Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
chore: bump version to 0.3.0
2026-03-17 19:03:08 +00:00 · 2026-03-13 15:14:46 -05:00 · 2026-03-13 20:11:58 +00:00
25 changed files with 191 additions and 2006 deletions
--- a/.github/workflows/scripts/create-github-release.sh
+++ b/.github/workflows/scripts/create-github-release.sh
@@ -58,8 +58,6 @@ 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, trae, 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, generic

 .PARAMETER Scripts
    Comma or space separated subset of script types to build (default: both)
@@ -454,11 +454,6 @@ 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
@@ -475,7 +470,7 @@ function Build-Variant {
 }

 # Define all agents and scripts
-$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'trae', 'generic')
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', '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 trae 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 generic (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -291,9 +291,6 @@ build_variant() {
    kimi)
      mkdir -p "$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" ;;
@@ -303,7 +300,7 @@ 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 trae 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 generic)
 ALL_SCRIPTS=(sh ps)

 norm_list() {
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -46,7 +46,6 @@ 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
@@ -7,26 +7,6 @@ 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 skills (#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)
-
-
 ## [0.3.0] - 2026-03-13

 ### Changed
@@ -55,7 +35,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

 ### 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`
--- a/README.md
+++ b/README.md
@@ -158,10 +158,6 @@ 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                                                                                                                                     |
@@ -188,7 +184,6 @@ 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
@@ -72,17 +72,12 @@ 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
@@ -359,15 +359,12 @@ specify extension add jira
      "installed_at": "2026-01-28T14:30:00Z",
      "source": "catalog",
      "manifest_hash": "sha256:abc123...",
-      "enabled": true,
-      "priority": 10
+      "enabled": true
    }
  }
 }
 ```

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

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

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

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

 **Options:**

- `--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)
+- `--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)

 #### `specify extension remove NAME`

@@ -1286,29 +1280,6 @@ $ 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
@@ -1,39 +1,8 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-03-16T00:00:00Z",
+  "updated_at": "2026-03-13T12:00:00Z",
  "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",
@@ -105,92 +74,6 @@
      "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",
@@ -241,12 +124,7 @@
        "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,
@@ -313,49 +191,13 @@
        "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",
@@ -407,15 +249,7 @@
        "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,
@@ -457,7 +291,7 @@
    "understanding": {
      "name": "Understanding",
      "id": "understanding",
-      "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.",
+      "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.",
      "author": "Ladislav Bihari",
      "version": "3.4.0",
      "download_url": "https://github.com/Testimonial/understanding/archive/refs/tags/v3.4.0.zip",
@@ -495,38 +329,6 @@
      "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/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.3.1"
+version = "0.3.0"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -14,7 +14,6 @@ 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
@@ -168,7 +168,7 @@ if $JSON_MODE; then
        if [[ ${#docs[@]} -eq 0 ]]; then
            json_docs="[]"
        else
-            json_docs=$(for d in "${docs[@]}"; do printf '"%s",' "$(json_escape "$d")"; done)
+            json_docs=$(printf '"%s",' "${docs[@]}")
            json_docs="[${json_docs%,}]"
        fi
        printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -161,7 +161,7 @@ has_jq() {
 }

 # 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).
+# Handles backslash, double-quote, and control characters (newline, tab, carriage return).
 json_escape() {
    local s="$1"
    s="${s//\\/\\\\}"
@@ -169,10 +169,6 @@ json_escape() {
    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"
 }

@@ -198,11 +194,9 @@ resolve_template() {
    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="$registry_file" python3 -c "
+            # Read preset IDs sorted by priority (lower number = higher precedence)
+            local sorted_presets
+            sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
 import json, sys, os
 try:
    with open(os.environ['SPECKIT_REGISTRY']) as f:
@@ -212,17 +206,14 @@ try:
        print(pid)
 except Exception:
    sys.exit(1)
-" 2>/dev/null); then
-                if [ -n "$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
+" 2>/dev/null)
+            if [ $? -eq 0 ] && [ -n "$sorted_presets" ]; then
+                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"
            else
-                # python3 failed (missing, or registry parse error) — fall back to unordered directory scan
+                # python3 returned empty list — fall through to directory scan
                for preset in "$presets_dir"/*/; do
                    [ -d "$preset" ] || continue
                    local candidate="$preset/templates/${template_name}.md"
@@ -255,9 +246,8 @@ except Exception:
    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=$(resolve_template ...) || true
-    return 1
+    # Return success with empty output so callers using set -e don't abort;
+    # callers check [ -n "$TEMPLATE" ] to detect "not found".
+    return 0
 }

--- 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 >/dev/null 2>&1 || true
+    git fetch --all --prune 2>/dev/null || true

    # Get highest number from ALL branches (not just matching short name)
    local highest_branch=$(get_highest_from_branches)
@@ -162,6 +162,17 @@ clean_branch_name() {
    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }

+# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
+json_escape() {
+    local s="$1"
+    s="${s//\\/\\\\}"
+    s="${s//\"/\\\"}"
+    s="${s//$'\n'/\\n}"
+    s="${s//$'\t'/\\t}"
+    s="${s//$'\r'/\\r}"
+    printf '%s' "$s"
+}
+
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
@@ -297,14 +308,9 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"

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

 # Inform the user how to persist the feature variable in their own shell
 printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2
--- a/scripts/bash/setup-plan.sh
+++ b/scripts/bash/setup-plan.sh
@@ -39,7 +39,7 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 mkdir -p "$FEATURE_DIR"

 # Copy plan template if it exists
-TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
+TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT")
 if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
    cp "$TEMPLATE" "$IMPL_PLAN"
    echo "Copied plan template to $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|trae|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|generic
 # Leave empty to update all existing agent files

 set -e
@@ -83,7 +83,6 @@ AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
 BOB_FILE="$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="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -676,82 +675,67 @@ update_specific_agent() {
        kimi)
            update_agent_file "$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|trae|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|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() {
-    _found_agent=false
-    _updated_paths=()
-    local _all_ok=true
+    local found_agent=false
+    local _updated_paths=()

-    _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
+    # 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.
