fix: only delete manifest when full tracked set was processed

When remove_tracked_files is called with an explicit files dict (subset),
skip manifest deletion to avoid losing tracking of entries not in the
subset. Manifest cleanup only runs when the full set is read from the
manifest itself (files=None).

AGENTS.md

@@ -427,4 +427,56 @@ When adding new agents:
 
 ---
 
+## Agent Pack System (new)
+
+The agent pack system is a declarative, self-contained replacement for the legacy `AGENT_CONFIG` + case/switch architecture. Each agent is defined by a `speckit-agent.yml` manifest and an optional `bootstrap.py` module. When `bootstrap.py` is absent, the built-in `DefaultBootstrap` class derives its directory layout from the manifest's `commands_dir` field.
+
+### `--agent` flag on `specify init`
+
+`specify init --agent <id>` uses the pack-based init flow instead of the legacy `--ai` flow. Both accept the same agent IDs, but `--agent` additionally enables installed-file tracking so that `specify agent switch` can cleanly tear down agent files later.
+
+```bash
+specify init my-project --agent claude          # Pack-based flow (with file tracking)
+specify init --here --agent gemini --ai-skills  # With skills
+```
+
+`--agent` and `--ai` are mutually exclusive. When `--agent` is used, `init-options.json` gains `"agent_pack": true`. The `generic` agent (which requires `--ai-commands-dir`) falls through to the legacy flow since it has no embedded pack.
+
+### `specify agent` subcommands
+
+| Command                         | Description |
+| ------------------------------- | ----------- |
+| `specify agent list`            | List all available agent packs |
+| `specify agent list --installed`| List only agents installed in the current project |
+| `specify agent info <id>`       | Show detailed information about an agent pack |
+| `specify agent switch <id>`     | Switch the active agent (tears down old, sets up new) |
+| `specify agent search [query]`  | Search agents by name, ID, description, or tags |
+| `specify agent validate <path>` | Validate an agent pack directory |
+| `specify agent export <id>`     | Export an agent pack for editing |
+| `specify agent add <id> --from <path>` | Install an agent pack from a local directory |
+| `specify agent remove <id>`     | Remove a cached/override agent pack |
+
+> **Note:** `specify agent add <id>` without `--from <path>` is reserved for future catalog-based installation, which is not yet implemented.
+
+### Pack resolution order
+
+Agent packs resolve by priority (highest first):
+1. **User-level** (`~/.specify/agents/<id>/`) — applies to all projects
+2. **Project-level** (`.specify/agents/<id>/`) — project-specific override
+3. **Catalog cache** (downloaded via `specify agent add`)
+4. **Embedded** (bundled in the specify-cli wheel)
+
+### Trust boundary
+
+Agent packs can include a `bootstrap.py` module that is dynamically imported and executed. Pack authors can run arbitrary code through this mechanism. Only install packs from trusted sources. The 4-level resolution stack means that placing a pack in any of the resolution directories causes its code to run when the agent is loaded.
+
+### Installed-file tracking
+
+When using `--agent`, all installed files are recorded in `.specify/agent-manifest-<id>.json` with SHA-256 hashes. During `specify agent switch`, the CLI:
+1. Checks for user-modified files before teardown
+2. Prompts for confirmation if files were changed
+3. Feeds tracked file lists into teardown for precise, file-level removal (directories are never deleted)
+
+---
+
 *This documentation should be updated whenever new agents are added to maintain accuracy and completeness.*

CHANGELOG.md

@@ -1,22 +1,11 @@
 # Changelog
 
-## [0.4.0] - 2026-03-23
+## [0.3.2] - 2026-03-19
 
 ### Changes
 
-- fix(cli): add allow_unicode=True and encoding="utf-8" to YAML I/O (#1936)
+- chore: bump version to 0.3.2
-- fix(codex): native skills fallback refresh + legacy prompt suppression (#1930)
+- Add conduct extension to community catalog (#1908)
-- feat(cli): embed core pack in wheel for offline/air-gapped deployment (#1803)
-- ci: increase stale workflow operations-per-run to 250 (#1922)
-- docs: update publishing guide with Category and Effect columns (#1913)
-- fix: Align native skills frontmatter with install_ai_skills (#1920)
-- feat: add timestamp-based branch naming option for `specify init` (#1911)
-- docs: add Extension Comparison Guide for community extensions (#1897)
-- docs: update SUPPORT.md, fix issue templates, add preset submission template (#1910)
-- Add support for Junie (#1831)
-- feat: migrate Codex/agy init to native skills workflow (#1906)
-- chore: bump version to 0.3.2 (#1909)
-
 - feat(extensions): add verify-tasks extension to community catalog (#1871)
 - feat(presets): add enable/disable toggle and update semantics (#1891)
 - feat: add iFlow CLI support (#1875)
@@ -32,13 +21,6 @@
 - Feature/spec kit add pi coding agent pullrequest (#1853)
 - feat: register spec-kit-learn extension (#1883)
 
-## [0.3.2] - 2026-03-19
-
-### Changes
-
-- chore: bump version to 0.3.2
-- Add conduct extension to community catalog (#1908)
-
 ## [0.3.1] - 2026-03-17
 
 ### Changed

extensions/git/README.md

@@ -1,71 +0,0 @@
-# Git Branching Workflow Extension
-
-Feature branch creation, numbering (sequential/timestamp), validation, and Git remote detection for Spec Kit.
-
-## Overview
-
-This extension provides Git branching operations as an optional, self-contained module. It manages:
-
-- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering
-- **Branch validation** to ensure branches follow naming conventions
-- **Git remote detection** for GitHub integration (e.g., issue creation)
-
-## Commands
-
-| Command | Description |
-|---------|-------------|
-| `speckit.git.feature` | Create a feature branch with sequential or timestamp numbering |
-| `speckit.git.validate` | Validate current branch follows feature branch naming conventions |
-| `speckit.git.remote` | Detect Git remote URL for GitHub integration |
-
-## Hooks
-
-| Event | Command | Optional | Description |
-|-------|---------|----------|-------------|
-| `before_specify` | `speckit.git.feature` | No | Create feature branch before specification |
-| `after_implement` | `speckit.git.validate` | Yes | Validate branch naming after implementation |
-
-## Configuration
-
-Configuration is stored in `.specify/extensions/git/git-config.yml`:
-
-```yaml
-# Branch numbering strategy: "sequential" or "timestamp"
-branch_numbering: sequential
-```
-
-## Installation
-
-```bash
-# Install from the bundled extension directory
-specify extension add extensions/git --dev
-
-# Or it auto-installs during specify init (migration period)
-```
-
-## Disabling
-
-```bash
-# Disable the git extension (spec creation continues without branching)
-specify extension disable git
-
-# Re-enable it
-specify extension enable git
-```
-
-## Graceful Degradation
-
-When Git is not installed or the directory is not a Git repository:
-- Spec directories are still created under `specs/`
-- Branch creation is skipped with a warning
-- Branch validation is skipped with a warning
-- Remote detection returns empty results
-
-## Scripts
-
-The extension bundles cross-platform scripts:
-
-- `scripts/bash/create-new-feature.sh` — Bash implementation
-- `scripts/bash/git-common.sh` — Shared Git utilities (Bash)
-- `scripts/powershell/create-new-feature.ps1` — PowerShell implementation
-- `scripts/powershell/git-common.ps1` — Shared Git utilities (PowerShell)

