trae**                   | `.trae/rules/`         | Markdown | N/A (IDE-based) | Trae IDE                    |
 | **Generic**                | User-specified via `--ai-commands-dir` | Markdown | N/A | Bring your own agent        |

 ### Step-by-Step Integration Guide
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,123 @@ Recent changes to the Specify CLI and templates are documented here.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## [0.3.1] - 2026-03-17
+
+### Changed
+
+- docs: add greenfield Spring Boot pirate-speak preset demo to README (#1878)
+- fix(ai-skills): exclude non-speckit copilot agent markdown from skill… (#1867)
+- feat: add Trae IDE support as a new agent (#1817)
+- feat(cli): polite deep merge for settings.json and support JSONC (#1874)
+- feat(extensions,presets): add priority-based resolution ordering (#1855)
+- fix(scripts): suppress stdout from git fetch in create-new-feature.sh (#1876)
+- fix(scripts): harden bash scripts — escape, compat, and error handling (#1869)
+- Add cognitive-squad to community extension catalog (#1870)
+- docs: add Go / React brownfield walkthrough to community walkthroughs (#1868)
+- chore: update DocGuard extension to v0.9.8 (#1859)
+- Feature: add specify status command (#1837)
+- fix(extensions): show extension ID in list output (#1843)
+- feat(extensions): add Archive and Reconcile extensions to community catalog (#1844)
+- feat: Add DocGuard CDD enforcement extension to community catalog (#1838)
+- chore: bump version to 0.3.0 (#1839)
+- feat(presets): Pluggable preset system with catalog, resolver, and skills propagation (#1787)
+- fix: match 'Last updated' timestamp with or without bold markers (#1836)
+- Add specify doctor command for project health diagnostics (#1828)
+- fix: harden bash scripts against shell injection and improve robustness (#1809)
+- fix: clean up command templates (specify, analyze) (#1810)
+- fix: migrate Qwen Code CLI from TOML to Markdown format (#1589) (#1730)
+- fix(cli): deprecate explicit command support for agy (#1798) (#1808)
+- Add /selftest.extension core extension to test other extensions (#1758)
+- feat(extensions): Quality of life improvements for RFC-aligned catalog integration (#1776)
+- Add Java brownfield walkthrough to community walkthroughs (#1820)
+- chore: bump version to 0.2.1 (#1813)
+- Added February 2026 newsletter (#1812)
+- feat: add Kimi Code CLI agent support (#1790)
+- docs: fix broken links in quickstart guide (#1759) (#1797)
+- docs: add catalog cli help documentation (#1793) (#1794)
+- fix: use quiet checkout to avoid exception on git checkout (#1792)
+- feat(extensions): support .extensionignore to exclude files during install (#1781)
+- feat: add Codex support for extension command registration (#1767)
+- chore: bump version to 0.2.0 (#1786)
+- fix: sync agent list comments with actual supported agents (#1785)
+- feat(extensions): support multiple active catalogs simultaneously (#1720)
+- Pavel/add tabnine cli support (#1503)
+- Add Understanding extension to community catalog (#1778)
+- Add ralph extension to community catalog (#1780)
+- Update README with project initialization instructions (#1772)
+- feat: add review extension to community catalog (#1775)
+- Add fleet extension to community catalog (#1771)
+- Integration of Mistral vibe support into speckit (#1725)
+- fix: Remove duplicate options in specify.md (#1765)
+- fix: use global branch numbering instead of per-short-name detection (#1757)
+- Add Community Walkthroughs section to README (#1766)
+- feat(extensions): add Jira Integration to community catalog (#1764)
+- Add Azure DevOps Integration extension to community catalog (#1734)
+- Fix docs: update Antigravity link and add initialization example (#1748)
+- fix: wire after_tasks and after_implement hook events into command templates (#1702)
+- make c ignores consistent with c++ (#1747)
+- chore: bump version to 0.1.13 (#1746)
+- feat: add kiro-cli and AGENT_CONFIG consistency coverage (#1690)
+- feat: add verify extension to community catalog (#1726)
+- Add Retrospective Extension to community catalog README table (#1741)
+- fix(scripts): add empty description validation and branch checkout error handling (#1559)
+- fix: correct Copilot extension command registration (#1724)
+- fix(implement): remove Makefile from C ignore patterns (#1558)
+- Add sync extension to community catalog (#1728)
+- fix(checklist): clarify file handling behavior for append vs create (#1556)
+- fix(clarify): correct conflicting question limit from 10 to 5 (#1557)
+- chore: bump version to 0.1.12 (#1737)
+- fix: use RELEASE_PAT so tag push triggers release workflow (#1736)
+- fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
+- fix: Split release process to sync pyproject.toml version with git tags (#1732)
+
+
+## [0.3.0] - 2026-03-13
+
+### Changed
+
+- No changes have been documented for this release yet.
+
+<!-- Entries for 0.2.x and earlier releases are documented in their respective sections below. -->
+- make c ignores consistent with c++ (#1747)
+- chore: bump version to 0.1.13 (#1746)
+- feat: add kiro-cli and AGENT_CONFIG consistency coverage (#1690)
+- feat: add verify extension to community catalog (#1726)
+- Add Retrospective Extension to community catalog README table (#1741)
+- fix(scripts): add empty description validation and branch checkout error handling (#1559)
+- fix: correct Copilot extension command registration (#1724)
+- fix(implement): remove Makefile from C ignore patterns (#1558)
+- Add sync extension to community catalog (#1728)
+- fix(checklist): clarify file handling behavior for append vs create (#1556)
+- fix(clarify): correct conflicting question limit from 10 to 5 (#1557)
+- chore: bump version to 0.1.12 (#1737)
+- fix: use RELEASE_PAT so tag push triggers release workflow (#1736)
+- fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
+- fix: Split release process to sync pyproject.toml version with git tags (#1732)
+
+
+## [Unreleased]
+
+### Added
+
+- feat(cli): polite deep merge for VSCode settings.json with JSONC support via `json5` and zero-data-loss fallbacks
+- feat(presets): Pluggable preset system with preset catalog and template resolver
+- Preset manifest (`preset.yml`) with validation for artifact, command, and script types
+- `PresetManifest`, `PresetRegistry`, `PresetManager`, `PresetCatalog`, `PresetResolver` classes in `src/specify_cli/presets.py`
+- CLI commands: `specify preset search`, `specify preset add`, `specify preset list`, `specify preset remove`, `specify preset resolve`, `specify preset info`
+- CLI commands: `specify preset catalog list`, `specify preset catalog add`, `specify preset catalog remove` for multi-catalog management
+- `PresetCatalogEntry` dataclass and multi-catalog support mirroring the extension catalog system
+- `--preset` option for `specify init` to install presets during initialization
+- Priority-based preset resolution: presets with lower priority number win (`--priority` flag)
+- `resolve_template()` / `Resolve-Template` helpers in bash and PowerShell common scripts
+- Template resolution priority stack: overrides → presets → extensions → core
+- Preset catalog files (`presets/catalog.json`, `presets/catalog.community.json`)
+- Preset scaffold directory (`presets/scaffold/`)
+- Scripts updated to use template resolution instead of hardcoded paths
+- feat(presets): Preset command overrides now propagate to agent skills when `--ai-skills` was used during init
+- feat: `specify init` persists CLI options to `.specify/init-options.json` for downstream operations
+- feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
+
 ## [0.2.1] - 2026-03-11

 ### Changed
@@ -51,13 +168,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
 - fix: Split release process to sync pyproject.toml version with git tags (#1732)

-
-## [Unreleased]
-
-### Added
-
- feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
-
 ## [0.2.0] - 2026-03-09

 ### Changed
--- a/README.md
+++ b/README.md
@@ -158,6 +158,10 @@ See Spec-Driven Development in action across different scenarios with these comm

 - **[Brownfield Java runtime extension](https://github.com/mnriem/spec-kit-java-brownfield-demo)** — Extends an existing open-source Jakarta EE runtime (Piranha, ~420,000 lines of Java, XML, JSP, HTML, and config files across 180 Maven modules) with a password-protected Server Admin Console, demonstrating spec-kit on a large multi-module Java project with no prior specs or constitution.

+- **[Brownfield Go / React dashboard demo](https://github.com/mnriem/spec-kit-go-brownfield-demo)** — Demonstrates spec-kit driven entirely from the **terminal using GitHub Copilot CLI**. Extends NASA's open-source Hermes ground support system (Go) with a lightweight React-based web telemetry dashboard, showing that the full constitution → specify → plan → tasks → implement workflow works from the terminal.
+
+- **[Greenfield Spring Boot MVC with a custom preset](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo)** — Builds a Spring Boot MVC application from scratch using a custom pirate-speak preset, demonstrating how presets can reshape the entire spec-kit experience: specifications become "Voyage Manifests," plans become "Battle Plans," and tasks become "Crew Assignments" — all generated in full pirate vernacular without changing any tooling.
+
 ## 🤖 Supported AI Agents

 | Agent                                                                                | Support | Notes                                                                                                                                     |
@@ -184,6 +188,7 @@ See Spec-Driven Development in action across different scenarios with these comm
 | [Kimi Code](https://code.kimi.com/)                                                  | ✅      |                                                                                                                                           |
 | [Windsurf](https://windsurf.com/)                                                    | ✅      |                                                                                                                                           |
 | [Antigravity (agy)](https://antigravity.google/)                                     | ✅      | Requires `--ai-skills` |
+| [Trae](https://www.trae.ai/)                                                         | ✅      |                                                                                                                                           |
 | Generic                                                                              | ✅      | Bring your own agent — use `--ai generic --ai-commands-dir <path>` for unsupported agents                                                 |

 ## 🔧 Specify CLI Reference
--- a/extensions/README.md
+++ b/extensions/README.md
@@ -72,11 +72,17 @@ The following community-contributed extensions are available in [`catalog.commun

 | Extension | Purpose | URL |
 |-----------|---------|-----|
+| Archive Extension | Archive merged features into main project memory. | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
 | Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
 | Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
+| Cognitive Squad | 19-function cognitive agent squad for autonomous pre-code analysis — 7 core agents, 7 specialists, 4 learning functions with feedback loop | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
+| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero dependencies. | [spec-kit-docguard](https://github.com/raccioly/docguard) |
 | Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
 | Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
+| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | [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 | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
+| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
 | Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
--- a/extensions/RFC-EXTENSION-SYSTEM.md
+++ b/extensions/RFC-EXTENSION-SYSTEM.md
@@ -359,12 +359,15 @@ specify extension add jira
      "installed_at": "2026-01-28T14:30:00Z",
      "source": "catalog",
      "manifest_hash": "sha256:abc123...",
-      "enabled": true
+      "enabled": true,
+      "priority": 10
    }
  }
 }
 ```

+**Priority Field**: Extensions are ordered by `priority` (lower = higher precedence). Default is 10. Used for template resolution when multiple extensions provide the same template.
+
 ### 3. Configuration

 ```bash
@@ -1084,11 +1087,15 @@ List installed extensions in current project.
 $ specify extension list

 Installed Extensions:
-  ✓ jira (v1.0.0) - Jira Integration
-    Commands: 3 | Hooks: 2 | Status: Enabled
+  ✓ Jira Integration (v1.0.0)
+     jira
+     Create Jira issues from spec-kit artifacts
+     Commands: 3 | Hooks: 2 | Priority: 10 | Status: Enabled

-  ✓ linear (v0.9.0) - Linear Integration
-    Commands: 1 | Hooks: 1 | Status: Enabled
+  ✓ Linear Integration (v0.9.0)
+     linear
+     Create Linear issues from spec-kit artifacts
+     Commands: 1 | Hooks: 1 | Priority: 10 | Status: Enabled
 ```

 **Options:**
@@ -1196,10 +1203,9 @@ Next steps:

 **Options:**

- `--from URL`: Install from custom URL or Git repo
- `--version VERSION`: Install specific version
- `--dev PATH`: Install from local path (development mode)
- `--no-register`: Skip command registration (manual setup)
+- `--from URL`: Install from a remote URL (archive). Does not accept Git repositories directly.
+- `--dev`: Install from a local path in development mode (the PATH is the positional `extension` argument).
+- `--priority NUMBER`: Set resolution priority (lower = higher precedence, default 10)

 #### `specify extension remove NAME`

@@ -1280,6 +1286,29 @@ $ specify extension disable jira
 To re-enable: specify extension enable jira
 ```

+#### `specify extension set-priority NAME PRIORITY`
+
+Change the resolution priority of an installed extension.
+
+```bash
+$ specify extension set-priority jira 5
+
+✓ Extension 'Jira Integration' priority changed: 10 → 5
+
+Lower priority = higher precedence in template resolution
+```
+
+**Priority Values:**
+
+- Lower numbers = higher precedence (checked first in resolution)
+- Default priority is 10
+- Must be a positive integer (1 or higher)
+
+**Use Cases:**
+
+- Ensure a critical extension's templates take precedence
+- Override default resolution order when multiple extensions provide similar templates
+
 ---

