Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

AGENTS.md

@@ -10,10 +10,6 @@ The toolkit supports multiple AI coding assistants, allowing teams to use their
 
 ---
 
-## General practices
-
-- Any changes to `__init__.py` for the Specify CLI require a version rev in `pyproject.toml` and addition of entries to `CHANGELOG.md`.
-
 ## Adding New Agent Support
 
 This section explains how to add support for new AI agents/assistants to the Specify CLI. Use this guide as a reference when integrating new AI tools into the Spec-Driven Development workflow.

CHANGELOG.md

@@ -7,6 +7,51 @@ 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).
 
+## [0.3.0] - 2026-03-13
+
+### Changed
+
+- No changes have been documented for this release yet.
+
+<!-- Entries for 0.2.x and earlier releases are documented in their respective sections below. -->
+- make c ignores consistent with c++ (#1747)
+- chore: bump version to 0.1.13 (#1746)
+- feat: add kiro-cli and AGENT_CONFIG consistency coverage (#1690)
+- feat: add verify extension to community catalog (#1726)
+- Add Retrospective Extension to community catalog README table (#1741)
+- fix(scripts): add empty description validation and branch checkout error handling (#1559)
+- fix: correct Copilot extension command registration (#1724)
+- fix(implement): remove Makefile from C ignore patterns (#1558)
+- Add sync extension to community catalog (#1728)
+- fix(checklist): clarify file handling behavior for append vs create (#1556)
+- fix(clarify): correct conflicting question limit from 10 to 5 (#1557)
+- chore: bump version to 0.1.12 (#1737)
+- fix: use RELEASE_PAT so tag push triggers release workflow (#1736)
+- fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
+- fix: Split release process to sync pyproject.toml version with git tags (#1732)
+
+
+## [Unreleased]
+
+### Added
+
+- feat(presets): Pluggable preset system with preset catalog and template resolver
+- Preset manifest (`preset.yml`) with validation for artifact, command, and script types
+- `PresetManifest`, `PresetRegistry`, `PresetManager`, `PresetCatalog`, `PresetResolver` classes in `src/specify_cli/presets.py`
+- CLI commands: `specify preset search`, `specify preset add`, `specify preset list`, `specify preset remove`, `specify preset resolve`, `specify preset info`
+- CLI commands: `specify preset catalog list`, `specify preset catalog add`, `specify preset catalog remove` for multi-catalog management
+- `PresetCatalogEntry` dataclass and multi-catalog support mirroring the extension catalog system
+- `--preset` option for `specify init` to install presets during initialization
+- Priority-based preset resolution: presets with lower priority number win (`--priority` flag)
+- `resolve_template()` / `Resolve-Template` helpers in bash and PowerShell common scripts
+- Template resolution priority stack: overrides → presets → extensions → core
+- Preset catalog files (`presets/catalog.json`, `presets/catalog.community.json`)
+- Preset scaffold directory (`presets/scaffold/`)
+- Scripts updated to use template resolution instead of hardcoded paths
+- feat(presets): Preset command overrides now propagate to agent skills when `--ai-skills` was used during init
+- feat: `specify init` persists CLI options to `.specify/init-options.json` for downstream operations
+- feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
+
 ## [0.2.1] - 2026-03-11
 
 ### Changed
@@ -51,13 +96,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
 - fix: Split release process to sync pyproject.toml version with git tags (#1732)
 
-
-## [Unreleased]
-
-### Added
-
-- feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
-
 ## [0.2.0] - 2026-03-09
 
 ### Changed

extensions/README.md

@@ -76,6 +76,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | 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) |
 | 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) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
 | 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) |

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-09T00:00:00Z",
+  "updated_at": "2026-03-13T12:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "azure-devops": {
@@ -74,6 +74,37 @@
       "created_at": "2026-02-22T00:00:00Z",
       "updated_at": "2026-02-22T00:00:00Z"
     },
+    "doctor": {
+      "name": "Project Health Check",
+      "id": "doctor",
+      "description": "Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-doctor/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-doctor",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-doctor",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-doctor/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-doctor/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "diagnostics",
+        "health-check",
+        "validation",
+        "project-structure"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-13T00:00:00Z",
+      "updated_at": "2026-03-13T00:00:00Z"
+    },
     "fleet": {
       "name": "Fleet Orchestrator",
       "id": "fleet",

presets/ARCHITECTURE.md

@@ -0,0 +1,157 @@
+# Preset System Architecture
+
+This document describes the internal architecture of the preset system — how template resolution, command registration, and catalog management work under the hood.
+
+For usage instructions, see [README.md](README.md).
+
+## Template Resolution
+
+When Spec Kit needs a template (e.g. `spec-template`), the `PresetResolver` walks a priority stack and returns the first match:
+
+```mermaid
+flowchart TD
+    A["resolve_template('spec-template')"] --> B{Override exists?}
+    B -- Yes --> C[".specify/templates/overrides/spec-template.md"]
+    B -- No --> D{Preset provides it?}
+    D -- Yes --> E[".specify/presets/‹preset-id›/templates/spec-template.md"]
+    D -- No --> F{Extension provides it?}
+    F -- Yes --> G[".specify/extensions/‹ext-id›/templates/spec-template.md"]
+    F -- No --> H[".specify/templates/spec-template.md"]
+
+    E -- "multiple presets?" --> I["lowest priority number wins"]
+    I --> E
+
+    style C fill:#4caf50,color:#fff
+    style E fill:#2196f3,color:#fff
+    style G fill:#ff9800,color:#fff
+    style H fill:#9e9e9e,color:#fff
+```
+
+| Priority | Source | Path | Use case |
+|----------|--------|------|----------|
+| 1 (highest) | Override | `.specify/templates/overrides/` | One-off project-local tweaks |
+| 2 | Preset | `.specify/presets/<id>/templates/` | Shareable, stackable customizations |
+| 3 | Extension | `.specify/extensions/<id>/templates/` | Extension-provided templates |
+| 4 (lowest) | Core | `.specify/templates/` | Shipped defaults |
+
+When multiple presets are installed, they're sorted by their `priority` field (lower number = higher precedence). This is set via `--priority` on `specify preset add`.
+
+The resolution is implemented three times to ensure consistency:
+- **Python**: `PresetResolver` in `src/specify_cli/presets.py`
+- **Bash**: `resolve_template()` in `scripts/bash/common.sh`
+- **PowerShell**: `Resolve-Template` in `scripts/powershell/common.ps1`
+
+## Command Registration
+
+When a preset is installed with `type: "command"` entries, the `PresetManager` registers them into all detected agent directories using the shared `CommandRegistrar` from `src/specify_cli/agents.py`.
+
+```mermaid
+flowchart TD
+    A["specify preset add my-preset"] --> B{Preset has type: command?}
+    B -- No --> Z["done (templates only)"]
+    B -- Yes --> C{Extension command?}
+    C -- "speckit.myext.cmd\n(3+ dot segments)" --> D{Extension installed?}
+    D -- No --> E["skip (extension not active)"]
+    D -- Yes --> F["register command"]
+    C -- "speckit.specify\n(core command)" --> F
+    F --> G["detect agent directories"]
+    G --> H[".claude/commands/"]
+    G --> I[".gemini/commands/"]
+    G --> J[".github/agents/"]
+    G --> K["... (17+ agents)"]
+    H --> L["write .md (Markdown format)"]
+    I --> M["write .toml (TOML format)"]
+    J --> N["write .agent.md + .prompt.md"]
+
+    style E fill:#ff5722,color:#fff
+    style L fill:#4caf50,color:#fff
+    style M fill:#4caf50,color:#fff
+    style N fill:#4caf50,color:#fff
+```
+
+### Extension safety check
+
+Command names follow the pattern `speckit.<ext-id>.<cmd-name>`. When a command has 3+ dot segments, the system extracts the extension ID and checks if `.specify/extensions/<ext-id>/` exists. If the extension isn't installed, the command is skipped — preventing orphan files referencing non-existent extensions.
+
+Core commands (e.g. `speckit.specify`, with only 2 segments) are always registered.
+
+### Agent format rendering
+
+The `CommandRegistrar` renders commands differently per agent:
+
+| Agent | Format | Extension | Arg placeholder |
+|-------|--------|-----------|-----------------|
+| Claude, Cursor, opencode, Windsurf, etc. | Markdown | `.md` | `$ARGUMENTS` |
+| Copilot | Markdown | `.agent.md` + `.prompt.md` | `$ARGUMENTS` |
+| Gemini, Qwen, Tabnine | TOML | `.toml` | `{{args}}` |
+
+### Cleanup on removal
+
+When `specify preset remove` is called, the registered commands are read from the registry metadata and the corresponding files are deleted from each agent directory, including Copilot companion `.prompt.md` files.
+
+## Catalog System
+
+```mermaid
+flowchart TD
+    A["specify preset search"] --> B["PresetCatalog.get_active_catalogs()"]
+    B --> C{SPECKIT_PRESET_CATALOG_URL set?}
+    C -- Yes --> D["single custom catalog"]
+    C -- No --> E{.specify/preset-catalogs.yml exists?}
+    E -- Yes --> F["project-level catalog stack"]
+    E -- No --> G{"~/.specify/preset-catalogs.yml exists?"}
+    G -- Yes --> H["user-level catalog stack"]
+    G -- No --> I["built-in defaults"]
+    I --> J["default (install allowed)"]
+    I --> K["community (discovery only)"]
+
+    style D fill:#ff9800,color:#fff
+    style F fill:#2196f3,color:#fff
+    style H fill:#2196f3,color:#fff
+    style J fill:#4caf50,color:#fff
+    style K fill:#9e9e9e,color:#fff
+```
+
+Catalogs are fetched with a 1-hour cache (per-URL, SHA256-hashed cache files). Each catalog entry has a `priority` (for merge ordering) and `install_allowed` flag.
+
+## Repository Layout
+
+```
+presets/
+├── ARCHITECTURE.md                         # This file
+├── PUBLISHING.md                           # Guide for submitting presets to the catalog
+├── README.md                               # User guide
+├── catalog.json                            # Official preset catalog
+├── catalog.community.json                  # Community preset catalog
+├── scaffold/                               # Scaffold for creating new presets
+│   ├── preset.yml                          # Example manifest
+│   ├── README.md                           # Guide for customizing the scaffold
+│   ├── commands/
+│   │   ├── speckit.specify.md              # Core command override example
+│   │   └── speckit.myext.myextcmd.md       # Extension command override example
+│   └── templates/
+│       ├── spec-template.md                # Core template override example
+│       └── myext-template.md               # Extension template override example
+└── self-test/                              # Self-test preset (overrides all core templates)
+    ├── preset.yml
+    ├── commands/
+    │   └── speckit.specify.md
+    └── templates/
+        ├── spec-template.md
+        ├── plan-template.md
+        ├── tasks-template.md
+        ├── checklist-template.md
+        ├── constitution-template.md
+        └── agent-file-template.md
+```
+
+## Module Structure
+
+```
+src/specify_cli/
+├── agents.py       # CommandRegistrar — shared infrastructure for writing
+│                    #   command files to agent directories
+├── presets.py       # PresetManifest, PresetRegistry, PresetManager,
+│                    #   PresetCatalog, PresetCatalogEntry, PresetResolver
+└── __init__.py      # CLI commands: specify preset list/add/remove/search/
+                     #   resolve/info, specify preset catalog list/add/remove
+```

