fix: correct 0.3.1 CHANGELOG.md entries (#1882 )

* Initial plan * fix: correct 0.3.1 CHANGELOG.md entries - fix truncated title and remove duplicates Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
chore: bump version to 0.3.1
2026-03-24 14:23:09 +00:00 · 2026-03-17 12:36:43 -05:00 · 2026-03-17 16:30:05 +00:00
43 changed files with 486 additions and 4363 deletions
--- a/.devcontainer/post-create.sh
+++ b/.devcontainer/post-create.sh
@@ -51,14 +51,6 @@ echo -e "\n🤖 Installing OpenCode CLI..."
 run_command "npm install -g opencode-ai@latest"
 echo "✅ Done"
 echo -e "\n🤖 Installing Junie CLI..."
 run_command "npm install -g @jetbrains/junie-cli@latest"
 echo "✅ Done"
 echo -e "\n🤖 Installing Pi Coding Agent..."
 run_command "npm install -g @mariozechner/pi-coding-agent@latest"
 echo "✅ Done"
 echo -e "\n🤖 Installing Kiro CLI..."
 # https://kiro.dev/docs/cli/
 KIRO_INSTALLER_URL="https://kiro.dev/install.sh"
--- a/.github/ISSUE_TEMPLATE/agent_request.yml
+++ b/.github/ISSUE_TEMPLATE/agent_request.yml
@@ -8,7 +8,7 @@ body:
      value: |
        Thanks for requesting a new agent! Before submitting, please check if the agent is already supported.
-        **Currently supported agents**: Claude Code, Gemini CLI, GitHub Copilot, Cursor, Qwen Code, opencode, Codex CLI, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy, Qoder CLI, Kiro CLI, Amp, SHAI, Tabnine CLI, Antigravity, IBM Bob, Mistral Vibe, Kimi Code, Trae, Pi Coding Agent, iFlow CLI
+        **Currently supported agents**: Claude Code, Gemini CLI, GitHub Copilot, Cursor, Qwen Code, opencode, Codex CLI, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy, Qoder CLI, Kiro CLI, Amp, SHAI, IBM Bob, Antigravity
  - type: input
    id: agent-name
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -7,7 +7,7 @@ contact_links:
    url: https://github.com/github/spec-kit/blob/main/README.md
    about: Read the Spec Kit documentation and guides
  - name: 🛠️ Extension Development Guide
-    url: https://github.com/github/spec-kit/blob/main/extensions/EXTENSION-DEVELOPMENT-GUIDE.md
+    url: https://github.com/manfredseee/spec-kit/blob/main/extensions/EXTENSION-DEVELOPMENT-GUIDE.md
    about: Learn how to develop and publish Spec Kit extensions
  - name: 🤝 Contributing Guide
    url: https://github.com/github/spec-kit/blob/main/CONTRIBUTING.md
--- a/.github/ISSUE_TEMPLATE/preset_submission.yml
+++ b/.github/ISSUE_TEMPLATE/preset_submission.yml
@@ -1,169 +0,0 @@
 name: Preset Submission
 description: Submit your preset to the Spec Kit preset catalog
 title: "[Preset]: Add "
 labels: ["preset-submission", "enhancement", "needs-triage"]
 body:
  - type: markdown
    attributes:
      value: |
        Thanks for contributing a preset! This template helps you submit your preset to the community catalog.
        **Before submitting:**
        - Review the [Preset Publishing Guide](https://github.com/github/spec-kit/blob/main/presets/PUBLISHING.md)
        - Ensure your preset has a valid `preset.yml` manifest
        - Create a GitHub release with a version tag (e.g., v1.0.0)
        - Test installation from the release archive: `specify preset add --from <download-url>`
  - type: input
    id: preset-id
    attributes:
      label: Preset ID
      description: Unique preset identifier (lowercase with hyphens only)
      placeholder: "e.g., healthcare-compliance"
    validations:
      required: true
  - type: input
    id: preset-name
    attributes:
      label: Preset Name
      description: Human-readable preset name
      placeholder: "e.g., Healthcare Compliance"
    validations:
      required: true
  - type: input
    id: version
    attributes:
      label: Version
      description: Semantic version number
      placeholder: "e.g., 1.0.0"
    validations:
      required: true
  - type: textarea
    id: description
    attributes:
      label: Description
      description: Brief description of what your preset does (under 200 characters)
      placeholder: Enforces HIPAA-compliant spec workflows with audit templates and compliance checklists
    validations:
      required: true
  - type: input
    id: author
    attributes:
      label: Author
      description: Your name or organization
      placeholder: "e.g., John Doe or Acme Corp"
    validations:
      required: true
  - type: input
    id: repository
    attributes:
      label: Repository URL
      description: GitHub repository URL for your preset
      placeholder: "https://github.com/your-org/spec-kit-your-preset"
    validations:
      required: true
  - type: input
    id: download-url
    attributes:
      label: Download URL
      description: URL to the GitHub release archive for your preset (e.g., https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip)
      placeholder: "https://github.com/your-org/spec-kit-preset-your-preset/archive/refs/tags/v1.0.0.zip"
    validations:
      required: true
  - type: input
    id: license
    attributes:
      label: License
      description: Open source license type
      placeholder: "e.g., MIT, Apache-2.0"
    validations:
      required: true
  - type: input
    id: speckit-version
    attributes:
      label: Required Spec Kit Version
      description: Minimum Spec Kit version required
      placeholder: "e.g., >=0.3.0"
    validations:
      required: true
  - type: textarea
    id: templates-provided
    attributes:
      label: Templates Provided
      description: List the template overrides your preset provides
      placeholder: |
        - spec-template.md — adds compliance section
        - plan-template.md — includes audit checkpoints
        - checklist-template.md — HIPAA compliance checklist
    validations:
      required: true
  - type: textarea
    id: commands-provided
    attributes:
      label: Commands Provided (optional)
      description: List any command overrides your preset provides
      placeholder: |
        - speckit.specify.md — customized for compliance workflows
  - type: textarea
    id: tags
    attributes:
      label: Tags
      description: 2-5 relevant tags (lowercase, separated by commas)
      placeholder: "compliance, healthcare, hipaa, audit"
    validations:
      required: true
  - type: textarea
    id: features
    attributes:
      label: Key Features
      description: List the main features and capabilities of your preset
      placeholder: |
        - HIPAA-compliant spec templates
        - Audit trail checklists
        - Compliance review workflow
    validations:
      required: true
  - type: checkboxes
    id: testing
    attributes:
      label: Testing Checklist
      description: Confirm that your preset has been tested
      options:
        - label: Preset installs successfully via `specify preset add`
          required: true
        - label: Template resolution works correctly after installation
          required: true
        - label: Documentation is complete and accurate
          required: true
        - label: Tested on at least one real project
          required: true
  - type: checkboxes
    id: requirements
    attributes:
      label: Submission Requirements
      description: Verify your preset meets all requirements
      options:
        - label: Valid `preset.yml` manifest included
          required: true
        - label: README.md with description and usage instructions
          required: true
        - label: LICENSE file included
          required: true
        - label: GitHub release created with version tag
          required: true
        - label: Preset ID follows naming conventions (lowercase-with-hyphens)
          required: true
--- a/.github/workflows/release-trigger.yml
+++ b/.github/workflows/release-trigger.yml
@@ -86,10 +86,8 @@ jobs:
          if [ -f "CHANGELOG.md" ]; then
            DATE=$(date +%Y-%m-%d)
-            # Get the previous tag by sorting all version tags numerically
+            # Get the previous tag to compare commits
-            # (git describe --tags only finds tags reachable from HEAD,
+            PREVIOUS_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "")
            #  which misses tags on unmerged release branches)
            PREVIOUS_TAG=$(git tag -l 'v*' --sort=-version:refname | head -n 1)
            echo "Generating changelog from commits..."
            if [[ -n "$PREVIOUS_TAG" ]]; then
@@ -106,7 +104,7 @@ jobs:
              echo ""
              echo "## [${{ steps.version.outputs.version }}] - $DATE"
              echo ""
-              echo "### Changes"
+              echo "### Changed"
              echo ""
              echo "$COMMITS"
              echo ""
--- a/.github/workflows/scripts/create-github-release.sh
+++ b/.github/workflows/scripts/create-github-release.sh
@@ -30,8 +30,6 @@ gh release create "$VERSION" \
  .genreleases/spec-kit-template-qwen-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-windsurf-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-windsurf-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-junie-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-junie-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-codex-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-codex-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-kilocode-sh-"$VERSION".zip \
@@ -62,10 +60,6 @@ gh release create "$VERSION" \
  .genreleases/spec-kit-template-kimi-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-trae-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-trae-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-pi-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-pi-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-iflow-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-iflow-ps-"$VERSION".zip \
  .genreleases/spec-kit-template-generic-sh-"$VERSION".zip \
  .genreleases/spec-kit-template-generic-ps-"$VERSION".zip \
  --title "Spec Kit Templates - $VERSION_NO_V" \
--- a/.github/workflows/scripts/create-release-packages.ps1
+++ b/.github/workflows/scripts/create-release-packages.ps1
@@ -14,7 +14,7 @@
 .PARAMETER Agents
    Comma or space separated subset of agents to build (default: all)
-    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, junie, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, trae, pi, iflow, generic
+    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, trae, generic
 .PARAMETER Scripts
    Comma or space separated subset of script types to build (default: both)
@@ -201,26 +201,20 @@ agent: $basename
    }
 }
-# Create skills in <skills_dir>\<name>\SKILL.md format.
+# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# current dotted-name exception (e.g. speckit.plan).
+# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-#
+function New-KimiSkills {
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
 # overrides (at minimum: name/description/compatibility/metadata.{author,source}).
 function New-Skills {
    param(
        [string]$SkillsDir,
-        [string]$ScriptVariant,
+        [string]$ScriptVariant
        [string]$AgentName,
        [string]$Separator = '-'
    )
    $templates = Get-ChildItem -Path "templates/commands/*.md" -File -ErrorAction SilentlyContinue
    foreach ($template in $templates) {
        $name = [System.IO.Path]::GetFileNameWithoutExtension($template.Name)
-        $skillName = "speckit${Separator}$name"
+        $skillName = "speckit.$name"
        $skillDir = Join-Path $SkillsDir $skillName
        New-Item -ItemType Directory -Force -Path $skillDir | Out-Null
@@ -273,7 +267,7 @@ function New-Skills {
        $body = $outputLines -join "`n"
        $body = $body -replace '\{ARGS\}', '$ARGUMENTS'
-        $body = $body -replace '__AGENT__', $AgentName
+        $body = $body -replace '__AGENT__', 'kimi'
        $body = Rewrite-Paths -Content $body
        # Strip existing frontmatter, keep only body
@@ -289,7 +283,7 @@ function New-Skills {
            if ($inBody) { $templateBody += "$line`n" }
        }
-        $skillContent = "---`nname: `"$skillName`"`ndescription: `"$description`"`ncompatibility: `"Requires spec-kit project structure with .specify/ directory`"`nmetadata:`n  author: `"github-spec-kit`"`n  source: `"templates/commands/$name.md`"`n---`n`n$templateBody"
+        $skillContent = "---`nname: `"$skillName`"`ndescription: `"$description`"`n---`n`n$templateBody"
        Set-Content -Path (Join-Path $skillDir "SKILL.md") -Value $skillContent -NoNewline
    }
 }
@@ -401,14 +395,9 @@ function Build-Variant {
            $cmdDir = Join-Path $baseDir ".windsurf/workflows"
            Generate-Commands -Agent 'windsurf' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
        }
        'junie' {
            $cmdDir = Join-Path $baseDir ".junie/commands"
            Generate-Commands -Agent 'junie' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
        }
        'codex' {
-            $skillsDir = Join-Path $baseDir ".agents/skills"
+            $cmdDir = Join-Path $baseDir ".codex/prompts"
-            New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
+            Generate-Commands -Agent 'codex' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'codex' -Separator '-'
        }
        'kilocode' {
            $cmdDir = Join-Path $baseDir ".kilocode/workflows"
@@ -463,21 +452,13 @@ function Build-Variant {
        'kimi' {
            $skillsDir = Join-Path $baseDir ".kimi/skills"
            New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
-            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi' -Separator '.'
+            New-KimiSkills -SkillsDir $skillsDir -ScriptVariant $Script
        }
        'trae' {
            $rulesDir = Join-Path $baseDir ".trae/rules"
            New-Item -ItemType Directory -Force -Path $rulesDir | Out-Null
            Generate-Commands -Agent 'trae' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $rulesDir -ScriptVariant $Script
        }
        'pi' {
            $cmdDir = Join-Path $baseDir ".pi/prompts"
            Generate-Commands -Agent 'pi' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
        }
        'iflow' {
            $cmdDir = Join-Path $baseDir ".iflow/commands"
            Generate-Commands -Agent 'iflow' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
        }
        'generic' {
            $cmdDir = Join-Path $baseDir ".speckit/commands"
            Generate-Commands -Agent 'generic' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
@@ -494,7 +475,7 @@ function Build-Variant {
 }
 # Define all agents and scripts
-$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'junie', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'trae', 'pi', 'iflow', 'generic')
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'trae', 'generic')
 $AllScripts = @('sh', 'ps')
 function Normalize-List {
--- a/.github/workflows/scripts/create-release-packages.sh
+++ b/.github/workflows/scripts/create-release-packages.sh
@@ -6,7 +6,7 @@ set -euo pipefail
 # Usage: .github/workflows/scripts/create-release-packages.sh <version>
 #   Version argument should include leading 'v'.
 #   Optionally set AGENTS and/or SCRIPTS env vars to limit what gets built.
-#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf junie codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae pi iflow generic (default: all)
+#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae generic (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -26,27 +26,9 @@ fi
 echo "Building release packages for $NEW_VERSION"
 # Create and use .genreleases directory for all build artifacts
-# Override via GENRELEASES_DIR env var (e.g. for tests writing to a temp dir)
+GENRELEASES_DIR=".genreleases"
 GENRELEASES_DIR="${GENRELEASES_DIR:-.genreleases}"
 # Guard against unsafe GENRELEASES_DIR values before cleaning
 if [[ -z "$GENRELEASES_DIR" ]]; then
  echo "GENRELEASES_DIR must not be empty" >&2
  exit 1
 fi
 case "$GENRELEASES_DIR" in
  '/'|'.'|'..')
    echo "Refusing to use unsafe GENRELEASES_DIR value: $GENRELEASES_DIR" >&2
    exit 1
    ;;
 esac
 if [[ "$GENRELEASES_DIR" == *".."* ]]; then
  echo "Refusing to use GENRELEASES_DIR containing '..' path segments: $GENRELEASES_DIR" >&2
  exit 1
 fi
 mkdir -p "$GENRELEASES_DIR"
-rm -rf "${GENRELEASES_DIR%/}/"* || true
+rm -rf "$GENRELEASES_DIR"/* || true
 rewrite_paths() {
  sed -E \
@@ -139,24 +121,18 @@ EOF
  done
 }
-# Create skills in <skills_dir>/<name>/SKILL.md format.
+# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# current dotted-name exception (e.g. speckit.plan).
+# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-#
+create_kimi_skills() {
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
 # overrides (at minimum: name/description/compatibility/metadata.{author,source}).
 create_skills() {
  local skills_dir="$1"
  local script_variant="$2"
  local agent_name="$3"
  local separator="${4:-"-"}"
  for template in templates/commands/*.md; do
    [[ -f "$template" ]] || continue
    local name
    name=$(basename "$template" .md)
-    local skill_name="speckit${separator}${name}"
+    local skill_name="speckit.${name}"
    local skill_dir="${skills_dir}/${skill_name}"
    mkdir -p "$skill_dir"
@@ -199,9 +175,9 @@ create_skills() {
      in_frontmatter && skip_scripts && /^[[:space:]]/ { next }
      { print }
    ')
-    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed "s/__AGENT__/$agent_name/g" | rewrite_paths)
+    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed 's/__AGENT__/kimi/g' | rewrite_paths)
-    # Strip existing frontmatter and prepend skills frontmatter.
+    # Strip existing frontmatter and prepend Kimi frontmatter
    local template_body
    template_body=$(printf '%s\n' "$body" | awk '/^---/{p++; if(p==2){found=1; next}} found')
@@ -209,10 +185,6 @@ create_skills() {
      printf -- '---\n'
      printf 'name: "%s"\n' "$skill_name"
      printf 'description: "%s"\n' "$description"
      printf 'compatibility: "%s"\n' "Requires spec-kit project structure with .specify/ directory"
      printf -- 'metadata:\n'
      printf '  author: "%s"\n' "github-spec-kit"
      printf '  source: "%s"\n' "templates/commands/${name}.md"
      printf -- '---\n\n'
      printf '%s\n' "$template_body"
    } > "$skill_dir/SKILL.md"
@@ -246,7 +218,7 @@ build_variant() {
    esac
  fi
-  [[ -d templates ]] && { mkdir -p "$SPEC_DIR/templates"; find templates -type f -not -path "templates/commands/*" -not -name "vscode-settings.json" | while IFS= read -r f; do d="$SPEC_DIR/$(dirname "$f")"; mkdir -p "$d"; cp "$f" "$d/"; done; echo "Copied templates -> .specify/templates"; }
+  [[ -d templates ]] && { mkdir -p "$SPEC_DIR/templates"; find templates -type f -not -path "templates/commands/*" -not -name "vscode-settings.json" -exec cp --parents {} "$SPEC_DIR"/ \; ; echo "Copied templates -> .specify/templates"; }
  case $agent in
    claude)
@@ -276,12 +248,9 @@ build_variant() {
    windsurf)
      mkdir -p "$base_dir/.windsurf/workflows"
      generate_commands windsurf md "\$ARGUMENTS" "$base_dir/.windsurf/workflows" "$script" ;;
    junie)
      mkdir -p "$base_dir/.junie/commands"
      generate_commands junie md "\$ARGUMENTS" "$base_dir/.junie/commands" "$script" ;;
    codex)
-      mkdir -p "$base_dir/.agents/skills"
+      mkdir -p "$base_dir/.codex/prompts"
-      create_skills "$base_dir/.agents/skills" "$script" "codex" "-" ;;
+      generate_commands codex md "\$ARGUMENTS" "$base_dir/.codex/prompts" "$script" ;;
    kilocode)
      mkdir -p "$base_dir/.kilocode/workflows"
      generate_commands kilocode md "\$ARGUMENTS" "$base_dir/.kilocode/workflows" "$script" ;;
@@ -321,16 +290,10 @@ build_variant() {
      generate_commands vibe md "\$ARGUMENTS" "$base_dir/.vibe/prompts" "$script" ;;
    kimi)
      mkdir -p "$base_dir/.kimi/skills"
-      create_skills "$base_dir/.kimi/skills" "$script" "kimi" "." ;;
+      create_kimi_skills "$base_dir/.kimi/skills" "$script" ;;
    trae)
      mkdir -p "$base_dir/.trae/rules"
      generate_commands trae md "\$ARGUMENTS" "$base_dir/.trae/rules" "$script" ;;
    pi)
      mkdir -p "$base_dir/.pi/prompts"
      generate_commands pi md "\$ARGUMENTS" "$base_dir/.pi/prompts" "$script" ;;
    iflow)
      mkdir -p "$base_dir/.iflow/commands"
      generate_commands iflow md "\$ARGUMENTS" "$base_dir/.iflow/commands" "$script" ;;
    generic)
      mkdir -p "$base_dir/.speckit/commands"
      generate_commands generic md "\$ARGUMENTS" "$base_dir/.speckit/commands" "$script" ;;
@@ -340,38 +303,37 @@ build_variant() {
 }
 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf junie codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae pi iflow generic)
+ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae generic)
 ALL_SCRIPTS=(sh ps)
 norm_list() {
  tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?"\n":"") $i);out=1}}}END{printf("\n")}'
 }
 validate_subset() {
-  local type=$1; shift
+  local type=$1; shift; local -n allowed=$1; shift; local items=("$@")
  local allowed_str="$1"; shift
  local invalid=0
-  for it in "$@"; do
+  for it in "${items[@]}"; do
    local found=0
-    for a in $allowed_str; do
+    for a in "${allowed[@]}"; do [[ $it == "$a" ]] && { found=1; break; }; done
      if [[ "$it" == "$a" ]]; then found=1; break; fi
    done
    if [[ $found -eq 0 ]]; then
-      echo "Error: unknown $type '$it' (allowed: $allowed_str)" >&2
+      echo "Error: unknown $type '$it' (allowed: ${allowed[*]})" >&2
      invalid=1
    fi
  done
  return $invalid
 }
 read_list() { tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?" ":"") $i);out=1}}}END{printf("\n")}'; }
 if [[ -n ${AGENTS:-} ]]; then
-  read -ra AGENT_LIST <<< "$(printf '%s' "$AGENTS" | read_list)"
+  mapfile -t AGENT_LIST < <(printf '%s' "$AGENTS" | norm_list)
-  validate_subset agent "${ALL_AGENTS[*]}" "${AGENT_LIST[@]}" || exit 1
+  validate_subset agent ALL_AGENTS "${AGENT_LIST[@]}" || exit 1
 else
  AGENT_LIST=("${ALL_AGENTS[@]}")
 fi
 if [[ -n ${SCRIPTS:-} ]]; then
-  read -ra SCRIPT_LIST <<< "$(printf '%s' "$SCRIPTS" | read_list)"
+  mapfile -t SCRIPT_LIST < <(printf '%s' "$SCRIPTS" | norm_list)
-  validate_subset script "${ALL_SCRIPTS[*]}" "${SCRIPT_LIST[@]}" || exit 1
+  validate_subset script ALL_SCRIPTS "${SCRIPT_LIST[@]}" || exit 1
 else
  SCRIPT_LIST=("${ALL_SCRIPTS[@]}")
 fi
--- a/.github/workflows/stale.yml
+++ b/.github/workflows/stale.yml
@@ -39,4 +39,4 @@ jobs:
          any-of-labels: ''
          # Operations per run (helps avoid rate limits)
-          operations-per-run: 250
+          operations-per-run: 100
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -33,12 +33,11 @@ Specify supports multiple AI agents by generating agent-specific command files a
 | **Cursor**                 | `.cursor/commands/`    | Markdown | `cursor-agent`  | Cursor CLI                  |
 | **Qwen Code**              | `.qwen/commands/`      | Markdown | `qwen`          | Alibaba's Qwen Code CLI     |
 | **opencode**               | `.opencode/command/`   | Markdown | `opencode`      | opencode CLI                |
-| **Codex CLI**              | `.agents/skills/`      | Markdown | `codex`         | Codex CLI (skills)          |
+| **Codex CLI**              | `.codex/commands/`     | Markdown | `codex`         | Codex CLI                   |
 | **Windsurf**               | `.windsurf/workflows/` | Markdown | N/A (IDE-based) | Windsurf IDE workflows      |
-| **Junie**                  | `.junie/commands/`     | Markdown | `junie`         | Junie by JetBrains          |
+| **Kilo Code**              | `.kilocode/rules/`     | Markdown | N/A (IDE-based) | Kilo Code IDE               |
-| **Kilo Code**              | `.kilocode/workflows/` | Markdown | N/A (IDE-based) | Kilo Code IDE               |
+| **Auggie CLI**             | `.augment/rules/`      | Markdown | `auggie`        | Auggie CLI                  |
-| **Auggie CLI**             | `.augment/commands/`   | Markdown | `auggie`        | Auggie CLI                  |
+| **Roo Code**               | `.roo/rules/`          | Markdown | N/A (IDE-based) | Roo Code IDE                |
 | **Roo Code**               | `.roo/commands/`       | Markdown | N/A (IDE-based) | Roo Code IDE                |
 | **CodeBuddy CLI**          | `.codebuddy/commands/` | Markdown | `codebuddy`     | CodeBuddy CLI               |
 | **Qoder CLI**              | `.qoder/commands/`     | Markdown | `qodercli`      | Qoder CLI                   |
 | **Kiro CLI**               | `.kiro/prompts/`       | Markdown | `kiro-cli`      | Kiro CLI                    |
@@ -46,8 +45,6 @@ Specify supports multiple AI agents by generating agent-specific command files a
 | **SHAI**                   | `.shai/commands/`      | Markdown | `shai`          | SHAI CLI                    |
 | **Tabnine CLI**            | `.tabnine/agent/commands/` | TOML | `tabnine`       | Tabnine CLI                 |
 | **Kimi Code**              | `.kimi/skills/`        | Markdown | `kimi`          | Kimi Code CLI (Moonshot AI) |
 | **Pi Coding Agent**        | `.pi/prompts/`         | Markdown | `pi`            | Pi terminal coding agent    |
 | **iFlow CLI**              | `.iflow/commands/`     | Markdown | `iflow`         | iFlow CLI (iflow-ai)        |
 | **IBM Bob**                | `.bob/commands/`       | Markdown | N/A (IDE-based) | IBM Bob IDE                 |
 | **Trae**                   | `.trae/rules/`         | Markdown | N/A (IDE-based) | Trae IDE                    |
 | **Generic**                | User-specified via `--ai-commands-dir` | Markdown | N/A | Bring your own agent        |
@@ -88,7 +85,7 @@ This eliminates the need for special-case mappings throughout the codebase.