+    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
+        update_agent_file "$file" "$name" || return 1
+        _updated_paths+=("$real_path")
+        found_agent=true
+    }
+
+    update_if_new "$CLAUDE_FILE" "Claude Code"
+    update_if_new "$GEMINI_FILE" "Gemini CLI"
+    update_if_new "$COPILOT_FILE" "GitHub Copilot"
+    update_if_new "$CURSOR_FILE" "Cursor IDE"
+    update_if_new "$QWEN_FILE" "Qwen Code"
+    update_if_new "$AGENTS_FILE" "Codex/opencode"
+    update_if_new "$AMP_FILE" "Amp"
+    update_if_new "$KIRO_FILE" "Kiro CLI"
+    update_if_new "$BOB_FILE" "IBM Bob"
+    update_if_new "$WINDSURF_FILE" "Windsurf"
+    update_if_new "$KILOCODE_FILE" "Kilo Code"
+    update_if_new "$AUGGIE_FILE" "Auggie CLI"
+    update_if_new "$ROO_FILE" "Roo Code"
+    update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"
+    update_if_new "$SHAI_FILE" "SHAI"
+    update_if_new "$TABNINE_FILE" "Tabnine CLI"
+    update_if_new "$QODER_FILE" "Qoder CLI"
+    update_if_new "$AGY_FILE" "Antigravity"
+    update_if_new "$VIBE_FILE" "Mistral Vibe"
+    update_if_new "$KIMI_FILE" "Kimi Code"

    # 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 "$CLAUDE_FILE" "Claude Code" || return 1
    fi
-
-    [[ "$_all_ok" == true ]]
 }
 print_summary() {
    echo
@@ -770,7 +754,7 @@ 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|trae|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|generic]"
 }

 #==============================================================================
--- 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, trae, 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, 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','trae','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','generic')]
    [string]$AgentType
 )

@@ -64,7 +64,6 @@ $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'

@@ -409,9 +408,8 @@ 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|trae|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|generic'; return $false }
    }
 }

@@ -437,7 +435,6 @@ 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
@@ -7,7 +7,6 @@
 #     "platformdirs",
 #     "readchar",
 #     "httpx",
-#     "json5",
 # ]
 # ///
 """
@@ -33,8 +32,6 @@ import tempfile
 import shutil
 import shlex
 import json
-import json5
-import stat
 import yaml
 from pathlib import Path
 from typing import Any, Optional, Tuple
@@ -275,13 +272,6 @@ AGENT_CONFIG = {
        "install_url": "https://code.kimi.com/",
        "requires_cli": True,
    },
-    "trae": {
-        "name": "Trae",
-        "folder": ".trae/",
-        "commands_subdir": "rules",  # Trae uses .trae/rules/ for project rules
-        "install_url": None,  # IDE-based
-        "requires_cli": False,
-    },
    "generic": {
        "name": "Generic (bring your own agent)",
        "folder": None,  # Set dynamically via --ai-commands-dir
@@ -664,82 +654,37 @@ def init_git_repo(project_path: Path, quiet: bool = False) -> Tuple[bool, Option
        os.chdir(original_cwd)

 def handle_vscode_settings(sub_item, dest_file, rel_path, verbose=False, tracker=None) -> None:
-    """Handle merging or copying of .vscode/settings.json files.
-
-    Note: when merge produces changes, rewritten output is normalized JSON and
-    existing JSONC comments/trailing commas are not preserved.
-    """
+    """Handle merging or copying of .vscode/settings.json files."""
    def log(message, color="green"):
        if verbose and not tracker:
            console.print(f"[{color}]{message}[/] {rel_path}")

-    def atomic_write_json(target_file: Path, payload: dict[str, Any]) -> None:
-        """Atomically write JSON while preserving existing mode bits when possible."""
-        temp_path: Optional[Path] = None
-        try:
-            with tempfile.NamedTemporaryFile(
-                mode='w',
-                encoding='utf-8',
-                dir=target_file.parent,
-                prefix=f"{target_file.name}.",
-                suffix=".tmp",
-                delete=False,
-            ) as f:
-                temp_path = Path(f.name)
-                json.dump(payload, f, indent=4)
-                f.write('\n')
-
-            if target_file.exists():
-                try:
-                    existing_stat = target_file.stat()
-                    os.chmod(temp_path, stat.S_IMODE(existing_stat.st_mode))
-                    if hasattr(os, "chown"):
-                        try:
-                            os.chown(temp_path, existing_stat.st_uid, existing_stat.st_gid)
-                        except PermissionError:
-                            # Best-effort owner/group preservation without requiring elevated privileges.
-                            pass
-                except OSError:
-                    # Best-effort metadata preservation; data safety is prioritized.
-                    pass
-
-            os.replace(temp_path, target_file)
-        except Exception:
-            if temp_path and temp_path.exists():
-                temp_path.unlink()
-            raise
-
    try:
        with open(sub_item, 'r', encoding='utf-8') as f:
-            # json5 natively supports comments and trailing commas (JSONC)
-            new_settings = json5.load(f)
+            new_settings = json.load(f)

        if dest_file.exists():
            merged = merge_json_files(dest_file, new_settings, verbose=verbose and not tracker)
-            if merged is not None:
-                atomic_write_json(dest_file, merged)
-                log("Merged:", "green")
-                log("Note: comments/trailing commas are normalized when rewritten", "yellow")
-            else:
-                log("Skipped merge (preserved existing settings)", "yellow")
+            with open(dest_file, 'w', encoding='utf-8') as f:
+                json.dump(merged, f, indent=4)
+                f.write('\n')
+            log("Merged:", "green")
        else:
            shutil.copy2(sub_item, dest_file)
            log("Copied (no existing settings.json):", "blue")

    except Exception as e:
-        log(f"Warning: Could not merge settings: {e}", "yellow")
-        if not dest_file.exists():
-            shutil.copy2(sub_item, dest_file)
+        log(f"Warning: Could not merge, copying instead: {e}", "yellow")
+        shutil.copy2(sub_item, dest_file)

-
-def merge_json_files(existing_path: Path, new_content: Any, verbose: bool = False) -> Optional[dict[str, Any]]:
+def merge_json_files(existing_path: Path, new_content: dict, verbose: bool = False) -> dict:
    """Merge new JSON content into existing JSON file.

-    Performs a polite deep merge where:
+    Performs a deep merge where:
    - New keys are added
-    - Existing keys are preserved (not overwritten) unless both values are dictionaries
-    - Nested dictionaries are merged recursively only when both sides are dictionaries
-    - Lists and other values are preserved from base if they exist
+    - Existing keys are preserved unless overwritten by new content
+    - Nested dictionaries are merged recursively
+    - Lists and other values are replaced (not merged)

    Args:
        existing_path: Path to existing JSON file
@@ -747,64 +692,28 @@ def merge_json_files(existing_path: Path, new_content: Any, verbose: bool = Fals
        verbose: Whether to print merge details

    Returns:
-        Merged JSON content as dict, or None if the existing file should be left untouched.