presets/PUBLISHING.md

@@ -0,0 +1,295 @@
+# Preset Publishing Guide
+
+This guide explains how to publish your preset to the Spec Kit preset catalog, making it discoverable by `specify preset search`.
+
+## Table of Contents
+
+1. [Prerequisites](#prerequisites)
+2. [Prepare Your Preset](#prepare-your-preset)
+3. [Submit to Catalog](#submit-to-catalog)
+4. [Verification Process](#verification-process)
+5. [Release Workflow](#release-workflow)
+6. [Best Practices](#best-practices)
+
+---
+
+## Prerequisites
+
+Before publishing a preset, ensure you have:
+
+1. **Valid Preset**: A working preset with a valid `preset.yml` manifest
+2. **Git Repository**: Preset hosted on GitHub (or other public git hosting)
+3. **Documentation**: README.md with description and usage instructions
+4. **License**: Open source license file (MIT, Apache 2.0, etc.)
+5. **Versioning**: Semantic versioning (e.g., 1.0.0)
+6. **Testing**: Preset tested on real projects with `specify preset add --dev`
+
+---
+
+## Prepare Your Preset
+
+### 1. Preset Structure
+
+Ensure your preset follows the standard structure:
+
+```text
+your-preset/
+├── preset.yml                 # Required: Preset manifest
+├── README.md                  # Required: Documentation
+├── LICENSE                    # Required: License file
+├── CHANGELOG.md               # Recommended: Version history
+│
+├── templates/                 # Template overrides
+│   ├── spec-template.md
+│   ├── plan-template.md
+│   └── ...
+│
+└── commands/                  # Command overrides (optional)
+    └── speckit.specify.md
+```
+
+Start from the [scaffold](scaffold/) if you're creating a new preset.
+
+### 2. preset.yml Validation
+
+Verify your manifest is valid:
+
+```yaml
+schema_version: "1.0"
+
+preset:
+  id: "your-preset"               # Unique lowercase-hyphenated ID
+  name: "Your Preset Name"        # Human-readable name
+  version: "1.0.0"                # Semantic version
+  description: "Brief description (one sentence)"
+  author: "Your Name or Organization"
+  repository: "https://github.com/your-org/spec-kit-preset-your-preset"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"      # Required spec-kit version
+
+provides:
+  templates:
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Custom spec template"
+      replaces: "spec-template"
+
+tags:                              # 2-5 relevant tags
+  - "category"
+  - "workflow"
+```
+
+**Validation Checklist**:
+
+- ✅ `id` is lowercase with hyphens only (no underscores, spaces, or special characters)
+- ✅ `version` follows semantic versioning (X.Y.Z)
+- ✅ `description` is concise (under 200 characters)
+- ✅ `repository` URL is valid and public
+- ✅ All template and command files exist in the preset directory
+- ✅ Template names are lowercase with hyphens only
+- ✅ Command names use dot notation (e.g. `speckit.specify`)
+- ✅ Tags are lowercase and descriptive
+
+### 3. Test Locally
+
+```bash
+# Install from local directory
+specify preset add --dev /path/to/your-preset
+
+# Verify templates resolve from your preset
+specify preset resolve spec-template
+
+# Verify preset info
+specify preset info your-preset
+
+# List installed presets
+specify preset list
+
+# Remove when done testing
+specify preset remove your-preset
+```
+
+If your preset includes command overrides, verify they appear in the agent directories:
+
+```bash
+# Check Claude commands (if using Claude)
+ls .claude/commands/speckit.*.md
+
+# Check Copilot commands (if using Copilot)
+ls .github/agents/speckit.*.agent.md
+
+# Check Gemini commands (if using Gemini)
+ls .gemini/commands/speckit.*.toml
+```
+
+### 4. Create GitHub Release
+
+Create a GitHub release for your preset version:
+
+```bash
+# Tag the release
+git tag v1.0.0
+git push origin v1.0.0
+```
+
+The release archive URL will be:
+
+```text
+https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip
+```
+
+### 5. Test Installation from Archive
+
+```bash
+specify preset add --from https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip
+```
+
+---
+
+## Submit to Catalog
+
+### Understanding the Catalogs
+
+Spec Kit uses a dual-catalog system:
+
+- **`catalog.json`** — Official, verified presets (install allowed by default)
+- **`catalog.community.json`** — Community-contributed presets (discovery only by default)
+
+All community presets should be submitted to `catalog.community.json`.
+
+### 1. Fork the spec-kit Repository
+
+```bash
+git clone https://github.com/YOUR-USERNAME/spec-kit.git
+cd spec-kit
+```
+
+### 2. Add Preset to Community Catalog
+
+Edit `presets/catalog.community.json` and add your preset.
+
+> **⚠️ Entries must be sorted alphabetically by preset ID.** Insert your preset in the correct position within the `"presets"` object.
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-10T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
+  "presets": {
+    "your-preset": {
+      "name": "Your Preset Name",
+      "description": "Brief description of what your preset provides",
+      "author": "Your Name",
+      "version": "1.0.0",
+      "download_url": "https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-preset-your-preset",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "templates": 3,
+        "commands": 1
+      },
+      "tags": [
+        "category",
+        "workflow"
+      ],
+      "created_at": "2026-03-10T00:00:00Z",
+      "updated_at": "2026-03-10T00:00:00Z"
+    }
+  }
+}
+```
+
+### 3. Submit Pull Request
+
+```bash
+git checkout -b add-your-preset
+git add presets/catalog.community.json
+git commit -m "Add your-preset to community catalog
+
+- Preset ID: your-preset
+- Version: 1.0.0
+- Author: Your Name
+- Description: Brief description
+"
+git push origin add-your-preset
+```
+
+**Pull Request Checklist**:
+
+```markdown
+## Preset Submission
+
+**Preset Name**: Your Preset Name
+**Preset ID**: your-preset
+**Version**: 1.0.0
+**Repository**: https://github.com/your-org/spec-kit-preset-your-preset
+
+### Checklist
+- [ ] Valid preset.yml manifest
+- [ ] README.md with description and usage
+- [ ] LICENSE file included
+- [ ] GitHub release created
+- [ ] Preset tested with `specify preset add --dev`
+- [ ] Templates resolve correctly (`specify preset resolve`)
+- [ ] Commands register to agent directories (if applicable)
+- [ ] Commands match template sections (command + template are coherent)
+- [ ] Added to presets/catalog.community.json
+```
+
+---
+
+## Verification Process
+
+After submission, maintainers will review:
+
+1. **Manifest validation** — valid `preset.yml`, all files exist
+2. **Template quality** — templates are useful and well-structured
+3. **Command coherence** — commands reference sections that exist in templates
+4. **Security** — no malicious content, safe file operations
+5. **Documentation** — clear README explaining what the preset does
+
+Once verified, `verified: true` is set and the preset appears in `specify preset search`.
+
+---
+
+## Release Workflow
+
+When releasing a new version:
+
+1. Update `version` in `preset.yml`
+2. Update CHANGELOG.md
+3. Tag and push: `git tag v1.1.0 && git push origin v1.1.0`
+4. Submit PR to update `version` and `download_url` in `presets/catalog.community.json`
+
+---
+
+## Best Practices
+
+### Template Design
+
+- **Keep sections clear** — use headings and placeholder text the LLM can replace
+- **Match commands to templates** — if your preset overrides a command, make sure it references the sections in your template
+- **Document customization points** — use HTML comments to guide users on what to change
+
+### Naming
+
+- Preset IDs should be descriptive: `healthcare-compliance`, `enterprise-safe`, `startup-lean`
+- Avoid generic names: `my-preset`, `custom`, `test`
+
+### Stacking
+
+- Design presets to work well when stacked with others
+- Only override templates you need to change
+- Document which templates and commands your preset modifies
+
+### Command Overrides
+
+- Only override commands when the workflow needs to change, not just the output format
+- If you only need different template sections, a template override is sufficient
+- Test command overrides with multiple agents (Claude, Gemini, Copilot)

presets/README.md

@@ -0,0 +1,115 @@
+# Presets
+
+Presets are stackable, priority-ordered collections of template and command overrides for Spec Kit. They let you customize both the artifacts produced by the Spec-Driven Development workflow (specs, plans, tasks, checklists, constitutions) and the commands that guide the LLM in creating them — without forking or modifying core files.
+
+## How It Works
+
+When Spec Kit needs a template (e.g. `spec-template`), it walks a resolution stack:
+
+1. `.specify/templates/overrides/` — project-local one-off overrides
+2. `.specify/presets/<preset-id>/templates/` — installed presets (sorted by priority)
+3. `.specify/extensions/<ext-id>/templates/` — extension-provided templates
+4. `.specify/templates/` — core templates shipped with Spec Kit
+
+If no preset is installed, core templates are used — exactly the same behavior as before presets existed.
+
+For detailed resolution and command registration flows, see [ARCHITECTURE.md](ARCHITECTURE.md).
+
+## Command Overrides
+
+Presets can also override the commands that guide the SDD workflow. Templates define *what* gets produced (specs, plans, constitutions); commands define *how* the LLM produces them (the step-by-step instructions).
+
+When a preset includes `type: "command"` entries, the commands are automatically registered into all detected agent directories (`.claude/commands/`, `.gemini/commands/`, etc.) in the correct format (Markdown or TOML with appropriate argument placeholders). When the preset is removed, the registered commands are cleaned up.
+
+## Quick Start
+
+```bash
+# Search available presets
+specify preset search
+
+# Install a preset from the catalog
+specify preset add healthcare-compliance
+
+# Install from a local directory (for development)
+specify preset add --dev ./my-preset
+
+# Install with a specific priority (lower = higher precedence)
+specify preset add healthcare-compliance --priority 5
+
+# List installed presets
+specify preset list
+
+# See which template a name resolves to
+specify preset resolve spec-template
+
+# Get detailed info about a preset
+specify preset info healthcare-compliance
+
+# Remove a preset
+specify preset remove healthcare-compliance
+```
+
+## Stacking Presets
+
+Multiple presets can be installed simultaneously. The `--priority` flag controls which one wins when two presets provide the same template (lower number = higher precedence):
+
+```bash
+specify preset add enterprise-safe --priority 10      # base layer
+specify preset add healthcare-compliance --priority 5  # overrides enterprise-safe
+specify preset add pm-workflow --priority 1            # overrides everything
+```
+
+Presets **override**, they don't merge. If two presets both provide `spec-template`, the one with the lowest priority number wins entirely.
+
+## Catalog Management
+
+Presets are discovered through catalogs. By default, Spec Kit uses the official and community catalogs:
+
+```bash
+# List active catalogs
+specify preset catalog list
+
+# Add a custom catalog
+specify preset catalog add https://example.com/catalog.json --name my-org --install-allowed
+
+# Remove a catalog
+specify preset catalog remove my-org
+```
+
+## Creating a Preset
+
+See [scaffold/](scaffold/) for a scaffold you can copy to create your own preset.
+
+1. Copy `scaffold/` to a new directory
+2. Edit `preset.yml` with your preset's metadata
+3. Add or replace templates in `templates/`
+4. Test locally with `specify preset add --dev .`
+5. Verify with `specify preset resolve spec-template`
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `SPECKIT_PRESET_CATALOG_URL` | Override the catalog URL (replaces all defaults) |
+
+## Configuration Files
+
+| File | Scope | Description |
+|------|-------|-------------|
+| `.specify/preset-catalogs.yml` | Project | Custom catalog stack for this project |
+| `~/.specify/preset-catalogs.yml` | User | Custom catalog stack for all projects |
+
+## Future Considerations
+
+The following enhancements are under consideration for future releases:
+
+- **Composition strategies** — Allow presets to declare a `strategy` per template instead of the default `replace`:
+
+  | Type | `replace` | `prepend` | `append` | `wrap` |
+  |------|-----------|-----------|----------|--------|
+  | **template** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **command** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **script** | ✓ (default) | — | — | ✓ |
+
+  For artifacts and commands (which are LLM directives), `wrap` would inject preset content before and after the core template using a `{CORE_TEMPLATE}` placeholder. For scripts, `wrap` would run custom logic before/after the core script via a `$CORE_SCRIPT` variable.
+- **Script overrides** — Enable presets to provide alternative versions of core scripts (e.g. `create-new-feature.sh`) for workflow customization. A `strategy: "wrap"` option could allow presets to run custom logic before/after the core script without fully replacing it.

presets/catalog.community.json

@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-09T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
+  "presets": {}
+}

presets/catalog.json

@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-03-10T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.json",
+  "presets": {}
+}

presets/scaffold/README.md

@@ -0,0 +1,46 @@
+# My Preset
+
+A custom preset for Spec Kit. Copy this directory and customize it to create your own.
+
+## Templates Included
+
+| Template | Type | Description |
+|----------|------|-------------|
+| `spec-template` | template | Custom feature specification template (overrides core and extensions) |
+| `myext-template` | template | Override of the myext extension's report template |
+| `speckit.specify` | command | Custom specification command (overrides core) |
+| `speckit.myext.myextcmd` | command | Override of the myext extension's myextcmd command |
+
+## Development
+
+1. Copy this directory: `cp -r presets/scaffold my-preset`
+2. Edit `preset.yml` — set your preset's ID, name, description, and templates
+3. Add or modify templates in `templates/`
+4. Test locally: `specify preset add --dev ./my-preset`
+5. Verify resolution: `specify preset resolve spec-template`
+6. Remove when done testing: `specify preset remove my-preset`
+
+## Manifest Reference (`preset.yml`)
+
+Required fields:
+- `schema_version` — always `"1.0"`
+- `preset.id` — lowercase alphanumeric with hyphens
+- `preset.name` — human-readable name
+- `preset.version` — semantic version (e.g. `1.0.0`)
+- `preset.description` — brief description
+- `requires.speckit_version` — version constraint (e.g. `>=0.1.0`)
+- `provides.templates` — list of templates with `type`, `name`, and `file`
+
+## Template Types
+
+- **template** — Document scaffolds (spec-template.md, plan-template.md, tasks-template.md, etc.)
+- **command** — AI agent workflow prompts (e.g. speckit.specify, speckit.plan)
+- **script** — Custom scripts (reserved for future use)
+
+## Publishing
+
+See the [Preset Publishing Guide](../PUBLISHING.md) for details on submitting to the catalog.
+
+## License
+
+MIT

presets/scaffold/commands/speckit.myext.myextcmd.md

@@ -0,0 +1,20 @@
+---
+description: "Override of the myext extension's myextcmd command"
+---
+
+<!-- Preset override for speckit.myext.myextcmd -->
+
+You are following a customized version of the myext extension's myextcmd command.
+
+When executing this command:
+
+1. Read the user's input from $ARGUMENTS
+2. Follow the standard myextcmd workflow
+3. Additionally, apply the following customizations from this preset:
+   - Add compliance checks before proceeding
+   - Include audit trail entries in the output
+
+> CUSTOMIZE: Replace the instructions above with your own.
+> This file overrides the command that the "myext" extension provides.
+> When this preset is installed, all agents (Claude, Gemini, Copilot, etc.)
+> will use this version instead of the extension's original.