 - `folder`: Directory where agent-specific files are stored (relative to project root)
 - `commands_subdir`: Subdirectory name within the agent folder where command/prompt files are stored (default: `"commands"`)
  - Most agents use `"commands"` (e.g., `.claude/commands/`)
-  - Some agents use alternative names: `"agents"` (copilot), `"workflows"` (windsurf, kilocode), `"prompts"` (codex, kiro-cli, pi), `"command"` (opencode - singular)
+  - Some agents use alternative names: `"agents"` (copilot), `"workflows"` (windsurf, kilocode), `"prompts"` (codex, kiro-cli), `"command"` (opencode - singular)
  - This field enables `--ai-skills` to locate command templates correctly for skill generation
 - `install_url`: Installation documentation URL (set to `None` for IDE-based agents)
 - `requires_cli`: Whether the agent requires a CLI tool check during initialization
@@ -319,7 +316,6 @@ Require a command-line tool to be installed:
 - **Cursor**: `cursor-agent` CLI
 - **Qwen Code**: `qwen` CLI
 - **opencode**: `opencode` CLI
 - **Junie**: `junie` CLI
 - **Kiro CLI**: `kiro-cli` CLI
 - **CodeBuddy CLI**: `codebuddy` CLI
 - **Qoder CLI**: `qodercli` CLI
@@ -327,7 +323,6 @@ Require a command-line tool to be installed:
 - **SHAI**: `shai` CLI
 - **Tabnine CLI**: `tabnine` CLI
 - **Kimi Code**: `kimi` CLI
 - **Pi Coding Agent**: `pi` CLI
 ### IDE-Based Agents
@@ -341,7 +336,7 @@ Work within integrated development environments:
 ### Markdown Format
-Used by: Claude, Cursor, opencode, Windsurf, Junie, Kiro CLI, Amp, SHAI, IBM Bob, Kimi Code, Qwen, Pi
+Used by: Claude, Cursor, opencode, Windsurf, Kiro CLI, Amp, SHAI, IBM Bob, Kimi Code, Qwen
 **Standard format:**
@@ -379,11 +374,6 @@ Command content with {SCRIPT} and {{args}} placeholders.
 ## Directory Conventions
 - **CLI agents**: Usually `.<agent-name>/commands/`
 - **Skills-based exceptions**:
  - Codex: `.agents/skills/` (skills, invoked as `$speckit-<command>`)
 - **Prompt-based exceptions**:
  - Kiro CLI: `.kiro/prompts/`
  - Pi: `.pi/prompts/`
 - **IDE agents**: Follow IDE-specific patterns:
  - Copilot: `.github/agents/`
  - Cursor: `.cursor/commands/`
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,49 +1,16 @@
 # Changelog
-## [0.3.2] - 2026-03-19
+<!-- markdownlint-disable MD024 -->
-### Changes
+Recent changes to the Specify CLI and templates are documented here.
- chore: bump version to 0.3.2
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
- Add conduct extension to community catalog (#1908)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [0.4.0] - 2026-03-23
 ### Changes
 - fix(cli): add allow_unicode=True and encoding="utf-8" to YAML I/O (#1936)
 - fix(codex): native skills fallback refresh + legacy prompt suppression (#1930)
 - 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)
 - feat(commands): wire before/after hook events into specify and plan templates (#1886)
 - docs(catalog): add speckit-utils to community catalog (#1896)
 - docs: Add Extensions & Presets section to README (#1898)
 - chore: update DocGuard extension to v0.9.11 (#1899)
 - Update cognitive-squad catalog entry — Triadic Model, full lifecycle (#1884)
 - feat: register spec-kit-iterate extension (#1887)
 - fix(scripts): add explicit positional binding to PowerShell create-new-feature params (#1885)
 - fix(scripts): encode residual JSON control chars as \uXXXX instead of stripping (#1872)
 - chore: update DocGuard extension to v0.9.10 (#1890)
 - Feature/spec kit add pi coding agent pullrequest (#1853)
 - feat: register spec-kit-learn extension (#1883)
 ## [0.3.1] - 2026-03-17
 ### Changed
 - chore: bump version to 0.3.1
 - docs: add greenfield Spring Boot pirate-speak preset demo to README (#1878)
 - fix(ai-skills): exclude non-speckit copilot agent markdown from skills (#1867)
 - feat: add Trae IDE support as a new agent (#1817)
@@ -59,21 +26,52 @@
 - feat(extensions): add Archive and Reconcile extensions to community catalog (#1844)
 - feat: Add DocGuard CDD enforcement extension to community catalog (#1838)
 ## [0.3.0] - 2026-03-13
 ### Changed
- chore: bump version to 0.3.0
+- No changes have been documented for this release yet.
- feat(presets): Pluggable preset system with catalog, resolver, and skills propagation (#1787)
+
- fix: match 'Last updated' timestamp with or without bold markers (#1836)
+<!-- Entries for 0.2.x and earlier releases are documented in their respective sections below. -->
- Add specify doctor command for project health diagnostics (#1828)
+- make c ignores consistent with c++ (#1747)
- fix: harden bash scripts against shell injection and improve robustness (#1809)
+- chore: bump version to 0.1.13 (#1746)
- fix: clean up command templates (specify, analyze) (#1810)
+- feat: add kiro-cli and AGENT_CONFIG consistency coverage (#1690)
- fix: migrate Qwen Code CLI from TOML to Markdown format (#1589) (#1730)
+- feat: add verify extension to community catalog (#1726)
- fix(cli): deprecate explicit command support for agy (#1798) (#1808)
+- Add Retrospective Extension to community catalog README table (#1741)
- Add /selftest.extension core extension to test other extensions (#1758)
+- fix(scripts): add empty description validation and branch checkout error handling (#1559)
- feat(extensions): Quality of life improvements for RFC-aligned catalog integration (#1776)
+- fix: correct Copilot extension command registration (#1724)
- Add Java brownfield walkthrough to community walkthroughs (#1820)
+- fix(implement): remove Makefile from C ignore patterns (#1558)
 - Add sync extension to community catalog (#1728)
 - fix(checklist): clarify file handling behavior for append vs create (#1556)
 - fix(clarify): correct conflicting question limit from 10 to 5 (#1557)
 - chore: bump version to 0.1.12 (#1737)
 - fix: use RELEASE_PAT so tag push triggers release workflow (#1736)
 - fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
 - fix: Split release process to sync pyproject.toml version with git tags (#1732)
 ## [Unreleased]
 ### Added
 - feat(cli): polite deep merge for VSCode settings.json with JSONC support via `json5` and zero-data-loss fallbacks
 - feat(presets): Pluggable preset system with preset catalog and template resolver
 - Preset manifest (`preset.yml`) with validation for artifact, command, and script types
 - `PresetManifest`, `PresetRegistry`, `PresetManager`, `PresetCatalog`, `PresetResolver` classes in `src/specify_cli/presets.py`
 - CLI commands: `specify preset search`, `specify preset add`, `specify preset list`, `specify preset remove`, `specify preset resolve`, `specify preset info`
 - CLI commands: `specify preset catalog list`, `specify preset catalog add`, `specify preset catalog remove` for multi-catalog management
 - `PresetCatalogEntry` dataclass and multi-catalog support mirroring the extension catalog system
 - `--preset` option for `specify init` to install presets during initialization
 - Priority-based preset resolution: presets with lower priority number win (`--priority` flag)
 - `resolve_template()` / `Resolve-Template` helpers in bash and PowerShell common scripts
 - Template resolution priority stack: overrides → presets → extensions → core
 - Preset catalog files (`presets/catalog.json`, `presets/catalog.community.json`)
 - Preset scaffold directory (`presets/scaffold/`)
 - Scripts updated to use template resolution instead of hardcoded paths
 - feat(presets): Preset command overrides now propagate to agent skills when `--ai-skills` was used during init
 - feat: `specify init` persists CLI options to `.specify/init-options.json` for downstream operations
 - feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
 ## [0.2.1] - 2026-03-11
@@ -300,3 +298,28 @@
 - Add pytest and Python linting (ruff) to CI (#1637)
 - feat: add pull request template for better contribution guidelines (#1634)
 ## [0.0.99] - 2026-02-19
 - Feat/ai skills (#1632)
 ## [0.0.98] - 2026-02-19
 - chore(deps): bump actions/stale from 9 to 10 (#1623)
 - feat: add dependabot configuration for pip and GitHub Actions updates (#1622)
 ## [0.0.97] - 2026-02-18
 - Remove Maintainers section from README.md (#1618)
 ## [0.0.96] - 2026-02-17
 - fix: typo in plan-template.md (#1446)
 ## [0.0.95] - 2026-02-12
 - Feat: add a new agent: Google Anti Gravity (#1220)
 ## [0.0.94] - 2026-02-11
 - Add stale workflow for 180-day inactive issues and PRs (#1594)
--- a/README.md
+++ b/README.md
@@ -25,7 +25,6 @@
 - [🚶 Community Walkthroughs](#-community-walkthroughs)
 - [🤖 Supported AI Agents](#-supported-ai-agents)
 - [🔧 Specify CLI Reference](#-specify-cli-reference)
 - [🧩 Making Spec Kit Your Own: Extensions & Presets](#-making-spec-kit-your-own-extensions--presets)
 - [📚 Core Philosophy](#-core-philosophy)
 - [🌟 Development Phases](#-development-phases)
 - [🎯 Experimental Goals](#-experimental-goals)
@@ -49,13 +48,9 @@ Choose your preferred installation method:
 #### Option 1: Persistent Installation (Recommended)
-Install once and use everywhere. Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
+Install once and use everywhere:
 ```bash
 # Install a specific stable release (recommended — replace vX.Y.Z with the latest tag)
 uv tool install specify-cli --from git+https://github.com/github/spec-kit.git@vX.Y.Z
 # Or install latest from main (may include unreleased changes)
 uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 ```
@@ -77,7 +72,7 @@ specify check
 To upgrade Specify, see the [Upgrade Guide](./docs/upgrade.md) for detailed instructions. Quick upgrade:
 ```bash
-uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@vX.Y.Z
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
 ```
 #### Option 2: One-time Usage
@@ -85,13 +80,13 @@ uv tool install specify-cli --force --from git+https://github.com/github/spec-ki
 Run directly without installing:
 ```bash
-# Create new project (pinned to a stable release — replace vX.Y.Z with the latest tag)
+# Create new project
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <PROJECT_NAME>
+uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
 # Or initialize in existing project
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init . --ai claude
+uvx --from git+https://github.com/github/spec-kit.git specify init . --ai claude
 # or
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here --ai claude
+uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai claude
 ```
 **Benefits of persistent installation:**
@@ -101,13 +96,9 @@ uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here
 - Better tool management with `uv tool list`, `uv tool upgrade`, `uv tool uninstall`
 - Cleaner shell configuration
 #### Option 3: Enterprise / Air-Gapped Installation
 If your environment blocks access to PyPI or GitHub, see the [Enterprise / Air-Gapped Installation](./docs/installation.md#enterprise--air-gapped-installation) guide for step-by-step instructions on using `pip download` to create portable, OS-specific wheel bundles on a connected machine.
 ### 2. Establish project principles
-Launch your AI assistant in the project directory. Most agents expose spec-kit as `/speckit.*` slash commands; Codex CLI in skills mode uses `$speckit-*` instead.
+Launch your AI assistant in the project directory. The `/speckit.*` commands are available in the assistant.
 Use the **`/speckit.constitution`** command to create your project's governing principles and development guidelines that will guide all subsequent development.
@@ -181,7 +172,7 @@ See Spec-Driven Development in action across different scenarios with these comm
 | [Auggie CLI](https://docs.augmentcode.com/cli/overview)                              | ✅      |                                                                                                                                           |
 | [Claude Code](https://www.anthropic.com/claude-code)                                 | ✅      |                                                                                                                                           |
 | [CodeBuddy CLI](https://www.codebuddy.ai/cli)                                        | ✅      |                                                                                                                                           |
-| [Codex CLI](https://github.com/openai/codex)                                         | ✅      | Requires `--ai-skills`. Codex recommends [skills](https://developers.openai.com/codex/skills) and treats [custom prompts](https://developers.openai.com/codex/custom-prompts) as deprecated. Spec-kit installs Codex skills into `.agents/skills` and invokes them as `$speckit-<command>`. |
+| [Codex CLI](https://github.com/openai/codex)                                         | ✅      |                                                                                                                                           |
 | [Cursor](https://cursor.sh/)                                                         | ✅      |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | ✅      |                                                                                                                                           |
 | [GitHub Copilot](https://code.visualstudio.com/)                                     | ✅      |                                                                                                                                           |
@@ -189,16 +180,13 @@ See Spec-Driven Development in action across different scenarios with these comm
 | [Jules](https://jules.google.com/)                                                   | ✅      |                                                                                                                                           |
 | [Kilo Code](https://github.com/Kilo-Org/kilocode)                                    | ✅      |                                                                                                                                           |
 | [opencode](https://opencode.ai/)                                                     | ✅      |                                                                                                                                           |
 | [Pi Coding Agent](https://pi.dev)                                                    | ✅      | Pi doesn't have MCP support out of the box, so `taskstoissues` won't work as intended. MCP support can be added via [extensions](https://github.com/badlogic/pi-mono/tree/main/packages/coding-agent#extensions) |
 | [Qwen Code](https://github.com/QwenLM/qwen-code)                                     | ✅      |                                                                                                                                           |
 | [Roo Code](https://roocode.com/)                                                     | ✅      |                                                                                                                                           |
 | [SHAI (OVHcloud)](https://github.com/ovh/shai)                                       | ✅      |                                                                                                                                           |
 | [Tabnine CLI](https://docs.tabnine.com/main/getting-started/tabnine-cli)             | ✅      |                                                                                                                                           |
 | [Mistral Vibe](https://github.com/mistralai/mistral-vibe)                            | ✅      |                                                                                                                                           |
 | [Kimi Code](https://code.kimi.com/)                                                  | ✅      |                                                                                                                                           |
 | [iFlow CLI](https://docs.iflow.cn/en/cli/quickstart)                                 | ✅      |                                                                                                                                           |
 | [Windsurf](https://windsurf.com/)                                                    | ✅      |                                                                                                                                           |
 | [Junie](https://junie.jetbrains.com/)                                                | ✅      |                                                                                                                                           |
 | [Antigravity (agy)](https://antigravity.google/)                                     | ✅      | Requires `--ai-skills` |
 | [Trae](https://www.trae.ai/)                                                         | ✅      |                                                                                                                                           |
 | Generic                                                                              | ✅      | Bring your own agent — use `--ai generic --ai-commands-dir <path>` for unsupported agents                                                 |
@@ -209,28 +197,27 @@ The `specify` command supports the following options:
 ### Commands
-| Command | Description                                                                                                                                                                                                                                                                              |
+| Command | Description                                                                                                                                             |
-| ------- |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `init`  | Initialize a new Specify project from the latest template                                                                                                                                                                                                                                |
+| `init`  | Initialize a new Specify project from the latest template                                                                                               |
-| `check` | Check for installed tools: `git` plus all CLI-based agents configured in `AGENT_CONFIG` (for example: `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `junie`, `qwen`, `opencode`, `codex`, `kiro-cli`, `shai`, `qodercli`, `vibe`, `kimi`, `iflow`, `pi`, etc.) |
+| `check` | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`, `kiro-cli`, `shai`, `qodercli`, `vibe`, `kimi`) |
 ### `specify init` Arguments & Options
-| Argument/Option        | Type     | Description                                                                                                                                                                                                                                                                                                                                                                               |
+| Argument/Option        | Type     | Description                                                                                                                                                                                  |
-| ---------------------- | -------- |-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| ---------------------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory)                                                                                                                                                                                                                                                                                        |
+| `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory)                                                                                           |
-| `--ai`                 | Option   | AI assistant to use (see `AGENT_CONFIG` for the full, up-to-date list). Common options include: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `junie`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, `shai`, `kiro-cli` (`kiro` alias), `agy`, `bob`, `qodercli`, `vibe`, `kimi`, `iflow`, `pi`, or `generic` (requires `--ai-commands-dir`) |
+| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, `shai`, `kiro-cli` (`kiro` alias), `agy`, `bob`, `qodercli`, `vibe`, `kimi`, or `generic` (requires `--ai-commands-dir`) |
-| `--ai-commands-dir`    | Option   | Directory for agent command files (required with `--ai generic`, e.g. `.myagent/commands/`)                                                                                                                                                                                                                                                                                               |
+| `--ai-commands-dir`    | Option   | Directory for agent command files (required with `--ai generic`, e.g. `.myagent/commands/`)                                                                                                  |
-| `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                                                                                                                                                                                                                                                                                                                               |
+| `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                                                                                                                                  |
-| `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                                                                                                                                                                                                                                                                                                                                           |
+| `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                                                                                                                                              |
-| `--no-git`             | Flag     | Skip git repository initialization                                                                                                                                                                                                                                                                                                                                                        |
+| `--no-git`             | Flag     | Skip git repository initialization                                                                                                                                                           |
-| `--here`               | Flag     | Initialize project in the current directory instead of creating a new one                                                                                                                                                                                                                                                                                                                 |
+| `--here`               | Flag     | Initialize project in the current directory instead of creating a new one                                                                                                                    |
-| `--force`              | Flag     | Force merge/overwrite when initializing in current directory (skip confirmation)                                                                                                                                                                                                                                                                                                          |
+| `--force`              | Flag     | Force merge/overwrite when initializing in current directory (skip confirmation)                                                                                                             |
-| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                                                                                                                                                                                                               |
+| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                  |
-| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                                                                                                                                                                                                                          |
+| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                             |
-| `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                                                                                                                                                                                                                 |
+| `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                    |
-| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                                                                                                                                                                                                                       |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                          |
 | `--branch-numbering`   | Option   | Branch numbering strategy: `sequential` (default — `001`, `002`, `003`) or `timestamp` (`YYYYMMDD-HHMMSS`). Timestamp mode is useful for distributed teams to avoid numbering conflicts                                                                                                                                                                                                  |
 ### Examples
@@ -265,12 +252,6 @@ specify init my-project --ai vibe
 # Initialize with IBM Bob support
 specify init my-project --ai bob
 # Initialize with Pi Coding Agent support
 specify init my-project --ai pi
 # Initialize with Codex CLI support
 specify init my-project --ai codex --ai-skills
 # Initialize with Antigravity support
 specify init my-project --ai agy --ai-skills
@@ -305,18 +286,13 @@ specify init my-project --ai claude --ai-skills
 # Initialize in current directory with agent skills
 specify init --here --ai gemini --ai-skills
 # Use timestamp-based branch numbering (useful for distributed teams)
 specify init my-project --ai claude --branch-numbering timestamp
 # Check system requirements
 specify check
 ```
 ### Available Slash Commands
-After running `specify init`, your AI coding agent will have access to these slash commands for structured development.
+After running `specify init`, your AI coding agent will have access to these slash commands for structured development:
 For Codex CLI, `--ai-skills` installs spec-kit as agent skills instead of slash-command prompt files. In Codex skills mode, invoke spec-kit as `$speckit-constitution`, `$speckit-specify`, `$speckit-plan`, `$speckit-tasks`, and `$speckit-implement`.
 #### Core Commands
@@ -346,68 +322,6 @@ Additional commands for enhanced quality and validation:
 | ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | `SPECIFY_FEATURE` | Override feature detection for non-Git repositories. Set to the feature directory name (e.g., `001-photo-albums`) to work on a specific feature when not using Git branches.<br/>\*\*Must be set in the context of the agent you're working with prior to using `/speckit.plan` or follow-up commands. |
 ## 🧩 Making Spec Kit Your Own: Extensions & Presets
 Spec Kit can be tailored to your needs through two complementary systems — **extensions** and **presets** — plus project-local overrides for one-off adjustments:
 ```mermaid
 block-beta
    columns 1
    overrides["⬆ Highest priority\nProject-Local Overrides\n.specify/templates/overrides/"]
    presets["Presets — Customize core & extensions\n.specify/presets/<preset-id>/templates/"]
    extensions["Extensions — Add new capabilities\n.specify/extensions/<ext-id>/templates/"]
    core["Spec Kit Core — Built-in SDD commands & templates\n.specify/templates/\n⬇ Lowest priority"]
    style overrides fill:transparent,stroke:#999
    style presets fill:transparent,stroke:#4a9eda
    style extensions fill:transparent,stroke:#4a9e4a
    style core fill:transparent,stroke:#e6a817
 ```
 **Templates** are resolved at **runtime** — Spec Kit walks the stack top-down and uses the first match. Project-local overrides (`.specify/templates/overrides/`) let you make one-off adjustments for a single project without creating a full preset. **Commands** are applied at **install time** — when you run `specify extension add` or `specify preset add`, command files are written into agent directories (e.g., `.claude/commands/`). If multiple presets or extensions provide the same command, the highest-priority version wins. On removal, the next-highest-priority version is restored automatically. If no overrides or customizations exist, Spec Kit uses its core defaults.
 ### Extensions — Add New Capabilities
 Use **extensions** when you need functionality that goes beyond Spec Kit's core. Extensions introduce new commands and templates — for example, adding domain-specific workflows that are not covered by the built-in SDD commands, integrating with external tools, or adding entirely new development phases. They expand *what Spec Kit can do*.
 ```bash
 # Search available extensions
 specify extension search
 # Install an extension
 specify extension add <extension-name>
 ```
 For example, extensions could add Jira integration, post-implementation code review, V-Model test traceability, or project health diagnostics.
 See the [Extensions README](./extensions/README.md) for the full guide, the complete community catalog, and how to build and publish your own.
 ### Presets — Customize Existing Workflows
 Use **presets** when you want to change *how* Spec Kit works without adding new capabilities. Presets override the templates and commands that ship with the core *and* with installed extensions — for example, enforcing a compliance-oriented spec format, using domain-specific terminology, or applying organizational standards to plans and tasks. They customize the artifacts and instructions that Spec Kit and its extensions produce.
 ```bash
 # Search available presets
 specify preset search
 # Install a preset
 specify preset add <preset-name>
 ```
 For example, presets could restructure spec templates to require regulatory traceability, adapt the workflow to fit the methodology you use (e.g., Agile, Kanban, Waterfall, jobs-to-be-done, or domain-driven design), add mandatory security review gates to plans, enforce test-first task ordering, or localize the entire workflow to a different language. The [pirate-speak demo](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo) shows just how deep the customization can go. Multiple presets can be stacked with priority ordering.
 See the [Presets README](./presets/README.md) for the full guide, including resolution order, priority, and how to create your own.
 ### When to Use Which
 | Goal | Use |
 | --- | --- |
 | Add a brand-new command or workflow | Extension |
 | Customize the format of specs, plans, or tasks | Preset |
 | Integrate an external tool or service | Extension |
 | Enforce organizational or regulatory standards | Preset |
 | Ship reusable domain-specific templates | Either — presets for template overrides, extensions for templates bundled with new commands |
 ## 📚 Core Philosophy
 Spec-Driven Development is a structured process that emphasizes:
@@ -502,11 +416,11 @@ specify init <project_name> --ai copilot
 # Or in current directory:
 specify init . --ai claude
-specify init . --ai codex --ai-skills
+specify init . --ai codex
 # or use --here flag
 specify init --here --ai claude
-specify init --here --ai codex --ai-skills
+specify init --here --ai codex
 # Force merge into a non-empty current directory
 specify init . --force --ai claude
@@ -515,7 +429,7 @@ specify init . --force --ai claude
 specify init --here --force --ai claude
 ```
-The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi, or Mistral Vibe installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
+The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, or Mistral Vibe installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
 ```bash
 specify init <project_name> --ai claude --ignore-agent-tools
--- a/SUPPORT.md
+++ b/SUPPORT.md
@@ -1,17 +1,18 @@
 # Support
-## How to get help
+## How to file issues and get help
-Please search existing [issues](https://github.com/github/spec-kit/issues) and [discussions](https://github.com/github/spec-kit/discussions) before creating new ones to avoid duplicates.