 ## Compatibility & Versioning
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,8 +1,39 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-03-09T00:00:00Z",
+  "updated_at": "2026-03-16T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
+    "archive": {
+      "name": "Archive Extension",
+      "id": "archive",
+      "description": "Archive merged features into main project memory, resolving gaps and conflicts.",
+      "author": "Stanislav Deviatov",
+      "version": "1.0.0",
+      "download_url": "https://github.com/stn1slv/spec-kit-archive/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/stn1slv/spec-kit-archive",
+      "homepage": "https://github.com/stn1slv/spec-kit-archive",
+      "documentation": "https://github.com/stn1slv/spec-kit-archive/blob/main/README.md",
+      "changelog": "https://github.com/stn1slv/spec-kit-archive/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "archive",
+        "memory",
+        "merge",
+        "changelog"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-14T00:00:00Z",
+      "updated_at": "2026-03-14T00:00:00Z"
+    },
    "azure-devops": {
      "name": "Azure DevOps Integration",
      "id": "azure-devops",
@@ -74,6 +105,123 @@
      "created_at": "2026-02-22T00:00:00Z",
      "updated_at": "2026-02-22T00:00:00Z"
    },
+    "cognitive-squad": {
+      "name": "Cognitive Squad",
+      "id": "cognitive-squad",
+      "description": "19-function cognitive agent squad for autonomous pre-code analysis — 7 core agents, 7 specialists, 4 learning functions with feedback loop",
+      "author": "Testimonial",
+      "version": "0.1.0",
+      "download_url": "https://github.com/Testimonial/cognitive-squad/archive/refs/tags/v0.1.0.zip",
+      "repository": "https://github.com/Testimonial/cognitive-squad",
+      "homepage": "https://github.com/Testimonial/cognitive-squad",
+      "documentation": "https://github.com/Testimonial/cognitive-squad/blob/main/README.md",
+      "changelog": "https://github.com/Testimonial/cognitive-squad/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0",
+        "tools": [
+          {
+            "name": "understanding",
+            "version": ">=3.4.0",
+            "required": false
+          },
+          {
+            "name": "spec-kit-reverse-eng",
+            "version": ">=1.0.0",
+            "required": false
+          }
+        ]
+      },
+      "provides": {
+        "commands": 7,
+        "hooks": 1
+      },
+      "tags": [
+        "ai-agents",
+        "cognitive",
+        "pre-code",
+        "analysis",
+        "multi-agent"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-16T00:00:00Z"
+    },
+    "docguard": {
+      "name": "DocGuard \u2014 CDD Enforcement",
+      "id": "docguard",
+      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero dependencies.",
+      "author": "raccioly",
+      "version": "0.9.8",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.9.8/spec-kit-docguard-v0.9.8.zip",
+      "repository": "https://github.com/raccioly/docguard",
+      "homepage": "https://www.npmjs.com/package/docguard-cli",
+      "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
+      "changelog": "https://github.com/raccioly/docguard/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "node",
+            "version": ">=18.0.0",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 6,
+        "hooks": 3
+      },
+      "tags": [
+        "documentation",
+        "validation",
+        "quality",
+        "cdd",
+        "traceability",
+        "ai-agents",
+        "enforcement",
+        "spec-kit"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-13T00:00:00Z",
+      "updated_at": "2026-03-15T20:00:00Z"
+    },
+    "doctor": {
+      "name": "Project Health Check",
+      "id": "doctor",
+      "description": "Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-doctor/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-doctor",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-doctor",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-doctor/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-doctor/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "diagnostics",
+        "health-check",
+        "validation",
+        "project-structure"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-13T00:00:00Z",
+      "updated_at": "2026-03-13T00:00:00Z"
+    },
    "fleet": {
      "name": "Fleet Orchestrator",
      "id": "fleet",
@@ -93,7 +241,12 @@
        "commands": 2,
        "hooks": 1
      },
-      "tags": ["orchestration", "workflow", "human-in-the-loop", "parallel"],
+      "tags": [
+        "orchestration",
+        "workflow",
+        "human-in-the-loop",
+        "parallel"
+      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
@@ -160,13 +313,49 @@
        "commands": 2,
        "hooks": 1
      },
-      "tags": ["implementation", "automation", "loop", "copilot"],
+      "tags": [
+        "implementation",
+        "automation",
+        "loop",
+        "copilot"
+      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-09T00:00:00Z",
      "updated_at": "2026-03-09T00:00:00Z"
    },
+    "reconcile": {
+      "name": "Reconcile Extension",
+      "id": "reconcile",
+      "description": "Reconcile implementation drift by surgically updating the feature's own spec, plan, and tasks.",
+      "author": "Stanislav Deviatov",
+      "version": "1.0.0",
+      "download_url": "https://github.com/stn1slv/spec-kit-reconcile/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/stn1slv/spec-kit-reconcile",
+      "homepage": "https://github.com/stn1slv/spec-kit-reconcile",
+      "documentation": "https://github.com/stn1slv/spec-kit-reconcile/blob/main/README.md",
+      "changelog": "https://github.com/stn1slv/spec-kit-reconcile/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "reconcile",
+        "drift",
+        "tasks",
+        "remediation"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-14T00:00:00Z",
+      "updated_at": "2026-03-14T00:00:00Z"
+    },
    "retrospective": {
      "name": "Retrospective Extension",
      "id": "retrospective",
@@ -218,7 +407,15 @@
        "commands": 7,
        "hooks": 1
      },
-      "tags": ["code-review", "quality", "review", "testing", "error-handling", "type-design", "simplification"],
+      "tags": [
+        "code-review",
+        "quality",
+        "review",
+        "testing",
+        "error-handling",
+        "type-design",
+        "simplification"
+      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
@@ -260,7 +457,7 @@
    "understanding": {
      "name": "Understanding",
      "id": "understanding",
-      "description": "Automated requirements quality analysis — validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
+      "description": "Automated requirements quality analysis \u2014 validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
      "author": "Ladislav Bihari",
      "version": "3.4.0",
      "download_url": "https://github.com/Testimonial/understanding/archive/refs/tags/v3.4.0.zip",
@@ -298,6 +495,38 @@
      "created_at": "2026-03-07T00:00:00Z",
      "updated_at": "2026-03-07T00:00:00Z"
    },
+    "status": {
+      "name": "Project Status",
+      "id": "status",
+      "description": "Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "status",
+        "workflow",
+        "progress",
+        "feature-tracking",
+        "task-progress"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-16T00:00:00Z"
+    },
    "v-model": {
      "name": "V-Model Extension Pack",
      "id": "v-model",
--- a/presets/ARCHITECTURE.md
+++ b/presets/ARCHITECTURE.md
@@ -0,0 +1,157 @@
+# Preset System Architecture
+
+This document describes the internal architecture of the preset system — how template resolution, command registration, and catalog management work under the hood.
+
+For usage instructions, see [README.md](README.md).
+
+## Template Resolution
+
+When Spec Kit needs a template (e.g. `spec-template`), the `PresetResolver` walks a priority stack and returns the first match:
+
+```mermaid
+flowchart TD
+    A["resolve_template('spec-template')"] --> B{Override exists?}
+    B -- Yes --> C[".specify/templates/overrides/spec-template.md"]
+    B -- No --> D{Preset provides it?}
+    D -- Yes --> E[".specify/presets/‹preset-id›/templates/spec-template.md"]
+    D -- No --> F{Extension provides it?}
+    F -- Yes --> G[".specify/extensions/‹ext-id›/templates/spec-template.md"]
+    F -- No --> H[".specify/templates/spec-template.md"]
+
+    E -- "multiple presets?" --> I["lowest priority number wins"]
+    I --> E
+
+    style C fill:#4caf50,color:#fff
+    style E fill:#2196f3,color:#fff
+    style G fill:#ff9800,color:#fff
+    style H fill:#9e9e9e,color:#fff
+```
+
+| Priority | Source | Path | Use case |
+|----------|--------|------|----------|
+| 1 (highest) | Override | `.specify/templates/overrides/` | One-off project-local tweaks |
+| 2 | Preset | `.specify/presets/<id>/templates/` | Shareable, stackable customizations |
+| 3 | Extension | `.specify/extensions/<id>/templates/` | Extension-provided templates |
+| 4 (lowest) | Core | `.specify/templates/` | Shipped defaults |
+
+When multiple presets are installed, they're sorted by their `priority` field (lower number = higher precedence). This is set via `--priority` on `specify preset add`.
+
+The resolution is implemented three times to ensure consistency:
+- **Python**: `PresetResolver` in `src/specify_cli/presets.py`
+- **Bash**: `resolve_template()` in `scripts/bash/common.sh`
+- **PowerShell**: `Resolve-Template` in `scripts/powershell/common.ps1`
+
+## Command Registration
+
+When a preset is installed with `type: "command"` entries, the `PresetManager` registers them into all detected agent directories using the shared `CommandRegistrar` from `src/specify_cli/agents.py`.
+
+```mermaid
+flowchart TD
+    A["specify preset add my-preset"] --> B{Preset has type: command?}
+    B -- No --> Z["done (templates only)"]
+    B -- Yes --> C{Extension command?}
+    C -- "speckit.myext.cmd\n(3+ dot segments)" --> D{Extension installed?}
+    D -- No --> E["skip (extension not active)"]
+    D -- Yes --> F["register command"]
+    C -- "speckit.specify\n(core command)" --> F
+    F --> G["detect agent directories"]
+    G --> H[".claude/commands/"]
+    G --> I[".gemini/commands/"]
+    G --> J[".github/agents/"]
+    G --> K["... (17+ agents)"]
+    H --> L["write .md (Markdown format)"]
+    I --> M["write .toml (TOML format)"]
+    J --> N["write .agent.md + .prompt.md"]
+
+    style E fill:#ff5722,color:#fff
+    style L fill:#4caf50,color:#fff
+    style M fill:#4caf50,color:#fff
+    style N fill:#4caf50,color:#fff
+```
+
+### Extension safety check
+
+Command names follow the pattern `speckit.<ext-id>.<cmd-name>`. When a command has 3+ dot segments, the system extracts the extension ID and checks if `.specify/extensions/<ext-id>/` exists. If the extension isn't installed, the command is skipped — preventing orphan files referencing non-existent extensions.
+
+Core commands (e.g. `speckit.specify`, with only 2 segments) are always registered.
+
+### Agent format rendering
+
+The `CommandRegistrar` renders commands differently per agent:
+
+| Agent | Format | Extension | Arg placeholder |
+|-------|--------|-----------|-----------------|
+| Claude, Cursor, opencode, Windsurf, etc. | Markdown | `.md` | `$ARGUMENTS` |
+| Copilot | Markdown | `.agent.md` + `.prompt.md` | `$ARGUMENTS` |
+| Gemini, Qwen, Tabnine | TOML | `.toml` | `{{args}}` |
+
+### Cleanup on removal
+
+When `specify preset remove` is called, the registered commands are read from the registry metadata and the corresponding files are deleted from each agent directory, including Copilot companion `.prompt.md` files.
+
+## Catalog System
+
+```mermaid
+flowchart TD
+    A["specify preset search"] --> B["PresetCatalog.get_active_catalogs()"]
+    B --> C{SPECKIT_PRESET_CATALOG_URL set?}
+    C -- Yes --> D["single custom catalog"]
+    C -- No --> E{.specify/preset-catalogs.yml exists?}
+    E -- Yes --> F["project-level catalog stack"]
+    E -- No --> G{"~/.specify/preset-catalogs.yml exists?"}
+    G -- Yes --> H["user-level catalog stack"]
+    G -- No --> I["built-in defaults"]
+    I --> J["default (install allowed)"]
+    I --> K["community (discovery only)"]
+
+    style D fill:#ff9800,color:#fff
+    style F fill:#2196f3,color:#fff
+    style H fill:#2196f3,color:#fff
+    style J fill:#4caf50,color:#fff
+    style K fill:#9e9e9e,color:#fff
+```
+
+Catalogs are fetched with a 1-hour cache (per-URL, SHA256-hashed cache files). Each catalog entry has a `priority` (for merge ordering) and `install_allowed` flag.
+
+## Repository Layout
+
+```
+presets/
+├── ARCHITECTURE.md                         # This file
+├── PUBLISHING.md                           # Guide for submitting presets to the catalog
+├── README.md                               # User guide
+├── catalog.json                            # Official preset catalog
+├── catalog.community.json                  # Community preset catalog
+├── scaffold/                               # Scaffold for creating new presets
+│   ├── preset.yml                          # Example manifest
+│   ├── README.md                           # Guide for customizing the scaffold
+│   ├── commands/
+│   │   ├── speckit.specify.md              # Core command override example
+│   │   └── speckit.myext.myextcmd.md       # Extension command override example
+│   └── templates/
+│       ├── spec-template.md                # Core template override example
+│       └── myext-template.md               # Extension template override example
+└── self-test/                              # Self-test preset (overrides all core templates)
+    ├── preset.yml
+    ├── commands/
+    │   └── speckit.specify.md
+    └── templates/
+        ├── spec-template.md
+        ├── plan-template.md
+        ├── tasks-template.md
+        ├── checklist-template.md
+        ├── constitution-template.md
+        └── agent-file-template.md
+```
+
+## Module Structure
+
+```
+src/specify_cli/
+├── agents.py       # CommandRegistrar — shared infrastructure for writing
+│                    #   command files to agent directories
+├── presets.py       # PresetManifest, PresetRegistry, PresetManager,
+│                    #   PresetCatalog, PresetCatalogEntry, PresetResolver
+└── __init__.py      # CLI commands: specify preset list/add/remove/search/
+                     #   resolve/info, specify preset catalog list/add/remove
+```
--- a/presets/PUBLISHING.md
+++ b/presets/PUBLISHING.md
@@ -0,0 +1,295 @@
+# Preset Publishing Guide
+
+This guide explains how to publish your preset to the Spec Kit preset catalog, making it discoverable by `specify preset search`.
+
+## Table of Contents
+
+1. [Prerequisites](#prerequisites)
+2. [Prepare Your Preset](#prepare-your-preset)
+3. [Submit to Catalog](#submit-to-catalog)
+4. [Verification Process](#verification-process)
+5. [Release Workflow](#release-workflow)
+6. [Best Practices](#best-practices)
+
+---
+
+## Prerequisites
+
+Before publishing a preset, ensure you have:
+
+1. **Valid Preset**: A working preset with a valid `preset.yml` manifest
+2. **Git Repository**: Preset hosted on GitHub (or other public git hosting)
+3. **Documentation**: README.md with description and usage instructions
+4. **License**: Open source license file (MIT, Apache 2.0, etc.)
+5. **Versioning**: Semantic versioning (e.g., 1.0.0)
+6. **Testing**: Preset tested on real projects with `specify preset add --dev`
+
+---
+
+## Prepare Your Preset
+
+### 1. Preset Structure
+
+Ensure your preset follows the standard structure:
+
+```text
+your-preset/
+├── preset.yml                 # Required: Preset manifest
+├── README.md                  # Required: Documentation
+├── LICENSE                    # Required: License file
+├── CHANGELOG.md               # Recommended: Version history
+│
+├── templates/                 # Template overrides
+│   ├── spec-template.md
+│   ├── plan-template.md
+│   └── ...
+│
+└── commands/                  # Command overrides (optional)
+    └── speckit.specify.md
+```
+
+Start from the [scaffold](scaffold/) if you're creating a new preset.
+
+### 2. preset.yml Validation
+
+Verify your manifest is valid:
+
+```yaml
+schema_version: "1.0"
+
+preset:
+  id: "your-preset"               # Unique lowercase-hyphenated ID
+  name: "Your Preset Name"        # Human-readable name
+  version: "1.0.0"                # Semantic version
+  description: "Brief description (one sentence)"
+  author: "Your Name or Organization"
+  repository: "https://github.com/your-org/spec-kit-preset-your-preset"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"      # Required spec-kit version
+
+provides:
+  templates:
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Custom spec template"
+      replaces: "spec-template"
+
+tags:                              # 2-5 relevant tags
+  - "category"
+  - "workflow"
+```
+
+**Validation Checklist**:
+
+- ✅ `id` is lowercase with hyphens only (no underscores, spaces, or special characters)
+- ✅ `version` follows semantic versioning (X.Y.Z)
+- ✅ `description` is concise (under 200 characters)
+- ✅ `repository` URL is valid and public
+- ✅ All template and command files exist in the preset directory
+- ✅ Template names are lowercase with hyphens only
+- ✅ Command names use dot notation (e.g. `speckit.specify`)
+- ✅ Tags are lowercase and descriptive
+
+### 3. Test Locally
+
+```bash
+# Install from local directory
+specify preset add --dev /path/to/your-preset
+
+# Verify templates resolve from your preset
+specify preset resolve spec-template
+
+# Verify preset info
+specify preset info your-preset
+
+# List installed presets
+specify preset list
+
+# Remove when done testing
+specify preset remove your-preset
+```
+
+If your preset includes command overrides, verify they appear in the agent directories:
+
+```bash
+# Check Claude commands (if using Claude)
+ls .claude/commands/speckit.*.md
+
+# Check Copilot commands (if using Copilot)
+ls .github/agents/speckit.*.agent.md
+
+# Check Gemini commands (if using Gemini)
+ls .gemini/commands/speckit.*.toml
+```
+
+### 4. Create GitHub Release
+
+Create a GitHub release for your preset version:
+
+```bash
+# Tag the release
+git tag v1.0.0
+git push origin v1.0.0
+```
+
+The release archive URL will be:
+
+```text
+https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip
+```
+
+### 5. Test Installation from Archive
+
+```bash
+specify preset add --from https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip
+```
+
+---
+
+## Submit to Catalog
+
+### Understanding the Catalogs
+
+Spec Kit uses a dual-catalog system:
+
+- **`catalog.json`** — Official, verified presets (install allowed by default)
+- **`catalog.community.json`** — Community-contributed presets (discovery only by default)
+
+All community presets should be submitted to `catalog.community.json`.
+
+### 1. Fork the spec-kit Repository
+
+```bash
+git clone https://github.com/YOUR-USERNAME/spec-kit.git
+cd spec-kit
+```
+
+### 2. Add Preset to Community Catalog
+
+Edit `presets/catalog.community.json` and add your preset.
+
+> **⚠️ Entries must be sorted alphabetically by preset ID.** Insert your preset in the correct position within the `"presets"` object.
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-10T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
+  "presets": {
+    "your-preset": {
+      "name": "Your Preset Name",
+      "description": "Brief description of what your preset provides",
+      "author": "Your Name",
+      "version": "1.0.0",
+      "download_url": "https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-preset-your-preset",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "templates": 3,
+        "commands": 1
+      },
+      "tags": [
+        "category",
+        "workflow"
+      ],
+      "created_at": "2026-03-10T00:00:00Z",
+      "updated_at": "2026-03-10T00:00:00Z"
+    }
+  }
+}
+```