presets/scaffold/commands/speckit.specify.md

@@ -0,0 +1,23 @@
+---
+description: "Create a feature specification (preset override)"
+scripts:
+  sh: scripts/bash/create-new-feature.sh "{ARGS}"
+  ps: scripts/powershell/create-new-feature.ps1 "{ARGS}"
+---
+
+## User Input
+
+```text
+$ARGUMENTS
+```
+
+Given the feature description above:
+
+1. **Create the feature branch** by running the script:
+   - Bash: `{SCRIPT} --json --short-name "<short-name>" "<description>"`
+   - The JSON output contains BRANCH_NAME and SPEC_FILE paths.
+
+2. **Read the spec-template** to see the sections you need to fill.
+
+3. **Write the specification** to SPEC_FILE, replacing the placeholders in each section
+   (Overview, Requirements, Acceptance Criteria) with details from the user's description.

presets/scaffold/preset.yml

@@ -0,0 +1,91 @@
+schema_version: "1.0"
+
+preset:
+  # CUSTOMIZE: Change 'my-preset' to your preset ID (lowercase, hyphen-separated)
+  id: "my-preset"
+
+  # CUSTOMIZE: Human-readable name for your preset
+  name: "My Preset"
+
+  # CUSTOMIZE: Update version when releasing (semantic versioning: X.Y.Z)
+  version: "1.0.0"
+
+  # CUSTOMIZE: Brief description (under 200 characters)
+  description: "Brief description of what your preset provides"
+
+  # CUSTOMIZE: Your name or organization name
+  author: "Your Name"
+
+  # CUSTOMIZE: GitHub repository URL (create before publishing)
+  repository: "https://github.com/your-org/spec-kit-preset-my-preset"
+
+  # REVIEW: License (MIT is recommended for open source)
+  license: "MIT"
+
+# Requirements for this preset
+requires:
+  # CUSTOMIZE: Minimum spec-kit version required
+  speckit_version: ">=0.1.0"
+
+# Templates provided by this preset
+provides:
+  templates:
+    # CUSTOMIZE: Define your template overrides
+    # Templates are document scaffolds (spec-template.md, plan-template.md, etc.)
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Custom feature specification template"
+      replaces: "spec-template"  # Which core template this overrides (optional)
+
+    # ADD MORE TEMPLATES: Copy this block for each template
+    # - type: "template"
+    #   name: "plan-template"
+    #   file: "templates/plan-template.md"
+    #   description: "Custom plan template"
+    #   replaces: "plan-template"
+
+    # OVERRIDE EXTENSION TEMPLATES:
+    # Presets sit above extensions in the resolution stack, so you can
+    # override templates provided by any installed extension.
+    # For example, if the "myext" extension provides a spec-template,
+    # the preset's version above will take priority automatically.
+
+    # Override a template provided by the "myext" extension:
+    - type: "template"
+      name: "myext-template"
+      file: "templates/myext-template.md"
+      description: "Override myext's report template"
+      replaces: "myext-template"
+
+    # Command overrides (AI agent workflow prompts)
+    # Presets can override both core and extension commands.
+    # Commands are automatically registered into all detected agent
+    # directories (.claude/commands/, .gemini/commands/, etc.)
+
+    # Override a core command:
+    - type: "command"
+      name: "speckit.specify"
+      file: "commands/speckit.specify.md"
+      description: "Custom specification command"
+      replaces: "speckit.specify"
+
+    # Override an extension command (e.g. from the "myext" extension):
+    - type: "command"
+      name: "speckit.myext.myextcmd"
+      file: "commands/speckit.myext.myextcmd.md"
+      description: "Override myext's myextcmd command with custom workflow"
+      replaces: "speckit.myext.myextcmd"
+
+    # Script templates (reserved for future use)
+    # - type: "script"
+    #   name: "create-new-feature"
+    #   file: "scripts/bash/create-new-feature.sh"
+    #   description: "Custom feature creation script"
+    #   replaces: "create-new-feature"
+
+# CUSTOMIZE: Add relevant tags (2-5 recommended)
+# Used for discovery in catalog
+tags:
+  - "example"
+  - "preset"

presets/scaffold/templates/myext-template.md

@@ -0,0 +1,24 @@
+# MyExt Report
+
+> This template overrides the one provided by the "myext" extension.
+> Customize it to match your needs.
+
+## Summary
+
+Brief summary of the report.
+
+## Details
+
+- Detail 1
+- Detail 2
+
+## Actions
+
+- [ ] Action 1
+- [ ] Action 2
+
+<!--
+  CUSTOMIZE: This template takes priority over the myext extension's
+  version of myext-template. The extension's original is still available
+  if you remove this preset.
+-->

presets/scaffold/templates/spec-template.md

@@ -0,0 +1,18 @@
+# Feature Specification: [FEATURE NAME]
+
+**Created**: [DATE]
+**Status**: Draft
+
+## Overview
+
+[Brief description of the feature]
+
+## Requirements
+
+- [ ] Requirement 1
+- [ ] Requirement 2
+
+## Acceptance Criteria
+
+- [ ] Criterion 1
+- [ ] Criterion 2

presets/self-test/commands/speckit.specify.md

@@ -0,0 +1,15 @@
+---
+description: "Self-test override of the specify command"
+---
+
+<!-- preset:self-test -->
+
+You are following the self-test preset's version of the specify command.
+
+When creating a specification, follow this process:
+
+1. Read the user's requirements from $ARGUMENTS
+2. Create a specification document using the spec-template
+3. Include all standard sections plus the self-test marker
+
+> This command is provided by the self-test preset.

presets/self-test/preset.yml

@@ -0,0 +1,61 @@
+schema_version: "1.0"
+
+preset:
+  id: "self-test"
+  name: "Self-Test Preset"
+  version: "1.0.0"
+  description: "A preset that overrides all core templates for testing purposes"
+  author: "github"
+  repository: "https://github.com/github/spec-kit"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+provides:
+  templates:
+    - type: "template"
+      name: "spec-template"
+      file: "templates/spec-template.md"
+      description: "Self-test spec template"
+      replaces: "spec-template"
+
+    - type: "template"
+      name: "plan-template"
+      file: "templates/plan-template.md"
+      description: "Self-test plan template"
+      replaces: "plan-template"
+
+    - type: "template"
+      name: "tasks-template"
+      file: "templates/tasks-template.md"
+      description: "Self-test tasks template"
+      replaces: "tasks-template"
+
+    - type: "template"
+      name: "checklist-template"
+      file: "templates/checklist-template.md"
+      description: "Self-test checklist template"
+      replaces: "checklist-template"
+
+    - type: "template"
+      name: "constitution-template"
+      file: "templates/constitution-template.md"
+      description: "Self-test constitution template"
+      replaces: "constitution-template"
+
+    - type: "template"
+      name: "agent-file-template"
+      file: "templates/agent-file-template.md"
+      description: "Self-test agent file template"
+      replaces: "agent-file-template"
+
+    - type: "command"
+      name: "speckit.specify"
+      file: "commands/speckit.specify.md"
+      description: "Self-test override of the specify command"
+      replaces: "speckit.specify"
+
+tags:
+  - "testing"
+  - "self-test"

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

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

presets/self-test/templates/checklist-template.md

@@ -0,0 +1,15 @@
+# Checklist (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Pre-Implementation
+
+- [ ] Spec reviewed
+- [ ] Plan approved
+
+## Post-Implementation
+
+- [ ] Tests passing
+- [ ] Documentation updated

presets/self-test/templates/constitution-template.md

@@ -0,0 +1,15 @@
+# Constitution (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Principles
+
+1. Principle 1
+2. Principle 2
+
+## Guidelines
+
+- Guideline 1
+- Guideline 2

presets/self-test/templates/plan-template.md

@@ -0,0 +1,22 @@
+# Implementation Plan (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Approach
+
+Describe the implementation approach.
+
+## Steps
+
+1. Step 1
+2. Step 2
+
+## Dependencies
+
+- Dependency 1
+
+## Risks
+
+- Risk 1

presets/self-test/templates/spec-template.md

@@ -0,0 +1,23 @@
+# Feature Specification (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Overview
+
+Brief description of the feature.
+
+## Requirements
+
+- Requirement 1
+- Requirement 2
+
+## Design
+
+Describe the design approach.
+
+## Acceptance Criteria
+
+- [ ] Criterion 1
+- [ ] Criterion 2

presets/self-test/templates/tasks-template.md

@@ -0,0 +1,17 @@
+# Tasks (Self-Test Preset)
+
+<!-- preset:self-test -->
+
+> This template is provided by the self-test preset.
+
+## Task List
+
+- [ ] Task 1
+- [ ] Task 2
+
+## Estimation
+
+| Task | Estimate |
+|------|----------|
+| Task 1 | TBD |
+| Task 2 | TBD |

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.2.1"
+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 = [

scripts/bash/check-prerequisites.sh

@@ -79,15 +79,28 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths and validate branch
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 
 # If paths-only mode, output paths and exit (support JSON + paths-only combined)
 if $PATHS_ONLY; then
     if $JSON_MODE; then
         # Minimal JSON paths payload (no validation performed)
-        printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
-            "$REPO_ROOT" "$CURRENT_BRANCH" "$FEATURE_DIR" "$FEATURE_SPEC" "$IMPL_PLAN" "$TASKS"
+        if has_jq; then
+            jq -cn \
+                --arg repo_root "$REPO_ROOT" \
+                --arg branch "$CURRENT_BRANCH" \
+                --arg feature_dir "$FEATURE_DIR" \
+                --arg feature_spec "$FEATURE_SPEC" \
+                --arg impl_plan "$IMPL_PLAN" \
+                --arg tasks "$TASKS" \
+                '{REPO_ROOT:$repo_root,BRANCH:$branch,FEATURE_DIR:$feature_dir,FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,TASKS:$tasks}'
+        else
+            printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
+                "$(json_escape "$REPO_ROOT")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$TASKS")"
+        fi
     else
         echo "REPO_ROOT: $REPO_ROOT"
         echo "BRANCH: $CURRENT_BRANCH"
@@ -141,14 +154,25 @@ fi
 # Output results
 if $JSON_MODE; then
     # Build JSON array of documents
-    if [[ ${#docs[@]} -eq 0 ]]; then
-        json_docs="[]"
+    if has_jq; then
+        if [[ ${#docs[@]} -eq 0 ]]; then
+            json_docs="[]"
+        else
+            json_docs=$(printf '%s\n' "${docs[@]}" | jq -R . | jq -s .)
+        fi
+        jq -cn \
+            --arg feature_dir "$FEATURE_DIR" \
+            --argjson docs "$json_docs" \
+            '{FEATURE_DIR:$feature_dir,AVAILABLE_DOCS:$docs}'
     else
-        json_docs=$(printf '"%s",' "${docs[@]}")
-        json_docs="[${json_docs%,}]"
+        if [[ ${#docs[@]} -eq 0 ]]; then
+            json_docs="[]"
+        else
+            json_docs=$(printf '"%s",' "${docs[@]}")
+            json_docs="[${json_docs%,}]"
+        fi
+        printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"
     fi
-    
-    printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$FEATURE_DIR" "$json_docs"
 else
     # Text output
     echo "FEATURE_DIR:$FEATURE_DIR"

scripts/bash/common.sh

@@ -120,7 +120,7 @@ find_feature_dir_by_prefix() {
         # Multiple matches - this shouldn't happen with proper naming convention
         echo "ERROR: Multiple spec directories found with prefix '$prefix': ${matches[*]}" >&2
         echo "Please ensure only one spec directory exists per numeric prefix." >&2
-        echo "$specs_dir/$branch_name"  # Return something to avoid breaking the script
+        return 1
     fi
 }
 