extensions/git/commands/speckit.git.feature.md

@@ -1,66 +0,0 @@
----
-description: "Create a feature branch with sequential or timestamp numbering"
----
-
-# Create Feature Branch
-
-Create a new feature branch for the given specification.
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Prerequisites
-
-- Verify Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, warn the user and skip branch creation (spec directory will still be created)
-
-## Branch Numbering Mode
-
-Determine the branch numbering strategy by checking configuration in this order:
-
-1. Check `.specify/extensions/git/git-config.yml` for `branch_numbering` value
-2. Check `.specify/init-options.json` for `branch_numbering` value (backward compatibility)
-3. Default to `sequential` if neither exists
-
-## Execution
-
-Generate a concise short name (2-4 words) for the branch:
-- Analyze the feature description and extract the most meaningful keywords
-- Use action-noun format when possible (e.g., "add-user-auth", "fix-payment-bug")
-- Preserve technical terms and acronyms (OAuth2, API, JWT, etc.)
-
-Run the appropriate script based on your platform:
-
-- **Bash**: `.specify/extensions/git/scripts/bash/create-new-feature.sh --json --short-name "<short-name>" "<feature description>"`
-- **Bash (timestamp)**: `.specify/extensions/git/scripts/bash/create-new-feature.sh --json --timestamp --short-name "<short-name>" "<feature description>"`
-- **PowerShell**: `.specify/extensions/git/scripts/powershell/create-new-feature.ps1 -Json -ShortName "<short-name>" "<feature description>"`
-- **PowerShell (timestamp)**: `.specify/extensions/git/scripts/powershell/create-new-feature.ps1 -Json -Timestamp -ShortName "<short-name>" "<feature description>"`
-
-**IMPORTANT**:
-- Do NOT pass `--number` — the script determines the correct next number automatically
-- Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
-- You must only ever run this script once per feature
-- The JSON output will contain BRANCH_NAME and SPEC_FILE paths
-
-If the extension scripts are not found at the `.specify/extensions/git/` path, fall back to:
-- **Bash**: `scripts/bash/create-new-feature.sh`
-- **PowerShell**: `scripts/powershell/create-new-feature.ps1`
-
-## Graceful Degradation
-
-If Git is not installed or the current directory is not a Git repository:
-- The script will still create the spec directory under `specs/`
-- A warning will be printed: `[specify] Warning: Git repository not detected; skipped branch creation`
-- The workflow continues normally without branch creation
-
-## Output
-
-The script outputs JSON with:
-- `BRANCH_NAME`: The created branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
-- `SPEC_FILE`: Path to the created spec file
-- `FEATURE_NUM`: The numeric or timestamp prefix used

extensions/git/commands/speckit.git.remote.md

@@ -1,45 +0,0 @@
----
-description: "Detect Git remote URL for GitHub integration"
----
-
-# Detect Git Remote URL
-
-Detect the Git remote URL for integration with GitHub services (e.g., issue creation).
-
-## Prerequisites
-
-- Check if Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, output a warning and return empty:
-  ```
-  [specify] Warning: Git repository not detected; cannot determine remote URL
-  ```
-
-## Execution
-
-Run the following command to get the remote URL:
-
-```bash
-git config --get remote.origin.url
-```
-
-## Output
-
-Parse the remote URL and determine:
-
-1. **Repository owner**: Extract from the URL (e.g., `github` from `https://github.com/github/spec-kit.git`)
-2. **Repository name**: Extract from the URL (e.g., `spec-kit` from `https://github.com/github/spec-kit.git`)
-3. **Is GitHub**: Whether the remote points to a GitHub repository
-
-Supported URL formats:
-- HTTPS: `https://github.com/<owner>/<repo>.git`
-- SSH: `git@github.com:<owner>/<repo>.git`
-
-> [!CAUTION]
-> ONLY report a GitHub repository if the remote URL actually points to github.com.
-> Do NOT assume the remote is GitHub if the URL format doesn't match.
-
-## Graceful Degradation
-
-If Git is not installed, the directory is not a Git repository, or no remote is configured:
-- Return an empty result
-- Do NOT error — other workflows should continue without Git remote information

extensions/git/commands/speckit.git.validate.md

@@ -1,49 +0,0 @@
----
-description: "Validate current branch follows feature branch naming conventions"
----
-
-# Validate Feature Branch
-
-Validate that the current Git branch follows the expected feature branch naming conventions.
-
-## Prerequisites
-
-- Check if Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, output a warning and skip validation:
-  ```
-  [specify] Warning: Git repository not detected; skipped branch validation
-  ```
-
-## Validation Rules
-
-Get the current branch name:
-
-```bash
-git rev-parse --abbrev-ref HEAD
-```
-
-The branch name must match one of these patterns:
-
-1. **Sequential**: `^[0-9]{3}-` (e.g., `001-feature-name`, `042-fix-bug`)
-2. **Timestamp**: `^[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`)
-
-## Execution
-
-If on a feature branch (matches either pattern):
-- Output: `✓ On feature branch: <branch-name>`
-- Check if the corresponding spec directory exists under `specs/`:
-  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the `###` portion
-  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion
-- If spec directory exists: `✓ Spec directory found: <path>`
-- If spec directory missing: `⚠ No spec directory found for prefix <prefix>`
-
-If NOT on a feature branch:
-- Output: `✗ Not on a feature branch. Current branch: <branch-name>`
-- Output: `Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name`
-
-## Graceful Degradation
-
-If Git is not installed or the directory is not a Git repository:
-- Check the `SPECIFY_FEATURE` environment variable as a fallback
-- If set, validate that value against the naming patterns
-- If not set, skip validation with a warning

extensions/git/config-template.yml

@@ -1,5 +0,0 @@
-# Git Branching Workflow Extension Configuration
-# Copy this file to .specify/extensions/git/git-config.yml to customize
-
-# Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
-branch_numbering: sequential

extensions/git/extension.yml

@@ -1,47 +0,0 @@
-schema_version: "1.0"
-
-extension:
-  id: git
-  name: "Git Branching Workflow"
-  version: "1.0.0"
-  description: "Feature branch creation, numbering (sequential/timestamp), validation, and Git remote detection"
-  author: spec-kit-core
-  repository: https://github.com/github/spec-kit
-  license: MIT
-
-requires:
-  speckit_version: ">=0.2.0"
-  tools:
-    - name: git
-      required: false
-
-provides:
-  commands:
-    - name: speckit.git.feature
-      file: commands/speckit.git.feature.md
-      description: "Create a feature branch with sequential or timestamp numbering"
-    - name: speckit.git.validate
-      file: commands/speckit.git.validate.md
-      description: "Validate current branch follows feature branch naming conventions"
-    - name: speckit.git.remote
-      file: commands/speckit.git.remote.md
-      description: "Detect Git remote URL for GitHub integration"
-
-hooks:
-  before_specify:
-    command: speckit.git.feature
-    optional: false
-    description: "Create feature branch before specification"
-  after_implement:
-    command: speckit.git.validate
-    optional: true
-    prompt: "Verify feature branch naming?"
-    description: "Validate branch naming after implementation"
-
-tags:
-  - "git"
-  - "branching"
-  - "workflow"
-
-defaults:
-  branch_numbering: sequential

