refactor: simplify finalize_setup scan to agent_root only, improve comments

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/054690bb-c048-41e0-b553-377d5cb36b78

.devcontainer/post-create.sh

@@ -51,6 +51,14 @@ 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"

.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, IBM Bob, Antigravity
+        **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
 
   - type: input
     id: agent-name

.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/manfredseee/spec-kit/blob/main/extensions/EXTENSION-DEVELOPMENT-GUIDE.md
+    url: https://github.com/github/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

.github/ISSUE_TEMPLATE/preset_submission.yml

@@ -0,0 +1,169 @@
+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

.github/workflows/release-trigger.yml

@@ -86,8 +86,10 @@ jobs:
           if [ -f "CHANGELOG.md" ]; then
             DATE=$(date +%Y-%m-%d)
 
-            # Get the previous tag to compare commits
-            PREVIOUS_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "")
+            # Get the previous tag by sorting all version tags numerically
+            # (git describe --tags only finds tags reachable from HEAD,
+            #  which misses tags on unmerged release branches)
+            PREVIOUS_TAG=$(git tag -l 'v*' --sort=-version:refname | head -n 1)
 
             echo "Generating changelog from commits..."
             if [[ -n "$PREVIOUS_TAG" ]]; then
@@ -104,7 +106,7 @@ jobs:
               echo ""
               echo "## [${{ steps.version.outputs.version }}] - $DATE"
               echo ""
-              echo "### Changed"
+              echo "### Changes"
               echo ""
               echo "$COMMITS"
               echo ""

.github/workflows/scripts/create-github-release.sh

@@ -30,6 +30,8 @@ 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-"$VERSION".zip \
@@ -58,6 +60,12 @@ gh release create "$VERSION" \
   .genreleases/spec-kit-template-vibe-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-kimi-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-kimi-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-trae-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-trae-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-pi-sh-"$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" \

.github/workflows/scripts/create-release-packages.ps1

@@ -14,7 +14,7 @@
 
 .PARAMETER Agents
     Comma or space separated subset of agents to build (default: all)
-    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, generic
+    Valid agents: claude, gemini, copilot, cursor-agent, qwen, opencode, windsurf, junie, codex, kilocode, auggie, roo, codebuddy, amp, kiro-cli, bob, qodercli, shai, tabnine, agy, vibe, kimi, trae, pi, iflow, generic
 
 .PARAMETER Scripts
     Comma or space separated subset of script types to build (default: both)
@@ -201,20 +201,26 @@ agent: $basename
     }
 }
 
-# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-function New-KimiSkills {
+# Create skills in <skills_dir>\<name>\SKILL.md format.
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
+#
+# 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)
-        $skillName = "speckit.$name"
+        $skillName = "speckit${Separator}$name"
         $skillDir = Join-Path $SkillsDir $skillName
         New-Item -ItemType Directory -Force -Path $skillDir | Out-Null
 
@@ -267,7 +273,7 @@ function New-KimiSkills {
 
         $body = $outputLines -join "`n"
         $body = $body -replace '\{ARGS\}', '$ARGUMENTS'
-        $body = $body -replace '__AGENT__', 'kimi'
+        $body = $body -replace '__AGENT__', $AgentName
         $body = Rewrite-Paths -Content $body
 
         # Strip existing frontmatter, keep only body
@@ -283,7 +289,7 @@ function New-KimiSkills {
             if ($inBody) { $templateBody += "$line`n" }
         }
 
-        $skillContent = "---`nname: `"$skillName`"`ndescription: `"$description`"`n---`n`n$templateBody"
+        $skillContent = "---`nname: `"$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"
         Set-Content -Path (Join-Path $skillDir "SKILL.md") -Value $skillContent -NoNewline
     }
 }
@@ -395,9 +401,14 @@ 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' {
-            $cmdDir = Join-Path $baseDir ".codex/prompts"
-            Generate-Commands -Agent 'codex' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+            $skillsDir = Join-Path $baseDir ".agents/skills"
+            New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'codex' -Separator '-'
         }
         'kilocode' {
             $cmdDir = Join-Path $baseDir ".kilocode/workflows"
@@ -452,7 +463,20 @@ function Build-Variant {
         'kimi' {
             $skillsDir = Join-Path $baseDir ".kimi/skills"
             New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
-            New-KimiSkills -SkillsDir $skillsDir -ScriptVariant $Script
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi' -Separator '.'
+        }
+        '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"
@@ -470,7 +494,7 @@ function Build-Variant {
 }
 