@@ -134,23 +134,120 @@ get_feature_paths() {
     fi
 
     # Use prefix-based lookup to support multiple branches per spec
-    local feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch")
+    local feature_dir
+    if ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
+        echo "ERROR: Failed to resolve feature directory" >&2
+        return 1
+    fi
 
-    cat <<EOF
-REPO_ROOT='$repo_root'
-CURRENT_BRANCH='$current_branch'
-HAS_GIT='$has_git_repo'
-FEATURE_DIR='$feature_dir'
-FEATURE_SPEC='$feature_dir/spec.md'
-IMPL_PLAN='$feature_dir/plan.md'
-TASKS='$feature_dir/tasks.md'
-RESEARCH='$feature_dir/research.md'
-DATA_MODEL='$feature_dir/data-model.md'
-QUICKSTART='$feature_dir/quickstart.md'
-CONTRACTS_DIR='$feature_dir/contracts'
-EOF
+    # Use printf '%q' to safely quote values, preventing shell injection
+    # via crafted branch names or paths containing special characters
+    printf 'REPO_ROOT=%q\n' "$repo_root"
+    printf 'CURRENT_BRANCH=%q\n' "$current_branch"
+    printf 'HAS_GIT=%q\n' "$has_git_repo"
+    printf 'FEATURE_DIR=%q\n' "$feature_dir"
+    printf 'FEATURE_SPEC=%q\n' "$feature_dir/spec.md"
+    printf 'IMPL_PLAN=%q\n' "$feature_dir/plan.md"
+    printf 'TASKS=%q\n' "$feature_dir/tasks.md"
+    printf 'RESEARCH=%q\n' "$feature_dir/research.md"
+    printf 'DATA_MODEL=%q\n' "$feature_dir/data-model.md"
+    printf 'QUICKSTART=%q\n' "$feature_dir/quickstart.md"
+    printf 'CONTRACTS_DIR=%q\n' "$feature_dir/contracts"
+}
+
+# Check if jq is available for safe JSON construction
+has_jq() {
+    command -v jq >/dev/null 2>&1
+}
+
+# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
+# Handles backslash, double-quote, and control characters (newline, tab, carriage return).
+json_escape() {
+    local s="$1"
+    s="${s//\\/\\\\}"
+    s="${s//\"/\\\"}"
+    s="${s//$'\n'/\\n}"
+    s="${s//$'\t'/\\t}"
+    s="${s//$'\r'/\\r}"
+    printf '%s' "$s"
 }
 
 check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 check_dir() { [[ -d "$1" && -n $(ls -A "$1" 2>/dev/null) ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 
+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+resolve_template() {
+    local template_name="$1"
+    local repo_root="$2"
+    local base="$repo_root/.specify/templates"
+
+    # Priority 1: Project overrides
+    local override="$base/overrides/${template_name}.md"
+    [ -f "$override" ] && echo "$override" && return 0
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    local presets_dir="$repo_root/.specify/presets"
+    if [ -d "$presets_dir" ]; then
+        local registry_file="$presets_dir/.registry"
+        if [ -f "$registry_file" ] && command -v python3 >/dev/null 2>&1; then
+            # Read preset IDs sorted by priority (lower number = higher precedence)
+            local sorted_presets
+            sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
+import json, sys, os
+try:
+    with open(os.environ['SPECKIT_REGISTRY']) as f:
+        data = json.load(f)
+    presets = data.get('presets', {})
+    for pid, meta in sorted(presets.items(), key=lambda x: x[1].get('priority', 10)):
+        print(pid)
+except Exception:
+    sys.exit(1)
+" 2>/dev/null)
+            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 returned empty list — fall through to directory scan
+                for preset in "$presets_dir"/*/; do
+                    [ -d "$preset" ] || continue
+                    local candidate="$preset/templates/${template_name}.md"
+                    [ -f "$candidate" ] && echo "$candidate" && return 0
+                done
+            fi
+        else
+            # Fallback: alphabetical directory order (no python3 available)
+            for preset in "$presets_dir"/*/; do
+                [ -d "$preset" ] || continue
+                local candidate="$preset/templates/${template_name}.md"
+                [ -f "$candidate" ] && echo "$candidate" && return 0
+            done
+        fi
+    fi
+
+    # Priority 3: Extension-provided templates
+    local ext_dir="$repo_root/.specify/extensions"
+    if [ -d "$ext_dir" ]; then
+        for ext in "$ext_dir"/*/; do
+            [ -d "$ext" ] || continue
+            # Skip hidden directories (e.g. .backup, .cache)
+            case "$(basename "$ext")" in .*) continue;; esac
+            local candidate="$ext/templates/${template_name}.md"
+            [ -f "$candidate" ] && echo "$candidate" && return 0
+        done
+    fi
+
+    # Priority 4: Core templates
+    local core="$base/${template_name}.md"
+    [ -f "$core" ] && echo "$core" && return 0
+
+    # Return success with empty output so callers using set -e don't abort;
+    # callers check [ -n "$TEMPLATE" ] to detect "not found".
+    return 0
+}
+

scripts/bash/create-new-feature.sh

@@ -162,10 +162,22 @@ 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.
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/common.sh"
 
 if git rev-parse --show-toplevel >/dev/null 2>&1; then
     REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -296,18 +308,26 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
-TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
+TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT")
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
+if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
 
-# Set the SPECIFY_FEATURE environment variable for the current session
-export SPECIFY_FEATURE="$BRANCH_NAME"
+# Inform the user how to persist the feature variable in their own shell
+printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2
 
 if $JSON_MODE; then
-    printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$BRANCH_NAME" "$SPEC_FILE" "$FEATURE_NUM"
+    if command -v jq >/dev/null 2>&1; then
+        jq -cn \
+            --arg branch_name "$BRANCH_NAME" \
+            --arg spec_file "$SPEC_FILE" \
+            --arg feature_num "$FEATURE_NUM" \
+            '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num}'
+    else
+        printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$(json_escape "$BRANCH_NAME")" "$(json_escape "$SPEC_FILE")" "$(json_escape "$FEATURE_NUM")"
+    fi
 else
     echo "BRANCH_NAME: $BRANCH_NAME"
     echo "SPEC_FILE: $SPEC_FILE"
     echo "FEATURE_NUM: $FEATURE_NUM"
-    echo "SPECIFY_FEATURE environment variable set to: $BRANCH_NAME"
+    printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
 fi

scripts/bash/setup-plan.sh

@@ -28,7 +28,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 
 # Check if we're on a proper feature branch (only for git repos)
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
@@ -37,20 +39,30 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 mkdir -p "$FEATURE_DIR"
 
 # Copy plan template if it exists
-TEMPLATE="$REPO_ROOT/.specify/templates/plan-template.md"
-if [[ -f "$TEMPLATE" ]]; then
+TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT")
+if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
     cp "$TEMPLATE" "$IMPL_PLAN"
     echo "Copied plan template to $IMPL_PLAN"
 else
-    echo "Warning: Plan template not found at $TEMPLATE"
+    echo "Warning: Plan template not found"
     # Create a basic plan file if template doesn't exist
     touch "$IMPL_PLAN"
 fi
 
 # Output results
 if $JSON_MODE; then
-    printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
-        "$FEATURE_SPEC" "$IMPL_PLAN" "$FEATURE_DIR" "$CURRENT_BRANCH" "$HAS_GIT"
+    if has_jq; then
+        jq -cn \
+            --arg feature_spec "$FEATURE_SPEC" \
+            --arg impl_plan "$IMPL_PLAN" \
+            --arg specs_dir "$FEATURE_DIR" \
+            --arg branch "$CURRENT_BRANCH" \
+            --arg has_git "$HAS_GIT" \
+            '{FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,SPECS_DIR:$specs_dir,BRANCH:$branch,HAS_GIT:$has_git}'
+    else
+        printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
+            "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$HAS_GIT")"
+    fi
 else
     echo "FEATURE_SPEC: $FEATURE_SPEC"
     echo "IMPL_PLAN: $IMPL_PLAN" 

scripts/bash/update-agent-context.sh

@@ -53,7 +53,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 
 NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
 AGENT_TYPE="${1:-}"
@@ -71,12 +73,14 @@ AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
 ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
 CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
 QODER_FILE="$REPO_ROOT/QODER.md"
-AMP_FILE="$REPO_ROOT/AGENTS.md"
+# AMP, Kiro CLI, and IBM Bob all share AGENTS.md — use AGENTS_FILE to avoid
+# updating the same file multiple times.
+AMP_FILE="$AGENTS_FILE"
 SHAI_FILE="$REPO_ROOT/SHAI.md"
 TABNINE_FILE="$REPO_ROOT/TABNINE.md"
-KIRO_FILE="$REPO_ROOT/AGENTS.md"
+KIRO_FILE="$AGENTS_FILE"
 AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
-BOB_FILE="$REPO_ROOT/AGENTS.md"
+BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
 
@@ -112,6 +116,8 @@ log_warning() {
 # Cleanup function for temporary files
 cleanup() {
     local exit_code=$?
+    # Disarm traps to prevent re-entrant loop
+    trap - EXIT INT TERM
     rm -f /tmp/agent_update_*_$$
     rm -f /tmp/manual_additions_$$
     exit $exit_code
@@ -476,7 +482,7 @@ update_existing_agent_file() {
         fi
         
         # Update timestamp
-        if [[ "$line" =~ \*\*Last\ updated\*\*:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
+        if [[ "$line" =~ (\*\*)?Last\ updated(\*\*)?:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
             echo "$line" | sed "s/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/$current_date/" >> "$temp_file"
         else
             echo "$line" >> "$temp_file"
@@ -607,67 +613,67 @@ update_specific_agent() {
     
     case "$agent_type" in
         claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code"
+            update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
             ;;
         gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI"
+            update_agent_file "$GEMINI_FILE" "Gemini CLI" || return 1
             ;;
         copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot"
+            update_agent_file "$COPILOT_FILE" "GitHub Copilot" || return 1
             ;;
         cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE"
+            update_agent_file "$CURSOR_FILE" "Cursor IDE" || return 1
             ;;
         qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code"
+            update_agent_file "$QWEN_FILE" "Qwen Code" || return 1
             ;;
         opencode)
-            update_agent_file "$AGENTS_FILE" "opencode"
+            update_agent_file "$AGENTS_FILE" "opencode" || return 1
             ;;
         codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI"
+            update_agent_file "$AGENTS_FILE" "Codex CLI" || return 1
             ;;
         windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf"
+            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
             ;;
         kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code"
+            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
             ;;
         auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI"
+            update_agent_file "$AUGGIE_FILE" "Auggie CLI" || return 1
             ;;
         roo)
-            update_agent_file "$ROO_FILE" "Roo Code"
+            update_agent_file "$ROO_FILE" "Roo Code" || return 1
             ;;
         codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
+            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI" || return 1
             ;;
         qodercli)
-            update_agent_file "$QODER_FILE" "Qoder CLI"
+            update_agent_file "$QODER_FILE" "Qoder CLI" || return 1
             ;;
         amp)
-            update_agent_file "$AMP_FILE" "Amp"
+            update_agent_file "$AMP_FILE" "Amp" || return 1
             ;;
         shai)
-            update_agent_file "$SHAI_FILE" "SHAI"
+            update_agent_file "$SHAI_FILE" "SHAI" || return 1
             ;;
         tabnine)
-            update_agent_file "$TABNINE_FILE" "Tabnine CLI"
+            update_agent_file "$TABNINE_FILE" "Tabnine CLI" || return 1
             ;;
         kiro-cli)
-            update_agent_file "$KIRO_FILE" "Kiro CLI"
+            update_agent_file "$KIRO_FILE" "Kiro CLI" || return 1
             ;;
         agy)
-            update_agent_file "$AGY_FILE" "Antigravity"
+            update_agent_file "$AGY_FILE" "Antigravity" || return 1
             ;;
         bob)
-            update_agent_file "$BOB_FILE" "IBM Bob"
+            update_agent_file "$BOB_FILE" "IBM Bob" || return 1
             ;;
         vibe)
-            update_agent_file "$VIBE_FILE" "Mistral Vibe"
+            update_agent_file "$VIBE_FILE" "Mistral Vibe" || return 1
             ;;
         kimi)
-            update_agent_file "$KIMI_FILE" "Kimi Code"
+            update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
             ;;
         generic)
             log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
@@ -682,106 +688,53 @@ update_specific_agent() {
 
 update_all_existing_agents() {
     local found_agent=false
-    
-    # Check each possible agent file and update if it exists
-    if [[ -f "$CLAUDE_FILE" ]]; then
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$GEMINI_FILE" ]]; then
-        update_agent_file "$GEMINI_FILE" "Gemini CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$COPILOT_FILE" ]]; then
-        update_agent_file "$COPILOT_FILE" "GitHub Copilot"
-        found_agent=true
-    fi
-    
-    if [[ -f "$CURSOR_FILE" ]]; then
-        update_agent_file "$CURSOR_FILE" "Cursor IDE"
-        found_agent=true
-    fi
-    
-    if [[ -f "$QWEN_FILE" ]]; then
-        update_agent_file "$QWEN_FILE" "Qwen Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$AGENTS_FILE" ]]; then
-        update_agent_file "$AGENTS_FILE" "Codex/opencode"
-        found_agent=true
-    fi
-    
-    if [[ -f "$WINDSURF_FILE" ]]; then
-        update_agent_file "$WINDSURF_FILE" "Windsurf"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KILOCODE_FILE" ]]; then
-        update_agent_file "$KILOCODE_FILE" "Kilo Code"
-        found_agent=true
-    fi
+    local _updated_paths=()
 