+This project uses GitHub issues to track bugs and feature requests. Please search the existing issues before filing new issues to avoid duplicates. For new issues, file your bug or feature request as a new issue.
- Review the [README](./README.md) for getting started instructions and troubleshooting tips
+For help or questions about using this project, please:
 - Open a [GitHub issue](https://github.com/github/spec-kit/issues/new) for bug reports, feature requests, or questions about the Spec-Driven Development methodology
 - Check the [comprehensive guide](./spec-driven.md) for detailed documentation on the Spec-Driven Development process
- Ask in [GitHub Discussions](https://github.com/github/spec-kit/discussions) for questions about using Spec Kit or the Spec-Driven Development methodology
+- Review the [README](./README.md) for getting started instructions and troubleshooting tips
 - Open a [GitHub issue](https://github.com/github/spec-kit/issues/new) for bug reports and feature requests
 ## Project Status
-**Spec Kit** is under active development and maintained by GitHub staff and the community. We will do our best to respond to support, feature requests, and community questions as time permits.
+**Spec Kit** is under active development and maintained by GitHub staff **AND THE COMMUNITY**. We will do our best to respond to support, feature requests, and community questions in a timely manner.
 ## GitHub Support Policy
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -3,7 +3,7 @@
 ## Prerequisites
 - **Linux/macOS** (or Windows; PowerShell scripts now supported without WSL)
- AI coding agent: [Claude Code](https://www.anthropic.com/claude-code), [GitHub Copilot](https://code.visualstudio.com/), [Codebuddy CLI](https://www.codebuddy.ai/cli), [Gemini CLI](https://github.com/google-gemini/gemini-cli), or [Pi Coding Agent](https://pi.dev)
+- AI coding agent: [Claude Code](https://www.anthropic.com/claude-code), [GitHub Copilot](https://code.visualstudio.com/), [Codebuddy CLI](https://www.codebuddy.ai/cli) or [Gemini CLI](https://github.com/google-gemini/gemini-cli)
 - [uv](https://docs.astral.sh/uv/) for package management
 - [Python 3.11+](https://www.python.org/downloads/)
 - [Git](https://git-scm.com/downloads)
@@ -12,22 +12,18 @@
 ### Initialize a New Project
-The easiest way to get started is to initialize a new project. Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
+The easiest way to get started is to initialize a new project:
 ```bash
 # Install from a specific stable release (recommended — replace vX.Y.Z with the latest tag)
 uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <PROJECT_NAME>
 # Or install latest from main (may include unreleased changes)
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
 ```
 Or initialize in the current directory:
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init .
+uvx --from git+https://github.com/github/spec-kit.git specify init .
 # or use the --here flag
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here
+uvx --from git+https://github.com/github/spec-kit.git specify init --here
 ```
 ### Specify AI Agent
@@ -35,11 +31,10 @@ uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here
 You can proactively specify your AI agent during initialization:
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai claude
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai claude
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai gemini
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai gemini
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai copilot
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai copilot
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai codebuddy
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai codebuddy
 uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai pi
 ```
 ### Specify Script Type (Shell vs PowerShell)
@@ -55,8 +50,8 @@ Auto behavior:
 Force a specific script type:
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --script sh
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --script sh
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --script ps
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --script ps
 ```
 ### Ignore Agent Tools Check
@@ -64,7 +59,7 @@ uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <proje
 If you prefer to get the templates without checking for the right tools:
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai claude --ignore-agent-tools
+uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai claude --ignore-agent-tools
 ```
 ## Verification
@@ -79,52 +74,6 @@ The `.specify/scripts` directory will contain both `.sh` and `.ps1` scripts.
 ## Troubleshooting
 ### Enterprise / Air-Gapped Installation
 If your environment blocks access to PyPI (you see 403 errors when running `uv tool install` or `pip install`), you can create a portable wheel bundle on a connected machine and transfer it to the air-gapped target.
 **Step 1: Build the wheel on a connected machine (same OS and Python version as the target)**
 ```bash
 # Clone the repository
 git clone https://github.com/github/spec-kit.git
 cd spec-kit
 # Build the wheel
 pip install build
 python -m build --wheel --outdir dist/
 # Download the wheel and all its runtime dependencies
 pip download -d dist/ dist/specify_cli-*.whl
 ```
 > **Important:** `pip download` resolves platform-specific wheels (e.g., PyYAML includes native extensions). You must run this step on a machine with the **same OS and Python version** as the air-gapped target. If you need to support multiple platforms, repeat this step on each target OS (Linux, macOS, Windows) and Python version.
 **Step 2: Transfer the `dist/` directory to the air-gapped machine**
 Copy the entire `dist/` directory (which contains the `specify-cli` wheel and all dependency wheels) to the target machine via USB, network share, or other approved transfer method.
 **Step 3: Install on the air-gapped machine**
 ```bash
 pip install --no-index --find-links=./dist specify-cli
 ```
 **Step 4: Initialize a project (no network required)**
 ```bash
 # Initialize a project — no GitHub access needed
 specify init my-project --ai claude --offline
 ```
 The `--offline` flag tells the CLI to use the templates, commands, and scripts bundled inside the wheel instead of downloading from GitHub.
 > **Deprecation notice:** Starting with v0.6.0, `specify init` will use bundled assets by default and the `--offline` flag will be removed. The GitHub download path will be retired because bundled assets eliminate the need for network access, avoid proxy/firewall issues, and guarantee that templates always match the installed CLI version. No action will be needed — `specify init` will simply work without network access out of the box.
 > **Note:** Python 3.11+ is required.
 > **Windows note:** Offline scaffolding requires PowerShell 7+ (`pwsh`), not Windows PowerShell 5.x (`powershell.exe`). Install from https://aka.ms/powershell.
 ### Git Credential Manager on Linux
 If you're having issues with Git authentication on Linux, you can install Git Credential Manager:
--- a/docs/upgrade.md
+++ b/docs/upgrade.md
@@ -8,7 +8,7 @@
 | What to Upgrade | Command | When to Use |
 |----------------|---------|-------------|
-| **CLI Tool Only** | `uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@vX.Y.Z` | Get latest CLI features without touching project files |
+| **CLI Tool Only** | `uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git` | Get latest CLI features without touching project files |
 | **Project Files** | `specify init --here --force --ai <your-agent>` | Update slash commands, templates, and scripts in your project |
 | **Both** | Run CLI upgrade, then project update | Recommended for major version updates |
@@ -20,18 +20,16 @@ The CLI tool (`specify`) is separate from your project files. Upgrade it to get
 ### If you installed with `uv tool install`
 Upgrade to a specific release (check [Releases](https://github.com/github/spec-kit/releases) for the latest tag):
 ```bash
-uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@vX.Y.Z
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
 ```
 ### If you use one-shot `uvx` commands
-Specify the desired release tag:
+No upgrade needed—`uvx` always fetches the latest version. Just run your commands as normal:
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here --ai copilot
+uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai copilot
 ```
 ### Verify the upgrade
@@ -291,9 +289,8 @@ This tells Spec Kit which feature directory to use when creating specs, plans, a
   ```bash
   ls -la .claude/commands/      # Claude Code
-   ls -la .gemini/commands/      # Gemini
+   ls -la .gemini/commands/       # Gemini
-   ls -la .cursor/commands/      # Cursor
+   ls -la .cursor/commands/       # Cursor
   ls -la .pi/prompts/           # Pi Coding Agent
   ```
 3. **Check agent-specific setup:**
@@ -401,7 +398,7 @@ The `specify` CLI tool is used for:
 - **Upgrades:** `specify init --here --force` to update templates and commands
 - **Diagnostics:** `specify check` to verify tool installation
-Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/speckit.plan`, etc.) are **permanently installed** in your project's agent folder (`.claude/`, `.github/prompts/`, `.pi/prompts/`, etc.). Your AI assistant reads these command files directly—no need to run `specify` again.
+Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/speckit.plan`, etc.) are **permanently installed** in your project's agent folder (`.claude/`, `.github/prompts/`, etc.). Your AI assistant reads these command files directly—no need to run `specify` again.
 **If your agent isn't recognizing slash commands:**
@@ -413,9 +410,6 @@ Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/s
   # For Claude
   ls -la .claude/commands/
   # For Pi
   ls -la .pi/prompts/
   ```
 2. **Restart your IDE/editor completely** (not just reload window)
--- a/extensions/EXTENSION-API-REFERENCE.md
+++ b/extensions/EXTENSION-API-REFERENCE.md
@@ -53,7 +53,7 @@ provides:
      required: boolean  # Default: false
 hooks:                   # Optional, event hooks
-  event_name:            # e.g., "after_specify", "after_plan", "after_tasks", "after_implement"
+  event_name:            # e.g., "after_tasks", "after_implement"
    command: string      # Command to execute
    optional: boolean    # Default: true
    prompt: string       # Prompt text for optional hooks
@@ -108,7 +108,7 @@ defaults:                # Optional, default configuration values
 #### `hooks`
 - **Type**: object
- **Keys**: Event names (e.g., `after_specify`, `after_plan`, `after_tasks`, `after_implement`, `before_commit`)
+- **Keys**: Event names (e.g., `after_tasks`, `after_implement`, `before_commit`)
 - **Description**: Hooks that execute at lifecycle events
 - **Events**: Defined by core spec-kit commands
@@ -551,16 +551,10 @@ hooks:
 Standard events (defined by core):
 - `before_specify` - Before specification generation
 - `after_specify` - After specification generation
 - `before_plan` - Before implementation planning
 - `after_plan` - After implementation planning
 - `before_tasks` - Before task generation
 - `after_tasks` - After task generation
 - `before_implement` - Before implementation
 - `after_implement` - After implementation
- `before_commit` - Before git commit *(planned - not yet wired into core templates)*
+- `before_commit` - Before git commit
- `after_commit` - After git commit *(planned - not yet wired into core templates)*
+- `after_commit` - After git commit
 ### Hook Configuration
--- a/extensions/EXTENSION-PUBLISHING-GUIDE.md
+++ b/extensions/EXTENSION-PUBLISHING-GUIDE.md
@@ -209,22 +209,9 @@ Edit `extensions/catalog.community.json` and add your extension:
 Add your extension to the Available Extensions table in `extensions/README.md`:
 ```markdown
-| Your Extension Name | Brief description of what it does | `<category>` | <effect> | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
+| Your Extension Name | Brief description of what it does | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
 ```
 **(Table) Category** — pick the one that best fits your extension:
 - `docs` — reads, validates, or generates spec artifacts
 - `code` — reviews, validates, or modifies source code
 - `process` — orchestrates workflow across phases
 - `integration` — syncs with external platforms
 - `visibility` — reports on project health or progress
 **Effect** — choose one:
 - Read-only — produces reports without modifying files
 - Read+Write — modifies files, creates artifacts, or updates specs
 Insert your extension in alphabetical order in the table.
 ### 4. Submit Pull Request
--- a/extensions/EXTENSION-USER-GUIDE.md
+++ b/extensions/EXTENSION-USER-GUIDE.md
@@ -387,9 +387,6 @@ settings:
  auto_execute_hooks: true
 # Hook configuration
 # Available events: before_specify, after_specify, before_plan, after_plan,
 #                   before_tasks, after_tasks, before_implement, after_implement
 # Planned (not yet wired into core templates): before_commit, after_commit
 hooks:
  after_tasks:
    - extension: jira
--- a/extensions/README.md
+++ b/extensions/README.md
@@ -70,34 +70,25 @@ specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/ta
 The following community-contributed extensions are available in [`catalog.community.json`](catalog.community.json):
-**Categories:** `docs` — reads, validates, or generates spec artifacts · `code` — reviews, validates, or modifies source code · `process` — orchestrates workflow across phases · `integration` — syncs with external platforms · `visibility` — reports on project health or progress
+| Extension | Purpose | URL |
-
+|-----------|---------|-----|
-**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
+| Archive Extension | Archive merged features into main project memory. | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
-
+| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
-| Extension | Purpose | Category | Effect | URL |
+| Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
-|-----------|---------|----------|--------|-----|
+| Cognitive Squad | 19-function cognitive agent squad for autonomous pre-code analysis — 7 core agents, 7 specialists, 4 learning functions with feedback loop | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
-| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
+| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero dependencies. | [spec-kit-docguard](https://github.com/raccioly/docguard) |
-| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
+| 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) |
-| 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 | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
+| 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) |
-| Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
+| 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) |
-| Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |
+| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| Ralph Loop | Autonomous implementation loop using AI agent CLI | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
-| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
+| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
-| Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
+| 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) |
-| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
+| 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) |
-| Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
+| Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
-| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
+| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | [understanding](https://github.com/Testimonial/understanding) |
-| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
+| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
-| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
+| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
 | Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [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 | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
 | Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | `docs` | Read-only | [understanding](https://github.com/Testimonial/understanding) |
 | V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
 | Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
 | Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
 ## Adding Your Extension
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-03-19T12:08:20Z",
+  "updated_at": "2026-03-16T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
    "archive": {
@@ -108,7 +108,7 @@
    "cognitive-squad": {
      "name": "Cognitive Squad",
      "id": "cognitive-squad",
-      "description": "Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing",
+      "description": "19-function cognitive agent squad for autonomous pre-code analysis — 7 core agents, 7 specialists, 4 learning functions with feedback loop",
      "author": "Testimonial",
      "version": "0.1.0",
      "download_url": "https://github.com/Testimonial/cognitive-squad/archive/refs/tags/v0.1.0.zip",
@@ -133,59 +133,29 @@
        ]
      },
      "provides": {
-        "commands": 10,
+        "commands": 7,
        "hooks": 1
      },
      "tags": [
        "ai-agents",
        "cognitive",
-        "full-lifecycle",
+        "pre-code",
-        "verification",
+        "analysis",
        "multi-agent"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-16T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
+      "updated_at": "2026-03-16T00:00:00Z"
    },
    "conduct": {
      "name": "Conduct Extension",
      "id": "conduct",
      "description": "Executes a single spec-kit phase via sub-agent delegation to reduce context pollution.",
      "author": "twbrandon7",
      "version": "1.0.0",
      "download_url": "https://github.com/twbrandon7/spec-kit-conduct-ext/archive/refs/tags/v1.0.0.zip",
      "repository": "https://github.com/twbrandon7/spec-kit-conduct-ext",
      "homepage": "https://github.com/twbrandon7/spec-kit-conduct-ext",
      "documentation": "https://github.com/twbrandon7/spec-kit-conduct-ext/blob/main/README.md",
      "changelog": "https://github.com/twbrandon7/spec-kit-conduct-ext/blob/main/CHANGELOG.md",
      "license": "MIT",
      "requires": {
        "speckit_version": ">=0.3.1"
      },
      "provides": {
        "commands": 1,
        "hooks": 0
      },
      "tags": [
        "conduct",
        "workflow",
        "automation"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-19T12:08:20Z",
      "updated_at": "2026-03-19T12:08:20Z"
    },
    "docguard": {
      "name": "DocGuard \u2014 CDD Enforcement",
      "id": "docguard",
-      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies.",
+      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero dependencies.",
      "author": "raccioly",
-      "version": "0.9.11",
+      "version": "0.9.8",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.9.11/spec-kit-docguard-v0.9.11.zip",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.9.8/spec-kit-docguard-v0.9.8.zip",
      "repository": "https://github.com/raccioly/docguard",
      "homepage": "https://www.npmjs.com/package/docguard-cli",
      "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -219,7 +189,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-03-18T18:53:31Z"
+      "updated_at": "2026-03-15T20:00:00Z"
    },
    "doctor": {
      "name": "Project Health Check",
@@ -283,36 +253,6 @@
      "created_at": "2026-03-06T00:00:00Z",
      "updated_at": "2026-03-06T00:00:00Z"
    },
    "iterate": {
      "name": "Iterate",
      "id": "iterate",
      "description": "Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building",
      "author": "Vianca Martinez",
      "version": "2.0.0",
      "download_url": "https://github.com/imviancagrace/spec-kit-iterate/archive/refs/tags/v2.0.0.zip",
      "repository": "https://github.com/imviancagrace/spec-kit-iterate",
      "homepage": "https://github.com/imviancagrace/spec-kit-iterate",
      "documentation": "https://github.com/imviancagrace/spec-kit-iterate/blob/main/README.md",
      "changelog": "https://github.com/imviancagrace/spec-kit-iterate/blob/main/CHANGELOG.md",
      "license": "MIT",
      "requires": {
        "speckit_version": ">=0.1.0"
      },
      "provides": {
        "commands": 2,
        "hooks": 0
      },
      "tags": [
        "iteration",
        "change-management",
        "spec-maintenance"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-17T00:00:00Z",
      "updated_at": "2026-03-17T00:00:00Z"
    },
    "jira": {
      "name": "Jira Integration",
      "id": "jira",
@@ -482,38 +422,6 @@
      "created_at": "2026-03-06T00:00:00Z",
      "updated_at": "2026-03-06T00:00:00Z"
    },
    "speckit-utils": {
      "name": "SDD Utilities",
      "id": "speckit-utils",
      "description": "Resume interrupted workflows, validate project health, and verify spec-to-task traceability.",
      "author": "mvanhorn",
      "version": "1.0.0",
      "download_url": "https://github.com/mvanhorn/speckit-utils/archive/refs/tags/v1.0.0.zip",
      "repository": "https://github.com/mvanhorn/speckit-utils",
      "homepage": "https://github.com/mvanhorn/speckit-utils",
      "documentation": "https://github.com/mvanhorn/speckit-utils/blob/main/README.md",
      "changelog": "https://github.com/mvanhorn/speckit-utils/blob/main/CHANGELOG.md",
      "license": "MIT",
      "requires": {
        "speckit_version": ">=0.1.0"
      },
      "provides": {
        "commands": 3,
        "hooks": 2
      },
      "tags": [
        "resume",
        "doctor",
        "validate",
        "workflow",
        "health-check"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-18T00:00:00Z",
      "updated_at": "2026-03-18T00:00:00Z"
    },
    "sync": {
      "name": "Spec Sync",
      "id": "sync",
@@ -651,37 +559,6 @@
      "created_at": "2026-02-20T00:00:00Z",
      "updated_at": "2026-02-22T00:00:00Z"
    },
    "learn": {
      "name": "Learning Extension",
      "id": "learn",
      "description": "Generate educational guides from implementations and enhance clarifications with mentoring context.",
      "author": "Vianca Martinez",
      "version": "1.0.0",
      "download_url": "https://github.com/imviancagrace/spec-kit-learn/archive/refs/tags/v1.0.0.zip",
      "repository": "https://github.com/imviancagrace/spec-kit-learn",
      "homepage": "https://github.com/imviancagrace/spec-kit-learn",
      "documentation": "https://github.com/imviancagrace/spec-kit-learn/blob/main/README.md",
      "changelog": "https://github.com/imviancagrace/spec-kit-learn/blob/main/CHANGELOG.md",
      "license": "MIT",
      "requires": {
        "speckit_version": ">=0.1.0"
      },
      "provides": {
        "commands": 2,
        "hooks": 1
      },
      "tags": [
        "learning",
        "education",
        "mentoring",
        "knowledge-transfer"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-17T00:00:00Z",
      "updated_at": "2026-03-17T00:00:00Z"
    },
    "verify": {
      "name": "Verify Extension",
      "id": "verify",
@@ -713,37 +590,6 @@
      "stars": 0,
      "created_at": "2026-03-03T00:00:00Z",
      "updated_at": "2026-03-03T00:00:00Z"
    },
    "verify-tasks": {
      "name": "Verify Tasks Extension",
      "id": "verify-tasks",
      "description": "Detect phantom completions: tasks marked [X] in tasks.md with no real implementation.",
      "author": "Dave Sharpe",
      "version": "1.0.0",
      "download_url": "https://github.com/datastone-inc/spec-kit-verify-tasks/archive/refs/tags/v1.0.0.zip",
      "repository": "https://github.com/datastone-inc/spec-kit-verify-tasks",
      "homepage": "https://github.com/datastone-inc/spec-kit-verify-tasks",
      "documentation": "https://github.com/datastone-inc/spec-kit-verify-tasks/blob/main/README.md",
      "changelog": "https://github.com/datastone-inc/spec-kit-verify-tasks/blob/main/CHANGELOG.md",
      "license": "MIT",
      "requires": {
        "speckit_version": ">=0.1.0"
      },
      "provides": {
        "commands": 1,
        "hooks": 1
      },
      "tags": [
        "verification",
        "quality",
        "phantom-completion",
        "tasks"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-16T00:00:00Z",
      "updated_at": "2026-03-16T00:00:00Z"
    }
  }
 }
--- a/presets/README.md
+++ b/presets/README.md
@@ -13,15 +13,13 @@ When Spec Kit needs a template (e.g. `spec-template`), it walks a resolution sta
 If no preset is installed, core templates are used — exactly the same behavior as before presets existed.
 Template resolution happens **at runtime** — although preset files are copied into `.specify/presets/<id>/` during installation, Spec Kit walks the resolution stack on every template lookup rather than merging templates into a single location.
 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).
-Unlike templates, command overrides are applied **at install time**. When a preset includes `type: "command"` entries, the commands are 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.
+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
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.4.0"
+version = "0.3.1"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -27,23 +27,6 @@ build-backend = "hatchling.build"
 [tool.hatch.build.targets.wheel]
 packages = ["src/specify_cli"]
 [tool.hatch.build.targets.wheel.force-include]
 # Bundle core assets so `specify init` works without network access (air-gapped / enterprise)
 # Page templates (exclude commands/ — bundled separately below to avoid duplication)
 "templates/agent-file-template.md" = "specify_cli/core_pack/templates/agent-file-template.md"
 "templates/checklist-template.md" = "specify_cli/core_pack/templates/checklist-template.md"
 "templates/constitution-template.md" = "specify_cli/core_pack/templates/constitution-template.md"
 "templates/plan-template.md" = "specify_cli/core_pack/templates/plan-template.md"
 "templates/spec-template.md" = "specify_cli/core_pack/templates/spec-template.md"
 "templates/tasks-template.md" = "specify_cli/core_pack/templates/tasks-template.md"
 "templates/vscode-settings.json" = "specify_cli/core_pack/templates/vscode-settings.json"
 # Command templates
 "templates/commands" = "specify_cli/core_pack/commands"
 "scripts/bash" = "specify_cli/core_pack/scripts/bash"
 "scripts/powershell" = "specify_cli/core_pack/scripts/powershell"
 ".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"
 [project.optional-dependencies]
 test = [
    "pytest>=7.0",
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -33,27 +33,16 @@ get_current_branch() {
    if [[ -d "$specs_dir" ]]; then
        local latest_feature=""
        local highest=0
        local latest_timestamp=""
        for dir in "$specs_dir"/*; do
            if [[ -d "$dir" ]]; then
                local dirname=$(basename "$dir")
-                if [[ "$dirname" =~ ^([0-9]{8}-[0-9]{6})- ]]; then
+                if [[ "$dirname" =~ ^([0-9]{3})- ]]; then
                    # Timestamp-based branch: compare lexicographically
                    local ts="${BASH_REMATCH[1]}"
                    if [[ "$ts" > "$latest_timestamp" ]]; then
                        latest_timestamp="$ts"
                        latest_feature=$dirname
                    fi
                elif [[ "$dirname" =~ ^([0-9]{3})- ]]; then
                    local number=${BASH_REMATCH[1]}
                    number=$((10#$number))
                    if [[ "$number" -gt "$highest" ]]; then
                        highest=$number
-                        # Only update if no timestamp branch found yet
+                        latest_feature=$dirname
                        if [[ -z "$latest_timestamp" ]]; then
                            latest_feature=$dirname
                        fi
                    fi
                fi
            fi
@@ -83,9 +72,9 @@ check_feature_branch() {
        return 0
    fi
-    if [[ ! "$branch" =~ ^[0-9]{3}- ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
+    if [[ ! "$branch" =~ ^[0-9]{3}- ]]; 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
+        echo "Feature branches should be named like: 001-feature-name" >&2
        return 1
    fi
@@ -101,18 +90,15 @@ find_feature_dir_by_prefix() {
    local branch_name="$2"
    local specs_dir="$repo_root/specs"
-    # Extract prefix from branch (e.g., "004" from "004-whatever" or "20260319-143022" from timestamp branches)
+    # Extract numeric prefix from branch (e.g., "004" from "004-whatever")
-    local prefix=""
+    if [[ ! "$branch_name" =~ ^([0-9]{3})- ]]; then
-    if [[ "$branch_name" =~ ^([0-9]{8}-[0-9]{6})- ]]; then
+        # If branch doesn't have numeric prefix, fall back to exact match
        prefix="${BASH_REMATCH[1]}"
    elif [[ "$branch_name" =~ ^([0-9]{3})- ]]; then
        prefix="${BASH_REMATCH[1]}"
    else
        # If branch doesn't have a recognized prefix, fall back to exact match
        echo "$specs_dir/$branch_name"
        return
    fi
    local prefix="${BASH_REMATCH[1]}"
    # Search for directories in specs/ that start with this prefix
    local matches=()
    if [[ -d "$specs_dir" ]]; then
@@ -133,7 +119,7 @@ find_feature_dir_by_prefix() {
    else
        # Multiple matches - this shouldn't happen with proper naming convention
        echo "ERROR: Multiple spec directories found with prefix '$prefix': ${matches[*]}" >&2
-        echo "Please ensure only one spec directory exists per prefix." >&2
+        echo "Please ensure only one spec directory exists per numeric prefix." >&2
        return 1
    fi
 }
@@ -185,21 +171,9 @@ json_escape() {
    s="${s//$'\r'/\\r}"
    s="${s//$'\b'/\\b}"
    s="${s//$'\f'/\\f}"
-    # Escape any remaining U+0001-U+001F control characters as \uXXXX.