+
+### 3. Submit Pull Request
+
+```bash
+git checkout -b add-your-preset
+git add presets/catalog.community.json
+git commit -m "Add your-preset to community catalog
+
+- Preset ID: your-preset
+- Version: 1.0.0
+- Author: Your Name
+- Description: Brief description
+"
+git push origin add-your-preset
+```
+
+**Pull Request Checklist**:
+
+```markdown
+## Preset Submission
+
+**Preset Name**: Your Preset Name
+**Preset ID**: your-preset
+**Version**: 1.0.0
+**Repository**: https://github.com/your-org/spec-kit-preset-your-preset
+
+### Checklist
+- [ ] Valid preset.yml manifest
+- [ ] README.md with description and usage
+- [ ] LICENSE file included
+- [ ] GitHub release created
+- [ ] Preset tested with `specify preset add --dev`
+- [ ] Templates resolve correctly (`specify preset resolve`)
+- [ ] Commands register to agent directories (if applicable)
+- [ ] Commands match template sections (command + template are coherent)
+- [ ] Added to presets/catalog.community.json
+```
+
+---
+
+## Verification Process
+
+After submission, maintainers will review:
+
+1. **Manifest validation** — valid `preset.yml`, all files exist
+2. **Template quality** — templates are useful and well-structured
+3. **Command coherence** — commands reference sections that exist in templates
+4. **Security** — no malicious content, safe file operations
+5. **Documentation** — clear README explaining what the preset does
+
+Once verified, `verified: true` is set and the preset appears in `specify preset search`.
+
+---
+
+## Release Workflow
+
+When releasing a new version:
+
+1. Update `version` in `preset.yml`
+2. Update CHANGELOG.md
+3. Tag and push: `git tag v1.1.0 && git push origin v1.1.0`
+4. Submit PR to update `version` and `download_url` in `presets/catalog.community.json`
+
+---
+
+## Best Practices
+
+### Template Design
+
+- **Keep sections clear** — use headings and placeholder text the LLM can replace
+- **Match commands to templates** — if your preset overrides a command, make sure it references the sections in your template
+- **Document customization points** — use HTML comments to guide users on what to change
+
+### Naming
+
+- Preset IDs should be descriptive: `healthcare-compliance`, `enterprise-safe`, `startup-lean`
+- Avoid generic names: `my-preset`, `custom`, `test`
+
+### Stacking
+
+- Design presets to work well when stacked with others
+- Only override templates you need to change
+- Document which templates and commands your preset modifies
+
+### Command Overrides
+
+- Only override commands when the workflow needs to change, not just the output format
+- If you only need different template sections, a template override is sufficient
+- Test command overrides with multiple agents (Claude, Gemini, Copilot)
--- a/presets/README.md
+++ b/presets/README.md
@@ -0,0 +1,115 @@
+# Presets
+
+Presets are stackable, priority-ordered collections of template and command overrides for Spec Kit. They let you customize both the artifacts produced by the Spec-Driven Development workflow (specs, plans, tasks, checklists, constitutions) and the commands that guide the LLM in creating them — without forking or modifying core files.
+
+## How It Works
+
+When Spec Kit needs a template (e.g. `spec-template`), it walks a resolution stack:
+
+1. `.specify/templates/overrides/` — project-local one-off overrides
+2. `.specify/presets/<preset-id>/templates/` — installed presets (sorted by priority)
+3. `.specify/extensions/<ext-id>/templates/` — extension-provided templates
+4. `.specify/templates/` — core templates shipped with Spec Kit
+
+If no preset is installed, core templates are used — exactly the same behavior as before presets existed.
+
+For detailed resolution and command registration flows, see [ARCHITECTURE.md](ARCHITECTURE.md).
+
+## Command Overrides
+
+Presets can also override the commands that guide the SDD workflow. Templates define *what* gets produced (specs, plans, constitutions); commands define *how* the LLM produces them (the step-by-step instructions).
+
+When a preset includes `type: "command"` entries, the commands are automatically registered into all detected agent directories (`.claude/commands/`, `.gemini/commands/`, etc.) in the correct format (Markdown or TOML with appropriate argument placeholders). When the preset is removed, the registered commands are cleaned up.
+
+## Quick Start
+
+```bash
+# Search available presets
+specify preset search
+
+# Install a preset from the catalog
+specify preset add healthcare-compliance
+
+# Install from a local directory (for development)
+specify preset add --dev ./my-preset
+
+# Install with a specific priority (lower = higher precedence)
+specify preset add healthcare-compliance --priority 5
+
+# List installed presets
+specify preset list
+
+# See which template a name resolves to
+specify preset resolve spec-template
+
+# Get detailed info about a preset
+specify preset info healthcare-compliance
+
+# Remove a preset
+specify preset remove healthcare-compliance
+```
+
+## Stacking Presets
+
+Multiple presets can be installed simultaneously. The `--priority` flag controls which one wins when two presets provide the same template (lower number = higher precedence):
+
+```bash
+specify preset add enterprise-safe --priority 10      # base layer
+specify preset add healthcare-compliance --priority 5  # overrides enterprise-safe
+specify preset add pm-workflow --priority 1            # overrides everything
+```
+
+Presets **override**, they don't merge. If two presets both provide `spec-template`, the one with the lowest priority number wins entirely.
+
+## Catalog Management
+
+Presets are discovered through catalogs. By default, Spec Kit uses the official and community catalogs:
+
+```bash
+# List active catalogs
+specify preset catalog list
+
+# Add a custom catalog
+specify preset catalog add https://example.com/catalog.json --name my-org --install-allowed
+
+# Remove a catalog
+specify preset catalog remove my-org
+```
+
+## Creating a Preset
+
+See [scaffold/](scaffold/) for a scaffold you can copy to create your own preset.
+
+1. Copy `scaffold/` to a new directory
+2. Edit `preset.yml` with your preset's metadata
+3. Add or replace templates in `templates/`
+4. Test locally with `specify preset add --dev .`
+5. Verify with `specify preset resolve spec-template`
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `SPECKIT_PRESET_CATALOG_URL` | Override the catalog URL (replaces all defaults) |
+
+## Configuration Files
+
+| File | Scope | Description |
+|------|-------|-------------|
+| `.specify/preset-catalogs.yml` | Project | Custom catalog stack for this project |
+| `~/.specify/preset-catalogs.yml` | User | Custom catalog stack for all projects |
+
+## Future Considerations
+
+The following enhancements are under consideration for future releases:
+
+- **Composition strategies** — Allow presets to declare a `strategy` per template instead of the default `replace`:
+
+  | Type | `replace` | `prepend` | `append` | `wrap` |
+  |------|-----------|-----------|----------|--------|
+  | **template** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **command** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **script** | ✓ (default) | — | — | ✓ |
+
+  For artifacts and commands (which are LLM directives), `wrap` would inject preset content before and after the core template using a `{CORE_TEMPLATE}` placeholder. For scripts, `wrap` would run custom logic before/after the core script via a `$CORE_SCRIPT` variable.
+- **Script overrides** — Enable presets to provide alternative versions of core scripts (e.g. `create-new-feature.sh`) for workflow customization. A `strategy: "wrap"` option could allow presets to run custom logic before/after the core script without fully replacing it.
--- a/presets/catalog.community.json
+++ b/presets/catalog.community.json
@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-09T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
+  "presets": {}
+}
--- a/presets/catalog.json
+++ b/presets/catalog.json
@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-10T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.json",
+  "presets": {}
+}
--- a/presets/scaffold/README.md
+++ b/presets/scaffold/README.md
@@ -0,0 +1,46 @@
+# My Preset
+
+A custom preset for Spec Kit. Copy this directory and customize it to create your own.
+
+## Templates Included
+
+| Template | Type | Description |
+|----------|------|-------------|
+| `spec-template` | template | Custom feature specification template (overrides core and extensions) |
+| `myext-template` | template | Override of the myext extension's report template |
+| `speckit.specify` | command | Custom specification command (overrides core) |
+| `speckit.myext.myextcmd` | command | Override of the myext extension's myextcmd command |
+
+## Development
+
+1. Copy this directory: `cp -r presets/scaffold my-preset`
+2. Edit `preset.yml` — set your preset's ID, name, description, and templates
+3. Add or modify templates in `templates/`
+4. Test locally: `specify preset add --dev ./my-preset`
+5. Verify resolution: `specify preset resolve spec-template`
+6. Remove when done testing: `specify preset remove my-preset`
+
+## Manifest Reference (`preset.yml`)
+
+Required fields:
+- `schema_version` — always `"1.0"`
+- `preset.id` — lowercase alphanumeric with hyphens
+- `preset.name` — human-readable name
+- `preset.version` — semantic version (e.g. `1.0.0`)
+- `preset.description` — brief description
+- `requires.speckit_version` — version constraint (e.g. `>=0.1.0`)
+- `provides.templates` — list of templates with `type`, `name`, and `file`
+
+## Template Types
+
+- **template** — Document scaffolds (spec-template.md, plan-template.md, tasks-template.md, etc.)
+- **command** — AI agent workflow prompts (e.g. speckit.specify, speckit.plan)
+- **script** — Custom scripts (reserved for future use)
+
+## Publishing
+
+See the [Preset Publishing Guide](../PUBLISHING.md) for details on submitting to the catalog.
+
+## License
+
+MIT
--- a/presets/scaffold/commands/speckit.myext.myextcmd.md
+++ b/presets/scaffold/commands/speckit.myext.myextcmd.md
@@ -0,0 +1,20 @@
+---
+description: "Override of the myext extension's myextcmd command"
+---
+
+<!-- Preset override for speckit.myext.myextcmd -->
+
+You are following a customized version of the myext extension's myextcmd command.
+
+When executing this command:
+
+1. Read the user's input from $ARGUMENTS
+2. Follow the standard myextcmd workflow
+3. Additionally, apply the following customizations from this preset:
+   - Add compliance checks before proceeding
+   - Include audit trail entries in the output
+
+> CUSTOMIZE: Replace the instructions above with your own.
+> This file overrides the command that the "myext" extension provides.
+> When this preset is installed, all agents (Claude, Gemini, Copilot, etc.)
+> will use this version instead of the extension's original.
--- a/presets/scaffold/commands/speckit.specify.md
+++ b/presets/scaffold/commands/speckit.specify.md
@@ -0,0 +1,23 @@
+---
+description: "Create a feature specification (preset override)"
+scripts:
+  sh: scripts/bash/create-new-feature.sh "{ARGS}"
+  ps: scripts/powershell/create-new-feature.ps1 "{ARGS}"
+---
+
+## User Input
+
+```text
+$ARGUMENTS
+```
+
+Given the feature description above:
+
+1. **Create the feature branch** by running the script:
+   - Bash: `{SCRIPT} --json --short-name "<short-name>" "<description>"`
+   - The JSON output contains BRANCH_NAME and SPEC_FILE paths.
+
+2. **Read the spec-template** to see the sections you need to fill.
+
+3. **Write the specification** to SPEC_FILE, replacing the placeholders in each section
+   (Overview, Requirements, Acceptance Criteria) with details from the user's description.
--- a/presets/scaffold/preset.yml
+++ b/presets/scaffold/preset.yml
@@ -0,0 +1,91 @@
+schema_version: "1.0"
+
+preset:
+  # CUSTOMIZE: Change 'my-preset' to your preset ID (lowercase, hyphen-separated)
+  id: "my-preset"
+
+  # CUSTOMIZE: Human-readable name for your preset
+  name: "My Preset"
+
+  # CUSTOMIZE: Update version when releasing (semantic versioning: X.Y.Z)
+  version: "1.0.0"
+
+  # CUSTOMIZE: Brief description (under 200 characters)
+  description: "Brief description of what your preset provides"
+
+  # CUSTOMIZE: Your name or organization name
+  author: "Your Name"
+
+  # CUSTOMIZE: GitHub repository URL (create before publishing)
+  repository: "https://github.com/your-org/spec-kit-preset-my-preset"
+
+  # REVIEW: License (MIT is recommended for open source)
+  license: "MIT"
+
+# Requirements for this preset
+requires:
+  # CUSTOMIZE: Minimum spec-kit version required
+  speckit_version: ">=0.1.0"
+
+# Templates provided by this preset
+provides:
+  templates:
+    # CUSTOMIZE: Define your template overrides
+    # Templates are document scaffolds (spec-template.md, plan-template.md, etc.)
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Custom feature specification template"
+      replaces: "spec-template"  # Which core template this overrides (optional)
+
+    # ADD MORE TEMPLATES: Copy this block for each template
+    # - type: "template"
+    #   name: "plan-template"
+    #   file: "templates/plan-template.md"
+    #   description: "Custom plan template"
+    #   replaces: "plan-template"
+
+    # OVERRIDE EXTENSION TEMPLATES:
+    # Presets sit above extensions in the resolution stack, so you can
+    # override templates provided by any installed extension.
+    # For example, if the "myext" extension provides a spec-template,
+    # the preset's version above will take priority automatically.
+
+    # Override a template provided by the "myext" extension:
+    - type: "template"
+      name: "myext-template"
+      file: "templates/myext-template.md"
+      description: "Override myext's report template"
+      replaces: "myext-template"
+
+    # Command overrides (AI agent workflow prompts)
+    # Presets can override both core and extension commands.
+    # Commands are automatically registered into all detected agent
+    # directories (.claude/commands/, .gemini/commands/, etc.)
+
+    # Override a core command:
+    - type: "command"
+      name: "speckit.specify"
+      file: "commands/speckit.specify.md"
+      description: "Custom specification command"
+      replaces: "speckit.specify"
+
+    # Override an extension command (e.g. from the "myext" extension):
+    - type: "command"
+      name: "speckit.myext.myextcmd"
+      file: "commands/speckit.myext.myextcmd.md"
+      description: "Override myext's myextcmd command with custom workflow"
+      replaces: "speckit.myext.myextcmd"
+
+    # Script templates (reserved for future use)
+    # - type: "script"
+    #   name: "create-new-feature"
+    #   file: "scripts/bash/create-new-feature.sh"
+    #   description: "Custom feature creation script"
+    #   replaces: "create-new-feature"
+
+# CUSTOMIZE: Add relevant tags (2-5 recommended)
+# Used for discovery in catalog
+tags:
+  - "example"
+  - "preset"
--- a/presets/scaffold/templates/myext-template.md
+++ b/presets/scaffold/templates/myext-template.md
@@ -0,0 +1,24 @@
+# MyExt Report
+
+> This template overrides the one provided by the "myext" extension.
+> Customize it to match your needs.
+
+## Summary
+
+Brief summary of the report.
+
+## Details
+
+- Detail 1
+- Detail 2
+
+## Actions
+
+- [ ] Action 1
+- [ ] Action 2
+
+<!--
+  CUSTOMIZE: This template takes priority over the myext extension's
+  version of myext-template. The extension's original is still available
+  if you remove this preset.
+-->
--- a/presets/scaffold/templates/spec-template.md
+++ b/presets/scaffold/templates/spec-template.md
@@ -0,0 +1,18 @@
+# Feature Specification: [FEATURE NAME]
+
+**Created**: [DATE]
+**Status**: Draft
+
+## Overview
+
+[Brief description of the feature]
+
+## Requirements
+
+- [ ] Requirement 1
+- [ ] Requirement 2
+
+## Acceptance Criteria
+
+- [ ] Criterion 1
+- [ ] Criterion 2
--- a/presets/self-test/commands/speckit.specify.md
+++ b/presets/self-test/commands/speckit.specify.md
@@ -0,0 +1,15 @@
+---
+description: "Self-test override of the specify command"
+---
+
+<!-- preset:self-test -->
+
+You are following the self-test preset's version of the specify command.
+
+When creating a specification, follow this process:
+
+1. Read the user's requirements from $ARGUMENTS
+2. Create a specification document using the spec-template
+3. Include all standard sections plus the self-test marker
+
+> This command is provided by the self-test preset.
--- a/presets/self-test/preset.yml
+++ b/presets/self-test/preset.yml
@@ -0,0 +1,61 @@
+schema_version: "1.0"
+
+preset:
+  id: "self-test"
+  name: "Self-Test Preset"
+  version: "1.0.0"
+  description: "A preset that overrides all core templates for testing purposes"
+  author: "github"
+  repository: "https://github.com/github/spec-kit"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+provides:
+  templates:
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Self-test spec template"
+      replaces: "spec-template"
+
+    - type: "template"
+      name: "plan-template"
+      file: "templates/plan-template.md"
+      description: "Self-test plan template"
+      replaces: "plan-template"
+
+    - type: "template"
+      name: "tasks-template"
+      file: "templates/tasks-template.md"
+      description: "Self-test tasks template"
+      replaces: "tasks-template"
+
+    - type: "template"
+      name: "checklist-template"
+      file: "templates/checklist-template.md"
+      description: "Self-test checklist template"
+      replaces: "checklist-template"
+
+    - type: "template"
+      name: "constitution-template"
+      file: "templates/constitution-template.md"
+      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"
+      description: "Self-test override of the specify command"
+      replaces: "speckit.specify"
+
+tags:
+  - "testing"
+  - "self-test"
--- a/presets/self-test/templates/agent-file-template.md
+++ b/presets/self-test/templates/agent-file-template.md
@@ -0,0 +1,9 @@
+# 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.
--- a/presets/self-test/templates/checklist-template.md
+++ b/presets/self-test/templates/checklist-template.md
@@ -0,0 +1,15 @@
+# Checklist (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Pre-Implementation
+
+- [ ] Spec reviewed
+- [ ] Plan approved
+
+## Post-Implementation
+
+- [ ] Tests passing
+- [ ] Documentation updated
--- a/presets/self-test/templates/constitution-template.md
+++ b/presets/self-test/templates/constitution-template.md
@@ -0,0 +1,15 @@
+# Constitution (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Principles
+
+1. Principle 1
+2. Principle 2
+
+## Guidelines
+
+- Guideline 1
+- Guideline 2
--- a/presets/self-test/templates/plan-template.md
+++ b/presets/self-test/templates/plan-template.md
@@ -0,0 +1,22 @@
+# Implementation Plan (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Approach
+
+Describe the implementation approach.
+
+## Steps
+
+1. Step 1
+2. Step 2
+
+## Dependencies
+
+- Dependency 1
+
+## Risks
+
+- Risk 1
--- a/presets/self-test/templates/spec-template.md
+++ b/presets/self-test/templates/spec-template.md
@@ -0,0 +1,23 @@
+# Feature Specification (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Overview
+
+Brief description of the feature.
+
+## Requirements
+
+- Requirement 1
+- Requirement 2
+
+## Design
+
+Describe the design approach.
+
+## Acceptance Criteria
+
+- [ ] Criterion 1
+- [ ] Criterion 2
--- a/presets/self-test/templates/tasks-template.md
+++ b/presets/self-test/templates/tasks-template.md
@@ -0,0 +1,17 @@
+# Tasks (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Task List
+
+- [ ] Task 1
+- [ ] Task 2
+
+## Estimation
+
+| Task | Estimate |
+|------|----------|
+| Task 1 | TBD |
+| Task 2 | TBD |
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.2.1"
+version = "0.3.1"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -14,6 +14,7 @@ dependencies = [
    "pyyaml>=6.0",
    "packaging>=23.0",
    "pathspec>=0.12.0",
+    "json5>=0.13.0",
 ]