-    if [[ -f "$AUGGIE_FILE" ]]; then
-        update_agent_file "$AUGGIE_FILE" "Auggie CLI"
+    # 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+=("$real_path")
         found_agent=true
-    fi
-    
-    if [[ -f "$ROO_FILE" ]]; then
-        update_agent_file "$ROO_FILE" "Roo Code"
-        found_agent=true
-    fi
+    }
 
-    if [[ -f "$CODEBUDDY_FILE" ]]; then
-        update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
-        found_agent=true
-    fi
+    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 [[ -f "$SHAI_FILE" ]]; then
-        update_agent_file "$SHAI_FILE" "SHAI"
-        found_agent=true
-    fi
-
-    if [[ -f "$TABNINE_FILE" ]]; then
-        update_agent_file "$TABNINE_FILE" "Tabnine CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$QODER_FILE" ]]; then
-        update_agent_file "$QODER_FILE" "Qoder CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$KIRO_FILE" ]]; then
-        update_agent_file "$KIRO_FILE" "Kiro CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$AGY_FILE" ]]; then
-        update_agent_file "$AGY_FILE" "Antigravity"
-        found_agent=true
-    fi
-    if [[ -f "$BOB_FILE" ]]; then
-        update_agent_file "$BOB_FILE" "IBM Bob"
-        found_agent=true
-    fi
-
-    if [[ -f "$VIBE_FILE" ]]; then
-        update_agent_file "$VIBE_FILE" "Mistral Vibe"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KIMI_FILE" ]]; then
-        update_agent_file "$KIMI_FILE" "Kimi Code"
-        found_agent=true
-    fi
-    
     # If no agent files exist, create a default Claude file
     if [[ "$found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
+        update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
     fi
 }
 print_summary() {

scripts/powershell/common.ps1

@@ -135,3 +135,70 @@ function Test-DirHasFiles {
     }
 }
 
+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+function Resolve-Template {
+    param(
+        [Parameter(Mandatory=$true)][string]$TemplateName,
+        [Parameter(Mandatory=$true)][string]$RepoRoot
+    )
+
+    $base = Join-Path $RepoRoot '.specify/templates'
+
+    # Priority 1: Project overrides
+    $override = Join-Path $base "overrides/$TemplateName.md"
+    if (Test-Path $override) { return $override }
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    $presetsDir = Join-Path $RepoRoot '.specify/presets'
+    if (Test-Path $presetsDir) {
+        $registryFile = Join-Path $presetsDir '.registry'
+        $sortedPresets = @()
+        if (Test-Path $registryFile) {
+            try {
+                $registryData = Get-Content $registryFile -Raw | ConvertFrom-Json
+                $presets = $registryData.presets
+                if ($presets) {
+                    $sortedPresets = $presets.PSObject.Properties |
+                        Sort-Object { if ($null -ne $_.Value.priority) { $_.Value.priority } else { 10 } } |
+                        ForEach-Object { $_.Name }
+                }
+            } catch {
+                # Fallback: alphabetical directory order
+                $sortedPresets = @()
+            }
+        }
+
+        if ($sortedPresets.Count -gt 0) {
+            foreach ($presetId in $sortedPresets) {
+                $candidate = Join-Path $presetsDir "$presetId/templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        } else {
+            # Fallback: alphabetical directory order
+            foreach ($preset in Get-ChildItem -Path $presetsDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' }) {
+                $candidate = Join-Path $preset.FullName "templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        }
+    }
+
+    # Priority 3: Extension-provided templates
+    $extDir = Join-Path $RepoRoot '.specify/extensions'
+    if (Test-Path $extDir) {
+        foreach ($ext in Get-ChildItem -Path $extDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' } | Sort-Object Name) {
+            $candidate = Join-Path $ext.FullName "templates/$TemplateName.md"
+            if (Test-Path $candidate) { return $candidate }
+        }
+    }
+
+    # Priority 4: Core templates
+    $core = Join-Path $base "$TemplateName.md"
+    if (Test-Path $core) { return $core }
+
+    return $null
+}
+

scripts/powershell/create-new-feature.ps1

@@ -141,6 +141,9 @@ if (-not $fallbackRoot) {
     exit 1
 }
 
+# Load common functions (includes Resolve-Template)
+. "$PSScriptRoot/common.ps1"
+
 try {
     $repoRoot = git rev-parse --show-toplevel 2>$null
     if ($LASTEXITCODE -eq 0) {
@@ -276,9 +279,9 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
 
-$template = Join-Path $repoRoot '.specify/templates/spec-template.md'
+$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
 $specFile = Join-Path $featureDir 'spec.md'
-if (Test-Path $template) { 
+if ($template -and (Test-Path $template)) { 
     Copy-Item $template $specFile -Force 
 } else { 
     New-Item -ItemType File -Path $specFile | Out-Null 

scripts/powershell/setup-plan.ps1

@@ -32,12 +32,12 @@ if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit $paths.HAS_GI
 New-Item -ItemType Directory -Path $paths.FEATURE_DIR -Force | Out-Null
 
 # Copy plan template if it exists, otherwise note it or create empty file
-$template = Join-Path $paths.REPO_ROOT '.specify/templates/plan-template.md'
-if (Test-Path $template) { 
+$template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
+if ($template -and (Test-Path $template)) { 
     Copy-Item $template $paths.IMPL_PLAN -Force
     Write-Output "Copied plan template to $($paths.IMPL_PLAN)"
 } else {
-    Write-Warning "Plan template not found at $template"
+    Write-Warning "Plan template not found"
     # Create a basic plan file if template doesn't exist
     New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
 }

scripts/powershell/update-agent-context.ps1

@@ -331,7 +331,7 @@ function Update-ExistingAgentFile {
             if ($existingChanges -lt 2) { $output.Add($line); $existingChanges++ }
             continue
         }
-        if ($line -match '\*\*Last updated\*\*: .*\d{4}-\d{2}-\d{2}') {
+        if ($line -match '(\*\*)?Last updated(\*\*)?: .*\d{4}-\d{2}-\d{2}') {
             $output.Add(($line -replace '\d{4}-\d{2}-\d{2}',$Date.ToString('yyyy-MM-dd')))
             continue
         }

src/specify_cli/__init__.py

@@ -34,7 +34,7 @@ import shlex
 import json
 import yaml
 from pathlib import Path
-from typing import Optional, Tuple
+from typing import Any, Optional, Tuple
 
 import typer
 import httpx
@@ -1067,6 +1067,36 @@ def ensure_constitution_from_template(project_path: Path, tracker: StepTracker |
         else:
             console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")
 
+
+INIT_OPTIONS_FILE = ".specify/init-options.json"
+
+
+def save_init_options(project_path: Path, options: dict[str, Any]) -> None:
+    """Persist the CLI options used during ``specify init``.
+
+    Writes a small JSON file to ``.specify/init-options.json`` so that
+    later operations (e.g. preset install) can adapt their behaviour
+    without scanning the filesystem.
+    """
+    dest = project_path / INIT_OPTIONS_FILE
+    dest.parent.mkdir(parents=True, exist_ok=True)
+    dest.write_text(json.dumps(options, indent=2, sort_keys=True))
+
+
+def load_init_options(project_path: Path) -> dict[str, Any]:
+    """Load the init options previously saved by ``specify init``.
+
+    Returns an empty dict if the file does not exist or cannot be parsed.
+    """
+    path = project_path / INIT_OPTIONS_FILE
+    if not path.exists():
+        return {}
+    try:
+        return json.loads(path.read_text())
+    except (json.JSONDecodeError, OSError):
+        return {}
+
+
 # Agent-specific skill directory overrides for agents whose skills directory
 # doesn't follow the standard <agent_folder>/skills/ pattern
 AGENT_SKILLS_DIR_OVERRIDES = {
@@ -1300,6 +1330,7 @@ def init(
     debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
     github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
     ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
+    preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
 ):
     """
     Initialize a new Specify project from the latest template.
@@ -1328,6 +1359,7 @@ def init(
         specify init my-project --ai claude --ai-skills   # Install agent skills
         specify init --here --ai gemini --ai-skills
         specify init my-project --ai generic --ai-commands-dir .myagent/commands/  # Unsupported agent
+        specify init my-project --ai claude --preset healthcare-compliance  # With preset
     """
 
     show_banner()
@@ -1589,6 +1621,50 @@ def init(
             else:
                 tracker.skip("git", "--no-git flag")
 
+            # Persist the CLI options so later operations (e.g. preset add)
+            # can adapt their behaviour without re-scanning the filesystem.
+            # Must be saved BEFORE preset install so _get_skills_dir() works.
+            save_init_options(project_path, {
+                "ai": selected_ai,
+                "ai_skills": ai_skills,
+                "ai_commands_dir": ai_commands_dir,
+                "here": here,
+                "preset": preset,
+                "script": selected_script,
+                "speckit_version": get_speckit_version(),
+            })
+
+            # Install preset if specified
+            if preset:
+                try:
+                    from .presets import PresetManager, PresetCatalog, PresetError
+                    preset_manager = PresetManager(project_path)
+                    speckit_ver = get_speckit_version()
+
+                    # Try local directory first, then catalog
+                    local_path = Path(preset).resolve()
+                    if local_path.is_dir() and (local_path / "preset.yml").exists():
+                        preset_manager.install_from_directory(local_path, speckit_ver)
+                    else:
+                        preset_catalog = PresetCatalog(project_path)
+                        pack_info = preset_catalog.get_pack_info(preset)
+                        if not pack_info:
+                            console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
+                        else:
+                            try:
+                                zip_path = preset_catalog.download_pack(preset)
+                                preset_manager.install_from_zip(zip_path, speckit_ver)
+                                # Clean up downloaded ZIP to avoid cache accumulation
+                                try:
+                                    zip_path.unlink(missing_ok=True)
+                                except OSError:
+                                    # Best-effort cleanup; failure to delete is non-fatal
+                                    pass
+                            except PresetError as preset_err:
+                                console.print(f"[yellow]Warning:[/yellow] Failed to install preset '{preset}': {preset_err}")
+                except Exception as preset_err:
+                    console.print(f"[yellow]Warning:[/yellow] Failed to install preset: {preset_err}")
+
             tracker.complete("final", "project ready")
         except Exception as e:
             tracker.error("final", str(e))
@@ -1826,6 +1902,20 @@ catalog_app = typer.Typer(
 )
 extension_app.add_typer(catalog_app, name="catalog")
 
+preset_app = typer.Typer(
+    name="preset",
+    help="Manage spec-kit presets",
+    add_completion=False,
+)
+app.add_typer(preset_app, name="preset")
+
+preset_catalog_app = typer.Typer(
+    name="catalog",
+    help="Manage preset catalogs",
+    add_completion=False,
+)
+preset_app.add_typer(preset_catalog_app, name="catalog")
+
 
 def get_speckit_version() -> str:
     """Get current spec-kit version."""
@@ -1848,6 +1938,490 @@ def get_speckit_version() -> str:
     return "unknown"
 