+    # Strip remaining control characters (U+0000–U+001F) not individually escaped above
-    # (U+0000/NUL cannot appear in bash strings and is excluded.)
+    s=$(printf '%s' "$s" | tr -d '\000-\007\013\016-\037')
-    # LC_ALL=C ensures ${#s} counts bytes and ${s:$i:1} yields single bytes,
+    printf '%s' "$s"
    # so multi-byte UTF-8 sequences (first byte >= 0xC0) pass through intact.
    local LC_ALL=C
    local i char code
    for (( i=0; i<${#s}; i++ )); do
        char="${s:$i:1}"
        printf -v code '%d' "'$char" 2>/dev/null || code=256
        if (( code >= 1 && code <= 31 )); then
            printf '\\u%04x' "$code"
        else
            printf '%s' "$char"
        fi
    done
 }
 check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
--- a/scripts/bash/create-new-feature.sh
+++ b/scripts/bash/create-new-feature.sh
@@ -5,14 +5,13 @@ 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) 
-            JSON_MODE=true
+            JSON_MODE=true 
            ;;
        --short-name)
            if [ $((i + 1)) -gt $# ]; then
@@ -41,27 +40,22 @@ while [ $i -le $# ]; do
            fi
            BRANCH_NUMBER="$next_arg"
            ;;
-        --timestamp)
+        --help|-h) 
-            USE_TIMESTAMP=true
+            echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>"
            ;;
        --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")
+            ARGS+=("$arg") 
            ;;
    esac
    i=$((i + 1))
@@ -69,7 +63,7 @@ done
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>" >&2
    exit 1
 fi
@@ -102,13 +96,10 @@ get_highest_from_specs() {
        for dir in "$specs_dir"/*; do
            [ -d "$dir" ] || continue
            dirname=$(basename "$dir")
-            # Only match sequential prefixes (###-*), skip timestamp dirs
+            number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
-            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
+            number=$((10#$number))
-                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
+            if [ "$number" -gt "$highest" ]; then
-                number=$((10#$number))
+                highest=$number
                if [ "$number" -gt "$highest" ]; then
                    highest=$number
                fi
            fi
        done
    fi
@@ -251,42 +242,29 @@ else
    BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
 fi
-# Warn if --number and --timestamp are both specified
+# Determine branch number
-if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
+if [ -z "$BRANCH_NUMBER" ]; then
-    >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
+    if [ "$HAS_GIT" = true ]; then
-    BRANCH_NUMBER=""
+        # Check existing branches on remotes
-fi
+        BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
-
+    else
-# Determine branch prefix
+        # Fall back to local directory check
-if [ "$USE_TIMESTAMP" = true ]; then
+        HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-    FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
+        BRANCH_NUMBER=$((HIGHEST + 1))
    BRANCH_NAME="${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}-${BRANCH_SUFFIX}"
 fi
 # Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
 FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
 BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
 # GitHub enforces a 244-byte limit on branch names
 # Validate and truncate if necessary
 MAX_BRANCH_LENGTH=244
 if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
    # Calculate how much we need to trim from suffix
-    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
+    # Account for: feature number (3) + hyphen (1) = 4 chars
-    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
+    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - 4))
    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)
@@ -305,11 +283,7 @@ if [ "$HAS_GIT" = true ]; then
    if ! git checkout -b "$BRANCH_NAME" 2>/dev/null; then
        # Check if branch already exists
        if git branch --list "$BRANCH_NAME" | grep -q .; then
-            if [ "$USE_TIMESTAMP" = true ]; then
+            >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
                >&2 echo "Error: Branch '$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."
--- a/scripts/bash/update-agent-context.sh
+++ b/scripts/bash/update-agent-context.sh
@@ -30,12 +30,12 @@
 #
 # 5. Multi-Agent Support
 #    - Handles agent-specific file paths and naming conventions
-#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Junie, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Tabnine CLI, Kiro CLI, Mistral Vibe, Kimi Code, Pi Coding Agent, iFlow CLI, Antigravity or Generic
+#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Tabnine CLI, Kiro CLI, Mistral Vibe, Kimi Code, Antigravity or Generic
 #    - Can update single agents or all existing agent files
 #    - Creates default Claude file if no agent files exist
 #
 # Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic
+# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic
 # Leave empty to update all existing agent files
 set -e
@@ -68,13 +68,12 @@ CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
 QWEN_FILE="$REPO_ROOT/QWEN.md"
 AGENTS_FILE="$REPO_ROOT/AGENTS.md"
 WINDSURF_FILE="$REPO_ROOT/.windsurf/rules/specify-rules.md"
 JUNIE_FILE="$REPO_ROOT/.junie/AGENTS.md"
 KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
 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, Kiro CLI, IBM Bob, and Pi all share AGENTS.md — use AGENTS_FILE to avoid
+# 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"
@@ -85,7 +84,6 @@ BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
 TRAE_FILE="$REPO_ROOT/.trae/rules/AGENTS.md"
 IFLOW_FILE="$REPO_ROOT/IFLOW.md"
 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -639,9 +637,6 @@ update_specific_agent() {
        windsurf)
            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
            ;;
        junie)
            update_agent_file "$JUNIE_FILE" "Junie" || return 1
            ;;
        kilocode)
            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
            ;;
@@ -684,18 +679,12 @@ update_specific_agent() {
        trae)
            update_agent_file "$TRAE_FILE" "Trae" || return 1
            ;;
        pi)
            update_agent_file "$AGENTS_FILE" "Pi Coding Agent" || return 1
            ;;
        iflow)
            update_agent_file "$IFLOW_FILE" "iFlow CLI" || return 1
            ;;
        generic)
            log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
            ;;
        *)
            log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic"
+            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic"
            exit 1
            ;;
    esac
@@ -744,7 +733,6 @@ update_all_existing_agents() {
    _update_if_new "$KIRO_FILE" "Kiro CLI"                 || _all_ok=false
    _update_if_new "$BOB_FILE" "IBM Bob"                   || _all_ok=false
    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
    _update_if_new "$JUNIE_FILE" "Junie"                || _all_ok=false
    _update_if_new "$KILOCODE_FILE" "Kilo Code"            || _all_ok=false
    _update_if_new "$AUGGIE_FILE" "Auggie CLI"             || _all_ok=false
    _update_if_new "$ROO_FILE" "Roo Code"                  || _all_ok=false
@@ -756,7 +744,6 @@ update_all_existing_agents() {
    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
    _update_if_new "$TRAE_FILE" "Trae"                     || _all_ok=false
    _update_if_new "$IFLOW_FILE" "iFlow CLI"               || _all_ok=false
    # If no agent files exist, create a default Claude file
    if [[ "$_found_agent" == false ]]; then
@@ -783,7 +770,7 @@ print_summary() {
    fi
    echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic]"
 }
 #==============================================================================
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -38,28 +38,17 @@ function Get-CurrentBranch {
    if (Test-Path $specsDir) {
        $latestFeature = ""
        $highest = 0
-        $latestTimestamp = ""
+        
        Get-ChildItem -Path $specsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{8}-\d{6})-') {
+            if ($_.Name -match '^(\d{3})-') {
                # Timestamp-based branch: compare lexicographically
                $ts = $matches[1]
                if ($ts -gt $latestTimestamp) {
                    $latestTimestamp = $ts
                    $latestFeature = $_.Name
                }
            } elseif ($_.Name -match '^(\d{3})-') {
                $num = [int]$matches[1]
                if ($num -gt $highest) {
                    $highest = $num
-                    # Only update if no timestamp branch found yet
+                    $latestFeature = $_.Name
                    if (-not $latestTimestamp) {
                        $latestFeature = $_.Name
                    }
                }
            }
        }
-
+        
        if ($latestFeature) {
            return $latestFeature
        }
@@ -90,9 +79,9 @@ function Test-FeatureBranch {
        return $true
    }
-    if ($Branch -notmatch '^[0-9]{3}-' -and $Branch -notmatch '^\d{8}-\d{6}-') {
+    if ($Branch -notmatch '^[0-9]{3}-') {
        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"
+        Write-Output "Feature branches should be named like: 001-feature-name"
        return $false
    }
    return $true
--- a/scripts/powershell/create-new-feature.ps1
+++ b/scripts/powershell/create-new-feature.ps1
@@ -4,36 +4,32 @@
 param(
    [switch]$Json,
    [string]$ShortName,
    [Parameter()]
    [int]$Number = 0,
    [switch]$Timestamp,
    [switch]$Help,
-    [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
+    [Parameter(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 "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] <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>"
+    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] <feature description>"
    exit 1
 }
@@ -75,7 +71,7 @@ function Get-HighestNumberFromSpecs {
    $highest = 0
    if (Test-Path $SpecsDir) {
        Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{3})-') {
+            if ($_.Name -match '^(\d+)') {
                $num = [int]$matches[1]
                if ($num -gt $highest) { $highest = $num }
            }
@@ -96,7 +92,7 @@ function Get-HighestNumberFromBranches {
                $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
                # Extract feature number if branch matches pattern ###-*
-                if ($cleanBranch -match '^(\d{3})-') {
+                if ($cleanBranch -match '^(\d+)-') {
                    $num = [int]$matches[1]
                    if ($num -gt $highest) { $highest = $num }
                }
@@ -219,40 +215,27 @@ if ($ShortName) {
    $branchSuffix = Get-BranchName -Description $featureDesc
 }
-# Warn if -Number and -Timestamp are both specified
+# Determine branch number
-if ($Timestamp -and $Number -ne 0) {
+if ($Number -eq 0) {
-    Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
+    if ($hasGit) {
-    $Number = 0
+        # Check existing branches on remotes
-}
+        $Number = Get-NextBranchNumber -SpecsDir $specsDir
-
+    } else {
-# Determine branch prefix
+        # Fall back to local directory check
-if ($Timestamp) {
+        $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
    $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"
 }
 $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
+    # Account for: feature number (3) + hyphen (1) = 4 chars
-    $prefixLength = $featureNum.Length + 1
+    $maxSuffixLength = $maxBranchLength - 4
    $maxSuffixLength = $maxBranchLength - $prefixLength
    # Truncate suffix
    $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
@@ -282,11 +265,7 @@ if ($hasGit) {
        # Check if branch already exists
        $existingBranch = git branch --list $branchName 2>$null
        if ($existingBranch) {
-            if ($Timestamp) {
+            Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
                Write-Error "Error: Branch '$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."
--- a/scripts/powershell/update-agent-context.ps1
+++ b/scripts/powershell/update-agent-context.ps1
@@ -9,7 +9,7 @@ Mirrors the behavior of scripts/bash/update-agent-context.sh:
 2. Plan Data Extraction
 3. Agent File Management (create from template or update existing)
 4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, junie, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, pi, iflow, generic)
+ 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, generic)
 .PARAMETER AgentType
 Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
@@ -25,7 +25,7 @@ Relies on common helper functions in common.ps1
 #>
 param(
    [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','junie','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','trae','pi','iflow','generic')]
+    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','trae','generic')]
    [string]$AgentType
 )
@@ -51,7 +51,6 @@ $CURSOR_FILE   = Join-Path $REPO_ROOT '.cursor/rules/specify-rules.mdc'
 $QWEN_FILE     = Join-Path $REPO_ROOT 'QWEN.md'
 $AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'
 $WINDSURF_FILE = Join-Path $REPO_ROOT '.windsurf/rules/specify-rules.md'
 $JUNIE_FILE = Join-Path $REPO_ROOT '.junie/AGENTS.md'
 $KILOCODE_FILE = Join-Path $REPO_ROOT '.kilocode/rules/specify-rules.md'
 $AUGGIE_FILE   = Join-Path $REPO_ROOT '.augment/rules/specify-rules.md'
 $ROO_FILE      = Join-Path $REPO_ROOT '.roo/rules/specify-rules.md'
@@ -66,7 +65,6 @@ $BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 $VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
 $KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
 $TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/AGENTS.md'
 $IFLOW_FILE    = Join-Path $REPO_ROOT 'IFLOW.md'
 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
@@ -398,7 +396,6 @@ function Update-SpecificAgent {
        'opencode' { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'opencode' }
        'codex'    { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Codex CLI' }
        'windsurf' { Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf' }
        'junie'    { Update-AgentFile -TargetFile $JUNIE_FILE    -AgentName 'Junie' }
        'kilocode' { Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code' }
        'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
        'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
@@ -413,10 +410,8 @@ function Update-SpecificAgent {
        'vibe'     { Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe' }
        'kimi'     { Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code' }
        'trae'     { Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae' }
        'pi'       { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Pi Coding Agent' }
        'iflow'    { Update-AgentFile -TargetFile $IFLOW_FILE    -AgentName 'iFlow CLI' }
        'generic'  { Write-Info 'Generic agent: no predefined context file. Use the agent-specific update script for your agent.' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic'; return $false }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|generic'; return $false }
    }
 }
@@ -430,7 +425,6 @@ function Update-AllExistingAgents {
    if (Test-Path $QWEN_FILE)     { if (-not (Update-AgentFile -TargetFile $QWEN_FILE     -AgentName 'Qwen Code')) { $ok = $false }; $found = $true }
    if (Test-Path $AGENTS_FILE)   { if (-not (Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Codex/opencode')) { $ok = $false }; $found = $true }
    if (Test-Path $WINDSURF_FILE) { if (-not (Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf')) { $ok = $false }; $found = $true }
    if (Test-Path $JUNIE_FILE)    { if (-not (Update-AgentFile -TargetFile $JUNIE_FILE    -AgentName 'Junie')) { $ok = $false }; $found = $true }
    if (Test-Path $KILOCODE_FILE) { if (-not (Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code')) { $ok = $false }; $found = $true }
    if (Test-Path $AUGGIE_FILE)   { if (-not (Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI')) { $ok = $false }; $found = $true }
    if (Test-Path $ROO_FILE)      { if (-not (Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code')) { $ok = $false }; $found = $true }
@@ -444,7 +438,6 @@ function Update-AllExistingAgents {
    if (Test-Path $VIBE_FILE)     { if (-not (Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe')) { $ok = $false }; $found = $true }
    if (Test-Path $KIMI_FILE)     { if (-not (Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code')) { $ok = $false }; $found = $true }
    if (Test-Path $TRAE_FILE)     { if (-not (Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae')) { $ok = $false }; $found = $true }
    if (Test-Path $IFLOW_FILE)    { if (-not (Update-AgentFile -TargetFile $IFLOW_FILE    -AgentName 'iFlow CLI')) { $ok = $false }; $found = $true }
    if (-not $found) {
        Write-Info 'No existing agent files found, creating default Claude file...'
        if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
@@ -459,7 +452,7 @@ function Print-Summary {
    if ($NEW_FRAMEWORK) { Write-Host "  - Added framework: $NEW_FRAMEWORK" }
    if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Host "  - Added database: $NEW_DB" }
    Write-Host ''
-    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic]'
+    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|generic]'
 }
 function Main {
--- a/src/specify_cli/init.py
+++ b/src/specify_cli/init.py
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -9,7 +9,6 @@ command files into agent-specific directories in the correct format.
 from pathlib import Path
 from typing import Dict, List, Any
 import platform
 import yaml
@@ -60,19 +59,13 @@ class CommandRegistrar:
            "extension": ".md"
        },
        "codex": {
-            "dir": ".agents/skills",
+            "dir": ".codex/prompts",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": "/SKILL.md",
        },
        "windsurf": {
            "dir": ".windsurf/workflows",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": ".md"
        },
-        "junie": {
+        "windsurf": {
-            "dir": ".junie/commands",
+            "dir": ".windsurf/workflows",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": ".md"
@@ -113,12 +106,6 @@ class CommandRegistrar:
            "args": "$ARGUMENTS",
            "extension": ".md"
        },
        "pi": {
            "dir": ".pi/prompts",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": ".md"
        },
        "amp": {
            "dir": ".agents/commands",
            "format": "markdown",
@@ -147,19 +134,13 @@ class CommandRegistrar:
            "dir": ".kimi/skills",
            "format": "markdown",
            "args": "$ARGUMENTS",
-            "extension": "/SKILL.md",
+            "extension": "/SKILL.md"
        },
        "trae": {
            "dir": ".trae/rules",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": ".md"
        },
        "iflow": {
            "dir": ".iflow/commands",
            "format": "markdown",
            "args": "$ARGUMENTS",
            "extension": ".md"
        }
    }
@@ -189,9 +170,6 @@ class CommandRegistrar:
        except yaml.YAMLError:
            frontmatter = {}
        if not isinstance(frontmatter, dict):
            frontmatter = {}
        return frontmatter, body
    @staticmethod
@@ -207,7 +185,7 @@ 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:
@@ -219,14 +197,11 @@ class CommandRegistrar:
        Returns:
            Modified frontmatter with adjusted paths
        """
-        for script_key in ("scripts", "agent_scripts"):
+        if "scripts" in frontmatter:
-            scripts = frontmatter.get(script_key)
+            for key in frontmatter["scripts"]:
-            if not isinstance(scripts, dict):
+                script_path = frontmatter["scripts"][key]
-                continue
+                if script_path.startswith("../../scripts/"):
-
+                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
            for key, script_path in scripts.items():
                if isinstance(script_path, str) and script_path.startswith("../../scripts/"):
                    scripts[key] = f".specify/scripts/{script_path[14:]}"
        return frontmatter
    def render_markdown_command(
@@ -283,101 +258,6 @@ class CommandRegistrar:
        return "\n".join(toml_lines)
    def render_skill_command(
        self,
        agent_name: str,
        skill_name: str,
        frontmatter: dict,
        body: str,
        source_id: str,
        source_file: str,
        project_root: Path,
    ) -> str:
        """Render a command override as a SKILL.md file.
        SKILL-target agents should receive the same skills-oriented
        frontmatter shape used elsewhere in the project instead of the
        original command frontmatter.
        Technical debt note:
        Spec-kit currently has multiple SKILL.md generators (template packaging,
        init-time conversion, and extension/preset overrides). Keep the skill
        frontmatter keys aligned (name/description/compatibility/metadata, with
        metadata.author and metadata.source subkeys) to avoid drift across agents.
        """
        if not isinstance(frontmatter, dict):
            frontmatter = {}
        if agent_name == "codex":
            body = self._resolve_codex_skill_placeholders(frontmatter, body, project_root)
        description = frontmatter.get("description", f"Spec-kit workflow command: {skill_name}")
        skill_frontmatter = {
            "name": skill_name,
            "description": description,
            "compatibility": "Requires spec-kit project structure with .specify/ directory",
            "metadata": {
                "author": "github-spec-kit",
                "source": f"{source_id}:{source_file}",
            },
        }
        return self.render_frontmatter(skill_frontmatter) + "\n" + body
    @staticmethod
    def _resolve_codex_skill_placeholders(frontmatter: dict, body: str, project_root: Path) -> str:
        """Resolve script placeholders for Codex skill overrides.
        This intentionally scopes the fix to Codex, which is the newly
        migrated runtime path in this PR. Existing Kimi behavior is left
        unchanged for now.
        """
        try:
            from . import load_init_options
        except ImportError:
            return body
        if not isinstance(frontmatter, dict):
            frontmatter = {}
        scripts = frontmatter.get("scripts", {}) or {}
        agent_scripts = frontmatter.get("agent_scripts", {}) or {}
        if not isinstance(scripts, dict):
            scripts = {}
        if not isinstance(agent_scripts, dict):
            agent_scripts = {}
        script_variant = load_init_options(project_root).get("script")
        if script_variant not in {"sh", "ps"}:
            fallback_order = []
            default_variant = "ps" if platform.system().lower().startswith("win") else "sh"
            secondary_variant = "sh" if default_variant == "ps" else "ps"
            if default_variant in scripts or default_variant in agent_scripts:
                fallback_order.append(default_variant)
            if secondary_variant in scripts or secondary_variant in agent_scripts:
                fallback_order.append(secondary_variant)
            for key in scripts:
                if key not in fallback_order:
                    fallback_order.append(key)
            for key in agent_scripts:
                if key not in fallback_order:
                    fallback_order.append(key)
            script_variant = fallback_order[0] if fallback_order else None
        script_command = scripts.get(script_variant) if script_variant else None
        if script_command:
            script_command = script_command.replace("{ARGS}", "$ARGUMENTS")
            body = body.replace("{SCRIPT}", script_command)
        agent_script_command = agent_scripts.get(script_variant) if script_variant else None
        if agent_script_command:
            agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
            body = body.replace("{AGENT_SCRIPT}", agent_script_command)
        return body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", "codex")
    def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
        """Convert argument placeholder format.
@@ -391,18 +271,6 @@ class CommandRegistrar:
        """
        return content.replace(from_placeholder, to_placeholder)
    @staticmethod
    def _compute_output_name(agent_name: str, cmd_name: str, agent_config: Dict[str, Any]) -> str:
        """Compute the on-disk command or skill name for an agent."""
        if agent_config["extension"] != "/SKILL.md":
            return cmd_name
        short_name = cmd_name
        if short_name.startswith("speckit."):
            short_name = short_name[len("speckit."):]
        return f"speckit.{short_name}" if agent_name == "kimi" else f"speckit-{short_name}"
    def register_commands(
        self,
        agent_name: str,
@@ -454,20 +322,14 @@ class CommandRegistrar:
                body, "$ARGUMENTS", agent_config["args"]
            )
-            output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+            if agent_config["format"] == "markdown":
            if agent_config["extension"] == "/SKILL.md":
                output = self.render_skill_command(
                    agent_name, output_name, frontmatter, body, source_id, cmd_file, project_root
                )
            elif 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"{output_name}{agent_config['extension']}"
+            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")
@@ -477,15 +339,9 @@ class CommandRegistrar:
            registered.append(cmd_name)
            for alias in cmd_info.get("aliases", []):
-                alias_output_name = self._compute_output_name(agent_name, alias, agent_config)
+                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
                alias_output = output
                if agent_config["extension"] == "/SKILL.md":
                    alias_output = self.render_skill_command(
                        agent_name, alias_output_name, frontmatter, body, source_id, cmd_file, project_root
                    )
                alias_file = commands_dir / f"{alias_output_name}{agent_config['extension']}"
                alias_file.parent.mkdir(parents=True, exist_ok=True)
-                alias_file.write_text(alias_output, encoding="utf-8")
+                alias_file.write_text(output, encoding="utf-8")
                if agent_name == "copilot":
                    self.write_copilot_prompt(project_root, alias)
                registered.append(alias)
@@ -528,7 +384,7 @@ class CommandRegistrar:
        results = {}
        for agent_name, agent_config in self.AGENT_CONFIGS.items():
-            agent_dir = project_root / agent_config["dir"]
+            agent_dir = project_root / agent_config["dir"].split("/")[0]
            if agent_dir.exists():
                try:
@@ -562,8 +418,7 @@ class CommandRegistrar:
            commands_dir = project_root / agent_config["dir"]
            for cmd_name in cmd_names:
-                output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+                cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
                cmd_file = commands_dir / f"{output_name}{agent_config['extension']}"
                if cmd_file.exists():
                    cmd_file.unlink()
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -222,17 +222,7 @@ class ExtensionRegistry:
        try:
            with open(self.registry_path, 'r') as f:
-                data = json.load(f)
+                return json.load(f)
            # Validate loaded data is a dict (handles corrupted registry files)
            if not isinstance(data, dict):
                return {
                    "schema_version": self.SCHEMA_VERSION,
                    "extensions": {}
                }
            # Normalize extensions field (handles corrupted extensions value)
            if not isinstance(data.get("extensions"), dict):
                data["extensions"] = {}
            return data
        except (json.JSONDecodeError, FileNotFoundError):
            # Corrupted or missing registry, start fresh
            return {
@@ -254,7 +244,7 @@ class ExtensionRegistry:
            metadata: Extension metadata (version, source, etc.)