 # Define all agents and scripts
-$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'generic')
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'junie', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'kiro-cli', 'bob', 'qodercli', 'shai', 'tabnine', 'agy', 'vibe', 'kimi', 'trae', 'pi', 'iflow', 'generic')
 $AllScripts = @('sh', 'ps')
 
 function Normalize-List {

.github/workflows/scripts/create-release-packages.sh

@@ -6,7 +6,7 @@ set -euo pipefail
 # Usage: .github/workflows/scripts/create-release-packages.sh <version>
 #   Version argument should include leading 'v'.
 #   Optionally set AGENTS and/or SCRIPTS env vars to limit what gets built.
-#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi generic (default: all)
+#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf junie codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae pi iflow generic (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -26,9 +26,27 @@ fi
 echo "Building release packages for $NEW_VERSION"
 
 # Create and use .genreleases directory for all build artifacts
-GENRELEASES_DIR=".genreleases"
+# Override via GENRELEASES_DIR env var (e.g. for tests writing to a temp dir)
+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 \
@@ -121,18 +139,24 @@ EOF
   done
 }
 
-# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-create_kimi_skills() {
+# Create skills in <skills_dir>/<name>/SKILL.md format.
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
+#
+# 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 "$template" .md)
-    local skill_name="speckit.${name}"
+    local skill_name="speckit${separator}${name}"
     local skill_dir="${skills_dir}/${skill_name}"
     mkdir -p "$skill_dir"
 
@@ -175,9 +199,9 @@ create_kimi_skills() {
       in_frontmatter && skip_scripts && /^[[:space:]]/ { next }
       { print }
     ')
-    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed 's/__AGENT__/kimi/g' | rewrite_paths)
+    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed "s/__AGENT__/$agent_name/g" | rewrite_paths)
 
-    # Strip existing frontmatter and prepend Kimi frontmatter
+    # Strip existing frontmatter and prepend skills frontmatter.
     local template_body
     template_body=$(printf '%s\n' "$body" | awk '/^---/{p++; if(p==2){found=1; next}} found')
 
@@ -185,6 +209,10 @@ create_kimi_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"
@@ -218,7 +246,7 @@ build_variant() {
     esac
   fi
 
-  [[ -d templates ]] && { mkdir -p "$SPEC_DIR/templates"; find templates -type f -not -path "templates/commands/*" -not -name "vscode-settings.json" -exec cp --parents {} "$SPEC_DIR"/ \; ; echo "Copied templates -> .specify/templates"; }
+  [[ -d templates ]] && { mkdir -p "$SPEC_DIR/templates"; find templates -type f -not -path "templates/commands/*" -not -name "vscode-settings.json" | while IFS= read -r f; do d="$SPEC_DIR/$(dirname "$f")"; mkdir -p "$d"; cp "$f" "$d/"; done; echo "Copied templates -> .specify/templates"; }
 
   case $agent in
     claude)
@@ -248,9 +276,12 @@ build_variant() {
     windsurf)
       mkdir -p "$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/.codex/prompts"
-      generate_commands codex md "\$ARGUMENTS" "$base_dir/.codex/prompts" "$script" ;;
+      mkdir -p "$base_dir/.agents/skills"
+      create_skills "$base_dir/.agents/skills" "$script" "codex" "-" ;;
     kilocode)
       mkdir -p "$base_dir/.kilocode/workflows"
       generate_commands kilocode md "\$ARGUMENTS" "$base_dir/.kilocode/workflows" "$script" ;;
@@ -290,7 +321,16 @@ build_variant() {
       generate_commands vibe md "\$ARGUMENTS" "$base_dir/.vibe/prompts" "$script" ;;
     kimi)
       mkdir -p "$base_dir/.kimi/skills"
-      create_kimi_skills "$base_dir/.kimi/skills" "$script" ;;
+      create_skills "$base_dir/.kimi/skills" "$script" "kimi" "." ;;
+    trae)
+      mkdir -p "$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" ;;
@@ -300,37 +340,38 @@ build_variant() {
 }
 