+        Merged JSON content as dict
    """
-    # Load existing content first to have a safe fallback
-    existing_content = None
-    exists = existing_path.exists()
-
-    if exists:
-        try:
-            with open(existing_path, 'r', encoding='utf-8') as f:
-                # Handle comments (JSONC) natively with json5
-                # Note: json5 handles BOM automatically
-                existing_content = json5.load(f)
-        except FileNotFoundError:
-            # Handle race condition where file is deleted after exists() check
-            exists = False
-        except Exception as e:
-            if verbose:
-                console.print(f"[yellow]Warning: Could not read or parse existing JSON in {existing_path.name} ({e}).[/yellow]")
-            # Skip merge to preserve existing file if unparseable or inaccessible (e.g. PermissionError)
-            return None
-
-    # Validate template content
-    if not isinstance(new_content, dict):
-        if verbose:
-            console.print(f"[yellow]Warning: Template content for {existing_path.name} is not a dictionary. Preserving existing settings.[/yellow]")
-        return None
-
-    if not exists:
+    try:
+        with open(existing_path, 'r', encoding='utf-8') as f:
+            existing_content = json.load(f)
+    except (FileNotFoundError, json.JSONDecodeError):
+        # If file doesn't exist or is invalid, just use new content
        return new_content

-    # If existing content parsed but is not a dict, skip merge to avoid data loss
-    if not isinstance(existing_content, dict):
-        if verbose:
-            console.print(f"[yellow]Warning: Existing JSON in {existing_path.name} is not an object. Skipping merge to avoid data loss.[/yellow]")
-        return None
-
-    def deep_merge_polite(base: dict[str, Any], update: dict[str, Any]) -> dict[str, Any]:
-        """Recursively merge update dict into base dict, preserving base values."""
+    def deep_merge(base: dict, update: dict) -> dict:
+        """Recursively merge update dict into base dict."""
        result = base.copy()
        for key, value in update.items():
-            if key not in result:
-                # Add new key
-                result[key] = value
-            elif isinstance(result[key], dict) and isinstance(value, dict):
+            if key in result and isinstance(result[key], dict) and isinstance(value, dict):
                # Recursively merge nested dictionaries
-                result[key] = deep_merge_polite(result[key], value)
+                result[key] = deep_merge(result[key], value)
            else:
-                # Key already exists and values are not both dicts; preserve existing value.
-                # This ensures user settings aren't overwritten by template defaults.
-                pass
+                # Add new key or replace existing value
+                result[key] = value
        return result

-    merged = deep_merge_polite(existing_content, new_content)
-
-    # Detect if anything actually changed. If not, return None so the caller
-    # can skip rewriting the file (preserving user's comments/formatting).
-    if merged == existing_content:
-        return None
+    merged = deep_merge(existing_content, new_content)

    if verbose:
        console.print(f"[cyan]Merged JSON file:[/cyan] {existing_path.name}")
@@ -1256,12 +1165,7 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
    else:
        templates_dir = project_path / commands_subdir

-    # Only consider speckit.*.md templates so that user-authored command
-    # files (e.g. custom slash commands, agent files) coexisting in the
-    # same commands directory are not incorrectly converted into skills.
-    template_glob = "speckit.*.md"
-
-    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
+    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
        # Fallback: try the repo-relative path (for running from source checkout)
        # This also covers agents whose extracted commands are in a different
        # format (e.g. gemini/tabnine use .toml, not .md).
@@ -1269,16 +1173,15 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
        fallback_dir = script_dir / "templates" / "commands"
        if fallback_dir.exists() and any(fallback_dir.glob("*.md")):
            templates_dir = fallback_dir
-            template_glob = "*.md"

-    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
+    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
        if tracker:
            tracker.error("ai-skills", "command templates not found")
        else:
            console.print("[yellow]Warning: command templates not found, skipping skills installation[/yellow]")
        return False

-    command_files = sorted(templates_dir.glob(template_glob))
+    command_files = sorted(templates_dir.glob("*.md"))
    if not command_files:
        if tracker:
            tracker.skip("ai-skills", "no command templates found")
@@ -1317,14 +1220,11 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
                body = content

            command_name = command_file.stem
-            # Normalize: extracted commands may be named "speckit.<cmd>.md"
-            # or "speckit.<cmd>.agent.md"; strip the "speckit." prefix and
-            # any trailing ".agent" suffix so skill names stay clean and
+            # Normalize: extracted commands may be named "speckit.<cmd>.md";
+            # strip the "speckit." prefix so skill names stay clean and
            # SKILL_DESCRIPTIONS lookups work.
            if command_name.startswith("speckit."):
                command_name = command_name[len("speckit."):]
-            if command_name.endswith(".agent"):
-                command_name = command_name[:-len(".agent")]
            # Kimi CLI discovers skills by directory name and invokes them as
            # /skill:<name> — use dot separator to match packaging convention.
            if selected_ai == "kimi":
@@ -1349,8 +1249,6 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
            source_name = command_file.name
            if source_name.startswith("speckit."):
                source_name = source_name[len("speckit."):]
-            if source_name.endswith(".agent.md"):
-                source_name = source_name[:-len(".agent.md")] + ".md"

            frontmatter_data = {
                "name": skill_name,
@@ -2102,11 +2000,6 @@ def preset_add(
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

-    # Validate priority
-    if priority < 1:
-        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
-        raise typer.Exit(1)
-
    manager = PresetManager(project_root)
    speckit_version = get_speckit_version()

@@ -2284,7 +2177,6 @@ def preset_info(
    pack_id: str = typer.Argument(..., help="Preset ID to get info about"),
 ):
    """Show detailed information about a preset."""
-    from .extensions import normalize_priority
    from .presets import PresetCatalog, PresetManager, PresetError

    project_root = Path.cwd()
@@ -2318,10 +2210,6 @@ def preset_info(
        if license_val:
            console.print(f"  License:     {license_val}")
        console.print("\n  [green]Status: installed[/green]")
-        # Get priority from registry
-        pack_metadata = manager.registry.get(pack_id)
-        priority = normalize_priority(pack_metadata.get("priority") if isinstance(pack_metadata, dict) else None)
-        console.print(f"  [dim]Priority:[/dim] {priority}")
        console.print()
        return

@@ -2353,58 +2241,6 @@ def preset_info(
    console.print()


-@preset_app.command("set-priority")
-def preset_set_priority(
-    pack_id: str = typer.Argument(help="Preset ID"),
-    priority: int = typer.Argument(help="New priority (lower = higher precedence)"),
-):
-    """Set the resolution priority of an installed preset."""