        """
        self.data["extensions"][extension_id] = {
-            **copy.deepcopy(metadata),
+            **metadata,
            "installed_at": datetime.now(timezone.utc).isoformat()
        }
        self._save()
@@ -277,16 +267,15 @@ class ExtensionRegistry:
        Raises:
            KeyError: If extension is not installed
        """
-        extensions = self.data.get("extensions")
+        if extension_id not in self.data["extensions"]:
        if not isinstance(extensions, dict) or extension_id not in extensions:
            raise KeyError(f"Extension '{extension_id}' is not installed")
        # Merge new metadata with existing, preserving original installed_at
-        existing = extensions[extension_id]
+        existing = self.data["extensions"][extension_id]
        # Handle corrupted registry entries (e.g., string/list instead of dict)
        if not isinstance(existing, dict):
            existing = {}
-        # Merge: existing fields preserved, new fields override (deep copy to prevent caller mutation)
+        # Merge: existing fields preserved, new fields override
-        merged = {**existing, **copy.deepcopy(metadata)}
+        merged = {**existing, **metadata}
        # Always preserve original installed_at based on key existence, not truthiness,
        # to handle cases where the field exists but may be falsy (legacy/corruption)
        if "installed_at" in existing:
@@ -294,7 +283,7 @@ class ExtensionRegistry:
        else:
            # If not present in existing, explicitly remove from merged if caller provided it
            merged.pop("installed_at", None)
-        extensions[extension_id] = merged
+        self.data["extensions"][extension_id] = merged
        self._save()
    def restore(self, extension_id: str, metadata: dict):
@@ -307,16 +296,8 @@ class ExtensionRegistry:
        Args:
            extension_id: Extension ID
            metadata: Complete extension metadata including installed_at
        Raises:
            ValueError: If metadata is None or not a dict
        """
-        if metadata is None or not isinstance(metadata, dict):
+        self.data["extensions"][extension_id] = dict(metadata)
            raise ValueError(f"Cannot restore '{extension_id}': metadata must be a dict")
        # Ensure extensions dict exists (handle corrupted registry)
        if not isinstance(self.data.get("extensions"), dict):
            self.data["extensions"] = {}
        self.data["extensions"][extension_id] = copy.deepcopy(metadata)
        self._save()
    def remove(self, extension_id: str):
@@ -325,11 +306,8 @@ class ExtensionRegistry:
        Args:
            extension_id: Extension ID
        """
-        extensions = self.data.get("extensions")
+        if extension_id in self.data["extensions"]:
-        if not isinstance(extensions, dict):
+            del self.data["extensions"][extension_id]
            return
        if extension_id in extensions:
            del extensions[extension_id]
            self._save()
    def get(self, extension_id: str) -> Optional[dict]:
@@ -342,49 +320,21 @@ class ExtensionRegistry:
            extension_id: Extension ID
        Returns:
-            Deep copy of extension metadata, or None if not found or corrupted
+            Deep copy of extension metadata, or None if not found
        """
-        extensions = self.data.get("extensions")
+        entry = self.data["extensions"].get(extension_id)
-        if not isinstance(extensions, dict):
+        return copy.deepcopy(entry) if entry is not None else None
            return None
        entry = extensions.get(extension_id)
        # Return None for missing or corrupted (non-dict) entries
        if entry is None or not isinstance(entry, dict):
            return None
        return copy.deepcopy(entry)
    def list(self) -> Dict[str, dict]:
-        """Get all installed extensions with valid metadata.
+        """Get all installed extensions.
-        Returns a deep copy of extensions with dict metadata only.
+        Returns a deep copy of the extensions mapping to prevent callers
-        Corrupted entries (non-dict values) are filtered out.
+        from accidentally mutating nested internal registry state.
        Returns:
-            Dictionary of extension_id -> metadata (deep copies), empty dict if corrupted
+            Dictionary of extension_id -> metadata (deep copies)
        """
-        extensions = self.data.get("extensions", {}) or {}
+        return copy.deepcopy(self.data["extensions"])
        if not isinstance(extensions, dict):
            return {}
        # Filter to only valid dict entries to match type contract
        return {
            ext_id: copy.deepcopy(meta)
            for ext_id, meta in extensions.items()
            if isinstance(meta, dict)
        }
    def keys(self) -> set:
        """Get all extension IDs including corrupted entries.
        Lightweight method that returns IDs without deep-copying metadata.
        Use this when you only need to check which extensions are tracked.
        Returns:
            Set of extension IDs (includes corrupted entries)
        """
        extensions = self.data.get("extensions", {}) or {}
        if not isinstance(extensions, dict):
            return set()
        return set(extensions.keys())
    def is_installed(self, extension_id: str) -> bool:
        """Check if extension is installed.
@@ -393,23 +343,17 @@ class ExtensionRegistry:
            extension_id: Extension ID
        Returns:
-            True if extension is installed, False if not or registry corrupted
+            True if extension is installed
        """
-        extensions = self.data.get("extensions")
+        return extension_id in self.data["extensions"]
        if not isinstance(extensions, dict):
            return False
        return extension_id in extensions
-    def list_by_priority(self, include_disabled: bool = False) -> List[tuple]:
+    def list_by_priority(self) -> List[tuple]:
        """Get all installed extensions sorted by priority.
        Lower priority number = higher precedence (checked first).
        Extensions with equal priority are sorted alphabetically by ID
        for deterministic ordering.
        Args:
            include_disabled: If True, include disabled extensions. Default False.
        Returns:
            List of (extension_id, metadata_copy) tuples sorted by priority.
            Metadata is deep-copied to prevent accidental mutation.
@@ -421,9 +365,6 @@ class ExtensionRegistry:
        for ext_id, meta in extensions.items():
            if not isinstance(meta, dict):
                continue
            # Skip disabled extensions unless explicitly requested
            if not include_disabled and not meta.get("enabled", True):
                continue
            metadata_copy = copy.deepcopy(meta)
            metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
            sortable_extensions.append((ext_id, metadata_copy))
@@ -692,7 +633,7 @@ class ExtensionManager:
        # Get registered commands before removal
        metadata = self.registry.get(extension_id)
-        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
+        registered_commands = metadata.get("registered_commands", {})
        extension_dir = self.extensions_dir / extension_id
@@ -975,8 +916,8 @@ 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 +1408,8 @@ 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 +1600,8 @@ 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 +1616,7 @@ 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):
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -238,17 +238,7 @@ class PresetRegistry:
        try:
            with open(self.registry_path, 'r') as f:
-                data = json.load(f)
+                return json.load(f)
            # Validate loaded data is a dict (handles corrupted registry files)
            if not isinstance(data, dict):
                return {
                    "schema_version": self.SCHEMA_VERSION,
                    "presets": {}
                }
            # Normalize presets field (handles corrupted presets value)
            if not isinstance(data.get("presets"), dict):
                data["presets"] = {}
            return data
        except (json.JSONDecodeError, FileNotFoundError):
            return {
                "schema_version": self.SCHEMA_VERSION,
@@ -269,7 +259,7 @@ class PresetRegistry:
            metadata: Pack metadata (version, source, etc.)
        """
        self.data["presets"][pack_id] = {
-            **copy.deepcopy(metadata),
+            **metadata,
            "installed_at": datetime.now(timezone.utc).isoformat()
        }
        self._save()
@@ -280,11 +270,8 @@ class PresetRegistry:
        Args:
            pack_id: Preset ID
        """
-        packs = self.data.get("presets")
+        if pack_id in self.data["presets"]:
-        if not isinstance(packs, dict):
+            del self.data["presets"][pack_id]
            return
        if pack_id in packs:
            del packs[pack_id]
            self._save()
    def update(self, pack_id: str, updates: dict):
@@ -301,15 +288,14 @@ class PresetRegistry:
        Raises:
            KeyError: If preset is not installed
        """
-        packs = self.data.get("presets")
+        if pack_id not in self.data["presets"]:
        if not isinstance(packs, dict) or pack_id not in packs:
            raise KeyError(f"Preset '{pack_id}' not found in registry")
-        existing = packs[pack_id]
+        existing = self.data["presets"][pack_id]
        # Handle corrupted registry entries (e.g., string/list instead of dict)
        if not isinstance(existing, dict):
            existing = {}
-        # Merge: existing fields preserved, new fields override (deep copy to prevent caller mutation)
+        # Merge: existing fields preserved, new fields override
-        merged = {**existing, **copy.deepcopy(updates)}
+        merged = {**existing, **updates}
        # Always preserve original installed_at based on key existence, not truthiness,
        # to handle cases where the field exists but may be falsy (legacy/corruption)
        if "installed_at" in existing:
@@ -317,95 +303,35 @@ class PresetRegistry:
        else:
            # If not present in existing, explicitly remove from merged if caller provided it
            merged.pop("installed_at", None)
-        packs[pack_id] = merged
+        self.data["presets"][pack_id] = merged
        self._save()
    def restore(self, pack_id: str, metadata: dict):
        """Restore preset metadata to registry without modifying timestamps.
        Use this method for rollback scenarios where you have a complete backup
        of the registry entry (including installed_at) and want to restore it
        exactly as it was.
        Args:
            pack_id: Preset ID
            metadata: Complete preset metadata including installed_at
        Raises:
            ValueError: If metadata is None or not a dict
        """
        if metadata is None or not isinstance(metadata, dict):
            raise ValueError(f"Cannot restore '{pack_id}': metadata must be a dict")
        # Ensure presets dict exists (handle corrupted registry)
        if not isinstance(self.data.get("presets"), dict):
            self.data["presets"] = {}
        self.data["presets"][pack_id] = copy.deepcopy(metadata)
        self._save()
    def get(self, pack_id: str) -> Optional[dict]:
        """Get preset metadata from registry.
        Returns a deep copy to prevent callers from accidentally mutating
        nested internal registry state without going through the write path.
        Args:
            pack_id: Preset ID
        Returns:
-            Deep copy of preset metadata, or None if not found or corrupted
+            Pack metadata or None if not found
        """
-        packs = self.data.get("presets")
+        return self.data["presets"].get(pack_id)
        if not isinstance(packs, dict):
            return None
        entry = packs.get(pack_id)
        # Return None for missing or corrupted (non-dict) entries
        if entry is None or not isinstance(entry, dict):
            return None
        return copy.deepcopy(entry)
    def list(self) -> Dict[str, dict]:
-        """Get all installed presets with valid metadata.
+        """Get all installed presets.
        Returns a deep copy of presets with dict metadata only.
        Corrupted entries (non-dict values) are filtered out.
        Returns:
-            Dictionary of pack_id -> metadata (deep copies), empty dict if corrupted
+            Dictionary of pack_id -> metadata
        """
-        packs = self.data.get("presets", {}) or {}
+        return self.data["presets"]
        if not isinstance(packs, dict):
            return {}
        # Filter to only valid dict entries to match type contract
        return {
            pack_id: copy.deepcopy(meta)
            for pack_id, meta in packs.items()
            if isinstance(meta, dict)
        }
-    def keys(self) -> set:
+    def list_by_priority(self) -> List[tuple]:
        """Get all preset IDs including corrupted entries.
        Lightweight method that returns IDs without deep-copying metadata.
        Use this when you only need to check which presets are tracked.
        Returns:
            Set of preset IDs (includes corrupted entries)
        """
        packs = self.data.get("presets", {}) or {}
        if not isinstance(packs, dict):
            return set()
        return set(packs.keys())
    def list_by_priority(self, include_disabled: bool = False) -> List[tuple]:
        """Get all installed presets sorted by priority.
        Lower priority number = higher precedence (checked first).
        Presets with equal priority are sorted alphabetically by ID
        for deterministic ordering.
        Args:
            include_disabled: If True, include disabled presets. Default False.
        Returns:
            List of (pack_id, metadata_copy) tuples sorted by priority.
            Metadata is deep-copied to prevent accidental mutation.
@@ -417,9 +343,6 @@ class PresetRegistry:
        for pack_id, meta in packs.items():
            if not isinstance(meta, dict):
                continue
            # Skip disabled presets unless explicitly requested
            if not include_disabled and not meta.get("enabled", True):
                continue
            metadata_copy = copy.deepcopy(meta)
            metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
            sortable_packs.append((pack_id, metadata_copy))
@@ -435,12 +358,9 @@ class PresetRegistry:
            pack_id: Preset ID
        Returns:
-            True if pack is installed, False if not or registry corrupted
+            True if pack is installed
        """
-        packs = self.data.get("presets")
+        return pack_id in self.data["presets"]
        if not isinstance(packs, dict):
            return False
        return pack_id in packs
 class PresetManager:
@@ -646,6 +566,8 @@ class PresetManager:
            short_name = cmd_name
            if short_name.startswith("speckit."):
                short_name = short_name[len("speckit."):]
            # Kimi CLI discovers skills by directory name and invokes them as
            # /skill:<name> — use dot separator to match packaging convention.
            if selected_ai == "kimi":
                skill_name = f"speckit.{short_name}"
            else:
@@ -1062,8 +984,8 @@ 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}"
            )
@@ -1544,20 +1466,12 @@ class PresetResolver:
            return []
        registry = ExtensionRegistry(self.extensions_dir)
-        # Use keys() to track ALL extensions (including corrupted entries) without deep copy
+        registered_extensions = registry.list_by_priority()
-        # This prevents corrupted entries from being picked up as "unregistered" dirs
+        registered_extension_ids = {ext_id for ext_id, _ in registered_extensions}
        registered_extension_ids = registry.keys()
        # Get all registered extensions including disabled; we filter disabled manually below
        all_registered = registry.list_by_priority(include_disabled=True)
        all_extensions: list[tuple[int, str, dict | None]] = []
-        # Only include enabled extensions in the result
+        for ext_id, metadata in registered_extensions:
        for ext_id, metadata in all_registered:
            # Skip disabled extensions
            if not metadata.get("enabled", True):
                continue
            priority = normalize_priority(metadata.get("priority") if metadata else None)
            all_extensions.append((priority, ext_id, metadata))
--- a/templates/commands/implement.md
+++ b/templates/commands/implement.md
@@ -19,7 +19,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 - Check if `.specify/extensions.yml` exists in the project root.
 - If it exists, read it and look for entries under the `hooks.before_implement` key
 - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- Filter to only hooks where `enabled: true`
 - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
@@ -174,7 +174,7 @@ Note: This command assumes a complete task breakdown exists in tasks.md. If task
 10. **Check for extension hooks**: After completion validation, check if `.specify/extensions.yml` exists in the project root.
    - If it exists, read it and look for entries under the `hooks.after_implement` key
    - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-    - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+    - Filter to only hooks where `enabled: true`
    - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
      - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
      - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
--- a/templates/commands/plan.md
+++ b/templates/commands/plan.md
@@ -24,40 +24,6 @@ $ARGUMENTS
 You **MUST** consider the user input before proceeding (if not empty).
 ## Pre-Execution Checks
 **Check for extension hooks (before planning)**:
 - Check if `.specify/extensions.yml` exists in the project root.
 - If it exists, read it and look for entries under the `hooks.before_plan` key
 - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
 - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
 - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
 - For each executable hook, output the following based on its `optional` flag:
  - **Optional hook** (`optional: true`):
    ```
    ## Extension Hooks
    **Optional Pre-Hook**: {extension}
    Command: `/{command}`
    Description: {description}
    Prompt: {prompt}
    To execute: `/{command}`
    ```
  - **Mandatory hook** (`optional: false`):
    ```
    ## Extension Hooks
    **Automatic Pre-Hook**: {extension}
    Executing: `/{command}`
    EXECUTE_COMMAND: {command}
    Wait for the result of the hook command before proceeding to the Outline.
    ```
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 ## Outline
 1. **Setup**: Run `{SCRIPT}` from repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
@@ -75,35 +41,6 @@ You **MUST** consider the user input before proceeding (if not empty).
 4. **Stop and report**: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
 5. **Check for extension hooks**: After reporting, check if `.specify/extensions.yml` exists in the project root.
   - If it exists, read it and look for entries under the `hooks.after_plan` key
   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
   - For each executable hook, output the following based on its `optional` flag:
     - **Optional hook** (`optional: true`):
       ```
       ## Extension Hooks
       **Optional Hook**: {extension}
       Command: `/{command}`
       Description: {description}
       Prompt: {prompt}
       To execute: `/{command}`
       ```
     - **Mandatory hook** (`optional: false`):
       ```
       ## Extension Hooks
       **Automatic Hook**: {extension}
       Executing: `/{command}`
       EXECUTE_COMMAND: {command}
       ```
   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 ## Phases
 ### Phase 0: Outline & Research
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -21,40 +21,6 @@ $ARGUMENTS
 You **MUST** consider the user input before proceeding (if not empty).
 ## Pre-Execution Checks
 **Check for extension hooks (before specification)**:
 - Check if `.specify/extensions.yml` exists in the project root.
 - If it exists, read it and look for entries under the `hooks.before_specify` key
 - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
 - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
 - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
 - For each executable hook, output the following based on its `optional` flag:
  - **Optional hook** (`optional: true`):
    ```
    ## Extension Hooks
    **Optional Pre-Hook**: {extension}
    Command: `/{command}`
    Description: {description}
    Prompt: {prompt}
    To execute: `/{command}`
    ```
  - **Mandatory hook** (`optional: false`):
    ```
    ## Extension Hooks
    **Automatic Pre-Hook**: {extension}
    Executing: `/{command}`
    EXECUTE_COMMAND: {command}
    Wait for the result of the hook command before proceeding to the Outline.
    ```
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 ## Outline
 The text the user typed after `/speckit.specify` in the triggering message **is** the feature description. Assume you always have it available in this conversation even if `{ARGS}` appears literally below. Do not ask the user to repeat it unless they provided an empty command.
@@ -73,16 +39,10 @@ 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** 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:
+2. **Create the feature branch** by running the script with `--short-name` (and `--json`), and do NOT pass `--number` (the script auto-detects the next globally available number across all branches and spec directories):
   **Branch numbering mode**: Before running the script, check if `.specify/init-options.json` exists and read the `branch_numbering` value.
   - If `"timestamp"`, add `--timestamp` (Bash) or `-Timestamp` (PowerShell) to the script invocation
   - If `"sequential"` or absent, do not add any extra flag (default behavior)
   - 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"`
   - PowerShell (timestamp): `{SCRIPT} -Json -Timestamp -ShortName "user-auth" "Add user authentication"`
   **IMPORTANT**:
   - Do NOT pass `--number` — the script determines the correct next number automatically
@@ -216,35 +176,6 @@ Given that feature description, do this:
 7. Report completion with branch name, spec file path, checklist results, and readiness for the next phase (`/speckit.clarify` or `/speckit.plan`).
 8. **Check for extension hooks**: After reporting completion, check if `.specify/extensions.yml` exists in the project root.
   - If it exists, read it and look for entries under the `hooks.after_specify` key
   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
   - For each executable hook, output the following based on its `optional` flag:
     - **Optional hook** (`optional: true`):
       ```
       ## Extension Hooks
       **Optional Hook**: {extension}
       Command: `/{command}`
       Description: {description}
       Prompt: {prompt}
       To execute: `/{command}`
       ```
     - **Mandatory hook** (`optional: false`):
       ```
       ## Extension Hooks
       **Automatic Hook**: {extension}
       Executing: `/{command}`
       EXECUTE_COMMAND: {command}
       ```
   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 **NOTE:** The script creates and checks out the new branch and initializes the spec file before writing.
 ## Quick Guidelines
--- a/templates/commands/tasks.md
+++ b/templates/commands/tasks.md
@@ -28,7 +28,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 - Check if `.specify/extensions.yml` exists in the project root.
 - If it exists, read it and look for entries under the `hooks.before_tasks` key
 - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- Filter to only hooks where `enabled: true`
 - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
@@ -100,7 +100,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 6. **Check for extension hooks**: After tasks.md is generated, check if `.specify/extensions.yml` exists in the project root.
   - If it exists, read it and look for entries under the `hooks.after_tasks` key
   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
-   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+   - Filter to only hooks where `enabled: true`
   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
--- a/tests/test_agent_config_consistency.py
+++ b/tests/test_agent_config_consistency.py
@@ -29,17 +29,11 @@ class TestAgentConfigConsistency:
        assert "q" not in cfg
    def test_extension_registrar_includes_codex(self):
-        """Extension command registrar should include codex targeting .agents/skills."""
+        """Extension command registrar should include codex targeting .codex/prompts."""
        cfg = CommandRegistrar.AGENT_CONFIGS
        assert "codex" in cfg
-        assert cfg["codex"]["dir"] == ".agents/skills"
+        assert cfg["codex"]["dir"] == ".codex/prompts"
        assert cfg["codex"]["extension"] == "/SKILL.md"
    def test_runtime_codex_uses_native_skills(self):
        """Codex runtime config should point at .agents/skills."""
        assert AGENT_CONFIG["codex"]["folder"] == ".agents/"
        assert AGENT_CONFIG["codex"]["commands_subdir"] == "skills"
    def test_release_agent_lists_include_kiro_cli_and_exclude_q(self):
        """Bash and PowerShell release scripts should agree on agent key set for Kiro."""
@@ -77,16 +71,6 @@ class TestAgentConfigConsistency:
        assert re.search(r"shai\)\s*\n.*?\.shai/commands", sh_text, re.S) is not None
        assert re.search(r"agy\)\s*\n.*?\.agent/commands", sh_text, re.S) is not None
    def test_release_scripts_generate_codex_skills(self):
        """Release scripts should generate Codex skills in .agents/skills."""
        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
        assert ".agents/skills" in sh_text
        assert ".agents/skills" in ps_text
        assert re.search(r"codex\)\s*\n.*?create_skills.*?\.agents/skills.*?\"-\"", sh_text, re.S) is not None
        assert re.search(r"'codex'\s*\{.*?\.agents/skills.*?New-Skills.*?-Separator '-'", ps_text, re.S) is not None
    def test_init_ai_help_includes_roo_and_kiro_alias(self):
        """CLI help text for --ai should stay in sync with agent config and alias guidance."""
        assert "roo" in AI_ASSISTANT_HELP
@@ -325,145 +309,3 @@ class TestAgentConfigConsistency:
    def test_ai_help_includes_trae(self):
        """CLI help text for --ai should include trae."""
        assert "trae" in AI_ASSISTANT_HELP
    # --- Pi Coding Agent consistency checks ---
    def test_pi_in_agent_config(self):
        """AGENT_CONFIG should include pi with correct folder and commands_subdir."""
        assert "pi" in AGENT_CONFIG
        assert AGENT_CONFIG["pi"]["folder"] == ".pi/"
        assert AGENT_CONFIG["pi"]["commands_subdir"] == "prompts"
        assert AGENT_CONFIG["pi"]["requires_cli"] is True
        assert AGENT_CONFIG["pi"]["install_url"] is not None
    def test_pi_in_extension_registrar(self):
        """Extension command registrar should include pi using .pi/prompts."""
        cfg = CommandRegistrar.AGENT_CONFIGS
        assert "pi" in cfg
        pi_cfg = cfg["pi"]
        assert pi_cfg["dir"] == ".pi/prompts"
        assert pi_cfg["format"] == "markdown"
        assert pi_cfg["args"] == "$ARGUMENTS"
        assert pi_cfg["extension"] == ".md"
    def test_pi_in_release_agent_lists(self):
        """Bash and PowerShell release scripts should include pi in agent lists."""
        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
        sh_match = re.search(r"ALL_AGENTS=\(([^)]*)\)", sh_text)
        assert sh_match is not None
        sh_agents = sh_match.group(1).split()
        ps_match = re.search(r"\$AllAgents = @\(([^)]*)\)", ps_text)
        assert ps_match is not None
        ps_agents = re.findall(r"'([^']+)'", ps_match.group(1))
        assert "pi" in sh_agents
        assert "pi" in ps_agents
    def test_release_scripts_generate_pi_prompt_templates(self):
        """Release scripts should generate Markdown prompt templates for pi in .pi/prompts."""