extensions/git/scripts/bash/create-new-feature.sh

@@ -1,394 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-JSON_MODE=false
-SHORT_NAME=""
-BRANCH_NUMBER=""
-USE_TIMESTAMP=false
-ARGS=()
-i=1
-while [ $i -le $# ]; do
-    arg="${!i}"
-    case "$arg" in
-        --json)
-            JSON_MODE=true
-            ;;
-        --short-name)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            # Check if the next argument is another option (starts with --)
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            SHORT_NAME="$next_arg"
-            ;;
-        --number)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            BRANCH_NUMBER="$next_arg"
-            ;;
-        --timestamp)
-            USE_TIMESTAMP=true
-            ;;
-        --help|-h)
-            echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
-            echo ""
-            echo "Options:"
-            echo "  --json              Output in JSON format"
-            echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
-            echo "  --number N          Specify branch number manually (overrides auto-detection)"
-            echo "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
-            echo "  --help, -h          Show this help message"
-            echo ""
-            echo "Examples:"
-            echo "  $0 'Add user authentication system' --short-name 'user-auth'"
-            echo "  $0 'Implement OAuth2 integration for API' --number 5"
-            echo "  $0 --timestamp --short-name 'user-auth' 'Add user authentication'"
-            exit 0
-            ;;
-        *)
-            ARGS+=("$arg")
-            ;;
-    esac
-    i=$((i + 1))
-done
-
-FEATURE_DESCRIPTION="${ARGS[*]}"
-if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
-    exit 1
-fi
-
-# Trim whitespace and validate description is not empty (e.g., user passed only whitespace)
-FEATURE_DESCRIPTION=$(echo "$FEATURE_DESCRIPTION" | xargs)
-if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Error: Feature description cannot be empty or contain only whitespace" >&2
-    exit 1
-fi
-
-# Function to find the repository root by searching for existing project markers
-find_repo_root() {
-    local dir="$1"
-    while [ "$dir" != "/" ]; do
-        if [ -d "$dir/.git" ] || [ -d "$dir/.specify" ]; then
-            echo "$dir"
-            return 0
-        fi
-        dir="$(dirname "$dir")"
-    done
-    return 1
-}
-
-# Function to get highest number from specs directory
-get_highest_from_specs() {
-    local specs_dir="$1"
-    local highest=0
-    
-    if [ -d "$specs_dir" ]; then
-        for dir in "$specs_dir"/*; do
-            [ -d "$dir" ] || continue
-            dirname=$(basename "$dir")
-            # Only match sequential prefixes (###-*), skip timestamp dirs
-            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
-                number=$((10#$number))
-                if [ "$number" -gt "$highest" ]; then
-                    highest=$number
-                fi
-            fi
-        done
-    fi
-    
-    echo "$highest"
-}
-
-# Function to get highest number from git branches
-get_highest_from_branches() {
-    local highest=0
-    
-    # Get all branches (local and remote)
-    branches=$(git branch -a 2>/dev/null || echo "")
-    
-    if [ -n "$branches" ]; then
-        while IFS= read -r branch; do
-            # Clean branch name: remove leading markers and remote prefixes
-            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
-            
-            # Extract feature number if branch matches pattern ###-*
-            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
-                number=$((10#$number))
-                if [ "$number" -gt "$highest" ]; then
-                    highest=$number
-                fi
-            fi
-        done <<< "$branches"
-    fi
-    
-    echo "$highest"
-}
-
-# Function to check existing branches (local and remote) and return next available number
-check_existing_branches() {
-    local specs_dir="$1"
-
-    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    git fetch --all --prune >/dev/null 2>&1 || true
-
-    # Get highest number from ALL branches (not just matching short name)
-    local highest_branch=$(get_highest_from_branches)
-
-    # Get highest number from ALL specs (not just matching short name)
-    local highest_spec=$(get_highest_from_specs "$specs_dir")
-
-    # Take the maximum of both
-    local max_num=$highest_branch
-    if [ "$highest_spec" -gt "$max_num" ]; then
-        max_num=$highest_spec
-    fi
-
-    # Return next number
-    echo $((max_num + 1))
-}
-
-# Function to clean and format a branch name
-clean_branch_name() {
-    local name="$1"
-    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed '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 common.sh using the following priority:
-#  1. common.sh next to this script (source checkout layout)
-#  2. .specify/scripts/bash/common.sh under the project root (installed project)
-#  3. scripts/bash/common.sh under the project root (source checkout fallback)
-#  4. git-common.sh next to this script (minimal fallback)
-_common_loaded=false
-
-if [ -f "$SCRIPT_DIR/common.sh" ]; then
-    source "$SCRIPT_DIR/common.sh"
-    _common_loaded=true
-else
-    # When running from an extension install (.specify/extensions/git/scripts/bash/),
-    # resolve to .specify/ (4 levels up), then to the project root (5 levels up).
-    _dot_specify="$(cd "$SCRIPT_DIR/../../../.." 2>/dev/null && pwd)"
-    _project_root="$(cd "$SCRIPT_DIR/../../../../.." 2>/dev/null && pwd)"
-
-    if [ -n "$_dot_specify" ] && [ -f "$_dot_specify/scripts/bash/common.sh" ]; then
-        source "$_dot_specify/scripts/bash/common.sh"
-        _common_loaded=true
-    elif [ -n "$_project_root" ] && [ -f "$_project_root/scripts/bash/common.sh" ]; then
-        source "$_project_root/scripts/bash/common.sh"
-        _common_loaded=true
-    elif [ -f "$SCRIPT_DIR/git-common.sh" ]; then
-        source "$SCRIPT_DIR/git-common.sh"
-        _common_loaded=true
-    fi
-fi
-
-if [ "$_common_loaded" != "true" ]; then
-    echo "Error: Could not locate common.sh or git-common.sh. Please ensure the Specify core scripts are installed." >&2
-    exit 1
-fi
-
-# If only git-common.sh was loaded, verify that the required helpers
-# (resolve_template, json_escape) are available.  These are provided by the
-# core common.sh; git-common.sh only supplies has_git / check_feature_branch.
-if ! type resolve_template >/dev/null 2>&1 || ! type json_escape >/dev/null 2>&1; then
-    echo "Error: resolve_template/json_escape not defined.  The core common.sh is required but could not be located." >&2
-    echo "Tried: $SCRIPT_DIR/common.sh, .specify/scripts/bash/common.sh, scripts/bash/common.sh" >&2
-    exit 1
-fi
-
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
-    REPO_ROOT=$(git rev-parse --show-toplevel)
-    HAS_GIT=true
-else
-    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
-    if [ -z "$REPO_ROOT" ]; then
-        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
-        exit 1
-    fi
-    HAS_GIT=false
-fi
-
-cd "$REPO_ROOT"
-
-SPECS_DIR="$REPO_ROOT/specs"
-mkdir -p "$SPECS_DIR"
-
-# Function to generate branch name with stop word filtering and length filtering
-generate_branch_name() {
-    local description="$1"
-    
-    # Common stop words to filter out
-    local stop_words="^(i|a|an|the|to|for|of|in|on|at|by|with|from|is|are|was|were|be|been|being|have|has|had|do|does|did|will|would|should|could|can|may|might|must|shall|this|that|these|those|my|your|our|their|want|need|add|get|set)$"
-    
-    # Convert to lowercase and split into words
-    local clean_name=$(echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/ /g')
-    
-    # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
-    local meaningful_words=()
-    for word in $clean_name; do
-        # Skip empty words
-        [ -z "$word" ] && continue
-        
-        # Keep words that are NOT stop words AND (length >= 3 OR are potential acronyms)
-        if ! echo "$word" | grep -qiE "$stop_words"; then
-            if [ ${#word} -ge 3 ]; then
-                meaningful_words+=("$word")
-            elif echo "$description" | grep -q "\b${word^^}\b"; then
-                # Keep short words if they appear as uppercase in original (likely acronyms)
-                meaningful_words+=("$word")
-            fi
-        fi
-    done
-    
-    # If we have meaningful words, use first 3-4 of them
-    if [ ${#meaningful_words[@]} -gt 0 ]; then
-        local max_words=3
-        if [ ${#meaningful_words[@]} -eq 4 ]; then max_words=4; fi
-        
-        local result=""
-        local count=0
-        for word in "${meaningful_words[@]}"; do
-            if [ $count -ge $max_words ]; then break; fi
-            if [ -n "$result" ]; then result="$result-"; fi
-            result="$result$word"
-            count=$((count + 1))
-        done
-        echo "$result"
-    else
-        # Fallback to original logic if no meaningful words found
-        local cleaned=$(clean_branch_name "$description")
-        echo "$cleaned" | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
-    fi
-}
-
-# Generate branch name
-if [ -n "$SHORT_NAME" ]; then
-    # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
-else
-    # Generate from description with smart filtering
-    BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
-fi
-
-# Warn if --number and --timestamp are both specified
-if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
-    >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
-    BRANCH_NUMBER=""
-fi
-
-# Determine branch prefix
-if [ "$USE_TIMESTAMP" = true ]; then
-    FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-else
-    # Determine branch number
-    if [ -z "$BRANCH_NUMBER" ]; then
-        if [ "$HAS_GIT" = true ]; then
-            # Check existing branches on remotes
-            BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
-        else
-            # Fall back to local directory check
-            HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-            BRANCH_NUMBER=$((HIGHEST + 1))
-        fi
-    fi
-
-    # Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
-    FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-fi
-
-# GitHub enforces a 244-byte limit on branch names
-# Validate and truncate if necessary
-MAX_BRANCH_LENGTH=244
-if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
-    # Calculate how much we need to trim from suffix
-    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
-    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
-    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
-    
-    # Truncate suffix at word boundary if possible
-    TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
-    # Remove trailing hyphen if truncation created one
-    TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
-    
-    ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
-    BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"
-    
-    >&2 echo "[specify] Warning: Branch name exceeded GitHub's 244-byte limit"
-    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${#ORIGINAL_BRANCH_NAME} bytes)"
-    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"
-fi
-
-if [ "$HAS_GIT" = true ]; then
-    if ! git checkout -q -b "$BRANCH_NAME" >/dev/null 2>&1; then
-        # Check if branch already exists
-        if git branch --list "$BRANCH_NAME" | grep -q .; then
-            if [ "$USE_TIMESTAMP" = true ]; then
-                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Rerun to get a new timestamp or use a different --short-name."
-            else
-                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
-            fi
-            exit 1
-        else
-            >&2 echo "Error: Failed to create git branch '$BRANCH_NAME'. Please check your git configuration and try again."
-            exit 1
-        fi
-    fi
-else
-    >&2 echo "[specify] Warning: Git repository not detected; skipped branch creation for $BRANCH_NAME"
-fi
-
-FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
-mkdir -p "$FEATURE_DIR"
-
-TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
-SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
-    cp "$TEMPLATE" "$SPEC_FILE"
-else
-    echo "Warning: Spec template not found; created empty spec file" >&2
-    touch "$SPEC_FILE"
-fi
-
-# 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 $JSON_MODE; then
-    if command -v jq >/dev/null 2>&1; then
-        jq -cn \
-            --arg branch_name "$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: $FEATURE_NUM"
-    printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
-fi