-    from .presets import PresetManager
-
-    project_root = Path.cwd()
-
-    # Check if we're in a spec-kit project
-    specify_dir = project_root / ".specify"
-    if not specify_dir.exists():
-        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
-        console.print("Run this command from a spec-kit project root")
-        raise typer.Exit(1)
-
-    # Validate priority
-    if priority < 1:
-        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
-        raise typer.Exit(1)
-
-    manager = PresetManager(project_root)
-
-    # Check if preset is installed
-    if not manager.registry.is_installed(pack_id):
-        console.print(f"[red]Error:[/red] Preset '{pack_id}' is not installed")
-        raise typer.Exit(1)
-
-    # Get current metadata
-    metadata = manager.registry.get(pack_id)
-    if metadata is None or not isinstance(metadata, dict):
-        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
-        raise typer.Exit(1)
-
-    from .extensions import normalize_priority
-    raw_priority = metadata.get("priority")
-    # Only skip if the stored value is already a valid int equal to requested priority
-    # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
-        console.print(f"[yellow]Preset '{pack_id}' already has priority {priority}[/yellow]")
-        raise typer.Exit(0)
-
-    old_priority = normalize_priority(raw_priority)
-
-    # Update priority
-    manager.registry.update(pack_id, {"priority": priority})
-
-    console.print(f"[green]✓[/green] Preset '{pack_id}' priority changed: {old_priority} → {priority}")
-    console.print("\n[dim]Lower priority = higher precedence in template resolution[/dim]")
-
-
 # ===== Preset Catalog Commands =====


@@ -2740,9 +2576,8 @@ def extension_list(
            status_color = "green" if ext["enabled"] else "red"

            console.print(f"  [{status_color}]{status_icon}[/{status_color}] [bold]{ext['name']}[/bold] (v{ext['version']})")
-            console.print(f"     [dim]{ext['id']}[/dim]")
            console.print(f"     {ext['description']}")
-            console.print(f"     Commands: {ext['command_count']} | Hooks: {ext['hook_count']} | Priority: {ext['priority']} | Status: {'Enabled' if ext['enabled'] else 'Disabled'}")
+            console.print(f"     Commands: {ext['command_count']} | Hooks: {ext['hook_count']} | Status: {'Enabled' if ext['enabled'] else 'Disabled'}")
            console.print()

    if available or all_extensions:
@@ -2930,7 +2765,6 @@ def extension_add(
    extension: str = typer.Argument(help="Extension name or path"),
    dev: bool = typer.Option(False, "--dev", help="Install from local directory"),
    from_url: Optional[str] = typer.Option(None, "--from", help="Install from custom URL"),
-    priority: int = typer.Option(10, "--priority", help="Resolution priority (lower = higher precedence, default 10)"),
 ):
    """Install an extension."""
    from .extensions import ExtensionManager, ExtensionCatalog, ExtensionError, ValidationError, CompatibilityError
@@ -2944,11 +2778,6 @@ def extension_add(
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

-    # Validate priority
-    if priority < 1:
-        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
-        raise typer.Exit(1)
-
    manager = ExtensionManager(project_root)
    speckit_version = get_speckit_version()

@@ -2965,7 +2794,7 @@ def extension_add(
                    console.print(f"[red]Error:[/red] No extension.yml found in {source_path}")
                    raise typer.Exit(1)

-                manifest = manager.install_from_directory(source_path, speckit_version, priority=priority)
+                manifest = manager.install_from_directory(source_path, speckit_version)

            elif from_url:
                # Install from URL (ZIP file)
@@ -2998,7 +2827,7 @@ def extension_add(
                    zip_path.write_bytes(zip_data)

                    # Install from downloaded ZIP
-                    manifest = manager.install_from_zip(zip_path, speckit_version, priority=priority)
+                    manifest = manager.install_from_zip(zip_path, speckit_version)
                except urllib.error.URLError as e:
                    console.print(f"[red]Error:[/red] Failed to download from {from_url}: {e}")
                    raise typer.Exit(1)
@@ -3042,7 +2871,7 @@ def extension_add(

                try:
                    # Install from downloaded ZIP
-                    manifest = manager.install_from_zip(zip_path, speckit_version, priority=priority)
+                    manifest = manager.install_from_zip(zip_path, speckit_version)
                finally:
                    # Clean up downloaded ZIP
                    if zip_path.exists():
@@ -3218,7 +3047,7 @@ def extension_info(
    extension: str = typer.Argument(help="Extension ID or name"),
 ):
    """Show detailed information about an extension."""
-    from .extensions import ExtensionCatalog, ExtensionManager, normalize_priority
+    from .extensions import ExtensionCatalog, ExtensionManager

    project_root = Path.cwd()

@@ -3255,15 +3084,8 @@ def extension_info(
        # Get local manifest info
        ext_manifest = manager.get_extension(resolved_installed_id)
        metadata = manager.registry.get(resolved_installed_id)
-        metadata_is_dict = isinstance(metadata, dict)
-        if not metadata_is_dict:
-            console.print(
-                "[yellow]Warning:[/yellow] Extension metadata appears to be corrupted; "
-                "some information may be unavailable."
-            )
-        version = metadata.get("version", "unknown") if metadata_is_dict else "unknown"

-        console.print(f"\n[bold]{resolved_installed_name}[/bold] (v{version})")
+        console.print(f"\n[bold]{resolved_installed_name}[/bold] (v{metadata.get('version', 'unknown')})")
        console.print(f"ID: {resolved_installed_id}")
        console.print()

@@ -3291,8 +3113,6 @@ def extension_info(

        console.print()
        console.print("[green]✓ Installed[/green]")
-        priority = normalize_priority(metadata.get("priority") if metadata_is_dict else None)
-        console.print(f"[dim]Priority:[/dim] {priority}")
        console.print(f"\nTo remove: specify extension remove {resolved_installed_id}")
        return

@@ -3308,8 +3128,6 @@ def extension_info(

 def _print_extension_info(ext_info: dict, manager):
    """Print formatted extension info from catalog data."""
-    from .extensions import normalize_priority
-
    # Header
    verified_badge = " [green]✓ Verified[/green]" if ext_info.get("verified") else ""
    console.print(f"\n[bold]{ext_info['name']}[/bold] (v{ext_info['version']}){verified_badge}")
@@ -3388,9 +3206,6 @@ def _print_extension_info(ext_info: dict, manager):
    install_allowed = ext_info.get("_install_allowed", True)
    if is_installed:
        console.print("[green]✓ Installed[/green]")
-        metadata = manager.registry.get(ext_info['id'])
-        priority = normalize_priority(metadata.get("priority") if isinstance(metadata, dict) else None)
-        console.print(f"[dim]Priority:[/dim] {priority}")
        console.print(f"\nTo remove: specify extension remove {ext_info['id']}")
    elif install_allowed:
        console.print("[yellow]Not installed[/yellow]")
@@ -3417,7 +3232,6 @@ def extension_update(
        ValidationError,
        CommandRegistrar,
        HookExecutor,
-        normalize_priority,
    )
    from packaging import version as pkg_version
    import shutil
@@ -3457,7 +3271,7 @@ def extension_update(
        for ext_id in extensions_to_update:
            # Get installed version
            metadata = manager.registry.get(ext_id)
-            if metadata is None or not isinstance(metadata, dict) or "version" not in metadata:
+            if metadata is None or "version" not in metadata:
                console.print(f"⚠  {ext_id}: Registry entry corrupted or missing (skipping)")
                continue
            try:
@@ -3642,13 +3456,13 @@ def extension_update(
                                shutil.copy2(cfg_file, new_extension_dir / cfg_file.name)

                    # 9. Restore metadata from backup (installed_at, enabled state)
-                    if backup_registry_entry and isinstance(backup_registry_entry, dict):
+                    if backup_registry_entry:
                        # Copy current registry entry to avoid mutating internal
                        # registry state before explicit restore().
                        current_metadata = manager.registry.get(extension_id)
-                        if current_metadata is None or not isinstance(current_metadata, dict):
+                        if current_metadata is None:
                            raise RuntimeError(
-                                f"Registry entry for '{extension_id}' missing or corrupted after install — update incomplete"
+                                f"Registry entry for '{extension_id}' missing after install — update incomplete"
                            )
                        new_metadata = dict(current_metadata)

@@ -3656,10 +3470,6 @@ def extension_update(
                        if "installed_at" in backup_registry_entry:
                            new_metadata["installed_at"] = backup_registry_entry["installed_at"]

-                        # Preserve the original priority (normalized to handle corruption)
-                        if "priority" in backup_registry_entry:
-                            new_metadata["priority"] = normalize_priority(backup_registry_entry["priority"])
-
                        # If extension was disabled before update, disable it again
                        if not backup_registry_entry.get("enabled", True):
                            new_metadata["enabled"] = False
@@ -3713,7 +3523,7 @@ def extension_update(
                    # (files that weren't in the original backup)
                    try:
                        new_registry_entry = manager.registry.get(extension_id)
-                        if new_registry_entry is None or not isinstance(new_registry_entry, dict):
+                        if new_registry_entry is None:
                            new_registered_commands = {}
                        else:
                            new_registered_commands = new_registry_entry.get("registered_commands", {})
@@ -3833,10 +3643,10 @@ def extension_enable(

    # Update registry
    metadata = manager.registry.get(extension_id)
-    if metadata is None or not isinstance(metadata, dict):
+    if metadata is None:
        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)
-
+    
    if metadata.get("enabled", True):
        console.print(f"[yellow]Extension '{display_name}' is already enabled[/yellow]")
        raise typer.Exit(0)
@@ -3881,10 +3691,10 @@ def extension_disable(

    # Update registry
    metadata = manager.registry.get(extension_id)
-    if metadata is None or not isinstance(metadata, dict):
+    if metadata is None:
        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)
-
+    
    if not metadata.get("enabled", True):
        console.print(f"[yellow]Extension '{display_name}' is already disabled[/yellow]")
        raise typer.Exit(0)
@@ -3906,57 +3716,6 @@ def extension_disable(
    console.print(f"To re-enable: specify extension enable {extension_id}")


-@extension_app.command("set-priority")
-def extension_set_priority(
-    extension: str = typer.Argument(help="Extension ID or name"),
-    priority: int = typer.Argument(help="New priority (lower = higher precedence)"),
-):
-    """Set the resolution priority of an installed extension."""
-    from .extensions import ExtensionManager
-
-    project_root = Path.cwd()
-
-    # Check if we're in a spec-kit project
-    specify_dir = project_root / ".specify"
-    if not specify_dir.exists():
-        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
-        console.print("Run this command from a spec-kit project root")
-        raise typer.Exit(1)
-
-    # Validate priority
-    if priority < 1:
-        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
-        raise typer.Exit(1)
-
-    manager = ExtensionManager(project_root)
-
-    # Resolve extension ID from argument (handles ambiguous names)
-    installed = manager.list_installed()
-    extension_id, display_name = _resolve_installed_extension(extension, installed, "set-priority")
-
-    # Get current metadata
-    metadata = manager.registry.get(extension_id)
-    if metadata is None or not isinstance(metadata, dict):
-        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
-        raise typer.Exit(1)
-
-    from .extensions import normalize_priority
-    raw_priority = metadata.get("priority")
-    # Only skip if the stored value is already a valid int equal to requested priority
-    # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
-        console.print(f"[yellow]Extension '{display_name}' already has priority {priority}[/yellow]")
-        raise typer.Exit(0)
-
-    old_priority = normalize_priority(raw_priority)
-
-    # Update priority
-    manager.registry.update(extension_id, {"priority": priority})
-
-    console.print(f"[green]✓[/green] Extension '{display_name}' priority changed: {old_priority} → {priority}")
-    console.print("\n[dim]Lower priority = higher precedence in template resolution[/dim]")
-
-
 def main():
    app()

--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -135,12 +135,6 @@ class CommandRegistrar:
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": "/SKILL.md"
-        },
-        "trae": {
-            "dir": ".trae/rules",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
        }
    }

--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -41,26 +41,6 @@ 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."""
@@ -271,9 +251,6 @@ 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,
@@ -347,32 +324,6 @@ 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."""
@@ -489,8 +440,7 @@ class ExtensionManager:
        self,
        source_dir: Path,
        speckit_version: str,
-        register_commands: bool = True,
-        priority: int = 10,
+        register_commands: bool = True
    ) -> ExtensionManifest:
        """Install extension from a local directory.

@@ -498,19 +448,14 @@ 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 or priority is invalid
+            ValidationError: If manifest 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)
@@ -552,7 +497,6 @@ class ExtensionManager:
            "source": "local",
            "manifest_hash": manifest.get_hash(),
            "enabled": True,
-            "priority": priority,
            "registered_commands": registered_commands
        })

@@ -561,27 +505,21 @@ class ExtensionManager:
    def install_from_zip(
        self,
        zip_path: Path,
-        speckit_version: str,
-        priority: int = 10,
+        speckit_version: str
    ) -> 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 or priority is invalid
+            ValidationError: If manifest 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)

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

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

    def remove(self, extension_id: str, keep_config: bool = False) -> bool:
        """Remove an installed extension.
@@ -694,9 +632,6 @@ 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"

@@ -708,7 +643,6 @@ 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)
@@ -721,7 +655,6 @@ 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
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -7,7 +7,6 @@ Presets are self-contained, versioned collections of templates
 customize the Spec-Driven Development workflow.
 """

-import copy
 import json
 import hashlib
 import os
@@ -24,8 +23,6 @@ import yaml
 from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier

-from .extensions import ExtensionRegistry, normalize_priority
-

@dataclass
 class PresetCatalogEntry:
@@ -274,38 +271,6 @@ class PresetRegistry:
            del self.data["presets"][pack_id]
            self._save()

-    def update(self, pack_id: str, updates: dict):
-        """Update preset metadata in registry.
-
-        Merges the provided updates with the existing entry, preserving any
-        fields not specified. The installed_at timestamp is always preserved
-        from the original entry.
-
-        Args:
-            pack_id: Preset ID
-            updates: Partial metadata to merge into existing metadata
-
-        Raises:
-            KeyError: If preset is not installed
-        """
-        if pack_id not in self.data["presets"]:
-            raise KeyError(f"Preset '{pack_id}' not found in registry")
-        existing = self.data["presets"][pack_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, **updates}
-        # Always preserve original installed_at based on key existence, not truthiness,
-        # to handle cases where the field exists but may be falsy (legacy/corruption)
-        if "installed_at" in existing:
-            merged["installed_at"] = existing["installed_at"]
-        else:
-            # If not present in existing, explicitly remove from merged if caller provided it
-            merged.pop("installed_at", None)
-        self.data["presets"][pack_id] = merged
-        self._save()
-
    def get(self, pack_id: str) -> Optional[dict]:
        """Get preset metadata from registry.