 [project.scripts]
--- a/scripts/bash/check-prerequisites.sh
+++ b/scripts/bash/check-prerequisites.sh
@@ -79,15 +79,28 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"

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

 # If paths-only mode, output paths and exit (support JSON + paths-only combined)
 if $PATHS_ONLY; then
    if $JSON_MODE; then
        # Minimal JSON paths payload (no validation performed)
-        printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
-            "$REPO_ROOT" "$CURRENT_BRANCH" "$FEATURE_DIR" "$FEATURE_SPEC" "$IMPL_PLAN" "$TASKS"
+        if has_jq; then
+            jq -cn \
+                --arg repo_root "$REPO_ROOT" \
+                --arg branch "$CURRENT_BRANCH" \
+                --arg feature_dir "$FEATURE_DIR" \
+                --arg feature_spec "$FEATURE_SPEC" \
+                --arg impl_plan "$IMPL_PLAN" \
+                --arg tasks "$TASKS" \
+                '{REPO_ROOT:$repo_root,BRANCH:$branch,FEATURE_DIR:$feature_dir,FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,TASKS:$tasks}'
+        else
+            printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
+                "$(json_escape "$REPO_ROOT")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$TASKS")"
+        fi
    else
        echo "REPO_ROOT: $REPO_ROOT"
        echo "BRANCH: $CURRENT_BRANCH"
@@ -141,14 +154,25 @@ fi
 # Output results
 if $JSON_MODE; then
    # Build JSON array of documents
-    if [[ ${#docs[@]} -eq 0 ]]; then
-        json_docs="[]"
+    if has_jq; then
+        if [[ ${#docs[@]} -eq 0 ]]; then
+            json_docs="[]"
+        else
+            json_docs=$(printf '%s\n' "${docs[@]}" | jq -R . | jq -s .)
+        fi
+        jq -cn \
+            --arg feature_dir "$FEATURE_DIR" \
+            --argjson docs "$json_docs" \
+            '{FEATURE_DIR:$feature_dir,AVAILABLE_DOCS:$docs}'
    else
-        json_docs=$(printf '"%s",' "${docs[@]}")
-        json_docs="[${json_docs%,}]"
+        if [[ ${#docs[@]} -eq 0 ]]; then
+            json_docs="[]"
+        else
+            json_docs=$(for d in "${docs[@]}"; do printf '"%s",' "$(json_escape "$d")"; done)
+            json_docs="[${json_docs%,}]"
+        fi
+        printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"
    fi
-    
-    printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$FEATURE_DIR" "$json_docs"
 else
    # Text output
    echo "FEATURE_DIR:$FEATURE_DIR"
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -120,7 +120,7 @@ find_feature_dir_by_prefix() {
        # Multiple matches - this shouldn't happen with proper naming convention
        echo "ERROR: Multiple spec directories found with prefix '$prefix': ${matches[*]}" >&2
        echo "Please ensure only one spec directory exists per numeric prefix." >&2
-        echo "$specs_dir/$branch_name"  # Return something to avoid breaking the script
+        return 1
    fi
 }

@@ -134,23 +134,130 @@ get_feature_paths() {
    fi

    # Use prefix-based lookup to support multiple branches per spec
-    local feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch")
+    local feature_dir
+    if ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
+        echo "ERROR: Failed to resolve feature directory" >&2
+        return 1
+    fi

-    cat <<EOF
-REPO_ROOT='$repo_root'
-CURRENT_BRANCH='$current_branch'
-HAS_GIT='$has_git_repo'
-FEATURE_DIR='$feature_dir'
-FEATURE_SPEC='$feature_dir/spec.md'
-IMPL_PLAN='$feature_dir/plan.md'
-TASKS='$feature_dir/tasks.md'
-RESEARCH='$feature_dir/research.md'
-DATA_MODEL='$feature_dir/data-model.md'
-QUICKSTART='$feature_dir/quickstart.md'
-CONTRACTS_DIR='$feature_dir/contracts'
-EOF
+    # Use printf '%q' to safely quote values, preventing shell injection
+    # via crafted branch names or paths containing special characters
+    printf 'REPO_ROOT=%q\n' "$repo_root"
+    printf 'CURRENT_BRANCH=%q\n' "$current_branch"
+    printf 'HAS_GIT=%q\n' "$has_git_repo"
+    printf 'FEATURE_DIR=%q\n' "$feature_dir"
+    printf 'FEATURE_SPEC=%q\n' "$feature_dir/spec.md"
+    printf 'IMPL_PLAN=%q\n' "$feature_dir/plan.md"
+    printf 'TASKS=%q\n' "$feature_dir/tasks.md"
+    printf 'RESEARCH=%q\n' "$feature_dir/research.md"
+    printf 'DATA_MODEL=%q\n' "$feature_dir/data-model.md"
+    printf 'QUICKSTART=%q\n' "$feature_dir/quickstart.md"
+    printf 'CONTRACTS_DIR=%q\n' "$feature_dir/contracts"
+}
+
+# Check if jq is available for safe JSON construction
+has_jq() {
+    command -v jq >/dev/null 2>&1
+}
+
+# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
+# Handles backslash, double-quote, and JSON-required control character escapes (RFC 8259).
+json_escape() {
+    local s="$1"
+    s="${s//\\/\\\\}"
+    s="${s//\"/\\\"}"
+    s="${s//$'\n'/\\n}"
+    s="${s//$'\t'/\\t}"
+    s="${s//$'\r'/\\r}"
+    s="${s//$'\b'/\\b}"
+    s="${s//$'\f'/\\f}"
+    # Strip remaining control characters (U+0000–U+001F) not individually escaped above
+    s=$(printf '%s' "$s" | tr -d '\000-\007\013\016-\037')
+    printf '%s' "$s"
 }

 check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 check_dir() { [[ -d "$1" && -n $(ls -A "$1" 2>/dev/null) ]] && echo "  ✓ $2" || echo "  ✗ $2"; }

+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+resolve_template() {
+    local template_name="$1"
+    local repo_root="$2"
+    local base="$repo_root/.specify/templates"
+
+    # Priority 1: Project overrides
+    local override="$base/overrides/${template_name}.md"
+    [ -f "$override" ] && echo "$override" && return 0
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    local presets_dir="$repo_root/.specify/presets"
+    if [ -d "$presets_dir" ]; then
+        local registry_file="$presets_dir/.registry"
+        if [ -f "$registry_file" ] && command -v python3 >/dev/null 2>&1; then
+            # Read preset IDs sorted by priority (lower number = higher precedence).
+            # The python3 call is wrapped in an if-condition so that set -e does not
+            # abort the function when python3 exits non-zero (e.g. invalid JSON).
+            local sorted_presets=""
+            if sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
+import json, sys, os
+try:
+    with open(os.environ['SPECKIT_REGISTRY']) as f:
+        data = json.load(f)
+    presets = data.get('presets', {})
+    for pid, meta in sorted(presets.items(), key=lambda x: x[1].get('priority', 10)):
+        print(pid)
+except Exception:
+    sys.exit(1)
+" 2>/dev/null); then
+                if [ -n "$sorted_presets" ]; then
+                    # python3 succeeded and returned preset IDs — search in priority order
+                    while IFS= read -r preset_id; do
+                        local candidate="$presets_dir/$preset_id/templates/${template_name}.md"
+                        [ -f "$candidate" ] && echo "$candidate" && return 0
+                    done <<< "$sorted_presets"
+                fi
+                # python3 succeeded but registry has no presets — nothing to search
+            else
+                # python3 failed (missing, or registry parse error) — fall back to unordered directory scan
+                for preset in "$presets_dir"/*/; do
+                    [ -d "$preset" ] || continue
+                    local candidate="$preset/templates/${template_name}.md"
+                    [ -f "$candidate" ] && echo "$candidate" && return 0
+                done
+            fi
+        else
+            # Fallback: alphabetical directory order (no python3 available)
+            for preset in "$presets_dir"/*/; do
+                [ -d "$preset" ] || continue
+                local candidate="$preset/templates/${template_name}.md"
+                [ -f "$candidate" ] && echo "$candidate" && return 0
+            done
+        fi
+    fi
+
+    # Priority 3: Extension-provided templates
+    local ext_dir="$repo_root/.specify/extensions"
+    if [ -d "$ext_dir" ]; then
+        for ext in "$ext_dir"/*/; do
+            [ -d "$ext" ] || continue
+            # Skip hidden directories (e.g. .backup, .cache)
+            case "$(basename "$ext")" in .*) continue;; esac
+            local candidate="$ext/templates/${template_name}.md"
+            [ -f "$candidate" ] && echo "$candidate" && return 0
+        done
+    fi
+
+    # Priority 4: Core templates
+    local core="$base/${template_name}.md"
+    [ -f "$core" ] && echo "$core" && return 0
+
+    # Template not found in any location.
+    # Return 1 so callers can distinguish "not found" from "found".
+    # Callers running under set -e should use: TEMPLATE=$(resolve_template ...) || true
+    return 1
+}
+
--- a/scripts/bash/create-new-feature.sh
+++ b/scripts/bash/create-new-feature.sh
@@ -138,7 +138,7 @@ check_existing_branches() {
    local specs_dir="$1"

    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    git fetch --all --prune 2>/dev/null || true
+    git fetch --all --prune >/dev/null 2>&1 || true

    # Get highest number from ALL branches (not just matching short name)
    local highest_branch=$(get_highest_from_branches)
@@ -166,6 +166,7 @@ clean_branch_name() {
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/common.sh"

 if git rev-parse --show-toplevel >/dev/null 2>&1; then
    REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -296,18 +297,31 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"

-TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
+TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
+if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
+    cp "$TEMPLATE" "$SPEC_FILE"
+else
+    echo "Warning: Spec template not found; created empty spec file" >&2
+    touch "$SPEC_FILE"
+fi

-# Set the SPECIFY_FEATURE environment variable for the current session
-export SPECIFY_FEATURE="$BRANCH_NAME"
+# Inform the user how to persist the feature variable in their own shell
+printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2

 if $JSON_MODE; then
-    printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$BRANCH_NAME" "$SPEC_FILE" "$FEATURE_NUM"
+    if command -v jq >/dev/null 2>&1; then
+        jq -cn \
+            --arg branch_name "$BRANCH_NAME" \
+            --arg spec_file "$SPEC_FILE" \
+            --arg feature_num "$FEATURE_NUM" \
+            '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num}'
+    else
+        printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$(json_escape "$BRANCH_NAME")" "$(json_escape "$SPEC_FILE")" "$(json_escape "$FEATURE_NUM")"
+    fi
 else
    echo "BRANCH_NAME: $BRANCH_NAME"
    echo "SPEC_FILE: $SPEC_FILE"
    echo "FEATURE_NUM: $FEATURE_NUM"
-    echo "SPECIFY_FEATURE environment variable set to: $BRANCH_NAME"
+    printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
 fi
--- a/scripts/bash/setup-plan.sh
+++ b/scripts/bash/setup-plan.sh
@@ -28,7 +28,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"

 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output

 # Check if we're on a proper feature branch (only for git repos)
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
@@ -37,20 +39,30 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 mkdir -p "$FEATURE_DIR"

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

 # Output results
 if $JSON_MODE; then
-    printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
-        "$FEATURE_SPEC" "$IMPL_PLAN" "$FEATURE_DIR" "$CURRENT_BRANCH" "$HAS_GIT"
+    if has_jq; then
+        jq -cn \
+            --arg feature_spec "$FEATURE_SPEC" \
+            --arg impl_plan "$IMPL_PLAN" \
+            --arg specs_dir "$FEATURE_DIR" \
+            --arg branch "$CURRENT_BRANCH" \
+            --arg has_git "$HAS_GIT" \
+            '{FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,SPECS_DIR:$specs_dir,BRANCH:$branch,HAS_GIT:$has_git}'
+    else
+        printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
+            "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$HAS_GIT")"
+    fi
 else
    echo "FEATURE_SPEC: $FEATURE_SPEC"
    echo "IMPL_PLAN: $IMPL_PLAN" 
--- a/scripts/bash/update-agent-context.sh
+++ b/scripts/bash/update-agent-context.sh
@@ -35,7 +35,7 @@
 #    - Creates default Claude file if no agent files exist
 #
 # Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic
+# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic
 # Leave empty to update all existing agent files

 set -e
@@ -53,7 +53,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"

 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output

 NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
 AGENT_TYPE="${1:-}"
@@ -71,14 +73,17 @@ AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
 ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
 CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
 QODER_FILE="$REPO_ROOT/QODER.md"
-AMP_FILE="$REPO_ROOT/AGENTS.md"
+# AMP, Kiro CLI, and IBM Bob all share AGENTS.md — use AGENTS_FILE to avoid
+# updating the same file multiple times.
+AMP_FILE="$AGENTS_FILE"
 SHAI_FILE="$REPO_ROOT/SHAI.md"
 TABNINE_FILE="$REPO_ROOT/TABNINE.md"
-KIRO_FILE="$REPO_ROOT/AGENTS.md"
+KIRO_FILE="$AGENTS_FILE"
 AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
-BOB_FILE="$REPO_ROOT/AGENTS.md"
+BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
+TRAE_FILE="$REPO_ROOT/.trae/rules/AGENTS.md"

 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -112,6 +117,8 @@ log_warning() {
 # Cleanup function for temporary files
 cleanup() {
    local exit_code=$?
+    # Disarm traps to prevent re-entrant loop
+    trap - EXIT INT TERM
    rm -f /tmp/agent_update_*_$$
    rm -f /tmp/manual_additions_$$
    exit $exit_code
@@ -476,7 +483,7 @@ update_existing_agent_file() {
        fi
        
        # Update timestamp
-        if [[ "$line" =~ \*\*Last\ updated\*\*:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
+        if [[ "$line" =~ (\*\*)?Last\ updated(\*\*)?:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
            echo "$line" | sed "s/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/$current_date/" >> "$temp_file"
        else
            echo "$line" >> "$temp_file"
@@ -607,182 +614,144 @@ update_specific_agent() {
    
    case "$agent_type" in
        claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code"
+            update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
            ;;
        gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI"
+            update_agent_file "$GEMINI_FILE" "Gemini CLI" || return 1
            ;;
        copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot"
+            update_agent_file "$COPILOT_FILE" "GitHub Copilot" || return 1
            ;;
        cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE"
+            update_agent_file "$CURSOR_FILE" "Cursor IDE" || return 1
            ;;
        qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code"
+            update_agent_file "$QWEN_FILE" "Qwen Code" || return 1
            ;;
        opencode)
-            update_agent_file "$AGENTS_FILE" "opencode"
+            update_agent_file "$AGENTS_FILE" "opencode" || return 1
            ;;
        codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI"
+            update_agent_file "$AGENTS_FILE" "Codex CLI" || return 1
            ;;
        windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf"
+            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
            ;;
        kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code"
+            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
            ;;
        auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI"
+            update_agent_file "$AUGGIE_FILE" "Auggie CLI" || return 1
            ;;
        roo)
-            update_agent_file "$ROO_FILE" "Roo Code"
+            update_agent_file "$ROO_FILE" "Roo Code" || return 1
            ;;
        codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
+            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI" || return 1
            ;;
        qodercli)
-            update_agent_file "$QODER_FILE" "Qoder CLI"
+            update_agent_file "$QODER_FILE" "Qoder CLI" || return 1
            ;;
        amp)
-            update_agent_file "$AMP_FILE" "Amp"
+            update_agent_file "$AMP_FILE" "Amp" || return 1
            ;;
        shai)
-            update_agent_file "$SHAI_FILE" "SHAI"
+            update_agent_file "$SHAI_FILE" "SHAI" || return 1
            ;;
        tabnine)
-            update_agent_file "$TABNINE_FILE" "Tabnine CLI"
+            update_agent_file "$TABNINE_FILE" "Tabnine CLI" || return 1
            ;;
        kiro-cli)
-            update_agent_file "$KIRO_FILE" "Kiro CLI"
+            update_agent_file "$KIRO_FILE" "Kiro CLI" || return 1
            ;;
        agy)
-            update_agent_file "$AGY_FILE" "Antigravity"
+            update_agent_file "$AGY_FILE" "Antigravity" || return 1
            ;;
        bob)
-            update_agent_file "$BOB_FILE" "IBM Bob"
+            update_agent_file "$BOB_FILE" "IBM Bob" || return 1
            ;;
        vibe)
-            update_agent_file "$VIBE_FILE" "Mistral Vibe"
+            update_agent_file "$VIBE_FILE" "Mistral Vibe" || return 1
            ;;
        kimi)
-            update_agent_file "$KIMI_FILE" "Kimi Code"
+            update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
+            ;;
+        trae)
+            update_agent_file "$TRAE_FILE" "Trae" || return 1
            ;;
        generic)
            log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
            ;;
        *)
            log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic"
+            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic"
            exit 1
            ;;
    esac
 }