extensions/git/scripts/bash/git-common.sh

@@ -1,30 +0,0 @@
-#!/usr/bin/env bash
-# Git-specific common functions for the git extension.
-# Extracted from scripts/bash/common.sh — contains only git-specific
-# branch validation and detection logic.
-
-# Check if we have git available
-has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
-}
-
-# Validate that a branch name matches the expected feature branch pattern.
-# Accepts sequential (###-*) or timestamp (YYYYMMDD-HHMMSS-*) formats.
-check_feature_branch() {
-    local branch="$1"
-    local has_git_repo="$2"
-
-    # For non-git repos, we can't enforce branch naming but still provide output
-    if [[ "$has_git_repo" != "true" ]]; then
-        echo "[specify] Warning: Git repository not detected; skipped branch validation" >&2
-        return 0
-    fi
-
-    if [[ ! "$branch" =~ ^[0-9]{3}- ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
-        echo "ERROR: Not on a feature branch. Current branch: $branch" >&2
-        echo "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name" >&2
-        return 1
-    fi
-
-    return 0
-}

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

@@ -1,368 +0,0 @@
-#!/usr/bin/env pwsh
-# Create a new feature
-[CmdletBinding()]
-param(
-    [switch]$Json,
-    [string]$ShortName,
-    [Parameter()]
-    [int]$Number = 0,
-    [switch]$Timestamp,
-    [switch]$Help,
-    [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
-    [string[]]$FeatureDescription
-)
-$ErrorActionPreference = 'Stop'
-
-# Show help if requested
-if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
-    Write-Host ""
-    Write-Host "Options:"
-    Write-Host "  -Json               Output in JSON format"
-    Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
-    Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
-    Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
-    Write-Host "  -Help               Show this help message"
-    Write-Host ""
-    Write-Host "Examples:"
-    Write-Host "  ./create-new-feature.ps1 'Add user authentication system' -ShortName 'user-auth'"
-    Write-Host "  ./create-new-feature.ps1 'Implement OAuth2 integration for API'"
-    Write-Host "  ./create-new-feature.ps1 -Timestamp -ShortName 'user-auth' 'Add user authentication'"
-    exit 0
-}
-
-# Check if feature description provided
-if (-not $FeatureDescription -or $FeatureDescription.Count -eq 0) {
-    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
-    exit 1
-}
-
-$featureDesc = ($FeatureDescription -join ' ').Trim()
-
-# Validate description is not empty after trimming (e.g., user passed only whitespace)
-if ([string]::IsNullOrWhiteSpace($featureDesc)) {
-    Write-Error "Error: Feature description cannot be empty or contain only whitespace"
-    exit 1
-}
-
-# 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 initialized with --no-git.
-function Find-RepositoryRoot {
-    param(
-        [string]$StartDir,
-        [string[]]$Markers = @('.git', '.specify')
-    )
-    $current = Resolve-Path $StartDir
-    while ($true) {
-        foreach ($marker in $Markers) {
-            if (Test-Path (Join-Path $current $marker)) {
-                return $current
-            }
-        }
-        $parent = Split-Path $current -Parent
-        if ($parent -eq $current) {
-            # Reached filesystem root without finding markers
-            return $null
-        }
-        $current = $parent
-    }
-}
-
-function Get-HighestNumberFromSpecs {
-    param([string]$SpecsDir)
-    
-    $highest = 0
-    if (Test-Path $SpecsDir) {
-        Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{3})-') {
-                $num = [int]$matches[1]
-                if ($num -gt $highest) { $highest = $num }
-            }
-        }
-    }
-    return $highest
-}
-
-function Get-HighestNumberFromBranches {
-    param()
-    
-    $highest = 0
-    try {
-        $branches = git branch -a 2>$null
-        if ($LASTEXITCODE -eq 0) {
-            foreach ($branch in $branches) {
-                # Clean branch name: remove leading markers and remote prefixes
-                $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
-                
-                # Extract feature number if branch matches pattern ###-*
-                if ($cleanBranch -match '^(\d{3})-') {
-                    $num = [int]$matches[1]
-                    if ($num -gt $highest) { $highest = $num }
-                }
-            }
-        }
-    } catch {
-        # If git command fails, return 0
-        Write-Verbose "Could not check Git branches: $_"
-    }
-    return $highest
-}
-
-function Get-NextBranchNumber {
-    param(
-        [string]$SpecsDir
-    )
-
-    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    try {
-        git fetch --all --prune 2>$null | Out-Null
-    } catch {
-        # Ignore fetch errors
-    }
-
-    # Get highest number from ALL branches (not just matching short name)
-    $highestBranch = Get-HighestNumberFromBranches
-
-    # Get highest number from ALL specs (not just matching short name)
-    $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
-
-    # Take the maximum of both
-    $maxNum = [Math]::Max($highestBranch, $highestSpec)
-
-    # Return next number
-    return $maxNum + 1
-}
-
-function ConvertTo-CleanBranchName {
-    param([string]$Name)
-    
-    return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
-}
-$fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
-if (-not $fallbackRoot) {
-    Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
-    exit 1
-}
-
-# Load common functions (includes Resolve-Template).
-# Search locations in priority order:
-#  1. common.ps1 next to this script (source checkout layout)
-#  2. .specify/scripts/powershell/common.ps1 under the project root (installed project)
-#  3. scripts/powershell/common.ps1 under the project root (source checkout fallback)
-#  4. git-common.ps1 next to this script (minimal fallback)
-$commonLoaded = $false
-
-if (Test-Path "$PSScriptRoot/common.ps1") {
-    . "$PSScriptRoot/common.ps1"
-    $commonLoaded = $true
-} else {
-    $coreCommonCandidates = @()
-
-    if ($fallbackRoot) {
-        $coreCommonCandidates += (Join-Path $fallbackRoot ".specify/scripts/powershell/common.ps1")
-        $coreCommonCandidates += (Join-Path $fallbackRoot "scripts/powershell/common.ps1")
-    }
-
-    $coreCommonCandidates += "$PSScriptRoot/git-common.ps1"
-
-    foreach ($candidate in $coreCommonCandidates) {
-        if ($candidate -and (Test-Path $candidate)) {
-            . $candidate
-            $commonLoaded = $true
-            break
-        }
-    }
-}
-
-if (-not $commonLoaded) {
-    throw "Unable to locate common script file. Please ensure the Specify core scripts are installed."
-}
-
-# If only git-common.ps1 was loaded, verify that Resolve-Template is available.
-# Resolve-Template is provided by the core common.ps1; git-common.ps1 only
-# supplies Test-HasGit / Test-FeatureBranch.
-if (-not (Get-Command Resolve-Template -ErrorAction SilentlyContinue)) {
-    throw ("Resolve-Template not defined. The core common.ps1 is required but could not be located. " +
-           "Tried: $PSScriptRoot/common.ps1, .specify/scripts/powershell/common.ps1, scripts/powershell/common.ps1")
-}
-
-try {
-    $repoRoot = git rev-parse --show-toplevel 2>$null
-    if ($LASTEXITCODE -eq 0) {
-        $hasGit = $true
-    } else {
-        throw "Git not available"
-    }
-} catch {
-    $repoRoot = $fallbackRoot
-    $hasGit = $false
-}
-
-Set-Location $repoRoot
-
-$specsDir = Join-Path $repoRoot 'specs'
-New-Item -ItemType Directory -Path $specsDir -Force | Out-Null
-
-# Function to generate branch name with stop word filtering and length filtering
-function Get-BranchName {
-    param([string]$Description)
-    
-    # Common stop words to filter out
-    $stopWords = @(
-        'i', 'a', 'an', 'the', 'to', 'for', 'of', 'in', 'on', 'at', 'by', 'with', 'from',
-        'is', 'are', 'was', 'were', 'be', 'been', 'being', 'have', 'has', 'had',
-        'do', 'does', 'did', 'will', 'would', 'should', 'could', 'can', 'may', 'might', 'must', 'shall',
-        'this', 'that', 'these', 'those', 'my', 'your', 'our', 'their',
-        'want', 'need', 'add', 'get', 'set'
-    )
-    
-    # Convert to lowercase and extract words (alphanumeric only)
-    $cleanName = $Description.ToLower() -replace '[^a-z0-9\s]', ' '
-    $words = $cleanName -split '\s+' | Where-Object { $_ }
-    
-    # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
-    $meaningfulWords = @()
-    foreach ($word in $words) {
-        # Skip stop words
-        if ($stopWords -contains $word) { continue }
-        
-        # Keep words that are length >= 3 OR appear as uppercase in original (likely acronyms)
-        if ($word.Length -ge 3) {
-            $meaningfulWords += $word
-        } elseif ($Description -match "\b$($word.ToUpper())\b") {
-            # Keep short words if they appear as uppercase in original (likely acronyms)
-            $meaningfulWords += $word
-        }
-    }
-    
-    # If we have meaningful words, use first 3-4 of them
-    if ($meaningfulWords.Count -gt 0) {
-        $maxWords = if ($meaningfulWords.Count -eq 4) { 4 } else { 3 }
-        $result = ($meaningfulWords | Select-Object -First $maxWords) -join '-'
-        return $result
-    } else {
-        # Fallback to original logic if no meaningful words found
-        $result = ConvertTo-CleanBranchName -Name $Description
-        $fallbackWords = ($result -split '-') | Where-Object { $_ } | Select-Object -First 3
-        return [string]::Join('-', $fallbackWords)
-    }
-}
-
-# Generate branch name
-if ($ShortName) {
-    # Use provided short name, just clean it up
-    $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
-} else {
-    # Generate from description with smart filtering
-    $branchSuffix = Get-BranchName -Description $featureDesc
-}
-
-# Warn if -Number and -Timestamp are both specified
-if ($Timestamp -and $Number -ne 0) {
-    Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
-    $Number = 0
-}
-
-# Determine branch prefix
-if ($Timestamp) {
-    $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
-    $branchName = "$featureNum-$branchSuffix"
-} else {
-    # Determine branch number
-    if ($Number -eq 0) {
-        if ($hasGit) {
-            # Check existing branches on remotes
-            $Number = Get-NextBranchNumber -SpecsDir $specsDir
-        } else {
-            # Fall back to local directory check
-            $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
-        }
-    }
-
-    $featureNum = ('{0:000}' -f $Number)
-    $branchName = "$featureNum-$branchSuffix"
-}
-
-# GitHub enforces a 244-byte limit on branch names
-# Validate and truncate if necessary
-$maxBranchLength = 244
-if ($branchName.Length -gt $maxBranchLength) {
-    # Calculate how much we need to trim from suffix
-    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
-    $prefixLength = $featureNum.Length + 1
-    $maxSuffixLength = $maxBranchLength - $prefixLength
-    
-    # Truncate suffix
-    $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
-    # Remove trailing hyphen if truncation created one
-    $truncatedSuffix = $truncatedSuffix -replace '-$', ''
-    
-    $originalBranchName = $branchName
-    $branchName = "$featureNum-$truncatedSuffix"
-    
-    Write-Warning "[specify] Branch name exceeded GitHub's 244-byte limit"
-    Write-Warning "[specify] Original: $originalBranchName ($($originalBranchName.Length) bytes)"
-    Write-Warning "[specify] Truncated to: $branchName ($($branchName.Length) bytes)"
-}
-
-if ($hasGit) {
-    $branchCreated = $false
-    try {
-        git checkout -q -b $branchName 2>$null | Out-Null
-        if ($LASTEXITCODE -eq 0) {
-            $branchCreated = $true
-        }
-    } catch {
-        # Exception during git command
-    }
-
-    if (-not $branchCreated) {
-        # Check if branch already exists
-        $existingBranch = git branch --list $branchName 2>$null
-        if ($existingBranch) {
-            if ($Timestamp) {
-                Write-Error "Error: Branch '$branchName' already exists. Rerun to get a new timestamp or use a different -ShortName."
-            } else {
-                Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
-            }
-            exit 1
-        } else {
-            Write-Error "Error: Failed to create git branch '$branchName'. Please check your git configuration and try again."
-            exit 1
-        }
-    }
-} else {
-    Write-Warning "[specify] Warning: Git repository not detected; skipped branch creation for $branchName"
-}
-
-$featureDir = Join-Path $specsDir $branchName
-New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
-
-$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
-$specFile = Join-Path $featureDir 'spec.md'
-if ($template -and (Test-Path $template)) { 
-    Copy-Item $template $specFile -Force 
-} else { 
-    New-Item -ItemType File -Path $specFile | Out-Null 
-}
-
-# Set the SPECIFY_FEATURE environment variable for the current session
-$env:SPECIFY_FEATURE = $branchName
-
-if ($Json) {
-    $obj = [PSCustomObject]@{ 
-        BRANCH_NAME = $branchName
-        SPEC_FILE = $specFile
-        FEATURE_NUM = $featureNum
-        HAS_GIT = $hasGit
-    }
-    $obj | ConvertTo-Json -Compress
-} else {
-    Write-Output "BRANCH_NAME: $branchName"
-    Write-Output "SPEC_FILE: $specFile"
-    Write-Output "FEATURE_NUM: $featureNum"
-    Write-Output "HAS_GIT: $hasGit"
-    Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
-}
-