 
+# ===== Preset Commands =====
+
+
+@preset_app.command("list")
+def preset_list():
+    """List installed presets."""
+    from .presets import PresetManager
+
+    project_root = Path.cwd()
+
+    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)
+
+    manager = PresetManager(project_root)
+    installed = manager.list_installed()
+
+    if not installed:
+        console.print("[yellow]No presets installed.[/yellow]")
+        console.print("\nInstall a preset with:")
+        console.print("  [cyan]specify preset add <pack-name>[/cyan]")
+        return
+
+    console.print("\n[bold cyan]Installed Presets:[/bold cyan]\n")
+    for pack in installed:
+        status = "[green]enabled[/green]" if pack.get("enabled", True) else "[red]disabled[/red]"
+        pri = pack.get('priority', 10)
+        console.print(f"  [bold]{pack['name']}[/bold] ({pack['id']}) v{pack['version']} — {status} — priority {pri}")
+        console.print(f"    {pack['description']}")
+        if pack.get("tags"):
+            tags_str = ", ".join(pack["tags"])
+            console.print(f"    [dim]Tags: {tags_str}[/dim]")
+        console.print(f"    [dim]Templates: {pack['template_count']}[/dim]")
+        console.print()
+
+
+@preset_app.command("add")
+def preset_add(
+    pack_id: str = typer.Argument(None, help="Preset ID to install from catalog"),
+    from_url: str = typer.Option(None, "--from", help="Install from a URL (ZIP file)"),
+    dev: str = typer.Option(None, "--dev", help="Install from local directory (development mode)"),
+    priority: int = typer.Option(10, "--priority", help="Resolution priority (lower = higher precedence, default 10)"),
+):
+    """Install a preset."""
+    from .presets import (
+        PresetManager,
+        PresetCatalog,
+        PresetError,
+        PresetValidationError,
+        PresetCompatibilityError,
+    )
+
+    project_root = Path.cwd()
+
+    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)
+
+    manager = PresetManager(project_root)
+    speckit_version = get_speckit_version()
+
+    try:
+        if dev:
+            dev_path = Path(dev).resolve()
+            if not dev_path.exists():
+                console.print(f"[red]Error:[/red] Directory not found: {dev}")
+                raise typer.Exit(1)
+
+            console.print(f"Installing preset from [cyan]{dev_path}[/cyan]...")
+            manifest = manager.install_from_directory(dev_path, speckit_version, priority)
+            console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")
+
+        elif from_url:
+            # Validate URL scheme before downloading
+            from urllib.parse import urlparse as _urlparse
+            _parsed = _urlparse(from_url)
+            _is_localhost = _parsed.hostname in ("localhost", "127.0.0.1", "::1")
+            if _parsed.scheme != "https" and not (_parsed.scheme == "http" and _is_localhost):
+                console.print(f"[red]Error:[/red] URL must use HTTPS (got {_parsed.scheme}://). HTTP is only allowed for localhost.")
+                raise typer.Exit(1)
+
+            console.print(f"Installing preset from [cyan]{from_url}[/cyan]...")
+            import urllib.request
+            import urllib.error
+            import tempfile
+
+            with tempfile.TemporaryDirectory() as tmpdir:
+                zip_path = Path(tmpdir) / "preset.zip"
+                try:
+                    with urllib.request.urlopen(from_url, timeout=60) as response:
+                        zip_path.write_bytes(response.read())
+                except urllib.error.URLError as e:
+                    console.print(f"[red]Error:[/red] Failed to download: {e}")
+                    raise typer.Exit(1)
+
+                manifest = manager.install_from_zip(zip_path, speckit_version, priority)
+
+            console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")
+
+        elif pack_id:
+            catalog = PresetCatalog(project_root)
+            pack_info = catalog.get_pack_info(pack_id)
+
+            if not pack_info:
+                console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in catalog")
+                raise typer.Exit(1)
+
+            if not pack_info.get("_install_allowed", True):
+                catalog_name = pack_info.get("_catalog_name", "unknown")
+                console.print(f"[red]Error:[/red] Preset '{pack_id}' is from the '{catalog_name}' catalog which is discovery-only (install not allowed).")
+                console.print("Add the catalog with --install-allowed or install from the preset's repository directly with --from.")
+                raise typer.Exit(1)
+
+            console.print(f"Installing preset [cyan]{pack_info.get('name', pack_id)}[/cyan]...")
+
+            try:
+                zip_path = catalog.download_pack(pack_id)
+                manifest = manager.install_from_zip(zip_path, speckit_version, priority)
+                console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")
+            finally:
+                if 'zip_path' in locals() and zip_path.exists():
+                    zip_path.unlink(missing_ok=True)
+        else:
+            console.print("[red]Error:[/red] Specify a preset ID, --from URL, or --dev path")
+            raise typer.Exit(1)
+
+    except PresetCompatibilityError as e:
+        console.print(f"[red]Compatibility Error:[/red] {e}")
+        raise typer.Exit(1)
+    except PresetValidationError as e:
+        console.print(f"[red]Validation Error:[/red] {e}")
+        raise typer.Exit(1)
+    except PresetError as e:
+        console.print(f"[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+
+@preset_app.command("remove")
+def preset_remove(
+    pack_id: str = typer.Argument(..., help="Preset ID to remove"),
+):
+    """Remove an installed preset."""
+    from .presets import PresetManager
+
+    project_root = Path.cwd()
+
+    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)
+
+    manager = PresetManager(project_root)
+
+    if not manager.registry.is_installed(pack_id):
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' is not installed")
+        raise typer.Exit(1)
+
+    if manager.remove(pack_id):
+        console.print(f"[green]✓[/green] Preset '{pack_id}' removed successfully")
+    else:
+        console.print(f"[red]Error:[/red] Failed to remove preset '{pack_id}'")
+        raise typer.Exit(1)
+
+
+@preset_app.command("search")
+def preset_search(
+    query: str = typer.Argument(None, help="Search query"),
+    tag: str = typer.Option(None, "--tag", help="Filter by tag"),
+    author: str = typer.Option(None, "--author", help="Filter by author"),
+):
+    """Search for presets in the catalog."""
+    from .presets import PresetCatalog, PresetError
+
+    project_root = Path.cwd()
+
+    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)
+
+    catalog = PresetCatalog(project_root)
+
+    try:
+        results = catalog.search(query=query, tag=tag, author=author)
+    except PresetError as e:
+        console.print(f"[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+    if not results:
+        console.print("[yellow]No presets found matching your criteria.[/yellow]")
+        return
+
+    console.print(f"\n[bold cyan]Presets ({len(results)} found):[/bold cyan]\n")
+    for pack in results:
+        console.print(f"  [bold]{pack.get('name', pack['id'])}[/bold] ({pack['id']}) v{pack.get('version', '?')}")
+        console.print(f"    {pack.get('description', '')}")
+        if pack.get("tags"):
+            tags_str = ", ".join(pack["tags"])
+            console.print(f"    [dim]Tags: {tags_str}[/dim]")
+        console.print()
+
+
+@preset_app.command("resolve")
+def preset_resolve(
+    template_name: str = typer.Argument(..., help="Template name to resolve (e.g., spec-template)"),
+):
+    """Show which template will be resolved for a given name."""
+    from .presets import PresetResolver
+
+    project_root = Path.cwd()
+
+    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)
+
+    resolver = PresetResolver(project_root)
+    result = resolver.resolve_with_source(template_name)
+
+    if result:
+        console.print(f"  [bold]{template_name}[/bold]: {result['path']}")
+        console.print(f"    [dim](from: {result['source']})[/dim]")
+    else:
+        console.print(f"  [yellow]{template_name}[/yellow]: not found")
+        console.print("    [dim]No template with this name exists in the resolution stack[/dim]")
+
+
+@preset_app.command("info")
+def preset_info(
+    pack_id: str = typer.Argument(..., help="Preset ID to get info about"),
+):
+    """Show detailed information about a preset."""
+    from .presets import PresetCatalog, PresetManager, PresetError
+
+    project_root = Path.cwd()
+
+    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)
+
+    # Check if installed locally first
+    manager = PresetManager(project_root)
+    local_pack = manager.get_pack(pack_id)
+
+    if local_pack:
+        console.print(f"\n[bold cyan]Preset: {local_pack.name}[/bold cyan]\n")
+        console.print(f"  ID:          {local_pack.id}")
+        console.print(f"  Version:     {local_pack.version}")
+        console.print(f"  Description: {local_pack.description}")
+        if local_pack.author:
+            console.print(f"  Author:      {local_pack.author}")
+        if local_pack.tags:
+            console.print(f"  Tags:        {', '.join(local_pack.tags)}")
+        console.print(f"  Templates:   {len(local_pack.templates)}")
+        for tmpl in local_pack.templates:
+            console.print(f"    - {tmpl['name']} ({tmpl['type']}): {tmpl.get('description', '')}")
+        repo = local_pack.data.get("preset", {}).get("repository")
+        if repo:
+            console.print(f"  Repository:  {repo}")
+        license_val = local_pack.data.get("preset", {}).get("license")
+        if license_val:
+            console.print(f"  License:     {license_val}")
+        console.print("\n  [green]Status: installed[/green]")
+        console.print()
+        return
+
+    # Fall back to catalog
+    catalog = PresetCatalog(project_root)
+    try:
+        pack_info = catalog.get_pack_info(pack_id)
+    except PresetError:
+        pack_info = None
+
+    if not pack_info:
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found (not installed and not in catalog)")
+        raise typer.Exit(1)
+
+    console.print(f"\n[bold cyan]Preset: {pack_info.get('name', pack_id)}[/bold cyan]\n")
+    console.print(f"  ID:          {pack_info['id']}")
+    console.print(f"  Version:     {pack_info.get('version', '?')}")
+    console.print(f"  Description: {pack_info.get('description', '')}")
+    if pack_info.get("author"):
+        console.print(f"  Author:      {pack_info['author']}")
+    if pack_info.get("tags"):
+        console.print(f"  Tags:        {', '.join(pack_info['tags'])}")
+    if pack_info.get("repository"):
+        console.print(f"  Repository:  {pack_info['repository']}")
+    if pack_info.get("license"):
+        console.print(f"  License:     {pack_info['license']}")
+    console.print("\n  [yellow]Status: not installed[/yellow]")
+    console.print(f"  Install with: [cyan]specify preset add {pack_id}[/cyan]")
+    console.print()
+
+
+# ===== Preset Catalog Commands =====
+
+
+@preset_catalog_app.command("list")
+def preset_catalog_list():
+    """List all active preset catalogs."""
+    from .presets import PresetCatalog, PresetValidationError
+
+    project_root = Path.cwd()
+
+    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)
+
+    catalog = PresetCatalog(project_root)
+
+    try:
+        active_catalogs = catalog.get_active_catalogs()
+    except PresetValidationError as e:
+        console.print(f"[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+    console.print("\n[bold cyan]Active Preset Catalogs:[/bold cyan]\n")
+    for entry in active_catalogs:
+        install_str = (
+            "[green]install allowed[/green]"
+            if entry.install_allowed
+            else "[yellow]discovery only[/yellow]"
+        )
+        console.print(f"  [bold]{entry.name}[/bold] (priority {entry.priority})")
+        if entry.description:
+            console.print(f"     {entry.description}")
+        console.print(f"     URL: {entry.url}")
+        console.print(f"     Install: {install_str}")
+        console.print()
+
+    config_path = project_root / ".specify" / "preset-catalogs.yml"
+    user_config_path = Path.home() / ".specify" / "preset-catalogs.yml"
+    if os.environ.get("SPECKIT_PRESET_CATALOG_URL"):
+        console.print("[dim]Catalog configured via SPECKIT_PRESET_CATALOG_URL environment variable.[/dim]")
+    else:
+        try:
+            proj_loaded = config_path.exists() and catalog._load_catalog_config(config_path) is not None
+        except PresetValidationError:
+            proj_loaded = False
+        if proj_loaded:
+            console.print(f"[dim]Config: {config_path.relative_to(project_root)}[/dim]")
+        else:
+            try:
+                user_loaded = user_config_path.exists() and catalog._load_catalog_config(user_config_path) is not None
+            except PresetValidationError:
+                user_loaded = False
+            if user_loaded:
+                console.print("[dim]Config: ~/.specify/preset-catalogs.yml[/dim]")
+            else:
+                console.print("[dim]Using built-in default catalog stack.[/dim]")
+                console.print(
+                    "[dim]Add .specify/preset-catalogs.yml to customize.[/dim]"
+                )
+
+
+@preset_catalog_app.command("add")
+def preset_catalog_add(
+    url: str = typer.Argument(help="Catalog URL (must use HTTPS)"),
+    name: str = typer.Option(..., "--name", help="Catalog name"),
+    priority: int = typer.Option(10, "--priority", help="Priority (lower = higher priority)"),
+    install_allowed: bool = typer.Option(
+        False, "--install-allowed/--no-install-allowed",
+        help="Allow presets from this catalog to be installed",
+    ),
+    description: str = typer.Option("", "--description", help="Description of the catalog"),
+):
+    """Add a catalog to .specify/preset-catalogs.yml."""
+    from .presets import PresetCatalog, PresetValidationError
+
+    project_root = Path.cwd()
+
+    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 URL
+    tmp_catalog = PresetCatalog(project_root)
+    try:
+        tmp_catalog._validate_catalog_url(url)
+    except PresetValidationError as e:
+        console.print(f"[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+    config_path = specify_dir / "preset-catalogs.yml"
+
+    # Load existing config
+    if config_path.exists():
+        try:
+            config = yaml.safe_load(config_path.read_text()) or {}
+        except Exception as e:
+            console.print(f"[red]Error:[/red] Failed to read {config_path}: {e}")
+            raise typer.Exit(1)
+    else:
+        config = {}
+
+    catalogs = config.get("catalogs", [])
+    if not isinstance(catalogs, list):
+        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
+        raise typer.Exit(1)
+
+    # Check for duplicate name
+    for existing in catalogs:
+        if isinstance(existing, dict) and existing.get("name") == name:
+            console.print(f"[yellow]Warning:[/yellow] A catalog named '{name}' already exists.")
+            console.print("Use 'specify preset catalog remove' first, or choose a different name.")
+            raise typer.Exit(1)
+
+    catalogs.append({
+        "name": name,
+        "url": url,
+        "priority": priority,
+        "install_allowed": install_allowed,
+        "description": description,
+    })
+
+    config["catalogs"] = catalogs
+    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False))
+
+    install_label = "install allowed" if install_allowed else "discovery only"
+    console.print(f"\n[green]✓[/green] Added catalog '[bold]{name}[/bold]' ({install_label})")
+    console.print(f"  URL: {url}")
+    console.print(f"  Priority: {priority}")
+    console.print(f"\nConfig saved to {config_path.relative_to(project_root)}")
+
+
+@preset_catalog_app.command("remove")
+def preset_catalog_remove(
+    name: str = typer.Argument(help="Catalog name to remove"),
+):
+    """Remove a catalog from .specify/preset-catalogs.yml."""
+    project_root = Path.cwd()
+
+    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)
+
+    config_path = specify_dir / "preset-catalogs.yml"
+    if not config_path.exists():
+        console.print("[red]Error:[/red] No preset catalog config found. Nothing to remove.")
+        raise typer.Exit(1)
+
+    try:
+        config = yaml.safe_load(config_path.read_text()) or {}
+    except Exception:
+        console.print("[red]Error:[/red] Failed to read preset catalog config.")
+        raise typer.Exit(1)
+
+    catalogs = config.get("catalogs", [])
+    if not isinstance(catalogs, list):
+        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
+        raise typer.Exit(1)
+    original_count = len(catalogs)
+    catalogs = [c for c in catalogs if isinstance(c, dict) and c.get("name") != name]
+
+    if len(catalogs) == original_count:
+        console.print(f"[red]Error:[/red] Catalog '{name}' not found.")
+        raise typer.Exit(1)
+
+    config["catalogs"] = catalogs
+    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False))
+
+    console.print(f"[green]✓[/green] Removed catalog '{name}'")
+    if not catalogs:
+        console.print("\n[dim]No catalogs remain in config. Built-in defaults will be used.[/dim]")
+
+
+# ===== Extension Commands =====
+
+
 def _resolve_installed_extension(
     argument: str,
     installed_extensions: list,