+# Helper: skip non-existent files and files already updated (dedup by
+# realpath so that variables pointing to the same file — e.g. AMP_FILE,
+# KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
+# Uses a linear array instead of associative array for bash 3.2 compatibility.
+# Note: defined at top level because bash 3.2 does not support true
+# nested/local functions. _updated_paths, _found_agent, and _all_ok are
+# initialised exclusively inside update_all_existing_agents so that
+# sourcing this script has no side effects on the caller's environment.
+
+_update_if_new() {
+    local file="$1" name="$2"
+    [[ -f "$file" ]] || return 0
+    local real_path
+    real_path=$(realpath "$file" 2>/dev/null || echo "$file")
+    local p
+    if [[ ${#_updated_paths[@]} -gt 0 ]]; then
+        for p in "${_updated_paths[@]}"; do
+            [[ "$p" == "$real_path" ]] && return 0
+        done
+    fi
+    # Record the file as seen before attempting the update so that:
+    # (a) aliases pointing to the same path are not retried on failure
+    # (b) _found_agent reflects file existence, not update success
+    _updated_paths+=("$real_path")
+    _found_agent=true
+    update_agent_file "$file" "$name"
+}
+
 update_all_existing_agents() {
-    local found_agent=false
-    
-    # Check each possible agent file and update if it exists
-    if [[ -f "$CLAUDE_FILE" ]]; then
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$GEMINI_FILE" ]]; then
-        update_agent_file "$GEMINI_FILE" "Gemini CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$COPILOT_FILE" ]]; then
-        update_agent_file "$COPILOT_FILE" "GitHub Copilot"
-        found_agent=true
-    fi
-    
-    if [[ -f "$CURSOR_FILE" ]]; then
-        update_agent_file "$CURSOR_FILE" "Cursor IDE"
-        found_agent=true
-    fi
-    
-    if [[ -f "$QWEN_FILE" ]]; then
-        update_agent_file "$QWEN_FILE" "Qwen Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$AGENTS_FILE" ]]; then
-        update_agent_file "$AGENTS_FILE" "Codex/opencode"
-        found_agent=true
-    fi
-    
-    if [[ -f "$WINDSURF_FILE" ]]; then
-        update_agent_file "$WINDSURF_FILE" "Windsurf"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KILOCODE_FILE" ]]; then
-        update_agent_file "$KILOCODE_FILE" "Kilo Code"
-        found_agent=true
-    fi
+    _found_agent=false
+    _updated_paths=()
+    local _all_ok=true

-    if [[ -f "$AUGGIE_FILE" ]]; then
-        update_agent_file "$AUGGIE_FILE" "Auggie CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$ROO_FILE" ]]; then
-        update_agent_file "$ROO_FILE" "Roo Code"
-        found_agent=true
-    fi
+    _update_if_new "$CLAUDE_FILE" "Claude Code"           || _all_ok=false
+    _update_if_new "$GEMINI_FILE" "Gemini CLI"             || _all_ok=false
+    _update_if_new "$COPILOT_FILE" "GitHub Copilot"        || _all_ok=false
+    _update_if_new "$CURSOR_FILE" "Cursor IDE"             || _all_ok=false
+    _update_if_new "$QWEN_FILE" "Qwen Code"                || _all_ok=false
+    _update_if_new "$AGENTS_FILE" "Codex/opencode"         || _all_ok=false
+    _update_if_new "$AMP_FILE" "Amp"                       || _all_ok=false
+    _update_if_new "$KIRO_FILE" "Kiro CLI"                 || _all_ok=false
+    _update_if_new "$BOB_FILE" "IBM Bob"                   || _all_ok=false
+    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
+    _update_if_new "$KILOCODE_FILE" "Kilo Code"            || _all_ok=false
+    _update_if_new "$AUGGIE_FILE" "Auggie CLI"             || _all_ok=false
+    _update_if_new "$ROO_FILE" "Roo Code"                  || _all_ok=false
+    _update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"       || _all_ok=false
+    _update_if_new "$SHAI_FILE" "SHAI"                     || _all_ok=false
+    _update_if_new "$TABNINE_FILE" "Tabnine CLI"           || _all_ok=false
+    _update_if_new "$QODER_FILE" "Qoder CLI"               || _all_ok=false
+    _update_if_new "$AGY_FILE" "Antigravity"               || _all_ok=false
+    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
+    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
+    _update_if_new "$TRAE_FILE" "Trae"                     || _all_ok=false

-    if [[ -f "$CODEBUDDY_FILE" ]]; then
-        update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$SHAI_FILE" ]]; then
-        update_agent_file "$SHAI_FILE" "SHAI"
-        found_agent=true
-    fi
-
-    if [[ -f "$TABNINE_FILE" ]]; then
-        update_agent_file "$TABNINE_FILE" "Tabnine CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$QODER_FILE" ]]; then
-        update_agent_file "$QODER_FILE" "Qoder CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$KIRO_FILE" ]]; then
-        update_agent_file "$KIRO_FILE" "Kiro CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$AGY_FILE" ]]; then
-        update_agent_file "$AGY_FILE" "Antigravity"
-        found_agent=true
-    fi
-    if [[ -f "$BOB_FILE" ]]; then
-        update_agent_file "$BOB_FILE" "IBM Bob"
-        found_agent=true
-    fi
-
-    if [[ -f "$VIBE_FILE" ]]; then
-        update_agent_file "$VIBE_FILE" "Mistral Vibe"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KIMI_FILE" ]]; then
-        update_agent_file "$KIMI_FILE" "Kimi Code"
-        found_agent=true
-    fi
-    
    # If no agent files exist, create a default Claude file
-    if [[ "$found_agent" == false ]]; then
+    if [[ "$_found_agent" == false ]]; then
        log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
+        update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
    fi
+
+    [[ "$_all_ok" == true ]]
 }
 print_summary() {
    echo
@@ -801,7 +770,7 @@ print_summary() {
    fi
    
    echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic]"
 }

 #==============================================================================
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -135,3 +135,70 @@ function Test-DirHasFiles {
    }
 }

+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+function Resolve-Template {
+    param(
+        [Parameter(Mandatory=$true)][string]$TemplateName,
+        [Parameter(Mandatory=$true)][string]$RepoRoot
+    )
+
+    $base = Join-Path $RepoRoot '.specify/templates'
+
+    # Priority 1: Project overrides
+    $override = Join-Path $base "overrides/$TemplateName.md"
+    if (Test-Path $override) { return $override }
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    $presetsDir = Join-Path $RepoRoot '.specify/presets'
+    if (Test-Path $presetsDir) {
+        $registryFile = Join-Path $presetsDir '.registry'
+        $sortedPresets = @()
+        if (Test-Path $registryFile) {
+            try {
+                $registryData = Get-Content $registryFile -Raw | ConvertFrom-Json
+                $presets = $registryData.presets
+                if ($presets) {
+                    $sortedPresets = $presets.PSObject.Properties |
+                        Sort-Object { if ($null -ne $_.Value.priority) { $_.Value.priority } else { 10 } } |
+                        ForEach-Object { $_.Name }
+                }
+            } catch {
+                # Fallback: alphabetical directory order
+                $sortedPresets = @()
+            }
+        }
+
+        if ($sortedPresets.Count -gt 0) {
+            foreach ($presetId in $sortedPresets) {
+                $candidate = Join-Path $presetsDir "$presetId/templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        } else {
+            # Fallback: alphabetical directory order
+            foreach ($preset in Get-ChildItem -Path $presetsDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' }) {
+                $candidate = Join-Path $preset.FullName "templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        }
+    }
+
+    # Priority 3: Extension-provided templates
+    $extDir = Join-Path $RepoRoot '.specify/extensions'
+    if (Test-Path $extDir) {
+        foreach ($ext in Get-ChildItem -Path $extDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' } | Sort-Object Name) {
+            $candidate = Join-Path $ext.FullName "templates/$TemplateName.md"
+            if (Test-Path $candidate) { return $candidate }
+        }
+    }
+
+    # Priority 4: Core templates
+    $core = Join-Path $base "$TemplateName.md"
+    if (Test-Path $core) { return $core }
+
+    return $null
+}
+
--- a/scripts/powershell/create-new-feature.ps1
+++ b/scripts/powershell/create-new-feature.ps1
@@ -141,6 +141,9 @@ if (-not $fallbackRoot) {
    exit 1
 }

+# Load common functions (includes Resolve-Template)
+. "$PSScriptRoot/common.ps1"
+
 try {
    $repoRoot = git rev-parse --show-toplevel 2>$null
    if ($LASTEXITCODE -eq 0) {
@@ -276,9 +279,9 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null

-$template = Join-Path $repoRoot '.specify/templates/spec-template.md'
+$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
 $specFile = Join-Path $featureDir 'spec.md'
-if (Test-Path $template) { 
+if ($template -and (Test-Path $template)) { 
    Copy-Item $template $specFile -Force 
 } else { 
    New-Item -ItemType File -Path $specFile | Out-Null 
--- a/scripts/powershell/setup-plan.ps1
+++ b/scripts/powershell/setup-plan.ps1
@@ -32,12 +32,12 @@ if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit $paths.HAS_GI
 New-Item -ItemType Directory -Path $paths.FEATURE_DIR -Force | Out-Null

 # Copy plan template if it exists, otherwise note it or create empty file
-$template = Join-Path $paths.REPO_ROOT '.specify/templates/plan-template.md'
-if (Test-Path $template) { 
+$template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
+if ($template -and (Test-Path $template)) { 
    Copy-Item $template $paths.IMPL_PLAN -Force
    Write-Output "Copied plan template to $($paths.IMPL_PLAN)"
 } else {
-    Write-Warning "Plan template not found at $template"
+    Write-Warning "Plan template not found"
    # Create a basic plan file if template doesn't exist
    New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
 }
--- a/scripts/powershell/update-agent-context.ps1
+++ b/scripts/powershell/update-agent-context.ps1
@@ -9,7 +9,7 @@ Mirrors the behavior of scripts/bash/update-agent-context.sh:
 2. Plan Data Extraction
 3. Agent File Management (create from template or update existing)
 4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, generic)
+ 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, generic)

 .PARAMETER AgentType
 Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
@@ -25,7 +25,7 @@ Relies on common helper functions in common.ps1
 #>
 param(
    [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','generic')]
+    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','trae','generic')]
    [string]$AgentType
 )

@@ -64,6 +64,7 @@ $AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
 $BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 $VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
 $KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
+$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/AGENTS.md'

 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'

@@ -331,7 +332,7 @@ function Update-ExistingAgentFile {
            if ($existingChanges -lt 2) { $output.Add($line); $existingChanges++ }
            continue
        }
-        if ($line -match '\*\*Last updated\*\*: .*\d{4}-\d{2}-\d{2}') {
+        if ($line -match '(\*\*)?Last updated(\*\*)?: .*\d{4}-\d{2}-\d{2}') {
            $output.Add(($line -replace '\d{4}-\d{2}-\d{2}',$Date.ToString('yyyy-MM-dd')))
            continue
        }
@@ -408,8 +409,9 @@ function Update-SpecificAgent {
        'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
        'vibe'     { Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe' }
        'kimi'     { Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code' }
+        'trae'     { Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae' }
        'generic'  { Write-Info 'Generic agent: no predefined context file. Use the agent-specific update script for your agent.' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic'; return $false }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic'; return $false }
    }
 }

@@ -435,6 +437,7 @@ function Update-AllExistingAgents {
    if (Test-Path $BOB_FILE)      { if (-not (Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob')) { $ok = $false }; $found = $true }
    if (Test-Path $VIBE_FILE)     { if (-not (Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe')) { $ok = $false }; $found = $true }
    if (Test-Path $KIMI_FILE)     { if (-not (Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code')) { $ok = $false }; $found = $true }
+    if (Test-Path $TRAE_FILE)     { if (-not (Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae')) { $ok = $false }; $found = $true }
    if (-not $found) {
        Write-Info 'No existing agent files found, creating default Claude file...'
        if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
--- a/src/specify_cli/init.py
+++ b/src/specify_cli/init.py
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -0,0 +1,428 @@
+"""
+Agent Command Registrar for Spec Kit
+
+Shared infrastructure for registering commands with AI agents.
+Used by both the extension system and the preset system to write
+command files into agent-specific directories in the correct format.
+"""
+
+from pathlib import Path
+from typing import Dict, List, Any
+
+import yaml
+
+
+class CommandRegistrar:
+    """Handles registration of commands with AI agents.
+
+    Supports writing command files in Markdown or TOML format to the
+    appropriate agent directory, with correct argument placeholders
+    and companion files (e.g. Copilot .prompt.md).
+    """
+
+    # Agent configurations with directory, format, and argument placeholder
+    AGENT_CONFIGS = {
+        "claude": {
+            "dir": ".claude/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "gemini": {
+            "dir": ".gemini/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "copilot": {
+            "dir": ".github/agents",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".agent.md"
+        },
+        "cursor": {
+            "dir": ".cursor/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qwen": {
+            "dir": ".qwen/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "opencode": {
+            "dir": ".opencode/command",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codex": {
+            "dir": ".codex/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "windsurf": {
+            "dir": ".windsurf/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kilocode": {
+            "dir": ".kilocode/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "auggie": {
+            "dir": ".augment/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "roo": {
+            "dir": ".roo/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codebuddy": {
+            "dir": ".codebuddy/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qodercli": {
+            "dir": ".qoder/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kiro-cli": {
+            "dir": ".kiro/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "amp": {
+            "dir": ".agents/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "shai": {
+            "dir": ".shai/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "tabnine": {
+            "dir": ".tabnine/agent/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "bob": {
+            "dir": ".bob/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kimi": {
+            "dir": ".kimi/skills",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": "/SKILL.md"
+        },
+        "trae": {
+            "dir": ".trae/rules",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        }
+    }
+
+    @staticmethod
+    def parse_frontmatter(content: str) -> tuple[dict, str]:
+        """Parse YAML frontmatter from Markdown content.
+
+        Args:
+            content: Markdown content with YAML frontmatter
+
+        Returns:
+            Tuple of (frontmatter_dict, body_content)
+        """
+        if not content.startswith("---"):
+            return {}, content
+
+        # Find second ---
+        end_marker = content.find("---", 3)
+        if end_marker == -1:
+            return {}, content
+
+        frontmatter_str = content[3:end_marker].strip()
+        body = content[end_marker + 3:].strip()
+
+        try:
+            frontmatter = yaml.safe_load(frontmatter_str) or {}
+        except yaml.YAMLError:
+            frontmatter = {}
+
+        return frontmatter, body
+
+    @staticmethod
+    def render_frontmatter(fm: dict) -> str:
+        """Render frontmatter dictionary as YAML.
+
+        Args:
+            fm: Frontmatter dictionary
+
+        Returns:
+            YAML-formatted frontmatter with delimiters
+        """
+        if not fm:
+            return ""
+
+        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False)
+        return f"---\n{yaml_str}---\n"
+
+    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+        """Adjust script paths from extension-relative to repo-relative.
+
+        Args:
+            frontmatter: Frontmatter dictionary
+
+        Returns:
+            Modified frontmatter with adjusted paths
+        """
+        if "scripts" in frontmatter:
+            for key in frontmatter["scripts"]:
+                script_path = frontmatter["scripts"][key]
+                if script_path.startswith("../../scripts/"):
+                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
+        return frontmatter
+
+    def render_markdown_command(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str,
+        context_note: str = None
+    ) -> str:
+        """Render command in Markdown format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+            context_note: Custom context comment (default: <!-- Source: {source_id} -->)
+
+        Returns:
+            Formatted Markdown command file content
+        """
+        if context_note is None:
+            context_note = f"\n<!-- Source: {source_id} -->\n"
+        return self.render_frontmatter(frontmatter) + "\n" + context_note + body
+
+    def render_toml_command(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str
+    ) -> str:
+        """Render command in TOML format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+
+        Returns:
+            Formatted TOML command file content
+        """
+        toml_lines = []
+
+        if "description" in frontmatter:
+            desc = frontmatter["description"].replace('"', '\\"')
+            toml_lines.append(f'description = "{desc}"')
+            toml_lines.append("")
+
+        toml_lines.append(f"# Source: {source_id}")
+        toml_lines.append("")
+
+        toml_lines.append('prompt = """')
+        toml_lines.append(body)
+        toml_lines.append('"""')
+
+        return "\n".join(toml_lines)
+
+    def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
+        """Convert argument placeholder format.
+
+        Args:
+            content: Command content
+            from_placeholder: Source placeholder (e.g., "$ARGUMENTS")
+            to_placeholder: Target placeholder (e.g., "{{args}}")
+
+        Returns:
+            Content with converted placeholders
+        """
+        return content.replace(from_placeholder, to_placeholder)
+
+    def register_commands(
+        self,
+        agent_name: str,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> List[str]:
+        """Register commands for a specific agent.
+
+        Args:
+            agent_name: Agent name (claude, gemini, copilot, etc.)
+            commands: List of command info dicts with 'name', 'file', and optional 'aliases'
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            List of registered command names
+
+        Raises:
+            ValueError: If agent is not supported
+        """
+        if agent_name not in self.AGENT_CONFIGS:
+            raise ValueError(f"Unsupported agent: {agent_name}")
+
+        agent_config = self.AGENT_CONFIGS[agent_name]
+        commands_dir = project_root / agent_config["dir"]
+        commands_dir.mkdir(parents=True, exist_ok=True)
+
+        registered = []
+
+        for cmd_info in commands:
+            cmd_name = cmd_info["name"]
+            cmd_file = cmd_info["file"]
+
+            source_file = source_dir / cmd_file
+            if not source_file.exists():
+                continue
+
+            content = source_file.read_text(encoding="utf-8")
+            frontmatter, body = self.parse_frontmatter(content)
+
+            frontmatter = self._adjust_script_paths(frontmatter)
+
+            body = self._convert_argument_placeholder(
+                body, "$ARGUMENTS", agent_config["args"]
+            )
+
+            if agent_config["format"] == "markdown":
+                output = self.render_markdown_command(frontmatter, body, source_id, context_note)
+            elif agent_config["format"] == "toml":
+                output = self.render_toml_command(frontmatter, body, source_id)
+            else:
+                raise ValueError(f"Unsupported format: {agent_config['format']}")
+
+            dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+            dest_file.parent.mkdir(parents=True, exist_ok=True)
+            dest_file.write_text(output, encoding="utf-8")
+
+            if agent_name == "copilot":
+                self.write_copilot_prompt(project_root, cmd_name)
+
+            registered.append(cmd_name)
+
+            for alias in cmd_info.get("aliases", []):
+                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
+                alias_file.parent.mkdir(parents=True, exist_ok=True)
+                alias_file.write_text(output, encoding="utf-8")
+                if agent_name == "copilot":
+                    self.write_copilot_prompt(project_root, alias)
+                registered.append(alias)
+
+        return registered
+
+    @staticmethod
+    def write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
+        """Generate a companion .prompt.md file for a Copilot agent command.
+
+        Args:
+            project_root: Path to project root
+            cmd_name: Command name (e.g. 'speckit.my-ext.example')
+        """
+        prompts_dir = project_root / ".github" / "prompts"
+        prompts_dir.mkdir(parents=True, exist_ok=True)
+        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
+        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n", encoding="utf-8")
+
+    def register_commands_for_all_agents(
+        self,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> Dict[str, List[str]]:
+        """Register commands for all detected agents in the project.
+
+        Args:
+            commands: List of command info dicts
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            Dictionary mapping agent names to list of registered commands
+        """
+        results = {}
+
+        for agent_name, agent_config in self.AGENT_CONFIGS.items():
+            agent_dir = project_root / agent_config["dir"].split("/")[0]
+
+            if agent_dir.exists():
+                try:
+                    registered = self.register_commands(
+                        agent_name, commands, source_id, source_dir, project_root,
+                        context_note=context_note
+                    )
+                    if registered:
+                        results[agent_name] = registered
+                except ValueError:
+                    continue
+
+        return results
+
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories.
+
+        Args:
+            registered_commands: Dict mapping agent names to command name lists
+            project_root: Path to project root
+        """
+        for agent_name, cmd_names in registered_commands.items():
+            if agent_name not in self.AGENT_CONFIGS:
+                continue
+
+            agent_config = self.AGENT_CONFIGS[agent_name]
+            commands_dir = project_root / agent_config["dir"]
+
+            for cmd_name in cmd_names:
+                cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+                if cmd_file.exists():
+                    cmd_file.unlink()
+
+                if agent_name == "copilot":
+                    prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
+                    if prompt_file.exists():
+                        prompt_file.unlink()
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -41,6 +41,26 @@ class CompatibilityError(ExtensionError):
    pass