extensions/git/scripts/powershell/git-common.ps1

@@ -1,33 +0,0 @@
-#!/usr/bin/env pwsh
-# Git-specific common functions for the git extension.
-# Extracted from scripts/powershell/common.ps1 — contains only git-specific
-# branch validation and detection logic.
-
-function Test-HasGit {
-    try {
-        git rev-parse --show-toplevel 2>$null | Out-Null
-        return ($LASTEXITCODE -eq 0)
-    } catch {
-        return $false
-    }
-}
-
-function Test-FeatureBranch {
-    param(
-        [string]$Branch,
-        [bool]$HasGit = $true
-    )
-    
-    # For non-git repos, we can't enforce branch naming but still provide output
-    if (-not $HasGit) {
-        Write-Warning "[specify] Warning: Git repository not detected; skipped branch validation"
-        return $true
-    }
-    
-    if ($Branch -notmatch '^[0-9]{3}-' -and $Branch -notmatch '^\d{8}-\d{6}-') {
-        Write-Output "ERROR: Not on a feature branch. Current branch: $Branch"
-        Write-Output "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name"
-        return $false
-    }
-    return $true
-}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.4.0"
+version = "0.3.2"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -41,9 +41,10 @@ packages = ["src/specify_cli"]
 "templates/commands" = "specify_cli/core_pack/commands"
 "scripts/bash" = "specify_cli/core_pack/scripts/bash"
 "scripts/powershell" = "specify_cli/core_pack/scripts/powershell"
-"extensions/git" = "specify_cli/core_pack/extensions/git"
 ".github/workflows/scripts/create-release-packages.sh" = "specify_cli/core_pack/release_scripts/create-release-packages.sh"
 ".github/workflows/scripts/create-release-packages.ps1" = "specify_cli/core_pack/release_scripts/create-release-packages.ps1"
+# Official agent packs (embedded in wheel for zero-config offline operation)
+"src/specify_cli/core_pack/agents" = "specify_cli/core_pack/agents"
 
 [project.optional-dependencies]
 test = [

src/specify_cli/agents.py

@@ -47,6 +47,12 @@ class CommandRegistrar:
             "args": "$ARGUMENTS",
             "extension": ".md"
         },
+        "cursor-agent": {
+            "dir": ".cursor/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
         "qwen": {
             "dir": ".qwen/commands",
             "format": "markdown",
@@ -207,7 +213,7 @@ class CommandRegistrar:
         if not fm:
             return ""
 