src/specify_cli/agents.py

@@ -0,0 +1,422 @@
+"""
+Agent Command Registrar for Spec Kit
+
+Shared infrastructure for registering commands with AI agents.
+Used by both the extension system and the preset system to write
+command files into agent-specific directories in the correct format.
+"""
+
+from pathlib import Path
+from typing import Dict, List, Any
+
+import yaml
+
+
+class CommandRegistrar:
+    """Handles registration of commands with AI agents.
+
+    Supports writing command files in Markdown or TOML format to the
+    appropriate agent directory, with correct argument placeholders
+    and companion files (e.g. Copilot .prompt.md).
+    """
+
+    # Agent configurations with directory, format, and argument placeholder
+    AGENT_CONFIGS = {
+        "claude": {
+            "dir": ".claude/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "gemini": {
+            "dir": ".gemini/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "copilot": {
+            "dir": ".github/agents",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".agent.md"
+        },
+        "cursor": {
+            "dir": ".cursor/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qwen": {
+            "dir": ".qwen/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "opencode": {
+            "dir": ".opencode/command",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codex": {
+            "dir": ".codex/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "windsurf": {
+            "dir": ".windsurf/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kilocode": {
+            "dir": ".kilocode/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "auggie": {
+            "dir": ".augment/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "roo": {
+            "dir": ".roo/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codebuddy": {
+            "dir": ".codebuddy/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qodercli": {
+            "dir": ".qoder/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kiro-cli": {
+            "dir": ".kiro/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "amp": {
+            "dir": ".agents/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "shai": {
+            "dir": ".shai/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "tabnine": {
+            "dir": ".tabnine/agent/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "bob": {
+            "dir": ".bob/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kimi": {
+            "dir": ".kimi/skills",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": "/SKILL.md"
+        }
+    }
+
+    @staticmethod
+    def parse_frontmatter(content: str) -> tuple[dict, str]:
+        """Parse YAML frontmatter from Markdown content.
+
+        Args:
+            content: Markdown content with YAML frontmatter
+
+        Returns:
+            Tuple of (frontmatter_dict, body_content)
+        """
+        if not content.startswith("---"):
+            return {}, content
+
+        # Find second ---
+        end_marker = content.find("---", 3)
+        if end_marker == -1:
+            return {}, content
+
+        frontmatter_str = content[3:end_marker].strip()
+        body = content[end_marker + 3:].strip()
+
+        try:
+            frontmatter = yaml.safe_load(frontmatter_str) or {}
+        except yaml.YAMLError:
+            frontmatter = {}
+
+        return frontmatter, body
+
+    @staticmethod
+    def render_frontmatter(fm: dict) -> str:
+        """Render frontmatter dictionary as YAML.
+
+        Args:
+            fm: Frontmatter dictionary
+
+        Returns:
+            YAML-formatted frontmatter with delimiters
+        """
+        if not fm:
+            return ""
+
+        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False)
+        return f"---\n{yaml_str}---\n"
+
+    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+        """Adjust script paths from extension-relative to repo-relative.
+
+        Args:
+            frontmatter: Frontmatter dictionary
+
+        Returns:
+            Modified frontmatter with adjusted paths
+        """
+        if "scripts" in frontmatter:
+            for key in frontmatter["scripts"]:
+                script_path = frontmatter["scripts"][key]
+                if script_path.startswith("../../scripts/"):
+                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
+        return frontmatter
+
+    def render_markdown_command(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str,
+        context_note: str = None
+    ) -> str:
+        """Render command in Markdown format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+            context_note: Custom context comment (default: <!-- Source: {source_id} -->)
+
+        Returns:
+            Formatted Markdown command file content
+        """
+        if context_note is None:
+            context_note = f"\n<!-- Source: {source_id} -->\n"
+        return self.render_frontmatter(frontmatter) + "\n" + context_note + body
+
+    def render_toml_command(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str
+    ) -> str:
+        """Render command in TOML format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+
+        Returns:
+            Formatted TOML command file content
+        """
+        toml_lines = []
+
+        if "description" in frontmatter:
+            desc = frontmatter["description"].replace('"', '\\"')
+            toml_lines.append(f'description = "{desc}"')
+            toml_lines.append("")
+
+        toml_lines.append(f"# Source: {source_id}")
+        toml_lines.append("")
+
+        toml_lines.append('prompt = """')
+        toml_lines.append(body)
+        toml_lines.append('"""')
+
+        return "\n".join(toml_lines)
+
+    def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
+        """Convert argument placeholder format.
+
+        Args:
+            content: Command content
+            from_placeholder: Source placeholder (e.g., "$ARGUMENTS")
+            to_placeholder: Target placeholder (e.g., "{{args}}")
+
+        Returns:
+            Content with converted placeholders
+        """
+        return content.replace(from_placeholder, to_placeholder)
+
+    def register_commands(
+        self,
+        agent_name: str,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> List[str]:
+        """Register commands for a specific agent.
+
+        Args:
+            agent_name: Agent name (claude, gemini, copilot, etc.)
+            commands: List of command info dicts with 'name', 'file', and optional 'aliases'
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            List of registered command names
+
+        Raises:
+            ValueError: If agent is not supported
+        """
+        if agent_name not in self.AGENT_CONFIGS:
+            raise ValueError(f"Unsupported agent: {agent_name}")
+
+        agent_config = self.AGENT_CONFIGS[agent_name]
+        commands_dir = project_root / agent_config["dir"]
+        commands_dir.mkdir(parents=True, exist_ok=True)
+
+        registered = []
+
+        for cmd_info in commands:
+            cmd_name = cmd_info["name"]
+            cmd_file = cmd_info["file"]
+
+            source_file = source_dir / cmd_file
+            if not source_file.exists():
+                continue
+
+            content = source_file.read_text(encoding="utf-8")
+            frontmatter, body = self.parse_frontmatter(content)
+
+            frontmatter = self._adjust_script_paths(frontmatter)
+
+            body = self._convert_argument_placeholder(
+                body, "$ARGUMENTS", agent_config["args"]
+            )
+
+            if agent_config["format"] == "markdown":
+                output = self.render_markdown_command(frontmatter, body, source_id, context_note)
+            elif agent_config["format"] == "toml":
+                output = self.render_toml_command(frontmatter, body, source_id)
+            else:
+                raise ValueError(f"Unsupported format: {agent_config['format']}")
+
+            dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+            dest_file.parent.mkdir(parents=True, exist_ok=True)
+            dest_file.write_text(output, encoding="utf-8")
+
+            if agent_name == "copilot":
+                self.write_copilot_prompt(project_root, cmd_name)
+
+            registered.append(cmd_name)
+
+            for alias in cmd_info.get("aliases", []):
+                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
+                alias_file.parent.mkdir(parents=True, exist_ok=True)
+                alias_file.write_text(output, encoding="utf-8")
+                if agent_name == "copilot":
+                    self.write_copilot_prompt(project_root, alias)
+                registered.append(alias)
+
+        return registered
+
+    @staticmethod
+    def write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
+        """Generate a companion .prompt.md file for a Copilot agent command.
+
+        Args:
+            project_root: Path to project root
+            cmd_name: Command name (e.g. 'speckit.my-ext.example')
+        """
+        prompts_dir = project_root / ".github" / "prompts"
+        prompts_dir.mkdir(parents=True, exist_ok=True)
+        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
+        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n", encoding="utf-8")
+
+    def register_commands_for_all_agents(
+        self,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> Dict[str, List[str]]:
+        """Register commands for all detected agents in the project.
+
+        Args:
+            commands: List of command info dicts
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            Dictionary mapping agent names to list of registered commands
+        """
+        results = {}
+
+        for agent_name, agent_config in self.AGENT_CONFIGS.items():
+            agent_dir = project_root / agent_config["dir"].split("/")[0]
+
+            if agent_dir.exists():
+                try:
+                    registered = self.register_commands(
+                        agent_name, commands, source_id, source_dir, project_root,
+                        context_note=context_note
+                    )
+                    if registered:
+                        results[agent_name] = registered
+                except ValueError:
+                    continue
+
+        return results
+
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories.
+
+        Args:
+            registered_commands: Dict mapping agent names to command name lists
+            project_root: Path to project root
+        """
+        for agent_name, cmd_names in registered_commands.items():
+            if agent_name not in self.AGENT_CONFIGS:
+                continue
+
+            agent_config = self.AGENT_CONFIGS[agent_name]
+            commands_dir = project_root / agent_config["dir"]
+
+            for cmd_name in cmd_names:
+                cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+                if cmd_file.exists():
+                    cmd_file.unlink()
+
+                if agent_name == "copilot":
+                    prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
+                    if prompt_file.exists():
+                        prompt_file.unlink()

src/specify_cli/extensions.py

@@ -578,23 +578,7 @@ class ExtensionManager:
         # Unregister commands from all AI agents
         if registered_commands:
             registrar = CommandRegistrar()
-            for agent_name, cmd_names in registered_commands.items():
-                if agent_name not in registrar.AGENT_CONFIGS:
-                    continue
-
-                agent_config = registrar.AGENT_CONFIGS[agent_name]
-                commands_dir = self.project_root / agent_config["dir"]
-
-                for cmd_name in cmd_names:
-                    cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
-                    if cmd_file.exists():
-                        cmd_file.unlink()
-
-                    # Also remove companion .prompt.md for Copilot
-                    if agent_name == "copilot":
-                        prompt_file = self.project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
-                        if prompt_file.exists():
-                            prompt_file.unlink()
+            registrar.unregister_commands(registered_commands, self.project_root)
 
         if keep_config:
             # Preserve config files, only remove non-config files
@@ -718,255 +702,47 @@ def version_satisfies(current: str, required: str) -> bool:
 
 
 class CommandRegistrar:
-    """Handles registration of extension commands with AI agents."""
+    """Handles registration of extension commands with AI agents.
 