 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi generic)
+ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf junie codex kilocode auggie roo codebuddy amp shai tabnine kiro-cli agy bob vibe qodercli kimi trae pi iflow 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 -n allowed=$1; shift; local items=("$@")
+  local type=$1; shift
+  local allowed_str="$1"; shift
   local invalid=0
-  for it in "${items[@]}"; do
+  for it in "$@"; do
     local found=0
-    for a in "${allowed[@]}"; do [[ $it == "$a" ]] && { found=1; break; }; done
+    for a in $allowed_str; do
+      if [[ "$it" == "$a" ]]; then found=1; break; fi
+    done
     if [[ $found -eq 0 ]]; then
-      echo "Error: unknown $type '$it' (allowed: ${allowed[*]})" >&2
+      echo "Error: unknown $type '$it' (allowed: $allowed_str)" >&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 ${AGENTS:-} ]]; then
-  mapfile -t AGENT_LIST < <(printf '%s' "$AGENTS" | norm_list)
-  validate_subset agent ALL_AGENTS "${AGENT_LIST[@]}" || exit 1
+  read -ra AGENT_LIST <<< "$(printf '%s' "$AGENTS" | read_list)"
+  validate_subset agent "${ALL_AGENTS[*]}" "${AGENT_LIST[@]}" || exit 1
 else
   AGENT_LIST=("${ALL_AGENTS[@]}")
 fi
 
 if [[ -n ${SCRIPTS:-} ]]; then
-  mapfile -t SCRIPT_LIST < <(printf '%s' "$SCRIPTS" | norm_list)
-  validate_subset script ALL_SCRIPTS "${SCRIPT_LIST[@]}" || exit 1
+  read -ra SCRIPT_LIST <<< "$(printf '%s' "$SCRIPTS" | read_list)"
+  validate_subset script "${ALL_SCRIPTS[*]}" "${SCRIPT_LIST[@]}" || exit 1
 else
   SCRIPT_LIST=("${ALL_SCRIPTS[@]}")
 fi

.github/workflows/stale.yml

@@ -39,4 +39,4 @@ jobs:
           any-of-labels: ''
           
           # Operations per run (helps avoid rate limits)
-          operations-per-run: 100
+          operations-per-run: 250

AGENTS.md

@@ -10,10 +10,6 @@ The toolkit supports multiple AI coding assistants, allowing teams to use their
 
 ---
 
-## General practices
-
-- Any changes to `__init__.py` for the Specify CLI require a version rev in `pyproject.toml` and addition of entries to `CHANGELOG.md`.
-
 ## Adding New Agent Support
 
 This section explains how to add support for new AI agents/assistants to the Specify CLI. Use this guide as a reference when integrating new AI tools into the Spec-Driven Development workflow.
@@ -37,11 +33,12 @@ 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**              | `.codex/commands/`     | Markdown | `codex`         | Codex CLI                   |
+| **Codex CLI**              | `.agents/skills/`      | Markdown | `codex`         | Codex CLI (skills)          |
 | **Windsurf**               | `.windsurf/workflows/` | Markdown | N/A (IDE-based) | Windsurf IDE workflows      |
-| **Kilo Code**              | `.kilocode/rules/`     | Markdown | N/A (IDE-based) | Kilo Code IDE               |
-| **Auggie CLI**             | `.augment/rules/`      | Markdown | `auggie`        | Auggie CLI                  |
-| **Roo Code**               | `.roo/rules/`          | Markdown | N/A (IDE-based) | Roo Code IDE                |
+| **Junie**                  | `.junie/commands/`     | Markdown | `junie`         | Junie by JetBrains          |
+| **Kilo Code**              | `.kilocode/workflows/` | Markdown | N/A (IDE-based) | Kilo Code IDE               |
+| **Auggie CLI**             | `.augment/commands/`   | Markdown | `auggie`        | Auggie CLI                  |
+| **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                    |
@@ -49,7 +46,10 @@ 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        |
 