+def normalize_priority(value: Any, default: int = 10) -> int:
+    """Normalize a stored priority value for sorting and display.
+
+    Corrupted registry data may contain missing, non-numeric, or non-positive
+    values. In those cases, fall back to the default priority.
+
+    Args:
+        value: Priority value to normalize (may be int, str, None, etc.)
+        default: Default priority to use for invalid values (default: 10)
+
+    Returns:
+        Normalized priority as positive integer (>= 1)
+    """
+    try:
+        priority = int(value)
+    except (TypeError, ValueError):
+        return default
+    return priority if priority >= 1 else default
+
+
@dataclass
 class CatalogEntry:
    """Represents a single catalog entry in the catalog stack."""
@@ -251,6 +271,9 @@ class ExtensionRegistry:
            raise KeyError(f"Extension '{extension_id}' is not installed")
        # Merge new metadata with existing, preserving original installed_at
        existing = self.data["extensions"][extension_id]
+        # Handle corrupted registry entries (e.g., string/list instead of dict)
+        if not isinstance(existing, dict):
+            existing = {}
        # Merge: existing fields preserved, new fields override
        merged = {**existing, **metadata}
        # Always preserve original installed_at based on key existence, not truthiness,
@@ -324,6 +347,32 @@ class ExtensionRegistry:
        """
        return extension_id in self.data["extensions"]

+    def list_by_priority(self) -> List[tuple]:
+        """Get all installed extensions sorted by priority.
+
+        Lower priority number = higher precedence (checked first).
+        Extensions with equal priority are sorted alphabetically by ID
+        for deterministic ordering.
+
+        Returns:
+            List of (extension_id, metadata_copy) tuples sorted by priority.
+            Metadata is deep-copied to prevent accidental mutation.
+        """
+        extensions = self.data.get("extensions", {}) or {}
+        if not isinstance(extensions, dict):
+            extensions = {}
+        sortable_extensions = []
+        for ext_id, meta in extensions.items():
+            if not isinstance(meta, dict):
+                continue
+            metadata_copy = copy.deepcopy(meta)
+            metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
+            sortable_extensions.append((ext_id, metadata_copy))
+        return sorted(
+            sortable_extensions,
+            key=lambda item: (item[1]["priority"], item[0]),
+        )
+

 class ExtensionManager:
    """Manages extension lifecycle: installation, removal, updates."""
@@ -440,7 +489,8 @@ class ExtensionManager:
        self,
        source_dir: Path,
        speckit_version: str,
-        register_commands: bool = True
+        register_commands: bool = True,
+        priority: int = 10,
    ) -> ExtensionManifest:
        """Install extension from a local directory.

@@ -448,14 +498,19 @@ class ExtensionManager:
            source_dir: Path to extension directory
            speckit_version: Current spec-kit version
            register_commands: If True, register commands with AI agents
+            priority: Resolution priority (lower = higher precedence, default 10)

        Returns:
            Installed extension manifest

        Raises:
-            ValidationError: If manifest is invalid
+            ValidationError: If manifest is invalid or priority is invalid
            CompatibilityError: If extension is incompatible
        """
+        # Validate priority
+        if priority < 1:
+            raise ValidationError("Priority must be a positive integer (1 or higher)")
+
        # Load and validate manifest
        manifest_path = source_dir / "extension.yml"
        manifest = ExtensionManifest(manifest_path)
@@ -497,6 +552,7 @@ class ExtensionManager:
            "source": "local",
            "manifest_hash": manifest.get_hash(),
            "enabled": True,
+            "priority": priority,
            "registered_commands": registered_commands
        })

@@ -505,21 +561,27 @@ class ExtensionManager:
    def install_from_zip(
        self,
        zip_path: Path,
-        speckit_version: str
+        speckit_version: str,
+        priority: int = 10,
    ) -> ExtensionManifest:
        """Install extension from ZIP file.

        Args:
            zip_path: Path to extension ZIP file
            speckit_version: Current spec-kit version
+            priority: Resolution priority (lower = higher precedence, default 10)

        Returns:
            Installed extension manifest

        Raises:
-            ValidationError: If manifest is invalid
+            ValidationError: If manifest is invalid or priority is invalid
            CompatibilityError: If extension is incompatible
        """
+        # Validate priority early
+        if priority < 1:
+            raise ValidationError("Priority must be a positive integer (1 or higher)")
+
        with tempfile.TemporaryDirectory() as tmpdir:
            temp_path = Path(tmpdir)

@@ -554,7 +616,7 @@ class ExtensionManager:
                raise ValidationError("No extension.yml found in ZIP file")

            # Install from extracted directory
-            return self.install_from_directory(extension_dir, speckit_version)
+            return self.install_from_directory(extension_dir, speckit_version, priority=priority)

    def remove(self, extension_id: str, keep_config: bool = False) -> bool:
        """Remove an installed extension.
@@ -578,23 +640,7 @@ class ExtensionManager:
        # Unregister commands from all AI agents
        if registered_commands:
            registrar = CommandRegistrar()
-            for agent_name, cmd_names in registered_commands.items():
-                if agent_name not in registrar.AGENT_CONFIGS:
-                    continue
-
-                agent_config = registrar.AGENT_CONFIGS[agent_name]
-                commands_dir = self.project_root / agent_config["dir"]
-
-                for cmd_name in cmd_names:
-                    cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
-                    if cmd_file.exists():
-                        cmd_file.unlink()
-
-                    # Also remove companion .prompt.md for Copilot
-                    if agent_name == "copilot":
-                        prompt_file = self.project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
-                        if prompt_file.exists():
-                            prompt_file.unlink()
+            registrar.unregister_commands(registered_commands, self.project_root)

        if keep_config:
            # Preserve config files, only remove non-config files
@@ -648,6 +694,9 @@ class ExtensionManager:
        result = []

        for ext_id, metadata in self.registry.list().items():
+            # Ensure metadata is a dictionary to avoid AttributeError when using .get()
+            if not isinstance(metadata, dict):
+                metadata = {}
            ext_dir = self.extensions_dir / ext_id
            manifest_path = ext_dir / "extension.yml"

@@ -659,6 +708,7 @@ class ExtensionManager:
                    "version": metadata.get("version", "unknown"),
                    "description": manifest.description,
                    "enabled": metadata.get("enabled", True),
+                    "priority": normalize_priority(metadata.get("priority")),
                    "installed_at": metadata.get("installed_at"),
                    "command_count": len(manifest.commands),
                    "hook_count": len(manifest.hooks)
@@ -671,6 +721,7 @@ class ExtensionManager:
                    "version": metadata.get("version", "unknown"),
                    "description": "⚠️ Corrupted extension",
                    "enabled": False,
+                    "priority": normalize_priority(metadata.get("priority")),
                    "installed_at": metadata.get("installed_at"),
                    "command_count": 0,
                    "hook_count": 0
@@ -718,255 +769,47 @@ def version_satisfies(current: str, required: str) -> bool:


 class CommandRegistrar:
-    """Handles registration of extension commands with AI agents."""
+    """Handles registration of extension commands with AI agents.

-    # Agent configurations with directory, format, and argument placeholder
-    AGENT_CONFIGS = {
-        "claude": {
-            "dir": ".claude/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "gemini": {
-            "dir": ".gemini/commands",
-            "format": "toml",
-            "args": "{{args}}",
-            "extension": ".toml"
-        },
-        "copilot": {
-            "dir": ".github/agents",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".agent.md"
-        },
-        "cursor": {
-            "dir": ".cursor/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "qwen": {
-            "dir": ".qwen/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "opencode": {
-            "dir": ".opencode/command",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "codex": {
-            "dir": ".codex/prompts",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "windsurf": {
-            "dir": ".windsurf/workflows",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kilocode": {
-            "dir": ".kilocode/rules",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "auggie": {
-            "dir": ".augment/rules",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "roo": {
-            "dir": ".roo/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "codebuddy": {
-            "dir": ".codebuddy/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "qodercli": {
-            "dir": ".qoder/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kiro-cli": {
-            "dir": ".kiro/prompts",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "amp": {
-            "dir": ".agents/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "shai": {
-            "dir": ".shai/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "tabnine": {
-            "dir": ".tabnine/agent/commands",
-            "format": "toml",
-            "args": "{{args}}",
-            "extension": ".toml"
-        },
-        "bob": {
-            "dir": ".bob/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kimi": {
-            "dir": ".kimi/skills",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": "/SKILL.md"
-        }
-    }
+    This is a backward-compatible wrapper around the shared CommandRegistrar
+    in agents.py. Extension-specific methods accept ExtensionManifest objects
+    and delegate to the generic API.
+    """

+    # Re-export AGENT_CONFIGS at class level for direct attribute access
+    from .agents import CommandRegistrar as _AgentRegistrar
+    AGENT_CONFIGS = _AgentRegistrar.AGENT_CONFIGS
+
+    def __init__(self):
+        from .agents import CommandRegistrar as _Registrar
+        self._registrar = _Registrar()
+
+    # Delegate static/utility methods
    @staticmethod
    def parse_frontmatter(content: str) -> tuple[dict, str]:
-        """Parse YAML frontmatter from Markdown content.
-
-        Args:
-            content: Markdown content with YAML frontmatter
-
-        Returns:
-            Tuple of (frontmatter_dict, body_content)
-        """
-        if not content.startswith("---"):
-            return {}, content
-
-        # Find second ---
-        end_marker = content.find("---", 3)
-        if end_marker == -1:
-            return {}, content
-
-        frontmatter_str = content[3:end_marker].strip()
-        body = content[end_marker + 3:].strip()
-
-        try:
-            frontmatter = yaml.safe_load(frontmatter_str) or {}
-        except yaml.YAMLError:
-            frontmatter = {}
-
-        return frontmatter, body
+        from .agents import CommandRegistrar as _Registrar
+        return _Registrar.parse_frontmatter(content)

    @staticmethod
    def render_frontmatter(fm: dict) -> str:
-        """Render frontmatter dictionary as YAML.
+        from .agents import CommandRegistrar as _Registrar
+        return _Registrar.render_frontmatter(fm)

-        Args:
-            fm: Frontmatter dictionary
+    @staticmethod
+    def _write_copilot_prompt(project_root, cmd_name: str) -> None:
+        from .agents import CommandRegistrar as _Registrar
+        _Registrar.write_copilot_prompt(project_root, cmd_name)

-        Returns:
-            YAML-formatted frontmatter with delimiters
-        """
-        if not fm:
-            return ""
-
-        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False)
-        return f"---\n{yaml_str}---\n"
-
-    def _adjust_script_paths(self, frontmatter: dict) -> dict:
-        """Adjust script paths from extension-relative to repo-relative.
-
-        Args:
-            frontmatter: Frontmatter dictionary
-
-        Returns:
-            Modified frontmatter with adjusted paths
-        """
-        if "scripts" in frontmatter:
-            for key in frontmatter["scripts"]:
-                script_path = frontmatter["scripts"][key]
-                if script_path.startswith("../../scripts/"):
-                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
-        return frontmatter
-
-    def _render_markdown_command(
-        self,
-        frontmatter: dict,
-        body: str,
-        ext_id: str
-    ) -> str:
-        """Render command in Markdown format.
-
-        Args:
-            frontmatter: Command frontmatter
-            body: Command body content
-            ext_id: Extension ID
-
-        Returns:
-            Formatted Markdown command file content
-        """
+    def _render_markdown_command(self, frontmatter, body, ext_id):
+        # Preserve extension-specific comment format for backward compatibility
        context_note = f"\n<!-- Extension: {ext_id} -->\n<!-- Config: .specify/extensions/{ext_id}/ -->\n"
-        return self.render_frontmatter(frontmatter) + "\n" + context_note + body
+        return self._registrar.render_frontmatter(frontmatter) + "\n" + context_note + body