-        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False, allow_unicode=True)
+        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:

src/specify_cli/core_pack/agents/agy/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "agy"
+  name: "Antigravity"
+  version: "1.0.0"
+  description: "Antigravity IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'antigravity']
+
+command_registration:
+  commands_dir: ".agent/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/amp/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "amp"
+  name: "Amp"
+  version: "1.0.0"
+  description: "Amp CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://ampcode.com/manual#install"
+  cli_tool: "amp"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'amp']
+
+command_registration:
+  commands_dir: ".agents/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/auggie/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "auggie"
+  name: "Auggie CLI"
+  version: "1.0.0"
+  description: "Auggie CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://docs.augmentcode.com/cli/setup-auggie/install-auggie-cli"
+  cli_tool: "auggie"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'augment', 'auggie']
+
+command_registration:
+  commands_dir: ".augment/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/bob/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "bob"
+  name: "IBM Bob"
+  version: "1.0.0"
+  description: "IBM Bob IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'ibm', 'bob']
+
+command_registration:
+  commands_dir: ".bob/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/claude/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "claude"
+  name: "Claude Code"
+  version: "1.0.0"
+  description: "Anthropic's Claude Code CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://docs.anthropic.com/en/docs/claude-code/setup"
+  cli_tool: "claude"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'anthropic', 'claude']
+
+command_registration:
+  commands_dir: ".claude/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/codebuddy/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "codebuddy"
+  name: "CodeBuddy"
+  version: "1.0.0"
+  description: "CodeBuddy CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://www.codebuddy.ai/cli"
+  cli_tool: "codebuddy"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'codebuddy']
+
+command_registration:
+  commands_dir: ".codebuddy/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/codex/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "codex"
+  name: "Codex CLI"
+  version: "1.0.0"
+  description: "OpenAI Codex CLI with project skills support"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://github.com/openai/codex"
+  cli_tool: "codex"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'openai', 'codex', 'skills']
+
+command_registration:
+  commands_dir: ".agents/skills"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: "/SKILL.md"

src/specify_cli/core_pack/agents/copilot/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "copilot"
+  name: "GitHub Copilot"
+  version: "1.0.0"
+  description: "GitHub Copilot for AI-assisted development in VS Code"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'github', 'copilot']
+
+command_registration:
+  commands_dir: ".github/agents"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".agent.md"

src/specify_cli/core_pack/agents/cursor-agent/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "cursor-agent"
+  name: "Cursor"
+  version: "1.0.0"
+  description: "Cursor IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'cursor']
+
+command_registration:
+  commands_dir: ".cursor/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/gemini/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "gemini"
+  name: "Gemini CLI"
+  version: "1.0.0"
+  description: "Google's Gemini CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://github.com/google-gemini/gemini-cli"
+  cli_tool: "gemini"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'google', 'gemini']
+
+command_registration:
+  commands_dir: ".gemini/commands"
+  format: "toml"
+  arg_placeholder: "{{args}}"
+  file_extension: ".toml"

src/specify_cli/core_pack/agents/iflow/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "iflow"
+  name: "iFlow CLI"
+  version: "1.0.0"
+  description: "iFlow CLI by iflow-ai for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://docs.iflow.cn/en/cli/quickstart"
+  cli_tool: "iflow"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'iflow']
+
+command_registration:
+  commands_dir: ".iflow/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/junie/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "junie"
+  name: "Junie"
+  version: "1.0.0"
+  description: "Junie by JetBrains for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://junie.jetbrains.com/"
+  cli_tool: "junie"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'jetbrains', 'junie']
+
+command_registration:
+  commands_dir: ".junie/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/kilocode/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "kilocode"
+  name: "Kilo Code"
+  version: "1.0.0"
+  description: "Kilo Code IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'kilocode']
+
+command_registration:
+  commands_dir: ".kilocode/workflows"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/kimi/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "kimi"
+  name: "Kimi Code"
+  version: "1.0.0"
+  description: "Kimi Code CLI by Moonshot AI with skills support"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://code.kimi.com/"
+  cli_tool: "kimi"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'moonshot', 'kimi', 'skills']
+
+command_registration:
+  commands_dir: ".kimi/skills"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: "/SKILL.md"

src/specify_cli/core_pack/agents/kiro-cli/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "kiro-cli"
+  name: "Kiro CLI"
+  version: "1.0.0"
+  description: "Kiro CLI by Amazon for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://kiro.dev/docs/cli/"
+  cli_tool: "kiro-cli"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'amazon', 'kiro']
+
+command_registration:
+  commands_dir: ".kiro/prompts"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/opencode/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "opencode"
+  name: "opencode"
+  version: "1.0.0"
+  description: "opencode CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://opencode.ai"
+  cli_tool: "opencode"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'opencode']
+
+command_registration:
+  commands_dir: ".opencode/command"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/pi/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "pi"
+  name: "Pi Coding Agent"
+  version: "1.0.0"
+  description: "Pi terminal coding agent for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://www.npmjs.com/package/@mariozechner/pi-coding-agent"
+  cli_tool: "pi"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'pi']
+
+command_registration:
+  commands_dir: ".pi/prompts"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/qodercli/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "qodercli"
+  name: "Qoder CLI"
+  version: "1.0.0"
+  description: "Qoder CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://qoder.com/cli"
+  cli_tool: "qodercli"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'qoder']
+
+command_registration:
+  commands_dir: ".qoder/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/qwen/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "qwen"
+  name: "Qwen Code"
+  version: "1.0.0"
+  description: "Alibaba's Qwen Code CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://github.com/QwenLM/qwen-code"
+  cli_tool: "qwen"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'alibaba', 'qwen']
+
+command_registration:
+  commands_dir: ".qwen/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/roo/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "roo"
+  name: "Roo Code"
+  version: "1.0.0"
+  description: "Roo Code IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'roo']
+
+command_registration:
+  commands_dir: ".roo/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/shai/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "shai"
+  name: "SHAI"
+  version: "1.0.0"
+  description: "SHAI CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://github.com/ovh/shai"
+  cli_tool: "shai"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'ovh', 'shai']
+
+command_registration:
+  commands_dir: ".shai/commands"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/tabnine/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "tabnine"
+  name: "Tabnine CLI"
+  version: "1.0.0"
+  description: "Tabnine CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://docs.tabnine.com/main/getting-started/tabnine-cli"
+  cli_tool: "tabnine"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'tabnine']
+
+command_registration:
+  commands_dir: ".tabnine/agent/commands"
+  format: "toml"
+  arg_placeholder: "{{args}}"
+  file_extension: ".toml"

src/specify_cli/core_pack/agents/trae/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "trae"
+  name: "Trae"
+  version: "1.0.0"
+  description: "Trae IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'trae']
+
+command_registration:
+  commands_dir: ".trae/rules"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/vibe/speckit-agent.yml

@@ -0,0 +1,25 @@
+schema_version: "1.0"
+
+agent:
+  id: "vibe"
+  name: "Mistral Vibe"
+  version: "1.0.0"
+  description: "Mistral Vibe CLI for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: true
+  install_url: "https://github.com/mistralai/mistral-vibe"
+  cli_tool: "vibe"
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['cli', 'mistral', 'vibe']
+
+command_registration:
+  commands_dir: ".vibe/prompts"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/core_pack/agents/windsurf/speckit-agent.yml

@@ -0,0 +1,23 @@
+schema_version: "1.0"
+
+agent:
+  id: "windsurf"
+  name: "Windsurf"
+  version: "1.0.0"
+  description: "Windsurf IDE for AI-assisted development"
+  author: "github"
+  license: "MIT"
+
+runtime:
+  requires_cli: false
+
+requires:
+  speckit_version: ">=0.1.0"
+
+tags: ['ide', 'windsurf']
+
+command_registration:
+  commands_dir: ".windsurf/workflows"
+  format: "markdown"
+  arg_placeholder: "$ARGUMENTS"
+  file_extension: ".md"

src/specify_cli/extensions.py

@@ -975,8 +975,8 @@ class ExtensionCatalog:
         if not config_path.exists():
             return None
         try:
-            data = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
+            data = yaml.safe_load(config_path.read_text()) or {}
-        except (yaml.YAMLError, OSError, UnicodeError) as e:
+        except (yaml.YAMLError, OSError) as e:
             raise ValidationError(
                 f"Failed to read catalog config {config_path}: {e}"
             )
@@ -1467,8 +1467,8 @@ class ConfigManager:
             return {}
 
         try:
-            return yaml.safe_load(file_path.read_text(encoding="utf-8")) or {}
+            return yaml.safe_load(file_path.read_text()) or {}
-        except (yaml.YAMLError, OSError, UnicodeError):
+        except (yaml.YAMLError, OSError):
             return {}
 
     def _get_extension_defaults(self) -> Dict[str, Any]:
@@ -1659,8 +1659,8 @@ class HookExecutor:
             }
 