@@ -329,26 +294,14 @@ class PresetRegistry:
        """Get all installed presets sorted by priority.

        Lower priority number = higher precedence (checked first).
-        Presets with equal priority are sorted alphabetically by ID
-        for deterministic ordering.

        Returns:
-            List of (pack_id, metadata_copy) tuples sorted by priority.
-            Metadata is deep-copied to prevent accidental mutation.
+            List of (pack_id, metadata) tuples sorted by priority
        """
-        packs = self.data.get("presets", {}) or {}
-        if not isinstance(packs, dict):
-            packs = {}
-        sortable_packs = []
-        for pack_id, meta in packs.items():
-            if not isinstance(meta, dict):
-                continue
-            metadata_copy = copy.deepcopy(meta)
-            metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
-            sortable_packs.append((pack_id, metadata_copy))
+        packs = self.data["presets"]
        return sorted(
-            sortable_packs,
-            key=lambda item: (item[1]["priority"], item[0]),
+            packs.items(),
+            key=lambda item: item[1].get("priority", 10),
        )

    def is_installed(self, pack_id: str) -> bool:
@@ -727,13 +680,9 @@ class PresetManager:
            Installed preset manifest

        Raises:
-            PresetValidationError: If manifest is invalid or priority is invalid
+            PresetValidationError: If manifest is invalid
            PresetCompatibilityError: If pack is incompatible
        """
-        # Validate priority
-        if priority < 1:
-            raise PresetValidationError("Priority must be a positive integer (1 or higher)")
-
        manifest_path = source_dir / "preset.yml"
        manifest = PresetManifest(manifest_path)

@@ -780,19 +729,14 @@ class PresetManager:
        Args:
            zip_path: Path to preset ZIP file
            speckit_version: Current spec-kit version
-            priority: Resolution priority (lower = higher precedence, default 10)

        Returns:
            Installed preset manifest

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

@@ -864,9 +808,6 @@ class PresetManager:
        result = []

        for pack_id, metadata in self.registry.list().items():
-            # Ensure metadata is a dictionary to avoid AttributeError when using .get()
-            if not isinstance(metadata, dict):
-                metadata = {}
            pack_dir = self.presets_dir / pack_id
            manifest_path = pack_dir / "preset.yml"

@@ -875,13 +816,13 @@ class PresetManager:
                result.append({
                    "id": pack_id,
                    "name": manifest.name,
-                    "version": metadata.get("version", manifest.version),
+                    "version": metadata["version"],
                    "description": manifest.description,
                    "enabled": metadata.get("enabled", True),
                    "installed_at": metadata.get("installed_at"),
                    "template_count": len(manifest.templates),
                    "tags": manifest.tags,
-                    "priority": normalize_priority(metadata.get("priority")),
+                    "priority": metadata.get("priority", 10),
                })
            except PresetValidationError:
                result.append({
@@ -893,7 +834,7 @@ class PresetManager:
                    "installed_at": metadata.get("installed_at"),
                    "template_count": 0,
                    "tags": [],
-                    "priority": normalize_priority(metadata.get("priority")),
+                    "priority": metadata.get("priority", 10),
                })

        return result
@@ -1452,40 +1393,6 @@ class PresetResolver:
        self.overrides_dir = self.templates_dir / "overrides"
        self.extensions_dir = project_root / ".specify" / "extensions"

-    def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
-        """Build unified list of registered and unregistered extensions sorted by priority.
-
-        Registered extensions use their stored priority; unregistered directories
-        get implicit priority=10. Results are sorted by (priority, ext_id) for
-        deterministic ordering.
-
-        Returns:
-            List of (priority, ext_id, metadata_or_none) tuples sorted by priority.
-        """
-        if not self.extensions_dir.exists():
-            return []
-
-        registry = ExtensionRegistry(self.extensions_dir)
-        registered_extensions = registry.list_by_priority()
-        registered_extension_ids = {ext_id for ext_id, _ in registered_extensions}
-
-        all_extensions: list[tuple[int, str, dict | None]] = []
-
-        for ext_id, metadata in registered_extensions:
-            priority = normalize_priority(metadata.get("priority") if metadata else None)
-            all_extensions.append((priority, ext_id, metadata))
-
-        # Add unregistered directories with implicit priority=10
-        for ext_dir in self.extensions_dir.iterdir():
-            if not ext_dir.is_dir() or ext_dir.name.startswith("."):
-                continue
-            if ext_dir.name not in registered_extension_ids:
-                all_extensions.append((10, ext_dir.name, None))
-
-        # Sort by (priority, ext_id) for deterministic ordering
-        all_extensions.sort(key=lambda x: (x[0], x[1]))
-        return all_extensions
-
    def resolve(
        self,
        template_name: str,
@@ -1538,18 +1445,18 @@ class PresetResolver:
                    if candidate.exists():
                        return candidate

-        # Priority 3: Extension-provided templates (sorted by priority — lower number wins)
-        for _priority, ext_id, _metadata in self._get_all_extensions_by_priority():
-            ext_dir = self.extensions_dir / ext_id
-            if not ext_dir.is_dir():
-                continue
-            for subdir in subdirs:
-                if subdir:
-                    candidate = ext_dir / subdir / f"{template_name}{ext}"
-                else:
-                    candidate = ext_dir / f"{template_name}{ext}"
-                if candidate.exists():
-                    return candidate
+        # Priority 3: Extension-provided templates
+        if self.extensions_dir.exists():
+            for ext_dir in sorted(self.extensions_dir.iterdir()):
+                if not ext_dir.is_dir() or ext_dir.name.startswith("."):
+                    continue
+                for subdir in subdirs:
+                    if subdir:
+                        candidate = ext_dir / subdir / f"{template_name}{ext}"
+                    else:
+                        candidate = ext_dir / "templates" / f"{template_name}{ext}"
+                    if candidate.exists():
+                        return candidate

        # Priority 4: Core templates
        if template_type == "template":
@@ -1607,24 +1514,17 @@ class PresetResolver:
                except ValueError:
                    continue

-        for _priority, ext_id, ext_meta in self._get_all_extensions_by_priority():
-            ext_dir = self.extensions_dir / ext_id
-            if not ext_dir.is_dir():
-                continue
-            try:
-                resolved.relative_to(ext_dir)
-                if ext_meta:
-                    version = ext_meta.get("version", "?")