        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
        assert ".pi/prompts" in sh_text
        assert ".pi/prompts" in ps_text
        assert re.search(r"pi\)\s*\n.*?\.pi/prompts", sh_text, re.S) is not None
        assert re.search(r"'pi'\s*\{.*?\.pi/prompts", ps_text, re.S) is not None
    def test_pi_in_powershell_validate_set(self):
        """PowerShell update-agent-context script should include 'pi' in ValidateSet."""
        ps_text = (REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1").read_text(encoding="utf-8")
        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
        assert validate_set_match is not None
        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
        assert "pi" in validate_set_values
    def test_pi_in_github_release_output(self):
        """GitHub release script should include pi template packages."""
        gh_release_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-github-release.sh").read_text(encoding="utf-8")
        assert "spec-kit-template-pi-sh-" in gh_release_text
        assert "spec-kit-template-pi-ps-" in gh_release_text
    def test_agent_context_scripts_include_pi(self):
        """Agent context scripts should support pi agent type."""
        bash_text = (REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh").read_text(encoding="utf-8")
        pwsh_text = (REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1").read_text(encoding="utf-8")
        assert "pi" in bash_text
        assert "Pi Coding Agent" in bash_text
        assert "pi" in pwsh_text
        assert "Pi Coding Agent" in pwsh_text
    def test_ai_help_includes_pi(self):
        """CLI help text for --ai should include pi."""
        assert "pi" in AI_ASSISTANT_HELP
    # --- iFlow CLI consistency checks ---
    def test_iflow_in_agent_config(self):
        """AGENT_CONFIG should include iflow with correct folder and commands_subdir."""
        assert "iflow" in AGENT_CONFIG
        assert AGENT_CONFIG["iflow"]["folder"] == ".iflow/"
        assert AGENT_CONFIG["iflow"]["commands_subdir"] == "commands"
        assert AGENT_CONFIG["iflow"]["requires_cli"] is True
    def test_iflow_in_extension_registrar(self):
        """Extension command registrar should include iflow targeting .iflow/commands."""
        cfg = CommandRegistrar.AGENT_CONFIGS
        assert "iflow" in cfg
        assert cfg["iflow"]["dir"] == ".iflow/commands"
        assert cfg["iflow"]["format"] == "markdown"
        assert cfg["iflow"]["args"] == "$ARGUMENTS"
    def test_iflow_in_release_agent_lists(self):
        """Bash and PowerShell release scripts should include iflow in agent lists."""
        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
        sh_match = re.search(r"ALL_AGENTS=\(([^)]*)\)", sh_text)
        assert sh_match is not None
        sh_agents = sh_match.group(1).split()
        ps_match = re.search(r"\$AllAgents = @\(([^)]*)\)", ps_text)
        assert ps_match is not None
        ps_agents = re.findall(r"'([^']+)'", ps_match.group(1))
        assert "iflow" in sh_agents
        assert "iflow" in ps_agents
    def test_iflow_in_release_scripts_build_variant(self):
        """Release scripts should generate Markdown commands for iflow in .iflow/commands."""
        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
        assert ".iflow/commands" in sh_text
        assert ".iflow/commands" in ps_text
        assert re.search(r"'iflow'\s*\{.*?\.iflow/commands", ps_text, re.S) is not None
    def test_iflow_in_github_release_output(self):
        """GitHub release script should include iflow template packages."""
        gh_release_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-github-release.sh").read_text(encoding="utf-8")
        assert "spec-kit-template-iflow-sh-" in gh_release_text
        assert "spec-kit-template-iflow-ps-" in gh_release_text
    def test_iflow_in_agent_context_scripts(self):
        """Agent context scripts should support iflow agent type."""
        bash_text = (REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh").read_text(encoding="utf-8")
        pwsh_text = (REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1").read_text(encoding="utf-8")
        assert "iflow" in bash_text
        assert "IFLOW_FILE" in bash_text
        assert "iflow" in pwsh_text
        assert "IFLOW_FILE" in pwsh_text
    def test_ai_help_includes_iflow(self):
        """CLI help text for --ai should include iflow."""
        assert "iflow" in AI_ASSISTANT_HELP
--- a/tests/test_ai_skills.py
+++ b/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
@@ -184,11 +182,6 @@ class TestGetSkillsDir:
        result = _get_skills_dir(project_dir, "kiro-cli")
        assert result == project_dir / ".kiro" / "skills"
    def test_pi_skills_dir(self, project_dir):
        """Pi should use .pi/skills/."""
        result = _get_skills_dir(project_dir, "pi")
        assert result == project_dir / ".pi" / "skills"
    def test_unknown_agent_uses_default(self, project_dir):
        """Unknown agents should fall back to DEFAULT_SKILLS_DIR."""
        result = _get_skills_dir(project_dir, "nonexistent-agent")
@@ -429,27 +422,6 @@ class TestInstallAiSkills:
        assert (cmds_dir / "speckit.specify.md").exists()
        assert (cmds_dir / "speckit.plan.md").exists()
    def test_pi_prompt_dir_installs_skills(self, project_dir):
        """Pi should install skills directly from .pi/prompts/."""
        prompts_dir = project_dir / ".pi" / "prompts"
        prompts_dir.mkdir(parents=True)
        (prompts_dir / "speckit.specify.md").write_text(
            "---\ndescription: Create or update the feature specification.\n---\n\n# Specify\n\nBody.\n"
        )
        (prompts_dir / "speckit.plan.md").write_text(
            "---\ndescription: Generate implementation plan.\n---\n\n# Plan\n\nBody.\n"
        )
        result = install_ai_skills(project_dir, "pi")
        assert result is True
        skills_dir = project_dir / ".pi" / "skills"
        assert skills_dir.exists()
        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
        assert len(skill_dirs) >= 1
        assert (prompts_dir / "speckit.specify.md").exists()
        assert (prompts_dir / "speckit.plan.md").exists()
    @pytest.mark.parametrize("agent_key", [k for k in AGENT_CONFIG.keys() if k != "generic"])
    def test_skills_install_for_all_agents(self, temp_dir, agent_key):
        """install_ai_skills should produce skills for every configured agent."""
@@ -473,7 +445,8 @@ class TestInstallAiSkills:
        skills_dir = _get_skills_dir(proj, agent_key)
        assert skills_dir.exists()
        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
-        # Kimi uses dotted skill names; other agents use hyphen-separated names.
+        # Kimi uses dot-separator (speckit.specify) to match /skill:speckit.* invocation;
        # all other agents use hyphen-separator (speckit-specify).
        expected_skill_name = "speckit.specify" if agent_key == "kimi" else "speckit-specify"
        assert expected_skill_name in skill_dirs
        assert (skills_dir / expected_skill_name / "SKILL.md").exists()
@@ -695,175 +668,6 @@ class TestNewProjectCommandSkip:
        prompts_dir = target / ".kiro" / "prompts"
        assert not prompts_dir.exists()
    def test_codex_native_skills_preserved_without_conversion(self, tmp_path):
        """Codex should keep bundled .agents/skills and skip install_ai_skills conversion."""
        from typer.testing import CliRunner
        runner = CliRunner()
        target = tmp_path / "new-codex-proj"
        def fake_download(project_path, *args, **kwargs):
            skill_dir = project_path / ".agents" / "skills" / "speckit-specify"
            skill_dir.mkdir(parents=True, exist_ok=True)
            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
        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") 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(
                app,
                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
            )
        assert result.exit_code == 0
        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):
        """Codex should attempt fallback conversion when bundled skills are missing."""
        from typer.testing import CliRunner
        runner = CliRunner()
        target = tmp_path / "missing-codex-skills"
        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.is_git_repo", return_value=False), \
             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
            result = runner.invoke(
                app,
                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
            )
        assert result.exit_code == 1
        mock_skills.assert_called_once()
        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."""
        from typer.testing import CliRunner
        runner = CliRunner()
        target = tmp_path / "foreign-codex-skills"
        def fake_download(project_path, *args, **kwargs):
            skill_dir = project_path / ".agents" / "skills" / "other-tool"
            skill_dir.mkdir(parents=True, exist_ok=True)
            (skill_dir / "SKILL.md").write_text("---\ndescription: Foreign skill\n---\n\nBody.\n")
        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.is_git_repo", return_value=False), \
             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
            result = runner.invoke(
                app,
                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
            )
        assert result.exit_code == 0
        mock_skills.assert_called_once()
        assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
    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)."""
        from typer.testing import CliRunner
@@ -954,21 +758,6 @@ 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 =====
@@ -1022,17 +811,6 @@ class TestCliValidation:
        assert "Explicit command support was deprecated in Antigravity version 1.20.5." in result.output
        assert "--ai-skills" in result.output
    def test_codex_without_ai_skills_fails(self):
        """--ai codex without --ai-skills should fail with exit code 1."""
        from typer.testing import CliRunner
        runner = CliRunner()
        result = runner.invoke(app, ["init", "test-proj", "--ai", "codex"])
        assert result.exit_code == 1
        assert "Custom prompt-based spec-kit initialization is deprecated for Codex CLI" in result.output
        assert "--ai-skills" in result.output
    def test_interactive_agy_without_ai_skills_prompts_skills(self, monkeypatch):
        """Interactive selector returning agy without --ai-skills should automatically enable --ai-skills."""
        from typer.testing import CliRunner
@@ -1075,72 +853,6 @@ class TestCliValidation:
            assert result.exit_code == 0
            assert "Explicit command support was deprecated" not in result.output
    def test_interactive_codex_without_ai_skills_enables_skills(self, monkeypatch):
        """Interactive selector returning codex without --ai-skills should automatically enable --ai-skills."""
        from typer.testing import CliRunner
        def _fake_select_with_arrows(*args, **kwargs):
            options = kwargs.get("options")
            if options is None and len(args) >= 1:
                options = args[0]
            if isinstance(options, dict) and "codex" in options:
                return "codex"
            if isinstance(options, (list, tuple)) and "codex" in options:
                return "codex"
            if isinstance(options, dict) and options:
                return next(iter(options.keys()))
            if isinstance(options, (list, tuple)) and options:
                return options[0]
            return None
        monkeypatch.setattr("specify_cli.select_with_arrows", _fake_select_with_arrows)
        def _fake_download(*args, **kwargs):
            project_path = Path(args[0])
            skill_dir = project_path / ".agents" / "skills" / "speckit-specify"
            skill_dir.mkdir(parents=True, exist_ok=True)
            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
        runner = CliRunner()
        with runner.isolated_filesystem():
            result = runner.invoke(app, ["init", "test-proj", "--no-git", "--ignore-agent-tools"])
            assert result.exit_code == 0
            assert "Custom prompt-based spec-kit initialization is deprecated for Codex CLI" not in result.output
            assert ".agents/skills" in result.output
            assert "$speckit-constitution" in result.output
            assert "/speckit.constitution" not in result.output
            assert "Optional skills that you can use for your specs" in result.output
    def test_kimi_next_steps_show_skill_invocation(self, monkeypatch):
        """Kimi next-steps guidance should display /skill:speckit.* usage."""
        from typer.testing import CliRunner
        def _fake_download(*args, **kwargs):
            project_path = Path(args[0])
            skill_dir = project_path / ".kimi" / "skills" / "speckit.specify"
            skill_dir.mkdir(parents=True, exist_ok=True)
            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
        runner = CliRunner()
        with runner.isolated_filesystem():
            result = runner.invoke(
                app,
                ["init", "test-proj", "--ai", "kimi", "--no-git", "--ignore-agent-tools"],
            )
            assert result.exit_code == 0
            assert "/skill:speckit.constitution" in result.output
            assert "/speckit.constitution" not in result.output
            assert "Optional skills that you can use for your specs" in result.output
    def test_ai_skills_flag_appears_in_help(self):
        """--ai-skills should appear in init --help output."""
        from typer.testing import CliRunner
@@ -1160,12 +872,10 @@ class TestCliValidation:
        target = tmp_path / "kiro-alias-proj"
        with patch("specify_cli.download_and_extract_template") as mock_download, \
             patch("specify_cli.scaffold_from_core_pack", create=True) as mock_scaffold, \
             patch("specify_cli.ensure_executable_scripts"), \
             patch("specify_cli.ensure_constitution_from_template"), \
             patch("specify_cli.is_git_repo", return_value=False), \
             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
            mock_scaffold.return_value = True
            result = runner.invoke(
                app,
                [
@@ -1181,14 +891,9 @@ class TestCliValidation:
            )
        assert result.exit_code == 0
-        # Without --offline, the download path should be taken.
+        assert mock_download.called
-        assert mock_download.called, (
+        # download_and_extract_template(project_path, ai_assistant, script_type, ...)
            "Expected download_and_extract_template to be called (default non-offline path)"
        )
        assert mock_download.call_args.args[1] == "kiro-cli"
        assert not mock_scaffold.called, (
            "scaffold_from_core_pack should not be called without --offline"
        )
    def test_q_removed_from_agent_config(self):
        """Amazon Q legacy key should not remain in AGENT_CONFIG."""
--- a/tests/test_branch_numbering.py
+++ b/tests/test_branch_numbering.py
@@ -1,89 +0,0 @@
 """
 Unit tests for branch numbering options (sequential vs timestamp).
 Tests cover:
 - Persisting branch_numbering in init-options.json
 - Default value when branch_numbering is None
 - Validation of branch_numbering values
 """
 import json
 from pathlib import Path
 from specify_cli import save_init_options
 class TestSaveBranchNumbering:
    """Tests for save_init_options with branch_numbering."""
    def test_save_branch_numbering_timestamp(self, tmp_path: Path):
        opts = {"branch_numbering": "timestamp", "ai": "claude"}
        save_init_options(tmp_path, opts)
        saved = json.loads((tmp_path / ".specify/init-options.json").read_text())
        assert saved["branch_numbering"] == "timestamp"
    def test_save_branch_numbering_sequential(self, tmp_path: Path):
        opts = {"branch_numbering": "sequential", "ai": "claude"}
        save_init_options(tmp_path, opts)
        saved = json.loads((tmp_path / ".specify/init-options.json").read_text())
        assert saved["branch_numbering"] == "sequential"
    def test_branch_numbering_defaults_to_sequential(self, tmp_path: Path, monkeypatch):
        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
        saved = json.loads((project_dir / ".specify/init-options.json").read_text())
        assert saved["branch_numbering"] == "sequential"
 class TestBranchNumberingValidation:
    """Tests for branch_numbering CLI validation via CliRunner."""
    def test_invalid_branch_numbering_rejected(self, tmp_path: Path):
        from typer.testing import CliRunner
        from specify_cli import app
        runner = CliRunner()
        result = runner.invoke(app, ["init", str(tmp_path / "proj"), "--ai", "claude", "--branch-numbering", "foobar"])
        assert result.exit_code == 1
        assert "Invalid --branch-numbering" in result.output
    def test_valid_branch_numbering_sequential(self, tmp_path: Path, monkeypatch):
        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)
        runner = CliRunner()
        result = runner.invoke(app, ["init", str(tmp_path / "proj"), "--ai", "claude", "--branch-numbering", "sequential", "--ignore-agent-tools"])
        assert result.exit_code == 0
        assert "Invalid --branch-numbering" not in (result.output or "")
    def test_valid_branch_numbering_timestamp(self, tmp_path: Path, monkeypatch):
        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)
        runner = CliRunner()
        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 "")
--- a/tests/test_core_pack_scaffold.py
+++ b/tests/test_core_pack_scaffold.py
@@ -1,613 +0,0 @@
 """
 Validation tests for offline/air-gapped scaffolding (PR #1803).
 For every supported AI agent (except "generic") the scaffold output is verified
 against invariants and compared byte-for-byte with the canonical output produced
 by create-release-packages.sh.
 Since scaffold_from_core_pack() now invokes the release script at runtime, the
 parity test (section 9) runs the script independently and compares the results
 to ensure the integration is correct.
 Per-agent invariants verified
 ──────────────────────────────
  • Command files are written to the directory declared in AGENT_CONFIG
  • File count matches the number of source templates
  • Extension is correct: .toml (TOML agents), .agent.md (copilot), .md (rest)
  • No unresolved placeholders remain ({SCRIPT}, {ARGS}, __AGENT__)
  • Argument token is correct: {{args}} for TOML agents, $ARGUMENTS for others
  • Path rewrites applied: scripts/ → .specify/scripts/ etc.
  • TOML files have "description" and "prompt" fields
  • Markdown files have parseable YAML frontmatter
  • Copilot: companion speckit.*.prompt.md files are generated in prompts/
  • .specify/scripts/ contains at least one script file
  • .specify/templates/ contains at least one template file
 Parity invariant
 ────────────────
  Every file produced by scaffold_from_core_pack() must be byte-for-byte
  identical to the same file in the ZIP produced by the release script.
 """
 import os
 import re
 import shutil
 import subprocess
 import tomllib
 import zipfile
 from pathlib import Path
 import pytest
 import yaml
 from specify_cli import (
    AGENT_CONFIG,
    _TOML_AGENTS,
    _locate_core_pack,
    scaffold_from_core_pack,
 )
 _REPO_ROOT = Path(__file__).parent.parent
 _RELEASE_SCRIPT = _REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh"
 def _find_bash() -> str | None:
    """Return the path to a usable bash on this machine, or None."""
    # Prefer PATH lookup so non-standard install locations (Nix, CI) are found.
    on_path = shutil.which("bash")
    if on_path:
        return on_path
    candidates = [
        "/opt/homebrew/bin/bash",
        "/usr/local/bin/bash",
        "/bin/bash",
        "/usr/bin/bash",
    ]
    for candidate in candidates:
        try:
            result = subprocess.run(
                [candidate, "--version"],
                capture_output=True, text=True, timeout=5,
            )
            if result.returncode == 0:
                return candidate
        except (FileNotFoundError, subprocess.TimeoutExpired):
            continue
    return None
 def _run_release_script(agent: str, script_type: str, bash: str, output_dir: Path) -> Path:
    """Run create-release-packages.sh for *agent*/*script_type* and return the
    path to the generated ZIP.  *output_dir* receives the build artifacts so
    the repo working tree stays clean."""
    env = os.environ.copy()
    env["AGENTS"] = agent
    env["SCRIPTS"] = script_type
    env["GENRELEASES_DIR"] = str(output_dir)
    result = subprocess.run(
        [bash, str(_RELEASE_SCRIPT), "v0.0.0"],
        capture_output=True, text=True,
        cwd=str(_REPO_ROOT),
        env=env,
        timeout=300,
    )
    if result.returncode != 0:
        pytest.fail(
            f"Release script failed with exit code {result.returncode}\n"
            f"stdout:\n{result.stdout}\nstderr:\n{result.stderr}"
        )
    zip_pattern = f"spec-kit-template-{agent}-{script_type}-v0.0.0.zip"
    zip_path = output_dir / zip_pattern
    if not zip_path.exists():
        pytest.fail(
            f"Release script did not produce expected ZIP: {zip_path}\n"
            f"stdout:\n{result.stdout}\nstderr:\n{result.stderr}"
        )
    return zip_path
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
 # Number of source command templates (one per .md file in templates/commands/)
 def _commands_dir() -> Path:
    """Return the command templates directory (source-checkout or core_pack)."""
    core = _locate_core_pack()
    if core and (core / "commands").is_dir():
        return core / "commands"
    # Source-checkout fallback
    repo_root = Path(__file__).parent.parent
    return repo_root / "templates" / "commands"
 def _get_source_template_stems() -> list[str]:
    """Return the stems of source command template files (e.g. ['specify', 'plan', ...])."""
    return sorted(p.stem for p in _commands_dir().glob("*.md"))
 def _expected_cmd_dir(project_path: Path, agent: str) -> Path:
    """Return the expected command-files directory for a given agent."""
    cfg = AGENT_CONFIG[agent]
    folder = (cfg.get("folder") or "").rstrip("/")
    subdir = cfg.get("commands_subdir", "commands")
    if folder:
        return project_path / folder / subdir
    return project_path / ".speckit" / subdir
 # Agents whose commands are laid out as <skills_dir>/<name>/SKILL.md.
 # Maps agent -> separator used in skill directory names.
 _SKILL_AGENTS: dict[str, str] = {"codex": "-", "kimi": "."}
 def _expected_ext(agent: str) -> str:
    if agent in _TOML_AGENTS:
        return "toml"
    if agent == "copilot":
        return "agent.md"
    if agent in _SKILL_AGENTS:
        return "SKILL.md"
    return "md"
 def _list_command_files(cmd_dir: Path, agent: str) -> list[Path]:
    """List generated command files, handling skills-based directory layouts."""
    if agent in _SKILL_AGENTS:
        sep = _SKILL_AGENTS[agent]
        return sorted(cmd_dir.glob(f"speckit{sep}*/SKILL.md"))
    ext = _expected_ext(agent)
    return sorted(cmd_dir.glob(f"speckit.*.{ext}"))
 def _collect_relative_files(root: Path) -> dict[str, bytes]:
    """Walk *root* and return {relative_posix_path: file_bytes}."""
    result: dict[str, bytes] = {}
    for p in root.rglob("*"):
        if p.is_file():
            result[p.relative_to(root).as_posix()] = p.read_bytes()
    return result
 # ---------------------------------------------------------------------------
 # Fixtures
 # ---------------------------------------------------------------------------
@pytest.fixture(scope="session")
 def source_template_stems() -> list[str]:
    return _get_source_template_stems()
@pytest.fixture(scope="session")
 def scaffolded_sh(tmp_path_factory):
    """Session-scoped cache: scaffold once per agent with script_type='sh'."""
    cache = {}
    def _get(agent: str) -> Path:
        if agent not in cache:
            project = tmp_path_factory.mktemp(f"scaffold_sh_{agent}")
            ok = scaffold_from_core_pack(project, agent, "sh")
            assert ok, f"scaffold_from_core_pack returned False for agent '{agent}'"
            cache[agent] = project
        return cache[agent]
    return _get
@pytest.fixture(scope="session")
 def scaffolded_ps(tmp_path_factory):
    """Session-scoped cache: scaffold once per agent with script_type='ps'."""
    cache = {}
    def _get(agent: str) -> Path:
        if agent not in cache:
            project = tmp_path_factory.mktemp(f"scaffold_ps_{agent}")
            ok = scaffold_from_core_pack(project, agent, "ps")
            assert ok, f"scaffold_from_core_pack returned False for agent '{agent}'"
            cache[agent] = project
        return cache[agent]
    return _get
 # ---------------------------------------------------------------------------
 # Parametrize over all agents except "generic"
 # ---------------------------------------------------------------------------
 _TESTABLE_AGENTS = [a for a in AGENT_CONFIG if a != "generic"]
 # ---------------------------------------------------------------------------
 # 1. Bundled scaffold — directory structure
 # ---------------------------------------------------------------------------
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_creates_specify_scripts(agent, scaffolded_sh):
    """scaffold_from_core_pack copies at least one script into .specify/scripts/."""
    project = scaffolded_sh(agent)
    scripts_dir = project / ".specify" / "scripts" / "bash"
    assert scripts_dir.is_dir(), f".specify/scripts/bash/ missing for agent '{agent}'"
    assert any(scripts_dir.iterdir()), f".specify/scripts/bash/ is empty for agent '{agent}'"
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_creates_specify_templates(agent, scaffolded_sh):
    """scaffold_from_core_pack copies at least one page template into .specify/templates/."""
    project = scaffolded_sh(agent)
    tpl_dir = project / ".specify" / "templates"
    assert tpl_dir.is_dir(), f".specify/templates/ missing for agent '{agent}'"
    assert any(tpl_dir.iterdir()), ".specify/templates/ is empty"
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_command_dir_location(agent, scaffolded_sh):
    """Command files land in the directory declared by AGENT_CONFIG."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    assert cmd_dir.is_dir(), (
        f"Command dir '{cmd_dir.relative_to(project)}' not created for agent '{agent}'"
    )
 # ---------------------------------------------------------------------------
 # 2. Bundled scaffold — file count
 # ---------------------------------------------------------------------------
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_command_file_count(agent, scaffolded_sh, source_template_stems):
    """One command file is generated per source template for every agent."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    generated = _list_command_files(cmd_dir, agent)
    if cmd_dir.is_dir():
        dir_listing = list(cmd_dir.iterdir())
    else:
        dir_listing = f"<command dir missing: {cmd_dir}>"
    assert len(generated) == len(source_template_stems), (
        f"Agent '{agent}': expected {len(source_template_stems)} command files "
        f"({_expected_ext(agent)}), found {len(generated)}. Dir: {dir_listing}"
    )
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_command_file_names(agent, scaffolded_sh, source_template_stems):
    """Each source template stem maps to a corresponding speckit.<stem>.<ext> file."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for stem in source_template_stems:
        if agent in _SKILL_AGENTS:
            sep = _SKILL_AGENTS[agent]
            expected = cmd_dir / f"speckit{sep}{stem}" / "SKILL.md"
        else:
            ext = _expected_ext(agent)
            expected = cmd_dir / f"speckit.{stem}.{ext}"
        assert expected.is_file(), (
            f"Agent '{agent}': expected file '{expected.name}' not found in '{cmd_dir}'"
        )
 # ---------------------------------------------------------------------------
 # 3. Bundled scaffold — content invariants
 # ---------------------------------------------------------------------------
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_no_unresolved_script_placeholder(agent, scaffolded_sh):
    """{SCRIPT} must not appear in any generated command file."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in cmd_dir.rglob("*"):
        if f.is_file():
            content = f.read_text(encoding="utf-8")
            assert "{SCRIPT}" not in content, (
                f"Unresolved {{SCRIPT}} in '{f.relative_to(project)}' for agent '{agent}'"
            )
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_no_unresolved_agent_placeholder(agent, scaffolded_sh):
    """__AGENT__ must not appear in any generated command file."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in cmd_dir.rglob("*"):
        if f.is_file():
            content = f.read_text(encoding="utf-8")
            assert "__AGENT__" not in content, (
                f"Unresolved __AGENT__ in '{f.relative_to(project)}' for agent '{agent}'"
            )
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_no_unresolved_args_placeholder(agent, scaffolded_sh):
    """{ARGS} must not appear in any generated command file (replaced with agent-specific token)."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in cmd_dir.rglob("*"):
        if f.is_file():
            content = f.read_text(encoding="utf-8")
            assert "{ARGS}" not in content, (
                f"Unresolved {{ARGS}} in '{f.relative_to(project)}' for agent '{agent}'"
            )
 # Build a set of template stems that actually contain {ARGS} in their source.
 _TEMPLATES_WITH_ARGS: frozenset[str] = frozenset(
    p.stem
    for p in _commands_dir().glob("*.md")
    if "{ARGS}" in p.read_text(encoding="utf-8")
 )
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_argument_token_format(agent, scaffolded_sh):
    """For templates that carry an {ARGS} token:
    - TOML agents must emit {{args}}
    - Markdown agents must emit $ARGUMENTS
    Templates without {ARGS} (e.g. implement, plan) are skipped.