         try:
-            return yaml.safe_load(self.config_file.read_text(encoding="utf-8")) or {}
+            return yaml.safe_load(self.config_file.read_text()) or {}
-        except (yaml.YAMLError, OSError, UnicodeError):
+        except (yaml.YAMLError, OSError):
             return {
                 "installed": [],
                 "settings": {"auto_execute_hooks": True},
@@ -1675,8 +1675,7 @@ class HookExecutor:
         """
         self.config_file.parent.mkdir(parents=True, exist_ok=True)
         self.config_file.write_text(
-            yaml.dump(config, default_flow_style=False, sort_keys=False, allow_unicode=True),
+            yaml.dump(config, default_flow_style=False, sort_keys=False)
-            encoding="utf-8",
         )
 
     def register_hooks(self, manifest: ExtensionManifest):

src/specify_cli/presets.py

@@ -1062,8 +1062,8 @@ class PresetCatalog:
         if not config_path.exists():
             return None
         try:
-            data = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
+            data = yaml.safe_load(config_path.read_text()) or {}
-        except (yaml.YAMLError, OSError, UnicodeError) as e:
+        except (yaml.YAMLError, OSError) as e:
             raise PresetValidationError(
                 f"Failed to read catalog config {config_path}: {e}"
             )

templates/commands/specify.md

@@ -73,40 +73,12 @@ Given that feature description, do this:
      - "Create a dashboard for analytics" → "analytics-dashboard"
      - "Fix payment processing timeout bug" → "fix-payment-timeout"
 
-2. **Create the feature branch** (unless already handled by a `before_specify` hook — see Pre-Execution Checks above). If a mandatory `before_specify` hook for `speckit.git.feature` already executed and created the branch, **skip this step entirely** and use the branch/spec information from the hook result. Otherwise:
+2. **Create the feature branch** by running the script with `--short-name` (and `--json`). In sequential mode, do NOT pass `--number` — the script auto-detects the next available number. In timestamp mode, the script generates a `YYYYMMDD-HHMMSS` prefix automatically:
 
-   **Git extension check**: Before running the branch creation script, check if the git extension is enabled:
+   **Branch numbering mode**: Before running the script, check if `.specify/init-options.json` exists and read the `branch_numbering` value.
-   - Check if `.specify/extensions/.registry` exists (a single JSON file tracking all extensions)
-   - If it exists, read the JSON and look for an `extensions.git` entry
-   - **Only skip branching** when `extensions.git.enabled` is **present and explicitly `false`**. In all other cases — including when the registry file is missing, when `extensions.git` has no entry, or when `"enabled"` is `true` or absent — proceed with normal branch creation (extension script if present, else core `{SCRIPT}` fallback)
-   - If the git extension is **disabled** (explicitly `"enabled": false`), **skip branch creation entirely** — do **not** run the branch creation script. Instead:
-     - Derive a spec directory name from the short name, e.g. `specs/<short-name>/`
-     - Explicitly set the following variables so later steps can use them:
-       - `FEATURE_DIR="specs/<short-name>"`
-       - `SPEC_FILE="$FEATURE_DIR/spec.md"`
-     - Ensure the directory and spec file exist:
-       - Bash:
-         - `mkdir -p "$FEATURE_DIR"`
-         - `touch "$SPEC_FILE"`
-       - PowerShell:
-         - `New-Item -ItemType Directory -Path $FEATURE_DIR -Force | Out-Null`
-         - `New-Item -ItemType File -Path $SPEC_FILE -Force | Out-Null`
-     - Then proceed directly to step 3 using `FEATURE_DIR` and `SPEC_FILE`
-   - If the registry file does not exist, proceed with branch creation using the default behavior (backward compatibility)
-
-   Run the script with `--short-name` (and `--json`). In sequential mode, do NOT pass `--number` — the script auto-detects the next available number. In timestamp mode, the script generates a `YYYYMMDD-HHMMSS` prefix automatically:
-
-   **Branch numbering mode**: Before running the script, determine the branch numbering strategy:
-   1. Check `.specify/extensions/git/git-config.yml` for `branch_numbering` value (extension config takes precedence)
-   2. If not found, check `.specify/init-options.json` for `branch_numbering` value (backward compatibility)
-   3. Default to `sequential` if neither exists
    - If `"timestamp"`, add `--timestamp` (Bash) or `-Timestamp` (PowerShell) to the script invocation
    - If `"sequential"` or absent, do not add any extra flag (default behavior)
 
-   **Script resolution**: Use the extension's bundled scripts when available, falling back to core scripts:
-   - **Bash**: If `.specify/extensions/git/scripts/bash/create-new-feature.sh` exists, use it; otherwise, fall back to `{SCRIPT}`
-   - **PowerShell**: If `.specify/extensions/git/scripts/powershell/create-new-feature.ps1` exists, use it; otherwise, fall back to `{SCRIPT}`
-
    - Bash example: `{SCRIPT} --json --short-name "user-auth" "Add user authentication"`
    - Bash (timestamp): `{SCRIPT} --json --timestamp --short-name "user-auth" "Add user authentication"`
    - PowerShell example: `{SCRIPT} -Json -ShortName "user-auth" "Add user authentication"`

tests/test_ai_skills.py

@@ -11,12 +11,10 @@ Tests cover:
 """
 
 import re
-import zipfile
 import pytest
 import tempfile
 import shutil
 import yaml
-import typer
 from pathlib import Path
 from unittest.mock import patch
 
@@ -722,8 +720,8 @@ class TestNewProjectCommandSkip:
         mock_skills.assert_not_called()
         assert (target / ".agents" / "skills" / "speckit-specify" / "SKILL.md").exists()
 
-    def test_codex_native_skills_missing_falls_back_then_fails_cleanly(self, tmp_path):
+    def test_codex_native_skills_missing_fails_clearly(self, tmp_path):
-        """Codex should attempt fallback conversion when bundled skills are missing."""
+        """Codex native skills init should fail if bundled skills are missing."""
         from typer.testing import CliRunner
 
         runner = CliRunner()
@@ -732,7 +730,7 @@ class TestNewProjectCommandSkip:
         with patch("specify_cli.download_and_extract_template", lambda *args, **kwargs: None), \
              patch("specify_cli.ensure_executable_scripts"), \
              patch("specify_cli.ensure_constitution_from_template"), \
-             patch("specify_cli.install_ai_skills", return_value=False) as mock_skills, \
+             patch("specify_cli.install_ai_skills") as mock_skills, \
              patch("specify_cli.is_git_repo", return_value=False), \
              patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
             result = runner.invoke(
@@ -741,13 +739,11 @@ class TestNewProjectCommandSkip:
             )
 
         assert result.exit_code == 1
-        mock_skills.assert_called_once()
+        mock_skills.assert_not_called()
-        assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
         assert "Expected bundled agent skills" in result.output
-        assert "fallback conversion failed" in result.output
 
     def test_codex_native_skills_ignores_non_speckit_skill_dirs(self, tmp_path):
-        """Non-spec-kit SKILL.md files should trigger fallback conversion, not hard-fail."""
+        """Non-spec-kit SKILL.md files should not satisfy Codex bundled-skills validation."""
         from typer.testing import CliRunner
 
         runner = CliRunner()
@@ -761,7 +757,7 @@ class TestNewProjectCommandSkip:
         with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
              patch("specify_cli.ensure_executable_scripts"), \
              patch("specify_cli.ensure_constitution_from_template"), \
-             patch("specify_cli.install_ai_skills", return_value=True) as mock_skills, \
+             patch("specify_cli.install_ai_skills") as mock_skills, \
              patch("specify_cli.is_git_repo", return_value=False), \
              patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
             result = runner.invoke(
@@ -769,100 +765,9 @@ class TestNewProjectCommandSkip:
                 ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
             )
 