-    def _render_toml_command(
-        self,
-        frontmatter: dict,
-        body: str,
-        ext_id: str
-    ) -> str:
-        """Render command in TOML format.
-
-        Args:
-            frontmatter: Command frontmatter
-            body: Command body content
-            ext_id: Extension ID
-
-        Returns:
-            Formatted TOML command file content
-        """
-        # TOML format for Gemini/Qwen
-        toml_lines = []
-
-        # Add description if present
-        if "description" in frontmatter:
-            # Escape quotes in description
-            desc = frontmatter["description"].replace('"', '\\"')
-            toml_lines.append(f'description = "{desc}"')
-            toml_lines.append("")
-
-        # Add extension context as comments
-        toml_lines.append(f"# Extension: {ext_id}")
-        toml_lines.append(f"# Config: .specify/extensions/{ext_id}/")
-        toml_lines.append("")
-
-        # Add prompt content
-        toml_lines.append('prompt = """')
-        toml_lines.append(body)
-        toml_lines.append('"""')
-
-        return "\n".join(toml_lines)
-
-    def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
-        """Convert argument placeholder format.
-
-        Args:
-            content: Command content
-            from_placeholder: Source placeholder (e.g., "$ARGUMENTS")
-            to_placeholder: Target placeholder (e.g., "{{args}}")
-
-        Returns:
-            Content with converted placeholders
-        """
-        return content.replace(from_placeholder, to_placeholder)
+    def _render_toml_command(self, frontmatter, body, ext_id):
+        # Preserve extension-specific context comments for backward compatibility
+        base = self._registrar.render_toml_command(frontmatter, body, ext_id)
+        context_lines = f"# Extension: {ext_id}\n# Config: .specify/extensions/{ext_id}/\n"
+        return base.rstrip("\n") + "\n" + context_lines

    def register_commands_for_agent(
        self,
@@ -975,96 +818,14 @@ class CommandRegistrar:
        extension_dir: Path,
        project_root: Path
    ) -> List[str]:
-        """Register extension commands for a specific agent.
-
-        Args:
-            agent_name: Agent name (claude, gemini, copilot, etc.)
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            List of registered command names
-
-        Raises:
-            ExtensionError: If agent is not supported
-        """
+        """Register extension commands for a specific agent."""
        if agent_name not in self.AGENT_CONFIGS:
            raise ExtensionError(f"Unsupported agent: {agent_name}")
-
-        agent_config = self.AGENT_CONFIGS[agent_name]
-        commands_dir = project_root / agent_config["dir"]
-        commands_dir.mkdir(parents=True, exist_ok=True)
-
-        registered = []
-
-        for cmd_info in manifest.commands:
-            cmd_name = cmd_info["name"]
-            cmd_file = cmd_info["file"]
-
-            # Read source command file
-            source_file = extension_dir / cmd_file
-            if not source_file.exists():
-                continue
-
-            content = source_file.read_text()
-            frontmatter, body = self.parse_frontmatter(content)
-
-            # Adjust script paths
-            frontmatter = self._adjust_script_paths(frontmatter)
-
-            # Convert argument placeholders
-            body = self._convert_argument_placeholder(
-                body, "$ARGUMENTS", agent_config["args"]
-            )
-
-            # Render in agent-specific format
-            if agent_config["format"] == "markdown":
-                output = self._render_markdown_command(frontmatter, body, manifest.id)
-            elif agent_config["format"] == "toml":
-                output = self._render_toml_command(frontmatter, body, manifest.id)
-            else:
-                raise ExtensionError(f"Unsupported format: {agent_config['format']}")
-
-            # Write command file
-            dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
-            dest_file.parent.mkdir(parents=True, exist_ok=True)
-            dest_file.write_text(output)
-
-            # Generate companion .prompt.md for Copilot agents
-            if agent_name == "copilot":
-                self._write_copilot_prompt(project_root, cmd_name)
-
-            registered.append(cmd_name)
-
-            # Register aliases
-            for alias in cmd_info.get("aliases", []):
-                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
-                alias_file.parent.mkdir(parents=True, exist_ok=True)
-                alias_file.write_text(output)
-                # Generate companion .prompt.md for alias too
-                if agent_name == "copilot":
-                    self._write_copilot_prompt(project_root, alias)
-                registered.append(alias)
-
-        return registered
-
-    @staticmethod
-    def _write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
-        """Generate a companion .prompt.md file for a Copilot agent command.
-
-        Copilot requires a .prompt.md file in .github/prompts/ that references
-        the corresponding .agent.md file in .github/agents/ via an ``agent:``
-        frontmatter field.
-
-        Args:
-            project_root: Path to project root
-            cmd_name: Command name (used as the file stem, e.g. 'speckit.my-ext.example')
-        """
-        prompts_dir = project_root / ".github" / "prompts"
-        prompts_dir.mkdir(parents=True, exist_ok=True)
-        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
-        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n")
+        context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
+        return self._registrar.register_commands(
+            agent_name, manifest.commands, manifest.id, extension_dir, project_root,
+            context_note=context_note
+        )

    def register_commands_for_all_agents(
        self,
@@ -1072,35 +833,20 @@ class CommandRegistrar:
        extension_dir: Path,
        project_root: Path
    ) -> Dict[str, List[str]]:
-        """Register extension commands for all detected agents.
+        """Register extension commands for all detected agents."""
+        context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
+        return self._registrar.register_commands_for_all_agents(
+            manifest.commands, manifest.id, extension_dir, project_root,
+            context_note=context_note
+        )

-        Args:
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            Dictionary mapping agent names to list of registered commands
-        """
-        results = {}
-
-        # Detect which agents are present in the project
-        for agent_name, agent_config in self.AGENT_CONFIGS.items():
-            agent_dir = project_root / agent_config["dir"].split("/")[0]
-
-            # Register if agent directory exists
-            if agent_dir.exists():
-                try:
-                    registered = self.register_commands_for_agent(
-                        agent_name, manifest, extension_dir, project_root
-                    )
-                    if registered:
-                        results[agent_name] = registered
-                except ExtensionError:
-                    # Skip agent on error
-                    continue
-
-        return results
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories."""
+        self._registrar.unregister_commands(registered_commands, project_root)

    def register_commands_for_claude(
        self,
@@ -1108,16 +854,7 @@ class CommandRegistrar:
        extension_dir: Path,
        project_root: Path
    ) -> List[str]:
-        """Register extension commands for Claude Code agent.
-
-        Args:
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            List of registered command names
-        """
+        """Register extension commands for Claude Code agent."""
        return self.register_commands_for_agent("claude", manifest, extension_dir, project_root)


--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
--- a/tests/test_agent_config_consistency.py
+++ b/tests/test_agent_config_consistency.py
@@ -233,3 +233,79 @@ class TestAgentConfigConsistency:
    def test_ai_help_includes_kimi(self):
        """CLI help text for --ai should include kimi."""
        assert "kimi" in AI_ASSISTANT_HELP
+
+    # --- Trae IDE consistency checks ---
+
+    def test_trae_in_agent_config(self):
+        """AGENT_CONFIG should include trae with correct folder and commands_subdir."""
+        assert "trae" in AGENT_CONFIG
+        assert AGENT_CONFIG["trae"]["folder"] == ".trae/"
+        assert AGENT_CONFIG["trae"]["commands_subdir"] == "rules"
+        assert AGENT_CONFIG["trae"]["requires_cli"] is False
+        assert AGENT_CONFIG["trae"]["install_url"] is None
+
+    def test_trae_in_extension_registrar(self):
+        """Extension command registrar should include trae using .trae/rules and markdown, if present."""
+        cfg = CommandRegistrar.AGENT_CONFIGS
+
+        assert "trae" in cfg
+        trae_cfg = cfg["trae"]
+        assert trae_cfg["format"] == "markdown"
+        assert trae_cfg["args"] == "$ARGUMENTS"
+        assert trae_cfg["extension"] == ".md"
+
+    def test_trae_in_release_agent_lists(self):
+        """Bash and PowerShell release scripts should include trae in agent lists."""
+        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
+        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
+
+        sh_match = re.search(r"ALL_AGENTS=\(([^)]*)\)", sh_text)
+        assert sh_match is not None
+        sh_agents = sh_match.group(1).split()
+
+        ps_match = re.search(r"\$AllAgents = @\(([^)]*)\)", ps_text)
+        assert ps_match is not None
+        ps_agents = re.findall(r"'([^']+)'", ps_match.group(1))
+
+        assert "trae" in sh_agents
+        assert "trae" in ps_agents
+
+    def test_trae_in_release_scripts_generate_commands(self):
+        """Release scripts should generate markdown commands for trae in .trae/rules."""
+        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
+        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
+
+        assert ".trae/rules" in sh_text
+        assert ".trae/rules" in ps_text
+        assert re.search(r"'trae'\s*\{.*?\.trae/rules", ps_text, re.S) is not None
+
+    def test_trae_in_github_release_output(self):
+        """GitHub release script should include trae template packages."""
+        gh_release_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-github-release.sh").read_text(encoding="utf-8")
+
+        assert "spec-kit-template-trae-sh-" in gh_release_text
+        assert "spec-kit-template-trae-ps-" in gh_release_text
+
+    def test_trae_in_agent_context_scripts(self):
+        """Agent context scripts should support trae agent type."""
+        bash_text = (REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh").read_text(encoding="utf-8")
+        pwsh_text = (REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1").read_text(encoding="utf-8")
+
+        assert "trae" in bash_text
+        assert "TRAE_FILE" in bash_text
+        assert "trae" in pwsh_text
+        assert "TRAE_FILE" in pwsh_text
+
+    def test_trae_in_powershell_validate_set(self):
+        """PowerShell update-agent-context script should include 'trae' in ValidateSet."""
+        ps_text = (REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1").read_text(encoding="utf-8")
+
+        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
+        assert validate_set_match is not None
+        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
+
+        assert "trae" in validate_set_values
+
+    def test_ai_help_includes_trae(self):
+        """CLI help text for --ai should include trae."""
+        assert "trae" in AI_ASSISTANT_HELP
--- a/tests/test_ai_skills.py
+++ b/tests/test_ai_skills.py
@@ -62,7 +62,7 @@ def templates_dir(project_dir):
    tpl_root.mkdir(parents=True, exist_ok=True)

    # Template with valid YAML frontmatter
-    (tpl_root / "specify.md").write_text(
+    (tpl_root / "speckit.specify.md").write_text(
        "---\n"
        "description: Create or update the feature specification.\n"
        "handoffs:\n"
@@ -79,7 +79,7 @@ def templates_dir(project_dir):
    )

    # Template with minimal frontmatter
-    (tpl_root / "plan.md").write_text(
+    (tpl_root / "speckit.plan.md").write_text(
        "---\n"
        "description: Generate implementation plan.\n"
        "---\n"
@@ -91,7 +91,7 @@ def templates_dir(project_dir):
    )

    # Template with no frontmatter
-    (tpl_root / "tasks.md").write_text(
+    (tpl_root / "speckit.tasks.md").write_text(
        "# Tasks Command\n"
        "\n"
        "Body without frontmatter.\n",
@@ -99,7 +99,7 @@ def templates_dir(project_dir):
    )

    # Template with empty YAML frontmatter (yaml.safe_load returns None)
-    (tpl_root / "empty_fm.md").write_text(
+    (tpl_root / "speckit.empty_fm.md").write_text(
        "---\n"
        "---\n"
        "\n"
@@ -337,7 +337,7 @@ class TestInstallAiSkills:
        cmds_dir = project_dir / ".claude" / "commands"
        cmds_dir.mkdir(parents=True)

-        (cmds_dir / "broken.md").write_text(
+        (cmds_dir / "speckit.broken.md").write_text(
            "---\n"
            "description: [unclosed bracket\n"
            "  invalid: yaml: content: here\n"
@@ -430,9 +430,12 @@ class TestInstallAiSkills:

        # Place .md templates in the agent's commands directory
        agent_folder = AGENT_CONFIG[agent_key]["folder"]
-        cmds_dir = proj / agent_folder.rstrip("/") / "commands"
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
        cmds_dir.mkdir(parents=True)
-        (cmds_dir / "specify.md").write_text(
+        # Copilot uses speckit.*.agent.md templates; other agents use speckit.*.md
+        fname = "speckit.specify.agent.md" if agent_key == "copilot" else "speckit.specify.md"
+        (cmds_dir / fname).write_text(
            "---\ndescription: Test command\n---\n\n# Test\n\nBody.\n"
        )

@@ -448,7 +451,100 @@ class TestInstallAiSkills:
        assert expected_skill_name in skill_dirs
        assert (skills_dir / expected_skill_name / "SKILL.md").exists()

+    def test_copilot_ignores_non_speckit_agents(self, project_dir):
+        """Non-speckit markdown in .github/agents/ must not produce skills."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True, exist_ok=True)
+        (agents_dir / "speckit.plan.agent.md").write_text(
+            "---\ndescription: Generate implementation plan.\n---\n\n# Plan\n\nBody.\n"
+        )
+        (agents_dir / "my-custom-agent.agent.md").write_text(
+            "---\ndescription: A user custom agent\n---\n\n# Custom\n\nBody.\n"
+        )

+        result = install_ai_skills(project_dir, "copilot")
+
+        assert result is True
+        skills_dir = _get_skills_dir(project_dir, "copilot")
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-plan" in skill_dirs
+        assert "speckit-my-custom-agent.agent" not in skill_dirs
+        assert "speckit-my-custom-agent" not in skill_dirs
+
+    @pytest.mark.parametrize("agent_key,custom_file", [
+        ("claude", "review.md"),
+        ("cursor-agent", "deploy.md"),
+        ("qwen", "my-workflow.md"),
+    ])
+    def test_non_speckit_commands_ignored_for_all_agents(self, temp_dir, agent_key, custom_file):
+        """User-authored command files must not produce skills for any agent."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.md").write_text(
+            "---\ndescription: Create spec.\n---\n\n# Specify\n\nBody.\n"
+        )
+        (cmds_dir / custom_file).write_text(
+            "---\ndescription: User custom command\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-specify" in skill_dirs
+        custom_stem = Path(custom_file).stem
+        assert f"speckit-{custom_stem}" not in skill_dirs
+
+    def test_copilot_fallback_when_only_non_speckit_agents(self, project_dir):
+        """Fallback to templates/commands/ when .github/agents/ has no speckit.*.md files."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True, exist_ok=True)
+        # Only a user-authored agent, no speckit.* templates
+        (agents_dir / "my-custom-agent.agent.md").write_text(
+            "---\ndescription: A user custom agent\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(project_dir, "copilot")
+
+        # Should succeed via fallback to templates/commands/
+        assert result is True
+        skills_dir = _get_skills_dir(project_dir, "copilot")
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        # Should have skills from fallback templates, not from the custom agent
+        assert "speckit-plan" in skill_dirs
+        assert not any("my-custom" in d for d in skill_dirs)
+
+    @pytest.mark.parametrize("agent_key", ["claude", "cursor-agent", "qwen"])
+    def test_fallback_when_only_non_speckit_commands(self, temp_dir, agent_key):
+        """Fallback to templates/commands/ when agent dir has no speckit.*.md files."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
+        cmds_dir.mkdir(parents=True)
+        # Only a user-authored command, no speckit.* templates
+        (cmds_dir / "my-custom-command.md").write_text(
+            "---\ndescription: User custom command\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        # Should succeed via fallback to templates/commands/
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert not any("my-custom" in d for d in skill_dirs)

 class TestCommandCoexistence:
    """Verify install_ai_skills never touches command files.
@@ -460,14 +556,16 @@ class TestCommandCoexistence:

    def test_existing_commands_preserved_claude(self, project_dir, templates_dir, commands_dir_claude):
        """install_ai_skills must NOT remove pre-existing .claude/commands files."""
-        # Verify commands exist before
-        assert len(list(commands_dir_claude.glob("speckit.*"))) == 3
+        # Verify commands exist before (templates_dir adds 4 speckit.* files,
+        # commands_dir_claude overlaps with 3 of them)
+        before = list(commands_dir_claude.glob("speckit.*"))
+        assert len(before) >= 3

        install_ai_skills(project_dir, "claude")

        # Commands must still be there — install_ai_skills never touches them
        remaining = list(commands_dir_claude.glob("speckit.*"))
-        assert len(remaining) == 3
+        assert len(remaining) == len(before)

    def test_existing_commands_preserved_gemini(self, project_dir, templates_dir, commands_dir_gemini):
        """install_ai_skills must NOT remove pre-existing .gemini/commands files."""
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -26,6 +26,7 @@ from specify_cli.extensions import (
    ExtensionError,
    ValidationError,
    CompatibilityError,
+    normalize_priority,
    version_satisfies,
 )