+        if self.extensions_dir.exists():
+            for ext_dir in sorted(self.extensions_dir.iterdir()):
+                if not ext_dir.is_dir() or ext_dir.name.startswith("."):
+                    continue
+                try:
+                    resolved.relative_to(ext_dir)
                    return {
                        "path": resolved_str,
-                        "source": f"extension:{ext_id} v{version}",
+                        "source": f"extension:{ext_dir.name}",
                    }
-                else:
-                    return {
-                        "path": resolved_str,
-                        "source": f"extension:{ext_id} (unregistered)",
-                    }
-            except ValueError:
-                continue
+                except ValueError:
+                    continue

        return {"path": resolved_str, "source": "core"}
--- a/tests/test_agent_config_consistency.py
+++ b/tests/test_agent_config_consistency.py
@@ -233,79 +233,3 @@ 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 / "speckit.specify.md").write_text(
+    (tpl_root / "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 / "speckit.plan.md").write_text(
+    (tpl_root / "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 / "speckit.tasks.md").write_text(
+    (tpl_root / "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 / "speckit.empty_fm.md").write_text(
+    (tpl_root / "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 / "speckit.broken.md").write_text(
+        (cmds_dir / "broken.md").write_text(
            "---\n"
            "description: [unclosed bracket\n"
            "  invalid: yaml: content: here\n"
@@ -430,12 +430,9 @@ class TestInstallAiSkills:

        # Place .md templates in the agent's commands directory
        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 = proj / agent_folder.rstrip("/") / "commands"
        cmds_dir.mkdir(parents=True)
-        # 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(
+        (cmds_dir / "specify.md").write_text(
            "---\ndescription: Test command\n---\n\n# Test\n\nBody.\n"
        )

@@ -451,100 +448,7 @@ 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.
@@ -556,16 +460,14 @@ 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 (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
+        # Verify commands exist before
+        assert len(list(commands_dir_claude.glob("speckit.*"))) == 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) == len(before)
+        assert len(remaining) == 3

    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
@@ -26,7 +26,6 @@ from specify_cli.extensions import (
    ExtensionError,
    ValidationError,
    CompatibilityError,
-    normalize_priority,
    version_satisfies,
 )

@@ -122,57 +121,6 @@ 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:
@@ -2389,404 +2337,3 @@ 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
@@ -1,190 +0,0 @@
-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
@@ -32,7 +32,6 @@ from specify_cli.presets import (
    PresetCompatibilityError,
    VALID_PRESET_TEMPLATE_TYPES,
 )
-from specify_cli.extensions import ExtensionRegistry


 # ===== Fixtures =====
@@ -574,24 +573,6 @@ class TestRegistryPriority:
        assert sorted_packs[0][0] == "pack-b"
        assert sorted_packs[1][0] == "pack-a"

-    def test_list_by_priority_invalid_priority_defaults(self, temp_dir):
-        """Malformed priority values fall back to the default priority."""
-        packs_dir = temp_dir / "packs"
-        packs_dir.mkdir()
-        registry = PresetRegistry(packs_dir)
-
-        registry.add("pack-high", {"version": "1.0.0", "priority": 1})
-        registry.data["presets"]["pack-invalid"] = {
-            "version": "1.0.0",
-            "priority": "high",
-        }
-        registry._save()
-
-        sorted_packs = registry.list_by_priority()
-
-        assert [item[0] for item in sorted_packs] == ["pack-high", "pack-invalid"]
-        assert sorted_packs[1][1]["priority"] == 10
-

 # ===== PresetResolver Tests =====

@@ -697,11 +678,6 @@ class TestPresetResolver:
        ext_template = ext_templates_dir / "custom-template.md"
        ext_template.write_text("# Extension Custom Template\n")

-        # Register extension in registry
-        extensions_dir = project_dir / ".specify" / "extensions"
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("my-ext", {"version": "1.0.0", "priority": 10})
-
        resolver = PresetResolver(project_dir)
        result = resolver.resolve("custom-template")
        assert result is not None
@@ -765,15 +741,10 @@ class TestPresetResolver:
        ext_template = ext_templates_dir / "unique-template.md"
        ext_template.write_text("# Unique\n")

-        # Register extension in registry
-        extensions_dir = project_dir / ".specify" / "extensions"
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("my-ext", {"version": "1.0.0", "priority": 10})
-
        resolver = PresetResolver(project_dir)
        result = resolver.resolve_with_source("unique-template")
        assert result is not None
-        assert result["source"] == "extension:my-ext v1.0.0"
+        assert result["source"] == "extension:my-ext"

    def test_resolve_with_source_not_found(self, project_dir):
        """Test resolve_with_source for nonexistent template."""
@@ -794,104 +765,6 @@ class TestPresetResolver:
        assert result is None


-class TestExtensionPriorityResolution:
-    """Test extension priority resolution with registered and unregistered extensions."""
-
-    def test_unregistered_beats_registered_with_lower_precedence(self, project_dir):
-        """Unregistered extension (implicit priority 10) beats registered with priority 20."""
-        extensions_dir = project_dir / ".specify" / "extensions"
-        extensions_dir.mkdir(parents=True, exist_ok=True)
-
-        # Create registered extension with priority 20 (lower precedence than 10)
-        registered_dir = extensions_dir / "registered-ext"
-        (registered_dir / "templates").mkdir(parents=True)
-        (registered_dir / "templates" / "test-template.md").write_text("# From Registered\n")
-
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("registered-ext", {"version": "1.0.0", "priority": 20})
-
-        # Create unregistered extension directory (implicit priority 10)
-        unregistered_dir = extensions_dir / "unregistered-ext"
-        (unregistered_dir / "templates").mkdir(parents=True)
-        (unregistered_dir / "templates" / "test-template.md").write_text("# From Unregistered\n")
-
-        # Unregistered (priority 10) should beat registered (priority 20)
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("test-template")
-        assert result is not None
-        assert "From Unregistered" in result.read_text()
-
-    def test_registered_with_higher_precedence_beats_unregistered(self, project_dir):
-        """Registered extension with priority 5 beats unregistered (implicit priority 10)."""
-        extensions_dir = project_dir / ".specify" / "extensions"
-        extensions_dir.mkdir(parents=True, exist_ok=True)
-
-        # Create registered extension with priority 5 (higher precedence than 10)
-        registered_dir = extensions_dir / "registered-ext"
-        (registered_dir / "templates").mkdir(parents=True)
-        (registered_dir / "templates" / "test-template.md").write_text("# From Registered\n")
-
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("registered-ext", {"version": "1.0.0", "priority": 5})
-
-        # Create unregistered extension directory (implicit priority 10)
-        unregistered_dir = extensions_dir / "unregistered-ext"
-        (unregistered_dir / "templates").mkdir(parents=True)
-        (unregistered_dir / "templates" / "test-template.md").write_text("# From Unregistered\n")
-
-        # Registered (priority 5) should beat unregistered (priority 10)
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("test-template")
-        assert result is not None
-        assert "From Registered" in result.read_text()
-
-    def test_unregistered_attribution_with_priority_ordering(self, project_dir):
-        """Test resolve_with_source correctly attributes unregistered extension."""