-        assert result.exit_code == 0
+        assert result.exit_code == 1
-        mock_skills.assert_called_once()
+        mock_skills.assert_not_called()
-        assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
+        assert "Expected bundled agent skills" in result.output
-
-    def test_codex_ai_skills_here_mode_preserves_existing_codex_dir(self, tmp_path, monkeypatch):
-        """Codex --here skills init should not delete a pre-existing .codex directory."""
-        from typer.testing import CliRunner
-
-        runner = CliRunner()
-        target = tmp_path / "codex-preserve-here"
-        target.mkdir()
-        existing_prompts = target / ".codex" / "prompts"
-        existing_prompts.mkdir(parents=True)
-        (existing_prompts / "custom.md").write_text("custom")
-        monkeypatch.chdir(target)
-
-        with patch("specify_cli.download_and_extract_template", return_value=target), \
-             patch("specify_cli.ensure_executable_scripts"), \
-             patch("specify_cli.ensure_constitution_from_template"), \
-             patch("specify_cli.install_ai_skills", return_value=True), \
-             patch("specify_cli.is_git_repo", return_value=True), \
-             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
-            result = runner.invoke(
-                app,
-                ["init", "--here", "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
-                input="y\n",
-            )
-
-        assert result.exit_code == 0
-        assert (target / ".codex").exists()
-        assert (existing_prompts / "custom.md").exists()
-
-    def test_codex_ai_skills_fresh_dir_does_not_create_codex_dir(self, tmp_path):
-        """Fresh-directory Codex skills init should not leave legacy .codex from archive."""
-        target = tmp_path / "fresh-codex-proj"
-        archive = tmp_path / "codex-template.zip"
-
-        with zipfile.ZipFile(archive, "w") as zf:
-            zf.writestr("template-root/.codex/prompts/speckit.specify.md", "legacy")
-            zf.writestr("template-root/.specify/templates/constitution-template.md", "constitution")
-
-        fake_meta = {
-            "filename": archive.name,
-            "size": archive.stat().st_size,
-            "release": "vtest",
-            "asset_url": "https://example.invalid/template.zip",
-        }
-
-        with patch("specify_cli.download_template_from_github", return_value=(archive, fake_meta)):
-            specify_cli.download_and_extract_template(
-                target,
-                "codex",
-                "sh",
-                is_current_dir=False,
-                skip_legacy_codex_prompts=True,
-                verbose=False,
-            )
-
-        assert target.exists()
-        assert (target / ".specify").exists()
-        assert not (target / ".codex").exists()
-
-    @pytest.mark.parametrize("is_current_dir", [False, True])
-    def test_download_and_extract_template_blocks_zip_path_traversal(self, tmp_path, monkeypatch, is_current_dir):
-        """Extraction should reject ZIP members escaping the target directory."""
-        target = (tmp_path / "here-proj") if is_current_dir else (tmp_path / "new-proj")
-        if is_current_dir:
-            target.mkdir()
-            monkeypatch.chdir(target)
-
-        archive = tmp_path / "malicious-template.zip"
-        with zipfile.ZipFile(archive, "w") as zf:
-            zf.writestr("../evil.txt", "pwned")
-            zf.writestr("template-root/.specify/templates/constitution-template.md", "constitution")
-
-        fake_meta = {
-            "filename": archive.name,
-            "size": archive.stat().st_size,
-            "release": "vtest",
-            "asset_url": "https://example.invalid/template.zip",
-        }
-
-        with patch("specify_cli.download_template_from_github", return_value=(archive, fake_meta)):
-            with pytest.raises(typer.Exit):
-                specify_cli.download_and_extract_template(
-                    target,
-                    "codex",
-                    "sh",
-                    is_current_dir=is_current_dir,
-                    skip_legacy_codex_prompts=True,
-                    verbose=False,
-                )
-
-        assert not (tmp_path / "evil.txt").exists()
 
     def test_commands_preserved_when_skills_fail(self, tmp_path):
         """If skills fail, commands should NOT be removed (safety net)."""
@@ -954,21 +859,6 @@ class TestSkipIfExists:
         # All 4 templates should produce skills (specify, plan, tasks, empty_fm)
         assert len(skill_dirs) == 4
 
-    def test_existing_skill_overwritten_when_enabled(self, project_dir, templates_dir):
-        """When overwrite_existing=True, pre-existing SKILL.md should be replaced."""
-        skill_dir = project_dir / ".claude" / "skills" / "speckit-specify"
-        skill_dir.mkdir(parents=True)
-        custom_content = "# My Custom Specify Skill\nUser-modified content\n"
-        skill_file = skill_dir / "SKILL.md"
-        skill_file.write_text(custom_content)
-
-        result = install_ai_skills(project_dir, "claude", overwrite_existing=True)
-
-        assert result is True
-        updated_content = skill_file.read_text()
-        assert updated_content != custom_content
-        assert "name: speckit-specify" in updated_content
-
 
 # ===== SKILL_DESCRIPTIONS Coverage Tests =====
 

tests/test_branch_numbering.py

@@ -87,84 +87,3 @@ class TestBranchNumberingValidation:
         result = runner.invoke(app, ["init", str(tmp_path / "proj"), "--ai", "claude", "--branch-numbering", "timestamp", "--ignore-agent-tools"])
         assert result.exit_code == 0
         assert "Invalid --branch-numbering" not in (result.output or "")
-
-
-class TestGitExtensionAutoInstall:
-    """Tests for bundled git extension auto-install during specify init."""
-
-    def test_git_extension_installed_during_init(self, tmp_path: Path, monkeypatch):
-        """Verify that `specify init` auto-installs the bundled git extension."""
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        def _fake_download(project_path, *args, **kwargs):
-            Path(project_path).mkdir(parents=True, exist_ok=True)
-
-        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
-
-        project_dir = tmp_path / "proj"
-        runner = CliRunner()
-        result = runner.invoke(app, ["init", str(project_dir), "--ai", "claude", "--ignore-agent-tools"])
-        assert result.exit_code == 0
-
-        # Extension files should exist
-        ext_dir = project_dir / ".specify" / "extensions" / "git"
-        assert ext_dir.is_dir(), "git extension directory not created"
-        assert (ext_dir / "extension.yml").is_file(), "extension.yml not installed"
-
-        # Registry should contain the git extension
-        registry_file = project_dir / ".specify" / "extensions" / ".registry"
-        assert registry_file.is_file(), "extension registry not created"
-        registry = json.loads(registry_file.read_text())
-        assert "git" in registry.get("extensions", {}), "git not in registry"
-        assert registry["extensions"]["git"]["enabled"] is True
-
-    def test_git_extension_noop_when_already_installed(self, tmp_path: Path):
-        """_install_bundled_git_extension should no-op if git is already installed."""
-        from specify_cli import _install_bundled_git_extension
-        from specify_cli.extensions import ExtensionManager
-
-        project_dir = tmp_path / "proj"
-        (project_dir / ".specify").mkdir(parents=True)
-
-        # First install
-        result1 = _install_bundled_git_extension(project_dir)
-        assert result1 is True
-
-        # Second install should also succeed (no-op)
-        result2 = _install_bundled_git_extension(project_dir)
-        assert result2 is True
-
-        # Only one entry in registry
-        manager = ExtensionManager(project_dir)
-        assert manager.registry.is_installed("git")
-
-    def test_git_extension_reinstalls_when_directory_missing(self, tmp_path: Path):
-        """_install_bundled_git_extension should reinstall if registry says installed but directory is gone."""
-        import shutil
-        from specify_cli import _install_bundled_git_extension
-        from specify_cli.extensions import ExtensionManager
-
-        project_dir = tmp_path / "proj"
-        (project_dir / ".specify").mkdir(parents=True)
-
-        # First install
-        result1 = _install_bundled_git_extension(project_dir)
-        assert result1 is True
-
-        ext_dir = project_dir / ".specify" / "extensions" / "git"
-        assert ext_dir.is_dir()
-
-        # Simulate stale registry: delete extension directory but keep registry
-        shutil.rmtree(ext_dir)
-        assert not ext_dir.exists()
-
-        # Registry still says installed
-        manager = ExtensionManager(project_dir)
-        assert manager.registry.is_installed("git")
-
-        # Re-install should detect missing directory and reinstall
-        result2 = _install_bundled_git_extension(project_dir)
-        assert result2 is True
-        assert ext_dir.is_dir(), "extension directory should be reinstalled"
-        assert (ext_dir / "extension.yml").is_file(), "extension.yml should be reinstalled"

tests/test_extensions.py

@@ -747,18 +747,6 @@ $ARGUMENTS
         assert output.endswith("---\n")
         assert "description: Test command" in output
 
-    def test_render_frontmatter_unicode(self):
-        """Test rendering frontmatter preserves non-ASCII characters."""
-        frontmatter = {
-            "description": "Prüfe Konformität der Implementierung"
-        }
-
-        registrar = CommandRegistrar()
-        output = registrar.render_frontmatter(frontmatter)
-
-        assert "Prüfe Konformität" in output
-        assert "\\u" not in output
-
     def test_register_commands_for_claude(self, extension_dir, project_dir):
         """Test registering commands for Claude agent."""
         # Create .claude directory