@@ -121,6 +122,57 @@ def project_dir(temp_dir):
    return proj_dir


+# ===== normalize_priority Tests =====
+
+class TestNormalizePriority:
+    """Test normalize_priority helper function."""
+
+    def test_valid_integer(self):
+        """Test with valid integer priority."""
+        assert normalize_priority(5) == 5
+        assert normalize_priority(1) == 1
+        assert normalize_priority(100) == 100
+
+    def test_valid_string_number(self):
+        """Test with string that can be converted to int."""
+        assert normalize_priority("5") == 5
+        assert normalize_priority("10") == 10
+
+    def test_zero_returns_default(self):
+        """Test that zero priority returns default."""
+        assert normalize_priority(0) == 10
+        assert normalize_priority(0, default=5) == 5
+
+    def test_negative_returns_default(self):
+        """Test that negative priority returns default."""
+        assert normalize_priority(-1) == 10
+        assert normalize_priority(-100, default=5) == 5
+
+    def test_none_returns_default(self):
+        """Test that None returns default."""
+        assert normalize_priority(None) == 10
+        assert normalize_priority(None, default=5) == 5
+
+    def test_invalid_string_returns_default(self):
+        """Test that non-numeric string returns default."""
+        assert normalize_priority("invalid") == 10
+        assert normalize_priority("abc", default=5) == 5
+
+    def test_float_truncates(self):
+        """Test that float is truncated to int."""
+        assert normalize_priority(5.9) == 5
+        assert normalize_priority(3.1) == 3
+
+    def test_empty_string_returns_default(self):
+        """Test that empty string returns default."""
+        assert normalize_priority("") == 10
+
+    def test_custom_default(self):
+        """Test custom default value."""
+        assert normalize_priority(None, default=20) == 20
+        assert normalize_priority("invalid", default=1) == 1
+
+
 # ===== ExtensionManifest Tests =====

 class TestExtensionManifest:
@@ -2337,3 +2389,404 @@ class TestExtensionUpdateCLI:

        for cmd_file in command_files:
            assert cmd_file.exists(), f"Expected command file to be restored after rollback: {cmd_file}"
+
+
+class TestExtensionListCLI:
+    """Test extension list CLI output format."""
+
+    def test_list_shows_extension_id(self, extension_dir, project_dir):
+        """extension list should display the extension ID."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install the extension using the manager
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "list"])
+
+        assert result.exit_code == 0, result.output
+        # Verify the extension ID is shown in the output
+        assert "test-ext" in result.output
+        # Verify name and version are also shown
+        assert "Test Extension" in result.output
+        assert "1.0.0" in result.output
+
+
+class TestExtensionPriority:
+    """Test extension priority-based resolution."""
+
+    def test_list_by_priority_empty(self, temp_dir):
+        """Test list_by_priority on empty registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        result = registry.list_by_priority()
+
+        assert result == []
+
+    def test_list_by_priority_single(self, temp_dir):
+        """Test list_by_priority with single extension."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("test-ext", {"version": "1.0.0", "priority": 5})
+
+        result = registry.list_by_priority()
+
+        assert len(result) == 1
+        assert result[0][0] == "test-ext"
+        assert result[0][1]["priority"] == 5
+
+    def test_list_by_priority_ordering(self, temp_dir):
+        """Test list_by_priority returns extensions sorted by priority."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        # Add in non-priority order
+        registry.add("ext-low", {"version": "1.0.0", "priority": 20})
+        registry.add("ext-high", {"version": "1.0.0", "priority": 1})
+        registry.add("ext-mid", {"version": "1.0.0", "priority": 10})
+
+        result = registry.list_by_priority()
+
+        assert len(result) == 3
+        # Lower priority number = higher precedence (first)
+        assert result[0][0] == "ext-high"
+        assert result[1][0] == "ext-mid"
+        assert result[2][0] == "ext-low"
+
+    def test_list_by_priority_default(self, temp_dir):
+        """Test list_by_priority uses default priority of 10."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        # Add without explicit priority
+        registry.add("ext-default", {"version": "1.0.0"})
+        registry.add("ext-high", {"version": "1.0.0", "priority": 1})
+        registry.add("ext-low", {"version": "1.0.0", "priority": 20})
+
+        result = registry.list_by_priority()
+
+        assert len(result) == 3
+        # ext-high (1), ext-default (10), ext-low (20)
+        assert result[0][0] == "ext-high"
+        assert result[1][0] == "ext-default"
+        assert result[2][0] == "ext-low"
+
+    def test_list_by_priority_invalid_priority_defaults(self, temp_dir):
+        """Malformed priority values fall back to the default priority."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("ext-high", {"version": "1.0.0", "priority": 1})
+        registry.data["extensions"]["ext-invalid"] = {
+            "version": "1.0.0",
+            "priority": "high",
+        }
+        registry._save()
+
+        result = registry.list_by_priority()
+
+        assert [item[0] for item in result] == ["ext-high", "ext-invalid"]
+        assert result[1][1]["priority"] == 10
+
+    def test_install_with_priority(self, extension_dir, project_dir):
+        """Test that install_from_directory stores priority."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False, priority=5)
+
+        metadata = manager.registry.get("test-ext")
+        assert metadata["priority"] == 5
+
+    def test_install_default_priority(self, extension_dir, project_dir):
+        """Test that install_from_directory uses default priority of 10."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        metadata = manager.registry.get("test-ext")
+        assert metadata["priority"] == 10
+
+    def test_list_installed_includes_priority(self, extension_dir, project_dir):
+        """Test that list_installed includes priority in returned data."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False, priority=3)
+
+        installed = manager.list_installed()
+
+        assert len(installed) == 1
+        assert installed[0]["priority"] == 3
+
+    def test_priority_preserved_on_update(self, temp_dir):
+        """Test that registry update preserves priority."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("test-ext", {"version": "1.0.0", "priority": 5, "enabled": True})
+
+        # Update with new metadata (no priority specified)
+        registry.update("test-ext", {"enabled": False})
+
+        updated = registry.get("test-ext")
+        assert updated["priority"] == 5  # Preserved
+        assert updated["enabled"] is False  # Updated
+
+    def test_resolve_uses_unregistered_extension_dirs_when_registry_partially_corrupted(self, project_dir):
+        """Resolution scans unregistered extension dirs after valid registry entries."""
+        extensions_dir = project_dir / ".specify" / "extensions"
+
+        valid_dir = extensions_dir / "valid-ext" / "templates"
+        valid_dir.mkdir(parents=True)
+        (valid_dir / "other-template.md").write_text("# Valid\n")
+
+        broken_dir = extensions_dir / "broken-ext" / "templates"
+        broken_dir.mkdir(parents=True)
+        (broken_dir / "target-template.md").write_text("# Broken Target\n")
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("valid-ext", {"version": "1.0.0", "priority": 10})
+        registry.data["extensions"]["broken-ext"] = "corrupted"
+        registry._save()
+
+        from specify_cli.presets import PresetResolver
+
+        resolver = PresetResolver(project_dir)
+        resolved = resolver.resolve("target-template")
+        sourced = resolver.resolve_with_source("target-template")
+
+        assert resolved is not None
+        assert resolved.name == "target-template.md"
+        assert "Broken Target" in resolved.read_text()
+        assert sourced is not None
+        assert sourced["source"] == "extension:broken-ext (unregistered)"
+
+
+class TestExtensionPriorityCLI:
+    """Test extension priority CLI integration."""
+
+    def test_add_with_priority_option(self, extension_dir, project_dir):
+        """Test extension add command with --priority option."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, [
+                "extension", "add", str(extension_dir), "--dev", "--priority", "3"
+            ])
+
+        assert result.exit_code == 0, result.output
+
+        manager = ExtensionManager(project_dir)
+        metadata = manager.registry.get("test-ext")
+        assert metadata["priority"] == 3
+
+    def test_list_shows_priority(self, extension_dir, project_dir):
+        """Test extension list shows priority."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install extension with priority
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False, priority=7)
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "list"])
+
+        assert result.exit_code == 0, result.output
+        assert "Priority: 7" in result.output
+
+    def test_set_priority_changes_priority(self, extension_dir, project_dir):
+        """Test set-priority command changes extension priority."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install extension with default priority
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Verify default priority
+        assert manager.registry.get("test-ext")["priority"] == 10
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "test-ext", "5"])
+
+        assert result.exit_code == 0, result.output
+        assert "priority changed: 10 → 5" in result.output
+
+        # Reload registry to see updated value
+        manager2 = ExtensionManager(project_dir)
+        assert manager2.registry.get("test-ext")["priority"] == 5
+
+    def test_set_priority_same_value_no_change(self, extension_dir, project_dir):
+        """Test set-priority with same value shows already set message."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install extension with priority 5
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False, priority=5)
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "test-ext", "5"])
+
+        assert result.exit_code == 0, result.output
+        assert "already has priority 5" in result.output
+
+    def test_set_priority_invalid_value(self, extension_dir, project_dir):
+        """Test set-priority rejects invalid priority values."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install extension
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "test-ext", "0"])
+
+        assert result.exit_code == 1, result.output
+        assert "Priority must be a positive integer" in result.output
+
+    def test_set_priority_not_installed(self, project_dir):
+        """Test set-priority fails for non-installed extension."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Ensure .specify exists
+        (project_dir / ".specify").mkdir(parents=True, exist_ok=True)
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "nonexistent", "5"])
+
+        assert result.exit_code == 1, result.output
+        assert "not installed" in result.output.lower() or "no extensions installed" in result.output.lower()
+
+    def test_set_priority_by_display_name(self, extension_dir, project_dir):
+        """Test set-priority works with extension display name."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install extension
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Use display name "Test Extension" instead of ID "test-ext"
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "Test Extension", "3"])
+
+        assert result.exit_code == 0, result.output
+        assert "priority changed" in result.output
+
+        # Reload registry to see updated value
+        manager2 = ExtensionManager(project_dir)
+        assert manager2.registry.get("test-ext")["priority"] == 3
+
+
+class TestExtensionPriorityBackwardsCompatibility:
+    """Test backwards compatibility for extensions installed before priority feature."""
+
+    def test_legacy_extension_without_priority_field(self, temp_dir):
+        """Extensions installed before priority feature should default to 10."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        # Simulate legacy registry entry without priority field
+        registry = ExtensionRegistry(extensions_dir)
+        registry.data["extensions"]["legacy-ext"] = {
+            "version": "1.0.0",
+            "source": "local",
+            "enabled": True,
+            "installed_at": "2025-01-01T00:00:00Z",
+            # No "priority" field - simulates pre-feature extension
+        }
+        registry._save()
+
+        # Reload registry
+        registry2 = ExtensionRegistry(extensions_dir)
+
+        # list_by_priority should use default of 10
+        result = registry2.list_by_priority()
+        assert len(result) == 1
+        assert result[0][0] == "legacy-ext"
+        # Priority defaults to 10 and is normalized in returned metadata
+        assert result[0][1]["priority"] == 10
+
+    def test_legacy_extension_in_list_installed(self, extension_dir, project_dir):
+        """list_installed returns priority=10 for legacy extensions without priority field."""
+        manager = ExtensionManager(project_dir)
+
+        # Install extension normally
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Manually remove priority to simulate legacy extension
+        ext_data = manager.registry.data["extensions"]["test-ext"]
+        del ext_data["priority"]
+        manager.registry._save()
+
+        # list_installed should still return priority=10
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["priority"] == 10
+
+    def test_mixed_legacy_and_new_extensions_ordering(self, temp_dir):
+        """Legacy extensions (no priority) sort with default=10 among prioritized extensions."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        # Add extension with explicit priority=5
+        registry.add("ext-with-priority", {"version": "1.0.0", "priority": 5})
+
+        # Add legacy extension without priority (manually)
+        registry.data["extensions"]["legacy-ext"] = {
+            "version": "1.0.0",
+            "source": "local",
+            "enabled": True,
+            # No priority field
+        }
+        registry._save()
+
+        # Add extension with priority=15
+        registry.add("ext-low-priority", {"version": "1.0.0", "priority": 15})
+
+        # Reload and check ordering
+        registry2 = ExtensionRegistry(extensions_dir)
+        result = registry2.list_by_priority()
+
+        assert len(result) == 3
+        # Order: ext-with-priority (5), legacy-ext (defaults to 10), ext-low-priority (15)
+        assert result[0][0] == "ext-with-priority"
+        assert result[1][0] == "legacy-ext"
+        assert result[2][0] == "ext-low-priority"
--- a/tests/test_merge.py
+++ b/tests/test_merge.py
@@ -0,0 +1,190 @@
+import stat
+
+from specify_cli import merge_json_files
+from specify_cli import handle_vscode_settings
+
+# --- Dimension 2: Polite Deep Merge Strategy ---
+
+def test_merge_json_files_type_mismatch_preservation(tmp_path):
+    """If user has a string but template wants a dict, PRESERVE user's string."""
+    existing_file = tmp_path / "settings.json"
+    # User might have overridden a setting with a simple string or different type
+    existing_file.write_text('{"chat.editor.fontFamily": "CustomFont"}')
+    
+    # Template might expect a dict for the same key (hypothetically)
+    new_settings = {
+        "chat.editor.fontFamily": {"font": "TemplateFont"}
+    }
+    
+    merged = merge_json_files(existing_file, new_settings)
+    # Result is None because user settings were preserved and nothing else changed
+    assert merged is None
+
+def test_merge_json_files_deep_nesting(tmp_path):
+    """Verify deep recursive merging of new keys."""
+    existing_file = tmp_path / "settings.json"
+    existing_file.write_text("""
+    {
+        "a": {
+            "b": {
+                "c": 1
+            }
+        }
+    }
+    """)
+    
+    new_settings = {
+        "a": {
+            "b": {
+                "d": 2  # New nested key
+            },
+            "e": 3      # New mid-level key
+        }
+    }
+    
+    merged = merge_json_files(existing_file, new_settings)
+    assert merged["a"]["b"]["c"] == 1
+    assert merged["a"]["b"]["d"] == 2
+    assert merged["a"]["e"] == 3
+
+def test_merge_json_files_empty_existing(tmp_path):
+    """Merging into an empty/new file."""
+    existing_file = tmp_path / "empty.json"
+    existing_file.write_text("{}")
+    
+    new_settings = {"a": 1}
+    merged = merge_json_files(existing_file, new_settings)
+    assert merged == {"a": 1}
+
+# --- Dimension 3: Real-world Simulation ---
+
+def test_merge_vscode_realistic_scenario(tmp_path):
+    """A realistic VSCode settings.json with many existing preferences, comments, and trailing commas."""
+    existing_file = tmp_path / "vscode_settings.json"
+    existing_file.write_text("""
+    {
+        "editor.fontSize": 12,
+        "editor.formatOnSave": true, /* block comment */
+        "files.exclude": {
+            "**/.git": true,
+            "**/node_modules": true,
+        },
+        "chat.promptFilesRecommendations": {
+            "existing.tool": true,
+        } // User comment
+    }
+    """)
+    
+    template_settings = {
+        "chat.promptFilesRecommendations": {
+            "speckit.specify": True,
+            "speckit.plan": True
+        },
+        "chat.tools.terminal.autoApprove": {
+            ".specify/scripts/bash/": True
+        }
+    }
+    
+    merged = merge_json_files(existing_file, template_settings)
+    
+    # Check preservation
+    assert merged["editor.fontSize"] == 12
+    assert merged["files.exclude"]["**/.git"] is True
+    assert merged["chat.promptFilesRecommendations"]["existing.tool"] is True
+    
+    # Check additions
+    assert merged["chat.promptFilesRecommendations"]["speckit.specify"] is True
+    assert merged["chat.tools.terminal.autoApprove"][".specify/scripts/bash/"] is True
+
+# --- Dimension 4: Error Handling & Robustness ---
+
+def test_merge_json_files_with_bom(tmp_path):
+    """Test files with UTF-8 BOM (sometimes created on Windows)."""
+    existing_file = tmp_path / "bom.json"
+    content = '{"a": 1}'
+    # Prepend UTF-8 BOM
+    existing_file.write_bytes(b'\xef\xbb\xbf' + content.encode('utf-8'))
+    
+    new_settings = {"b": 2}
+    merged = merge_json_files(existing_file, new_settings)
+    assert merged == {"a": 1, "b": 2}
+
+def test_merge_json_files_not_a_dictionary_template(tmp_path):
+    """If for some reason new_content is not a dict, PRESERVE existing settings by returning None."""
+    existing_file = tmp_path / "ok.json"
+    existing_file.write_text('{"a": 1}')
+    
+    # Secure fallback: return None to skip writing and avoid clobbering
+    assert merge_json_files(existing_file, ["not", "a", "dict"]) is None
+
+def test_merge_json_files_unparseable_existing(tmp_path):
+    """If the existing file is unparseable JSON, return None to avoid overwriting it."""
+    bad_file = tmp_path / "bad.json"
+    bad_file.write_text('{"a": 1, missing_value}') # Invalid JSON
+    
+    assert merge_json_files(bad_file, {"b": 2}) is None
+
+
+def test_merge_json_files_list_preservation(tmp_path):
+    """Verify that existing list values are preserved and NOT merged or overwritten."""
+    existing_file = tmp_path / "list.json"
+    existing_file.write_text('{"my.list": ["user_item"]}')
+    
+    template_settings = {
+        "my.list": ["template_item"]
+    }
+    
+    merged = merge_json_files(existing_file, template_settings)
+    # The polite merge policy says: keep existing values if they exist and aren't both dicts.
+    # Since nothing changed, it returns None.
+    assert merged is None
+
+def test_merge_json_files_no_changes(tmp_path):
+    """If the merge doesn't introduce any new keys or changes, return None to skip rewrite."""
+    existing_file = tmp_path / "no_change.json"
+    existing_file.write_text('{"a": 1, "b": {"c": 2}}')
+    
+    template_settings = {
+        "a": 1,          # Already exists
+        "b": {"c": 2}    # Already exists nested
+    }
+    
+    # Should return None because result == existing
+    assert merge_json_files(existing_file, template_settings) is None
+
+def test_merge_json_files_type_mismatch_no_op(tmp_path):
+    """If a key exists with different type and we preserve it, it might still result in no change."""
+    existing_file = tmp_path / "mismatch_no_op.json"
+    existing_file.write_text('{"a": "user_string"}')
+    
+    template_settings = {
+        "a": {"key": "template_dict"} # Mismatch, will be ignored
+    }
+    
+    # Should return None because we preserved the user's string and nothing else changed
+    assert merge_json_files(existing_file, template_settings) is None
+
+
+def test_handle_vscode_settings_preserves_mode_on_atomic_write(tmp_path):
+    """Atomic rewrite should preserve existing file mode bits."""
+    vscode_dir = tmp_path / ".vscode"
+    vscode_dir.mkdir()
+    dest_file = vscode_dir / "settings.json"
+    template_file = tmp_path / "template_settings.json"
+
+    dest_file.write_text('{"a": 1}\n', encoding="utf-8")
+    dest_file.chmod(0o640)
+    before_mode = stat.S_IMODE(dest_file.stat().st_mode)
+
+    template_file.write_text('{"b": 2}\n', encoding="utf-8")
+
+    handle_vscode_settings(
+        template_file,
+        dest_file,
+        "settings.json",
+        verbose=False,
+        tracker=None,
+    )
+
+    after_mode = stat.S_IMODE(dest_file.stat().st_mode)
+    assert after_mode == before_mode
--- a/tests/test_presets.py
+++ b/tests/test_presets.py