-    # Agent configurations with directory, format, and argument placeholder
-    AGENT_CONFIGS = {
-        "claude": {
-            "dir": ".claude/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "gemini": {
-            "dir": ".gemini/commands",
-            "format": "toml",
-            "args": "{{args}}",
-            "extension": ".toml"
-        },
-        "copilot": {
-            "dir": ".github/agents",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".agent.md"
-        },
-        "cursor": {
-            "dir": ".cursor/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "qwen": {
-            "dir": ".qwen/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "opencode": {
-            "dir": ".opencode/command",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "codex": {
-            "dir": ".codex/prompts",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "windsurf": {
-            "dir": ".windsurf/workflows",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kilocode": {
-            "dir": ".kilocode/rules",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "auggie": {
-            "dir": ".augment/rules",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "roo": {
-            "dir": ".roo/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "codebuddy": {
-            "dir": ".codebuddy/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "qodercli": {
-            "dir": ".qoder/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kiro-cli": {
-            "dir": ".kiro/prompts",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "amp": {
-            "dir": ".agents/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "shai": {
-            "dir": ".shai/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "tabnine": {
-            "dir": ".tabnine/agent/commands",
-            "format": "toml",
-            "args": "{{args}}",
-            "extension": ".toml"
-        },
-        "bob": {
-            "dir": ".bob/commands",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": ".md"
-        },
-        "kimi": {
-            "dir": ".kimi/skills",
-            "format": "markdown",
-            "args": "$ARGUMENTS",
-            "extension": "/SKILL.md"
-        }
-    }
+    This is a backward-compatible wrapper around the shared CommandRegistrar
+    in agents.py. Extension-specific methods accept ExtensionManifest objects
+    and delegate to the generic API.
+    """
 
+    # Re-export AGENT_CONFIGS at class level for direct attribute access
+    from .agents import CommandRegistrar as _AgentRegistrar
+    AGENT_CONFIGS = _AgentRegistrar.AGENT_CONFIGS
+
+    def __init__(self):
+        from .agents import CommandRegistrar as _Registrar
+        self._registrar = _Registrar()
+
+    # Delegate static/utility methods
     @staticmethod
     def parse_frontmatter(content: str) -> tuple[dict, str]:
-        """Parse YAML frontmatter from Markdown content.
-
-        Args:
-            content: Markdown content with YAML frontmatter
-
-        Returns:
-            Tuple of (frontmatter_dict, body_content)
-        """
-        if not content.startswith("---"):
-            return {}, content
-
-        # Find second ---
-        end_marker = content.find("---", 3)
-        if end_marker == -1:
-            return {}, content
-
-        frontmatter_str = content[3:end_marker].strip()
-        body = content[end_marker + 3:].strip()
-
-        try:
-            frontmatter = yaml.safe_load(frontmatter_str) or {}
-        except yaml.YAMLError:
-            frontmatter = {}
-
-        return frontmatter, body
+        from .agents import CommandRegistrar as _Registrar
+        return _Registrar.parse_frontmatter(content)
 
     @staticmethod
     def render_frontmatter(fm: dict) -> str:
-        """Render frontmatter dictionary as YAML.
+        from .agents import CommandRegistrar as _Registrar
+        return _Registrar.render_frontmatter(fm)
 
-        Args:
-            fm: Frontmatter dictionary
+    @staticmethod
+    def _write_copilot_prompt(project_root, cmd_name: str) -> None:
+        from .agents import CommandRegistrar as _Registrar
+        _Registrar.write_copilot_prompt(project_root, cmd_name)
 
-        Returns:
-            YAML-formatted frontmatter with delimiters
-        """
-        if not fm:
-            return ""
-
-        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False)
-        return f"---\n{yaml_str}---\n"
-
-    def _adjust_script_paths(self, frontmatter: dict) -> dict:
-        """Adjust script paths from extension-relative to repo-relative.
-
-        Args:
-            frontmatter: Frontmatter dictionary
-
-        Returns:
-            Modified frontmatter with adjusted paths
-        """
-        if "scripts" in frontmatter:
-            for key in frontmatter["scripts"]:
-                script_path = frontmatter["scripts"][key]
-                if script_path.startswith("../../scripts/"):
-                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
-        return frontmatter
-
-    def _render_markdown_command(
-        self,
-        frontmatter: dict,
-        body: str,
-        ext_id: str
-    ) -> str:
-        """Render command in Markdown format.
-
-        Args:
-            frontmatter: Command frontmatter
-            body: Command body content
-            ext_id: Extension ID
-
-        Returns:
-            Formatted Markdown command file content
-        """
+    def _render_markdown_command(self, frontmatter, body, ext_id):
+        # Preserve extension-specific comment format for backward compatibility
         context_note = f"\n<!-- Extension: {ext_id} -->\n<!-- Config: .specify/extensions/{ext_id}/ -->\n"
-        return self.render_frontmatter(frontmatter) + "\n" + context_note + body
+        return self._registrar.render_frontmatter(frontmatter) + "\n" + context_note + body
 
-    def _render_toml_command(
-        self,
-        frontmatter: dict,
-        body: str,
-        ext_id: str
-    ) -> str:
-        """Render command in TOML format.
-
-        Args:
-            frontmatter: Command frontmatter
-            body: Command body content
-            ext_id: Extension ID
-
-        Returns:
-            Formatted TOML command file content
-        """
-        # TOML format for Gemini/Qwen
-        toml_lines = []
-
-        # Add description if present
-        if "description" in frontmatter:
-            # Escape quotes in description
-            desc = frontmatter["description"].replace('"', '\\"')
-            toml_lines.append(f'description = "{desc}"')
-            toml_lines.append("")
-
-        # Add extension context as comments
-        toml_lines.append(f"# Extension: {ext_id}")
-        toml_lines.append(f"# Config: .specify/extensions/{ext_id}/")
-        toml_lines.append("")
-
-        # Add prompt content
-        toml_lines.append('prompt = """')
-        toml_lines.append(body)
-        toml_lines.append('"""')
-
-        return "\n".join(toml_lines)
-
-    def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
-        """Convert argument placeholder format.
-
-        Args:
-            content: Command content
-            from_placeholder: Source placeholder (e.g., "$ARGUMENTS")
-            to_placeholder: Target placeholder (e.g., "{{args}}")
-
-        Returns:
-            Content with converted placeholders
-        """
-        return content.replace(from_placeholder, to_placeholder)
+    def _render_toml_command(self, frontmatter, body, ext_id):
+        # Preserve extension-specific context comments for backward compatibility
+        base = self._registrar.render_toml_command(frontmatter, body, ext_id)
+        context_lines = f"# Extension: {ext_id}\n# Config: .specify/extensions/{ext_id}/\n"
+        return base.rstrip("\n") + "\n" + context_lines
 
     def register_commands_for_agent(
         self,
@@ -975,96 +751,14 @@ class CommandRegistrar:
         extension_dir: Path,
         project_root: Path
     ) -> List[str]:
-        """Register extension commands for a specific agent.
-
-        Args:
-            agent_name: Agent name (claude, gemini, copilot, etc.)
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            List of registered command names
-
-        Raises:
-            ExtensionError: If agent is not supported
-        """
+        """Register extension commands for a specific agent."""
         if agent_name not in self.AGENT_CONFIGS:
             raise ExtensionError(f"Unsupported agent: {agent_name}")
-
-        agent_config = self.AGENT_CONFIGS[agent_name]
-        commands_dir = project_root / agent_config["dir"]
-        commands_dir.mkdir(parents=True, exist_ok=True)
-
-        registered = []
-
-        for cmd_info in manifest.commands:
-            cmd_name = cmd_info["name"]
-            cmd_file = cmd_info["file"]
-
-            # Read source command file
-            source_file = extension_dir / cmd_file
-            if not source_file.exists():
-                continue
-
-            content = source_file.read_text()
-            frontmatter, body = self.parse_frontmatter(content)
-
-            # Adjust script paths
-            frontmatter = self._adjust_script_paths(frontmatter)
-
-            # Convert argument placeholders
-            body = self._convert_argument_placeholder(
-                body, "$ARGUMENTS", agent_config["args"]
-            )
-
-            # Render in agent-specific format
-            if agent_config["format"] == "markdown":
-                output = self._render_markdown_command(frontmatter, body, manifest.id)
-            elif agent_config["format"] == "toml":
-                output = self._render_toml_command(frontmatter, body, manifest.id)
-            else:
-                raise ExtensionError(f"Unsupported format: {agent_config['format']}")
-
-            # Write command file
-            dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
-            dest_file.parent.mkdir(parents=True, exist_ok=True)
-            dest_file.write_text(output)
-
-            # Generate companion .prompt.md for Copilot agents
-            if agent_name == "copilot":
-                self._write_copilot_prompt(project_root, cmd_name)
-
-            registered.append(cmd_name)
-
-            # Register aliases
-            for alias in cmd_info.get("aliases", []):
-                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
-                alias_file.parent.mkdir(parents=True, exist_ok=True)
-                alias_file.write_text(output)
-                # Generate companion .prompt.md for alias too
-                if agent_name == "copilot":
-                    self._write_copilot_prompt(project_root, alias)
-                registered.append(alias)
-
-        return registered
-
-    @staticmethod
-    def _write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
-        """Generate a companion .prompt.md file for a Copilot agent command.
-
-        Copilot requires a .prompt.md file in .github/prompts/ that references
-        the corresponding .agent.md file in .github/agents/ via an ``agent:``
-        frontmatter field.
-
-        Args:
-            project_root: Path to project root
-            cmd_name: Command name (used as the file stem, e.g. 'speckit.my-ext.example')
-        """
-        prompts_dir = project_root / ".github" / "prompts"
-        prompts_dir.mkdir(parents=True, exist_ok=True)
-        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
-        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n")
+        context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
+        return self._registrar.register_commands(
+            agent_name, manifest.commands, manifest.id, extension_dir, project_root,
+            context_note=context_note
+        )
 
     def register_commands_for_all_agents(
         self,
@@ -1072,35 +766,20 @@ class CommandRegistrar:
         extension_dir: Path,
         project_root: Path
     ) -> Dict[str, List[str]]:
-        """Register extension commands for all detected agents.
+        """Register extension commands for all detected agents."""
+        context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
+        return self._registrar.register_commands_for_all_agents(
+            manifest.commands, manifest.id, extension_dir, project_root,
+            context_note=context_note
+        )
 
-        Args:
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            Dictionary mapping agent names to list of registered commands
-        """
-        results = {}
-
-        # Detect which agents are present in the project
-        for agent_name, agent_config in self.AGENT_CONFIGS.items():
-            agent_dir = project_root / agent_config["dir"].split("/")[0]
-
-            # Register if agent directory exists
-            if agent_dir.exists():
-                try:
-                    registered = self.register_commands_for_agent(
-                        agent_name, manifest, extension_dir, project_root
-                    )
-                    if registered:
-                        results[agent_name] = registered
-                except ExtensionError:
-                    # Skip agent on error
-                    continue
-
-        return results
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories."""
+        self._registrar.unregister_commands(registered_commands, project_root)
 
     def register_commands_for_claude(
         self,
@@ -1108,16 +787,7 @@ class CommandRegistrar:
         extension_dir: Path,
         project_root: Path
     ) -> List[str]:
-        """Register extension commands for Claude Code agent.
-
-        Args:
-            manifest: Extension manifest
-            extension_dir: Path to extension directory
-            project_root: Path to project root
-
-        Returns:
-            List of registered command names
-        """
+        """Register extension commands for Claude Code agent."""
         return self.register_commands_for_agent("claude", manifest, extension_dir, project_root)