    """
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in _list_command_files(cmd_dir, agent):
        # Recover the stem from the file path
        if agent in _SKILL_AGENTS:
            sep = _SKILL_AGENTS[agent]
            stem = f.parent.name.removeprefix(f"speckit{sep}")
        else:
            ext = _expected_ext(agent)
            stem = f.name.removeprefix("speckit.").removesuffix(f".{ext}")
        if stem not in _TEMPLATES_WITH_ARGS:
            continue  # this template has no argument token
        content = f.read_text(encoding="utf-8")
        if agent in _TOML_AGENTS:
            assert "{{args}}" in content, (
                f"TOML agent '{agent}': expected '{{{{args}}}}' in '{f.name}'"
            )
        else:
            assert "$ARGUMENTS" in content, (
                f"Markdown agent '{agent}': expected '$ARGUMENTS' in '{f.name}'"
            )
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_path_rewrites_applied(agent, scaffolded_sh):
    """Bare scripts/ and templates/ paths must be rewritten to .specify/ variants.
    YAML frontmatter 'source:' metadata fields are excluded — they reference
    the original template path for provenance, not a runtime path.
    """
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in cmd_dir.rglob("*"):
        if not f.is_file():
            continue
        content = f.read_text(encoding="utf-8")
        # Strip YAML frontmatter before checking — source: metadata is not a runtime path
        body = content
        if content.startswith("---"):
            parts = content.split("---", 2)
            if len(parts) >= 3:
                body = parts[2]
        # Should not contain bare (non-.specify/) script paths
        assert not re.search(r'(?<!\.specify/)scripts/', body), (
            f"Bare scripts/ path found in '{f.relative_to(project)}' for agent '{agent}'"
        )
        assert not re.search(r'(?<!\.specify/)templates/', body), (
            f"Bare templates/ path found in '{f.relative_to(project)}' for agent '{agent}'"
        )
 # ---------------------------------------------------------------------------
 # 4. TOML format checks
 # ---------------------------------------------------------------------------
@pytest.mark.parametrize("agent", sorted(_TOML_AGENTS))
 def test_toml_format_valid(agent, scaffolded_sh):
    """TOML agents: every command file must have description and prompt fields."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in cmd_dir.glob("speckit.*.toml"):
        content = f.read_text(encoding="utf-8")
        assert 'description = "' in content, (
            f"Missing 'description' in '{f.name}' for agent '{agent}'"
        )
        assert 'prompt = """' in content, (
            f"Missing 'prompt' block in '{f.name}' for agent '{agent}'"
        )
 # ---------------------------------------------------------------------------
 # 5. Markdown frontmatter checks
 # ---------------------------------------------------------------------------
 _MARKDOWN_AGENTS = [a for a in _TESTABLE_AGENTS if a not in _TOML_AGENTS]
@pytest.mark.parametrize("agent", _MARKDOWN_AGENTS)
 def test_markdown_has_frontmatter(agent, scaffolded_sh):
    """Markdown agents: every command file must start with valid YAML frontmatter."""
    project = scaffolded_sh(agent)
    cmd_dir = _expected_cmd_dir(project, agent)
    for f in _list_command_files(cmd_dir, agent):
        content = f.read_text(encoding="utf-8")
        assert content.startswith("---"), (
            f"No YAML frontmatter in '{f.name}' for agent '{agent}'"
        )
        parts = content.split("---", 2)
        assert len(parts) >= 3, f"Incomplete frontmatter in '{f.name}'"
        fm = yaml.safe_load(parts[1])
        assert fm is not None, f"Empty frontmatter in '{f.name}'"
        assert "description" in fm, (
            f"'description' key missing from frontmatter in '{f.name}' for agent '{agent}'"
        )
 # ---------------------------------------------------------------------------
 # 6. Copilot-specific: companion .prompt.md files
 # ---------------------------------------------------------------------------
 def test_copilot_companion_prompt_files(scaffolded_sh, source_template_stems):
    """Copilot: a speckit.<stem>.prompt.md companion is created for every .agent.md file."""
    project = scaffolded_sh("copilot")
    prompts_dir = project / ".github" / "prompts"
    assert prompts_dir.is_dir(), ".github/prompts/ not created for copilot"
    for stem in source_template_stems:
        prompt_file = prompts_dir / f"speckit.{stem}.prompt.md"
        assert prompt_file.is_file(), (
            f"Companion prompt file '{prompt_file.name}' missing for copilot"
        )
 def test_copilot_prompt_file_content(scaffolded_sh, source_template_stems):
    """Copilot companion .prompt.md files must reference their parent .agent.md."""
    project = scaffolded_sh("copilot")
    prompts_dir = project / ".github" / "prompts"
    for stem in source_template_stems:
        f = prompts_dir / f"speckit.{stem}.prompt.md"
        content = f.read_text(encoding="utf-8")
        assert f"agent: speckit.{stem}" in content, (
            f"Companion '{f.name}' does not reference 'speckit.{stem}'"
        )
 # ---------------------------------------------------------------------------
 # 7. PowerShell script variant
 # ---------------------------------------------------------------------------
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_scaffold_powershell_variant(agent, scaffolded_ps, source_template_stems):
    """scaffold_from_core_pack with script_type='ps' creates correct files."""
    project = scaffolded_ps(agent)
    scripts_dir = project / ".specify" / "scripts" / "powershell"
    assert scripts_dir.is_dir(), f".specify/scripts/powershell/ missing for '{agent}'"
    assert any(scripts_dir.iterdir()), ".specify/scripts/powershell/ is empty"
    cmd_dir = _expected_cmd_dir(project, agent)
    generated = _list_command_files(cmd_dir, agent)
    assert len(generated) == len(source_template_stems)
 # ---------------------------------------------------------------------------
 # 8. Parity: bundled vs. real create-release-packages.sh ZIP
 # ---------------------------------------------------------------------------
@pytest.fixture(scope="session")
 def release_script_trees(tmp_path_factory):
    """Session-scoped cache: run release script once per (agent, script_type)."""
    cache: dict[tuple[str, str], dict[str, bytes]] = {}
    bash = _find_bash()
    def _get(agent: str, script_type: str) -> dict[str, bytes] | None:
        if bash is None:
            return None
        key = (agent, script_type)
        if key not in cache:
            tmp = tmp_path_factory.mktemp(f"release_{agent}_{script_type}")
            gen_dir = tmp / "genreleases"
            gen_dir.mkdir()
            zip_path = _run_release_script(agent, script_type, bash, gen_dir)
            extracted = tmp / "extracted"
            extracted.mkdir()
            with zipfile.ZipFile(zip_path) as zf:
                zf.extractall(extracted)
            cache[key] = _collect_relative_files(extracted)
        return cache[key]
    return _get
@pytest.mark.parametrize("script_type", ["sh", "ps"])
@pytest.mark.parametrize("agent", _TESTABLE_AGENTS)
 def test_parity_bundled_vs_release_script(agent, script_type, scaffolded_sh, scaffolded_ps, release_script_trees):
    """scaffold_from_core_pack() file tree is identical to the ZIP produced by
    create-release-packages.sh for every agent and script type.
    This is the true end-to-end parity check: the Python offline path must
    produce exactly the same artifacts as the canonical shell release script.
    Both sides are session-cached: each agent/script_type combination is
    scaffolded and release-scripted only once across all tests.
    """
    script_tree = release_script_trees(agent, script_type)
    if script_tree is None:
        pytest.skip("bash required to run create-release-packages.sh")
    # Reuse session-cached scaffold output
    if script_type == "sh":
        bundled_dir = scaffolded_sh(agent)
    else:
        bundled_dir = scaffolded_ps(agent)
    bundled_tree = _collect_relative_files(bundled_dir)
    only_bundled = set(bundled_tree) - set(script_tree)
    only_script = set(script_tree) - set(bundled_tree)
    assert not only_bundled, (
        f"Agent '{agent}' ({script_type}): files only in bundled output (not in release ZIP):\n  "
        + "\n  ".join(sorted(only_bundled))
    )
    assert not only_script, (
        f"Agent '{agent}' ({script_type}): files only in release ZIP (not in bundled output):\n  "
        + "\n  ".join(sorted(only_script))
    )
    for name in bundled_tree:
        assert bundled_tree[name] == script_tree[name], (
            f"Agent '{agent}' ({script_type}): file '{name}' content differs between "
            f"bundled output and release script ZIP"
        )
 # ---------------------------------------------------------------------------
 # Section 10 – pyproject.toml force-include covers all template files
 # ---------------------------------------------------------------------------
 def test_pyproject_force_include_covers_all_templates():
    """Every file in templates/ (excluding commands/) must be listed in
    pyproject.toml's [tool.hatch.build.targets.wheel.force-include] section.
    This prevents new template files from being silently omitted from the
    wheel, which would break ``specify init --offline``.
    """
    templates_dir = _REPO_ROOT / "templates"
    # Collect all files directly in templates/ (not in subdirectories like commands/)
    repo_template_files = sorted(
        f.name for f in templates_dir.iterdir()
        if f.is_file()
    )
    assert repo_template_files, "Expected at least one template file in templates/"
    pyproject_path = _REPO_ROOT / "pyproject.toml"
    with open(pyproject_path, "rb") as f:
        pyproject = tomllib.load(f)
    force_include = pyproject.get("tool", {}).get("hatch", {}).get("build", {}).get("targets", {}).get("wheel", {}).get("force-include", {})
    missing = [
        name for name in repo_template_files
        if f"templates/{name}" not in force_include
    ]
    assert not missing, (
        "Template files not listed in pyproject.toml force-include "
        "(offline scaffolding will miss them):\n  "
        + "\n  ".join(missing)
    )
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -420,48 +420,6 @@ class TestExtensionRegistry:
        assert registry.is_installed("test-ext")
        assert registry.get("test-ext")["version"] == "1.0.0"
    def test_restore_rejects_none_metadata(self, temp_dir):
        """Test restore() raises ValueError for None metadata."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-ext", None)
    def test_restore_rejects_non_dict_metadata(self, temp_dir):
        """Test restore() raises ValueError for non-dict metadata."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-ext", "not-a-dict")
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-ext", ["list", "not", "dict"])
    def test_restore_uses_deep_copy(self, temp_dir):
        """Test restore() deep copies metadata to prevent mutation."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        original_metadata = {
            "version": "1.0.0",
            "nested": {"key": "original"},
        }
        registry.restore("test-ext", original_metadata)
        # Mutate the original metadata after restore
        original_metadata["version"] = "MUTATED"
        original_metadata["nested"]["key"] = "MUTATED"
        # Registry should have the original values
        stored = registry.get("test-ext")
        assert stored["version"] == "1.0.0"
        assert stored["nested"]["key"] == "original"
    def test_get_returns_deep_copy(self, temp_dir):
        """Test that get() returns deep copies for nested structures."""
        extensions_dir = temp_dir / "extensions"
@@ -481,26 +439,6 @@ class TestExtensionRegistry:
        internal = registry.data["extensions"]["test-ext"]
        assert internal["registered_commands"] == {"claude": ["cmd1"]}
    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
        """Test that get() returns None for corrupted (non-dict) entries."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        # Directly corrupt the registry with non-dict entries
        registry.data["extensions"]["corrupted-string"] = "not a dict"
        registry.data["extensions"]["corrupted-list"] = ["not", "a", "dict"]
        registry.data["extensions"]["corrupted-int"] = 42
        registry._save()
        # All corrupted entries should return None
        assert registry.get("corrupted-string") is None
        assert registry.get("corrupted-list") is None
        assert registry.get("corrupted-int") is None
        # Non-existent should also return None
        assert registry.get("nonexistent") is None
    def test_list_returns_deep_copy(self, temp_dir):
        """Test that list() returns deep copies for nested structures."""
        extensions_dir = temp_dir / "extensions"
@@ -520,20 +458,6 @@ class TestExtensionRegistry:
        internal = registry.data["extensions"]["test-ext"]
        assert internal["registered_commands"] == {"claude": ["cmd1"]}
    def test_list_returns_empty_dict_for_corrupted_registry(self, temp_dir):
        """Test that list() returns empty dict when extensions is not a dict."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        # Corrupt the registry - extensions is a list instead of dict
        registry.data["extensions"] = ["not", "a", "dict"]
        registry._save()
        # list() should return empty dict, not crash
        result = registry.list()
        assert result == {}
 # ===== ExtensionManager Tests =====
@@ -665,19 +589,9 @@ class TestCommandRegistrar:
        assert "q" not in CommandRegistrar.AGENT_CONFIGS
    def test_codex_agent_config_present(self):
-        """Codex should be mapped to .agents/skills."""
+        """Codex should be mapped to .codex/prompts."""
        assert "codex" in CommandRegistrar.AGENT_CONFIGS
-        assert CommandRegistrar.AGENT_CONFIGS["codex"]["dir"] == ".agents/skills"
+        assert CommandRegistrar.AGENT_CONFIGS["codex"]["dir"] == ".codex/prompts"
        assert CommandRegistrar.AGENT_CONFIGS["codex"]["extension"] == "/SKILL.md"
    def test_pi_agent_config_present(self):
        """Pi should be mapped to .pi/prompts."""
        assert "pi" in CommandRegistrar.AGENT_CONFIGS
        cfg = CommandRegistrar.AGENT_CONFIGS["pi"]
        assert cfg["dir"] == ".pi/prompts"
        assert cfg["format"] == "markdown"
        assert cfg["args"] == "$ARGUMENTS"
        assert cfg["extension"] == ".md"
    def test_qwen_agent_config_is_markdown(self):
        """Qwen should use Markdown format with $ARGUMENTS (not TOML)."""
@@ -718,21 +632,6 @@ $ARGUMENTS
        assert frontmatter == {}
        assert body == content
    def test_parse_frontmatter_non_mapping_returns_empty_dict(self):
        """Non-mapping YAML frontmatter should not crash downstream renderers."""
        content = """---
 - item1
 - item2
 ---
 # Command body
 """
        registrar = CommandRegistrar()
        frontmatter, body = registrar.parse_frontmatter(content)
        assert frontmatter == {}
        assert "Command body" in body
    def test_render_frontmatter(self):
        """Test rendering frontmatter to YAML."""
        frontmatter = {
@@ -747,18 +646,6 @@ $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
@@ -836,299 +723,6 @@ $ARGUMENTS
        assert (claude_dir / "speckit.alias.cmd.md").exists()
        assert (claude_dir / "speckit.shortcut.md").exists()
    def test_unregister_commands_for_codex_skills_uses_mapped_names(self, project_dir):
        """Codex skill cleanup should use the same mapped names as registration."""
        skills_dir = project_dir / ".agents" / "skills"
        (skills_dir / "speckit-specify").mkdir(parents=True)
        (skills_dir / "speckit-specify" / "SKILL.md").write_text("body")
        (skills_dir / "speckit-shortcut").mkdir(parents=True)
        (skills_dir / "speckit-shortcut" / "SKILL.md").write_text("body")
        registrar = CommandRegistrar()
        registrar.unregister_commands(
            {"codex": ["speckit.specify", "speckit.shortcut"]},
            project_dir,
        )
        assert not (skills_dir / "speckit-specify" / "SKILL.md").exists()
        assert not (skills_dir / "speckit-shortcut" / "SKILL.md").exists()
    def test_register_commands_for_all_agents_distinguishes_codex_from_amp(self, extension_dir, project_dir):
        """A Codex project under .agents/skills should not implicitly activate Amp."""
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(extension_dir / "extension.yml")
        registrar = CommandRegistrar()
        registered = registrar.register_commands_for_all_agents(manifest, extension_dir, project_dir)
        assert "codex" in registered
        assert "amp" not in registered
        assert not (project_dir / ".agents" / "commands").exists()
    def test_codex_skill_registration_writes_skill_frontmatter(self, extension_dir, project_dir):
        """Codex SKILL.md output should use skills-oriented frontmatter."""
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(extension_dir / "extension.yml")
        registrar = CommandRegistrar()
        registrar.register_commands_for_agent("codex", manifest, extension_dir, project_dir)
        skill_file = skills_dir / "speckit-test.hello" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        assert "name: speckit-test.hello" in content
        assert "description: Test hello command" in content
        assert "compatibility:" in content
        assert "metadata:" in content
        assert "source: test-ext:commands/hello.md" in content
        assert "<!-- Extension:" not in content
    def test_codex_skill_registration_resolves_script_placeholders(self, project_dir, temp_dir):
        """Codex SKILL.md overrides should resolve script placeholders."""
        import yaml
        ext_dir = temp_dir / "ext-scripted"
        ext_dir.mkdir()
        (ext_dir / "commands").mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "ext-scripted",
                "name": "Scripted Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.test.plan",
                        "file": "commands/plan.md",
                        "description": "Scripted command",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        (ext_dir / "commands" / "plan.md").write_text(
            """---
 description: "Scripted command"
 scripts:
  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
  ps: ../../scripts/powershell/setup-plan.ps1 -Json
 agent_scripts:
  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 Run {SCRIPT}
 Then {AGENT_SCRIPT}
 Agent __AGENT__
 """
        )
        init_options = project_dir / ".specify" / "init-options.json"
        init_options.parent.mkdir(parents=True, exist_ok=True)
        init_options.write_text('{"ai":"codex","ai_skills":true,"script":"sh"}')
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(ext_dir / "extension.yml")
        registrar = CommandRegistrar()
        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
        skill_file = skills_dir / "speckit-test.plan" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        assert "{SCRIPT}" not in content
        assert "{AGENT_SCRIPT}" not in content
        assert "__AGENT__" not in content
        assert "{ARGS}" not in content
        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
    def test_codex_skill_alias_frontmatter_matches_alias_name(self, project_dir, temp_dir):
        """Codex alias skills should render their own matching `name:` frontmatter."""
        import yaml
        ext_dir = temp_dir / "ext-alias-skill"
        ext_dir.mkdir()
        (ext_dir / "commands").mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "ext-alias-skill",
                "name": "Alias Skill Extension",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.alias.cmd",
                        "file": "commands/cmd.md",
                        "aliases": ["speckit.shortcut"],
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Alias skill\n---\n\nBody\n")
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(ext_dir / "extension.yml")
        registrar = CommandRegistrar()
        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
        primary = skills_dir / "speckit-alias.cmd" / "SKILL.md"
        alias = skills_dir / "speckit-shortcut" / "SKILL.md"
        assert primary.exists()
        assert alias.exists()
        assert "name: speckit-alias.cmd" in primary.read_text()
        assert "name: speckit-shortcut" in alias.read_text()
    def test_codex_skill_registration_uses_fallback_script_variant_without_init_options(
        self, project_dir, temp_dir
    ):
        """Codex placeholder substitution should still work without init-options.json."""
        import yaml
        ext_dir = temp_dir / "ext-script-fallback"
        ext_dir.mkdir()
        (ext_dir / "commands").mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "ext-script-fallback",
                "name": "Script fallback",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.fallback.plan",
                        "file": "commands/plan.md",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        (ext_dir / "commands" / "plan.md").write_text(
            """---
 description: "Fallback scripted command"
 scripts:
  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
  ps: ../../scripts/powershell/setup-plan.ps1 -Json
 agent_scripts:
  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
 ---
 Run {SCRIPT}
 Then {AGENT_SCRIPT}
 """
        )
        # Intentionally do NOT create .specify/init-options.json
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(ext_dir / "extension.yml")
        registrar = CommandRegistrar()
        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
        skill_file = skills_dir / "speckit-fallback.plan" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        assert "{SCRIPT}" not in content
        assert "{AGENT_SCRIPT}" not in content
        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
    def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
        self, project_dir, temp_dir, monkeypatch
    ):
        """Without init metadata, Windows fallback should prefer ps scripts over sh."""
        import yaml
        monkeypatch.setattr("specify_cli.agents.platform.system", lambda: "Windows")
        ext_dir = temp_dir / "ext-script-windows-fallback"
        ext_dir.mkdir()
        (ext_dir / "commands").mkdir()
        manifest_data = {
            "schema_version": "1.0",
            "extension": {
                "id": "ext-script-windows-fallback",
                "name": "Script fallback windows",
                "version": "1.0.0",
                "description": "Test",
            },
            "requires": {"speckit_version": ">=0.1.0"},
            "provides": {
                "commands": [
                    {
                        "name": "speckit.windows.plan",
                        "file": "commands/plan.md",
                    }
                ]
            },
        }
        with open(ext_dir / "extension.yml", "w") as f:
            yaml.dump(manifest_data, f)
        (ext_dir / "commands" / "plan.md").write_text(
            """---
 description: "Windows fallback scripted command"
 scripts:
  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
  ps: ../../scripts/powershell/setup-plan.ps1 -Json
 agent_scripts:
  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 Run {SCRIPT}
 Then {AGENT_SCRIPT}
 """
        )
        skills_dir = project_dir / ".agents" / "skills"
        skills_dir.mkdir(parents=True)
        manifest = ExtensionManifest(ext_dir / "extension.yml")
        registrar = CommandRegistrar()
        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
        skill_file = skills_dir / "speckit-windows.plan" / "SKILL.md"
        assert skill_file.exists()
        content = skill_file.read_text()
        assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
        assert ".specify/scripts/powershell/update-agent-context.ps1 -AgentType codex" in content
        assert ".specify/scripts/bash/setup-plan.sh" not in content
    def test_register_commands_for_copilot(self, extension_dir, project_dir):
        """Test registering commands for Copilot agent with .agent.md extension."""