-        extensions_dir = project_dir / ".specify" / "extensions"
-        extensions_dir.mkdir(parents=True, exist_ok=True)
-
-        # Create registered extension with priority 20
-        registered_dir = extensions_dir / "registered-ext"
-        (registered_dir / "templates").mkdir(parents=True)
-        (registered_dir / "templates" / "test-template.md").write_text("# From Registered\n")
-
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("registered-ext", {"version": "1.0.0", "priority": 20})
-
-        # Create unregistered extension (implicit priority 10)
-        unregistered_dir = extensions_dir / "unregistered-ext"
-        (unregistered_dir / "templates").mkdir(parents=True)
-        (unregistered_dir / "templates" / "test-template.md").write_text("# From Unregistered\n")
-
-        # Attribution should show unregistered extension
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve_with_source("test-template")
-        assert result is not None
-        assert "unregistered-ext" in result["source"]
-        assert "(unregistered)" in result["source"]
-
-    def test_same_priority_sorted_alphabetically(self, project_dir):
-        """Extensions with same priority are sorted alphabetically by ID."""
-        extensions_dir = project_dir / ".specify" / "extensions"
-        extensions_dir.mkdir(parents=True, exist_ok=True)
-
-        # Create two unregistered extensions (both implicit priority 10)
-        # "aaa-ext" should come before "zzz-ext" alphabetically
-        zzz_dir = extensions_dir / "zzz-ext"
-        (zzz_dir / "templates").mkdir(parents=True)
-        (zzz_dir / "templates" / "test-template.md").write_text("# From ZZZ\n")
-
-        aaa_dir = extensions_dir / "aaa-ext"
-        (aaa_dir / "templates").mkdir(parents=True)
-        (aaa_dir / "templates" / "test-template.md").write_text("# From AAA\n")
-
-        # AAA should win due to alphabetical ordering at same priority
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("test-template")
-        assert result is not None
-        assert "From AAA" in result.read_text()
-
-
 # ===== PresetCatalog Tests =====


@@ -1106,13 +979,8 @@ class TestIntegration:
        ext_templates_dir.mkdir(parents=True)
        (ext_templates_dir / "spec-template.md").write_text("# Extension\n")

-        # Register extension in registry
-        extensions_dir = project_dir / ".specify" / "extensions"
-        ext_registry = ExtensionRegistry(extensions_dir)
-        ext_registry.add("my-ext", {"version": "1.0.0", "priority": 10})
-
        result = resolver.resolve_with_source("spec-template")
-        assert result["source"] == "extension:my-ext v1.0.0"
+        assert result["source"] == "extension:my-ext"

        # Install pack — should win over extension
        manager = PresetManager(project_dir)
@@ -1842,162 +1710,3 @@ class TestPresetSkills:

        metadata = manager.registry.get("self-test")
        assert metadata.get("registered_skills", []) == []
-
-
-class TestPresetSetPriority:
-    """Test preset set-priority CLI command."""
-
-    def test_set_priority_changes_priority(self, project_dir, pack_dir):
-        """Test set-priority command changes preset priority."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        runner = CliRunner()
-
-        # Install preset with default priority
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(pack_dir, "0.1.5")
-
-        # Verify default priority
-        assert manager.registry.get("test-pack")["priority"] == 10
-
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(app, ["preset", "set-priority", "test-pack", "5"])
-
-        assert result.exit_code == 0, result.output
-        assert "priority changed: 10 → 5" in result.output
-
-        # Reload registry to see updated value
-        manager2 = PresetManager(project_dir)
-        assert manager2.registry.get("test-pack")["priority"] == 5
-
-    def test_set_priority_same_value_no_change(self, project_dir, pack_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 preset with priority 5
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(pack_dir, "0.1.5", priority=5)
-
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(app, ["preset", "set-priority", "test-pack", "5"])
-
-        assert result.exit_code == 0, result.output
-        assert "already has priority 5" in result.output
-
-    def test_set_priority_invalid_value(self, project_dir, pack_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 preset
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(pack_dir, "0.1.5")
-
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(app, ["preset", "set-priority", "test-pack", "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 preset."""
-        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, ["preset", "set-priority", "nonexistent", "5"])
-
-        assert result.exit_code == 1, result.output
-        assert "not installed" in result.output.lower()
-
-
-class TestPresetPriorityBackwardsCompatibility:
-    """Test backwards compatibility for presets installed before priority feature."""
-
-    def test_legacy_preset_without_priority_field(self, temp_dir):
-        """Presets installed before priority feature should default to 10."""
-        presets_dir = temp_dir / ".specify" / "presets"
-        presets_dir.mkdir(parents=True)
-
-        # Simulate legacy registry entry without priority field
-        registry = PresetRegistry(presets_dir)
-        registry.data["presets"]["legacy-pack"] = {
-            "version": "1.0.0",
-            "source": "local",
-            "enabled": True,
-            "installed_at": "2025-01-01T00:00:00Z",
-            # No "priority" field - simulates pre-feature preset
-        }
-        registry._save()
-
-        # Reload registry
-        registry2 = PresetRegistry(presets_dir)
-
-        # list_by_priority should use default of 10
-        result = registry2.list_by_priority()
-        assert len(result) == 1
-        assert result[0][0] == "legacy-pack"
-        # Priority defaults to 10 and is normalized in returned metadata
-        assert result[0][1]["priority"] == 10
-
-    def test_legacy_preset_in_list_installed(self, project_dir, pack_dir):
-        """list_installed returns priority=10 for legacy presets without priority field."""
-        manager = PresetManager(project_dir)
-
-        # Install preset normally
-        manager.install_from_directory(pack_dir, "0.1.5")
-
-        # Manually remove priority to simulate legacy preset
-        pack_data = manager.registry.data["presets"]["test-pack"]
-        del pack_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_presets_ordering(self, temp_dir):
-        """Legacy presets (no priority) sort with default=10 among prioritized presets."""
-        presets_dir = temp_dir / ".specify" / "presets"
-        presets_dir.mkdir(parents=True)
-
-        registry = PresetRegistry(presets_dir)
-
-        # Add preset with explicit priority=5
-        registry.add("pack-with-priority", {"version": "1.0.0", "priority": 5})
-
-        # Add legacy preset without priority (manually)
-        registry.data["presets"]["legacy-pack"] = {
-            "version": "1.0.0",
-            "source": "local",
-            "enabled": True,
-            # No priority field
-        }
-
-        # Add another preset with priority=15
-        registry.add("low-priority-pack", {"version": "1.0.0", "priority": 15})
-        registry._save()
-
-        # Reload and check ordering
-        registry2 = PresetRegistry(presets_dir)
-        sorted_presets = registry2.list_by_priority()
-
-        # Should be: pack-with-priority (5), legacy-pack (default 10), low-priority-pack (15)
-        assert [p[0] for p in sorted_presets] == [
-            "pack-with-priority",
-            "legacy-pack",
-            "low-priority-pack",
-        ]
Author	SHA1	Message	Date
Manfred Riem	9b10d440b1	Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>	2026-03-13 15:14:46 -05:00
github-actions[bot]	2656ee1df7	chore: bump version to 0.3.0	2026-03-13 20:11:58 +00:00