        # Create .github/agents directory (Copilot project)
@@ -2906,40 +2500,6 @@ class TestExtensionPriority:
        assert [item[0] for item in result] == ["ext-high", "ext-invalid"]
        assert result[1][1]["priority"] == 10
    def test_list_by_priority_excludes_disabled(self, temp_dir):
        """Test that list_by_priority excludes disabled extensions by default."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        registry.add("ext-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
        registry.add("ext-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
        registry.add("ext-default", {"version": "1.0.0", "priority": 10})  # no enabled field = True
        # Default: exclude disabled
        by_priority = registry.list_by_priority()
        ext_ids = [p[0] for p in by_priority]
        assert "ext-enabled" in ext_ids
        assert "ext-default" in ext_ids
        assert "ext-disabled" not in ext_ids
    def test_list_by_priority_includes_disabled_when_requested(self, temp_dir):
        """Test that list_by_priority includes disabled extensions when requested."""
        extensions_dir = temp_dir / "extensions"
        extensions_dir.mkdir()
        registry = ExtensionRegistry(extensions_dir)
        registry.add("ext-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
        registry.add("ext-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
        # Include disabled
        by_priority = registry.list_by_priority(include_disabled=True)
        ext_ids = [p[0] for p in by_priority]
        assert "ext-enabled" in ext_ids
        assert "ext-disabled" in ext_ids
        # Disabled ext has lower priority number, so it comes first when included
        assert ext_ids[0] == "ext-disabled"
    def test_install_with_priority(self, extension_dir, project_dir):
        """Test that install_from_directory stores priority."""
        manager = ExtensionManager(project_dir)
@@ -2981,8 +2541,8 @@ class TestExtensionPriority:
        assert updated["priority"] == 5  # Preserved
        assert updated["enabled"] is False  # Updated
-    def test_corrupted_extension_entry_not_picked_up_as_unregistered(self, project_dir):
+    def test_resolve_uses_unregistered_extension_dirs_when_registry_partially_corrupted(self, project_dir):
-        """Corrupted registry entries are still tracked and NOT picked up as unregistered."""
+        """Resolution scans unregistered extension dirs after valid registry entries."""
        extensions_dir = project_dir / ".specify" / "extensions"
        valid_dir = extensions_dir / "valid-ext" / "templates"
@@ -2995,21 +2555,20 @@ class TestExtensionPriority:
        registry = ExtensionRegistry(extensions_dir)
        registry.add("valid-ext", {"version": "1.0.0", "priority": 10})
        # Corrupt the entry - should still be tracked, not picked up as unregistered
        registry.data["extensions"]["broken-ext"] = "corrupted"
        registry._save()
        from specify_cli.presets import PresetResolver
        resolver = PresetResolver(project_dir)
        # Corrupted extension templates should NOT be resolved
        resolved = resolver.resolve("target-template")
-        assert resolved is None
+        sourced = resolver.resolve_with_source("target-template")
-        # Valid extension template should still resolve
+        assert resolved is not None
-        valid_resolved = resolver.resolve("other-template")
+        assert resolved.name == "target-template.md"
-        assert valid_resolved is not None
+        assert "Broken Target" in resolved.read_text()
-        assert "Valid" in valid_resolved.read_text()
+        assert sourced is not None
        assert sourced["source"] == "extension:broken-ext (unregistered)"
 class TestExtensionPriorityCLI:
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -369,172 +369,6 @@ class TestPresetRegistry:
        registry = PresetRegistry(packs_dir)
        assert registry.get("nonexistent") is None
    def test_restore(self, temp_dir):
        """Test restore() preserves timestamps exactly."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        # Create original entry with a specific timestamp
        original_metadata = {
            "version": "1.0.0",
            "source": "local",
            "installed_at": "2025-01-15T10:30:00+00:00",
            "enabled": True,
        }
        registry.restore("test-pack", original_metadata)
        # Verify exact restoration
        restored = registry.get("test-pack")
        assert restored["installed_at"] == "2025-01-15T10:30:00+00:00"
        assert restored["version"] == "1.0.0"
        assert restored["enabled"] is True
    def test_restore_rejects_none_metadata(self, temp_dir):
        """Test restore() raises ValueError for None metadata."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-pack", None)
    def test_restore_rejects_non_dict_metadata(self, temp_dir):
        """Test restore() raises ValueError for non-dict metadata."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-pack", "not-a-dict")
        with pytest.raises(ValueError, match="metadata must be a dict"):
            registry.restore("test-pack", ["list", "not", "dict"])
    def test_restore_uses_deep_copy(self, temp_dir):
        """Test restore() deep copies metadata to prevent mutation."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        original_metadata = {
            "version": "1.0.0",
            "nested": {"key": "original"},
        }
        registry.restore("test-pack", original_metadata)
        # Mutate the original metadata after restore
        original_metadata["version"] = "MUTATED"
        original_metadata["nested"]["key"] = "MUTATED"
        # Registry should have the original values
        stored = registry.get("test-pack")
        assert stored["version"] == "1.0.0"
        assert stored["nested"]["key"] == "original"
    def test_get_returns_deep_copy(self, temp_dir):
        """Test that get() returns a deep copy to prevent mutation."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        registry.add("test-pack", {"version": "1.0.0", "nested": {"key": "original"}})
        # Get and mutate the returned copy
        metadata = registry.get("test-pack")
        metadata["version"] = "MUTATED"
        metadata["nested"]["key"] = "MUTATED"
        # Original should be unchanged
        fresh = registry.get("test-pack")
        assert fresh["version"] == "1.0.0"
        assert fresh["nested"]["key"] == "original"
    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
        """Test that get() returns None for corrupted (non-dict) entries."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        # Directly corrupt the registry with non-dict entries
        registry.data["presets"]["corrupted-string"] = "not a dict"
        registry.data["presets"]["corrupted-list"] = ["not", "a", "dict"]
        registry.data["presets"]["corrupted-int"] = 42
        registry._save()
        # All corrupted entries should return None
        assert registry.get("corrupted-string") is None
        assert registry.get("corrupted-list") is None
        assert registry.get("corrupted-int") is None
        # Non-existent should also return None
        assert registry.get("nonexistent") is None
    def test_list_returns_deep_copy(self, temp_dir):
        """Test that list() returns deep copies to prevent mutation."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        registry.add("test-pack", {"version": "1.0.0", "nested": {"key": "original"}})
        # Get list and mutate
        all_packs = registry.list()
        all_packs["test-pack"]["version"] = "MUTATED"
        all_packs["test-pack"]["nested"]["key"] = "MUTATED"
        # Original should be unchanged
        fresh = registry.get("test-pack")
        assert fresh["version"] == "1.0.0"
        assert fresh["nested"]["key"] == "original"
    def test_list_returns_empty_dict_for_corrupted_registry(self, temp_dir):
        """Test that list() returns empty dict when presets is not a dict."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        # Corrupt the registry - presets is a list instead of dict
        registry.data["presets"] = ["not", "a", "dict"]
        registry._save()
        # list() should return empty dict, not crash
        result = registry.list()
        assert result == {}
    def test_list_by_priority_excludes_disabled(self, temp_dir):
        """Test that list_by_priority excludes disabled presets by default."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        registry.add("pack-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
        registry.add("pack-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
        registry.add("pack-default", {"version": "1.0.0", "priority": 10})  # no enabled field = True
        # Default: exclude disabled
        by_priority = registry.list_by_priority()
        pack_ids = [p[0] for p in by_priority]
        assert "pack-enabled" in pack_ids
        assert "pack-default" in pack_ids
        assert "pack-disabled" not in pack_ids
    def test_list_by_priority_includes_disabled_when_requested(self, temp_dir):
        """Test that list_by_priority includes disabled presets when requested."""
        packs_dir = temp_dir / "packs"
        packs_dir.mkdir()
        registry = PresetRegistry(packs_dir)
        registry.add("pack-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
        registry.add("pack-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
        # Include disabled
        by_priority = registry.list_by_priority(include_disabled=True)
        pack_ids = [p[0] for p in by_priority]
        assert "pack-enabled" in pack_ids
        assert "pack-disabled" in pack_ids
        # Disabled pack has lower priority number, so it comes first when included
        assert pack_ids[0] == "pack-disabled"
 # ===== PresetManager Tests =====
@@ -873,44 +707,6 @@ class TestPresetResolver:
        assert result is not None
        assert "Extension Custom Template" in result.read_text()
    def test_resolve_disabled_extension_templates_skipped(self, project_dir):
        """Test that disabled extension templates are not resolved."""
        # Create extension with templates
        ext_dir = project_dir / ".specify" / "extensions" / "disabled-ext"
        ext_templates_dir = ext_dir / "templates"
        ext_templates_dir.mkdir(parents=True)
        ext_template = ext_templates_dir / "disabled-template.md"
        ext_template.write_text("# Disabled Extension Template\n")
        # Register extension as disabled
        extensions_dir = project_dir / ".specify" / "extensions"
        ext_registry = ExtensionRegistry(extensions_dir)
        ext_registry.add("disabled-ext", {"version": "1.0.0", "priority": 1, "enabled": False})
        # Template should NOT be resolved because extension is disabled
        resolver = PresetResolver(project_dir)
        result = resolver.resolve("disabled-template")
        assert result is None, "Disabled extension template should not be resolved"
    def test_resolve_disabled_extension_not_picked_up_as_unregistered(self, project_dir):
        """Test that disabled extensions are not picked up via unregistered dir scan."""
        # Create extension directory with templates
        ext_dir = project_dir / ".specify" / "extensions" / "test-disabled-ext"
        ext_templates_dir = ext_dir / "templates"
        ext_templates_dir.mkdir(parents=True)
        ext_template = ext_templates_dir / "unique-disabled-template.md"
        ext_template.write_text("# Should Not Resolve\n")
        # Register the extension but disable it
        extensions_dir = project_dir / ".specify" / "extensions"
        ext_registry = ExtensionRegistry(extensions_dir)
        ext_registry.add("test-disabled-ext", {"version": "1.0.0", "enabled": False})
        # Verify the template is NOT resolved (even though the directory exists)
        resolver = PresetResolver(project_dir)
        result = resolver.resolve("unique-disabled-template")
        assert result is None, "Disabled extension should not be picked up as unregistered"
    def test_resolve_pack_over_extension(self, project_dir, pack_dir, temp_dir, valid_pack_data):
        """Test that pack templates take priority over extension templates."""
        # Create extension with templates
@@ -2205,189 +2001,3 @@ class TestPresetPriorityBackwardsCompatibility:
            "legacy-pack",
            "low-priority-pack",
        ]
 class TestPresetEnableDisable:
    """Test preset enable/disable CLI commands."""
    def test_disable_preset(self, project_dir, pack_dir):
        """Test disable command sets enabled=False."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        # Verify initially enabled
        assert manager.registry.get("test-pack").get("enabled", True) is True
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "disable", "test-pack"])
        assert result.exit_code == 0, result.output
        assert "disabled" in result.output.lower()
        # Reload registry to see updated value
        manager2 = PresetManager(project_dir)
        assert manager2.registry.get("test-pack")["enabled"] is False
    def test_enable_preset(self, project_dir, pack_dir):
        """Test enable command sets enabled=True."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset and disable it
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        manager.registry.update("test-pack", {"enabled": False})
        # Verify disabled
        assert manager.registry.get("test-pack")["enabled"] is False
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "enable", "test-pack"])
        assert result.exit_code == 0, result.output
        assert "enabled" in result.output.lower()
        # Reload registry to see updated value
        manager2 = PresetManager(project_dir)
        assert manager2.registry.get("test-pack")["enabled"] is True
    def test_disable_already_disabled(self, project_dir, pack_dir):
        """Test disable on already disabled preset shows warning."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset and disable it
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        manager.registry.update("test-pack", {"enabled": False})
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "disable", "test-pack"])
        assert result.exit_code == 0, result.output
        assert "already disabled" in result.output.lower()
    def test_enable_already_enabled(self, project_dir, pack_dir):
        """Test enable on already enabled preset shows warning."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset (enabled by default)
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "enable", "test-pack"])
        assert result.exit_code == 0, result.output
        assert "already enabled" in result.output.lower()
    def test_disable_not_installed(self, project_dir):
        """Test disable fails for non-installed preset."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "disable", "nonexistent"])
        assert result.exit_code == 1, result.output
        assert "not installed" in result.output.lower()
    def test_enable_not_installed(self, project_dir):
        """Test enable fails for non-installed preset."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "enable", "nonexistent"])
        assert result.exit_code == 1, result.output
        assert "not installed" in result.output.lower()
    def test_disabled_preset_excluded_from_resolution(self, project_dir, pack_dir):
        """Test that disabled presets are excluded from template resolution."""
        # Install preset with a template
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        # Create a template in the preset directory
        preset_template = project_dir / ".specify" / "presets" / "test-pack" / "templates" / "test-template.md"
        preset_template.parent.mkdir(parents=True, exist_ok=True)
        preset_template.write_text("# Template from test-pack")
        resolver = PresetResolver(project_dir)
        # Template should be found when enabled
        result = resolver.resolve("test-template", "template")
        assert result is not None
        assert "test-pack" in str(result)
        # Disable the preset
        manager.registry.update("test-pack", {"enabled": False})
        # Template should NOT be found when disabled
        resolver2 = PresetResolver(project_dir)
        result2 = resolver2.resolve("test-template", "template")
        assert result2 is None
    def test_enable_corrupted_registry_entry(self, project_dir, pack_dir):
        """Test enable fails gracefully for corrupted registry entry."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset then corrupt the registry entry
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        manager.registry.data["presets"]["test-pack"] = "corrupted-string"
        manager.registry._save()
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "enable", "test-pack"])
        assert result.exit_code == 1
        assert "corrupted state" in result.output.lower()
    def test_disable_corrupted_registry_entry(self, project_dir, pack_dir):
        """Test disable fails gracefully for corrupted registry entry."""
        from typer.testing import CliRunner
        from unittest.mock import patch
        from specify_cli import app
        runner = CliRunner()
        # Install preset then corrupt the registry entry
        manager = PresetManager(project_dir)
        manager.install_from_directory(pack_dir, "0.1.5")
        manager.registry.data["presets"]["test-pack"] = "corrupted-string"
        manager.registry._save()
        with patch.object(Path, "cwd", return_value=project_dir):
            result = runner.invoke(app, ["preset", "disable", "test-pack"])
        assert result.exit_code == 1
        assert "corrupted state" in result.output.lower()
--- a/tests/test_timestamp_branches.py
+++ b/tests/test_timestamp_branches.py
@@ -1,252 +0,0 @@
 """
 Pytest tests for timestamp-based branch naming in create-new-feature.sh and common.sh.
 Converted from tests/test_timestamp_branches.sh so they are discovered by `uv run pytest`.
 """
 import os
 import re
 import shutil
 import subprocess
 from pathlib import Path
 import pytest
 PROJECT_ROOT = Path(__file__).resolve().parent.parent
 CREATE_FEATURE = PROJECT_ROOT / "scripts" / "bash" / "create-new-feature.sh"
 COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
@pytest.fixture
 def git_repo(tmp_path: Path) -> Path:
    """Create a temp git repo with scripts and .specify dir."""
    subprocess.run(["git", "init", "-q"], cwd=tmp_path, check=True)
    subprocess.run(
        ["git", "config", "user.email", "test@example.com"], cwd=tmp_path, check=True
    )
    subprocess.run(
        ["git", "config", "user.name", "Test User"], cwd=tmp_path, check=True
    )
    subprocess.run(
        ["git", "commit", "--allow-empty", "-m", "init", "-q"],
        cwd=tmp_path,
        check=True,
    )
    scripts_dir = tmp_path / "scripts" / "bash"
    scripts_dir.mkdir(parents=True)
    shutil.copy(CREATE_FEATURE, scripts_dir / "create-new-feature.sh")
    shutil.copy(COMMON_SH, scripts_dir / "common.sh")
    (tmp_path / ".specify" / "templates").mkdir(parents=True)
    return tmp_path
@pytest.fixture
 def no_git_dir(tmp_path: Path) -> Path:
    """Create a temp directory without git, but with scripts."""
    scripts_dir = tmp_path / "scripts" / "bash"
    scripts_dir.mkdir(parents=True)
    shutil.copy(CREATE_FEATURE, scripts_dir / "create-new-feature.sh")
    shutil.copy(COMMON_SH, scripts_dir / "common.sh")
    (tmp_path / ".specify" / "templates").mkdir(parents=True)
    return tmp_path
 def run_script(cwd: Path, *args: str) -> subprocess.CompletedProcess:
    """Run create-new-feature.sh with given args."""
    cmd = ["bash", "scripts/bash/create-new-feature.sh", *args]
    return subprocess.run(
        cmd,
        cwd=cwd,
        capture_output=True,
        text=True,
    )
 def source_and_call(func_call: str, env: dict | None = None) -> subprocess.CompletedProcess:
    """Source common.sh and call a function."""
    cmd = f'source "{COMMON_SH}" && {func_call}'
    return subprocess.run(
        ["bash", "-c", cmd],
        capture_output=True,
        text=True,
        env={**os.environ, **(env or {})},
    )
 # ── Timestamp Branch Tests ───────────────────────────────────────────────────
 class TestTimestampBranch:
    def test_timestamp_creates_branch(self, git_repo: Path):
        """Test 1: --timestamp creates branch with YYYYMMDD-HHMMSS prefix."""
        result = run_script(git_repo, "--timestamp", "--short-name", "user-auth", "Add user auth")
        assert result.returncode == 0, result.stderr
        branch = None
        for line in result.stdout.splitlines():
            if line.startswith("BRANCH_NAME:"):
                branch = line.split(":", 1)[1].strip()
        assert branch is not None
        assert re.match(r"^\d{8}-\d{6}-user-auth$", branch), f"unexpected branch: {branch}"
    def test_number_and_timestamp_warns(self, git_repo: Path):
        """Test 3: --number + --timestamp warns and uses timestamp."""
        result = run_script(git_repo, "--timestamp", "--number", "42", "--short-name", "feat", "Feature")
        assert result.returncode == 0, result.stderr
        assert "Warning" in result.stderr and "--number" in result.stderr
    def test_json_output_keys(self, git_repo: Path):
        """Test 4: JSON output contains expected keys."""
        import json
        result = run_script(git_repo, "--json", "--timestamp", "--short-name", "api", "API feature")
        assert result.returncode == 0, result.stderr
        data = json.loads(result.stdout)
        for key in ("BRANCH_NAME", "SPEC_FILE", "FEATURE_NUM"):
            assert key in data, f"missing {key} in JSON: {data}"
        assert re.match(r"^\d{8}-\d{6}$", data["FEATURE_NUM"])
    def test_long_name_truncation(self, git_repo: Path):
        """Test 5: Long branch name is truncated to <= 244 chars."""
        long_name = "a-" * 150 + "end"
        result = run_script(git_repo, "--timestamp", "--short-name", long_name, "Long feature")
        assert result.returncode == 0, result.stderr
        branch = None
        for line in result.stdout.splitlines():
            if line.startswith("BRANCH_NAME:"):
                branch = line.split(":", 1)[1].strip()
        assert branch is not None
        assert len(branch) <= 244
        assert re.match(r"^\d{8}-\d{6}-", branch)
 # ── Sequential Branch Tests ──────────────────────────────────────────────────
 class TestSequentialBranch:
    def test_sequential_default_with_existing_specs(self, git_repo: Path):
        """Test 2: Sequential default with existing specs."""
        (git_repo / "specs" / "001-first-feat").mkdir(parents=True)
        (git_repo / "specs" / "002-second-feat").mkdir(parents=True)
        result = run_script(git_repo, "--short-name", "new-feat", "New feature")
        assert result.returncode == 0, result.stderr
        branch = None
        for line in result.stdout.splitlines():
            if line.startswith("BRANCH_NAME:"):
                branch = line.split(":", 1)[1].strip()
        assert branch is not None
        assert re.match(r"^\d{3}-new-feat$", branch), f"unexpected branch: {branch}"
    def test_sequential_ignores_timestamp_dirs(self, git_repo: Path):
        """Sequential numbering skips timestamp dirs when computing next number."""
        (git_repo / "specs" / "002-first-feat").mkdir(parents=True)
        (git_repo / "specs" / "20260319-143022-ts-feat").mkdir(parents=True)
        result = run_script(git_repo, "--short-name", "next-feat", "Next feature")
        assert result.returncode == 0, result.stderr
        branch = None
        for line in result.stdout.splitlines():
            if line.startswith("BRANCH_NAME:"):
                branch = line.split(":", 1)[1].strip()
        assert branch == "003-next-feat", f"expected 003-next-feat, got: {branch}"
 # ── check_feature_branch Tests ───────────────────────────────────────────────
 class TestCheckFeatureBranch:
    def test_accepts_timestamp_branch(self):
        """Test 6: check_feature_branch accepts timestamp branch."""
        result = source_and_call('check_feature_branch "20260319-143022-feat" "true"')
        assert result.returncode == 0
    def test_accepts_sequential_branch(self):
        """Test 7: check_feature_branch accepts sequential branch."""
        result = source_and_call('check_feature_branch "004-feat" "true"')
        assert result.returncode == 0
    def test_rejects_main(self):
        """Test 8: check_feature_branch rejects main."""
        result = source_and_call('check_feature_branch "main" "true"')
        assert result.returncode != 0
    def test_rejects_partial_timestamp(self):
        """Test 9: check_feature_branch rejects 7-digit date."""
        result = source_and_call('check_feature_branch "2026031-143022-feat" "true"')
        assert result.returncode != 0
 # ── find_feature_dir_by_prefix Tests ─────────────────────────────────────────
 class TestFindFeatureDirByPrefix:
    def test_timestamp_branch(self, tmp_path: Path):
        """Test 10: find_feature_dir_by_prefix with timestamp branch."""
        (tmp_path / "specs" / "20260319-143022-user-auth").mkdir(parents=True)
        result = source_and_call(
            f'find_feature_dir_by_prefix "{tmp_path}" "20260319-143022-user-auth"'
        )
        assert result.returncode == 0
        assert result.stdout.strip() == f"{tmp_path}/specs/20260319-143022-user-auth"
    def test_cross_branch_prefix(self, tmp_path: Path):
        """Test 11: find_feature_dir_by_prefix cross-branch (different suffix, same timestamp)."""
        (tmp_path / "specs" / "20260319-143022-original-feat").mkdir(parents=True)
        result = source_and_call(
            f'find_feature_dir_by_prefix "{tmp_path}" "20260319-143022-different-name"'
        )
        assert result.returncode == 0
        assert result.stdout.strip() == f"{tmp_path}/specs/20260319-143022-original-feat"
 # ── get_current_branch Tests ─────────────────────────────────────────────────
 class TestGetCurrentBranch:
    def test_env_var(self):
        """Test 12: get_current_branch returns SPECIFY_FEATURE env var."""
        result = source_and_call("get_current_branch", env={"SPECIFY_FEATURE": "my-custom-branch"})
        assert result.stdout.strip() == "my-custom-branch"
 # ── No-git Tests ─────────────────────────────────────────────────────────────
 class TestNoGitTimestamp:
    def test_no_git_timestamp(self, no_git_dir: Path):
        """Test 13: No-git repo + timestamp creates spec dir with warning."""
        result = run_script(no_git_dir, "--timestamp", "--short-name", "no-git-feat", "No git feature")
        assert result.returncode == 0, result.stderr
        spec_dirs = list((no_git_dir / "specs").iterdir()) if (no_git_dir / "specs").exists() else []
        assert len(spec_dirs) > 0, "spec dir not created"
        assert "git" in result.stderr.lower() or "warning" in result.stderr.lower()
 # ── E2E Flow Tests ───────────────────────────────────────────────────────────
 class TestE2EFlow:
    def test_e2e_timestamp(self, git_repo: Path):
        """Test 14: E2E timestamp flow — branch, dir, validation."""
        run_script(git_repo, "--timestamp", "--short-name", "e2e-ts", "E2E timestamp test")
        branch = subprocess.run(
            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
            cwd=git_repo,
            capture_output=True,
            text=True,
        ).stdout.strip()
        assert re.match(r"^\d{8}-\d{6}-e2e-ts$", branch), f"branch: {branch}"
        assert (git_repo / "specs" / branch).is_dir()
        val = source_and_call(f'check_feature_branch "{branch}" "true"')
        assert val.returncode == 0
    def test_e2e_sequential(self, git_repo: Path):
        """Test 15: E2E sequential flow (regression guard)."""
        run_script(git_repo, "--short-name", "seq-feat", "Sequential feature")
        branch = subprocess.run(
            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
            cwd=git_repo,
            capture_output=True,
            text=True,
        ).stdout.strip()
        assert re.match(r"^\d{3}-seq-feat$", branch), f"branch: {branch}"
        assert (git_repo / "specs" / branch).is_dir()
        val = source_and_call(f'check_feature_branch "{branch}" "true"')
        assert val.returncode == 0