 ### Step-by-Step Integration Guide
@@ -88,7 +88,7 @@ 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), `"command"` (opencode - singular)
+  - Some agents use alternative names: `"agents"` (copilot), `"workflows"` (windsurf, kilocode), `"prompts"` (codex, kiro-cli, pi), `"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
@@ -319,6 +319,7 @@ 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
@@ -326,6 +327,7 @@ 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
 
@@ -339,7 +341,7 @@ Work within integrated development environments:
 
 ### Markdown Format
 
-Used by: Claude, Cursor, opencode, Windsurf, Kiro CLI, Amp, SHAI, IBM Bob, Kimi Code, Qwen
+Used by: Claude, Cursor, opencode, Windsurf, Junie, Kiro CLI, Amp, SHAI, IBM Bob, Kimi Code, Qwen, Pi
 
 **Standard format:**
 
@@ -377,6 +379,11 @@ 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/`

CHANGELOG.md

@@ -1,11 +1,61 @@
 # Changelog
 
-<!-- markdownlint-disable MD024 -->
+## [0.3.2] - 2026-03-19
 
-Recent changes to the Specify CLI and templates are documented here.
+### Changes
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+- chore: bump version to 0.3.2
+- Add conduct extension to community catalog (#1908)
+- 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)
+- feat(cli): polite deep merge for settings.json and support JSONC (#1874)
+- feat(extensions,presets): add priority-based resolution ordering (#1855)
+- fix(scripts): suppress stdout from git fetch in create-new-feature.sh (#1876)
+- fix(scripts): harden bash scripts — escape, compat, and error handling (#1869)
+- Add cognitive-squad to community extension catalog (#1870)
+- docs: add Go / React brownfield walkthrough to community walkthroughs (#1868)
+- chore: update DocGuard extension to v0.9.8 (#1859)
+- Feature: add specify status command (#1837)
+- fix(extensions): show extension ID in list output (#1843)
+- feat(extensions): add Archive and Reconcile extensions to community catalog (#1844)
+- feat: Add DocGuard CDD enforcement extension to community catalog (#1838)
+
+## [0.3.0] - 2026-03-13
+
+### Changed
+
+- chore: bump version to 0.3.0
+- feat(presets): Pluggable preset system with catalog, resolver, and skills propagation (#1787)
+- fix: match 'Last updated' timestamp with or without bold markers (#1836)
+- Add specify doctor command for project health diagnostics (#1828)
+- fix: harden bash scripts against shell injection and improve robustness (#1809)
+- fix: clean up command templates (specify, analyze) (#1810)
+- fix: migrate Qwen Code CLI from TOML to Markdown format (#1589) (#1730)
+- fix(cli): deprecate explicit command support for agy (#1798) (#1808)
+- Add /selftest.extension core extension to test other extensions (#1758)
+- feat(extensions): Quality of life improvements for RFC-aligned catalog integration (#1776)
+- Add Java brownfield walkthrough to community walkthroughs (#1820)
 
 ## [0.2.1] - 2026-03-11
 
@@ -51,13 +101,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fix: release-trigger uses release branch + PR instead of direct push to main (#1733)
 - fix: Split release process to sync pyproject.toml version with git tags (#1732)
 
-
-## [Unreleased]
-
-### Added
-
-- feat(extensions): support `.extensionignore` to exclude files/folders during `specify extension add` (#1781)
-
 ## [0.2.0] - 2026-03-09
 
 ### Changed
@@ -239,28 +282,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - 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)

README.md

@@ -25,6 +25,7 @@
 - [🚶 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)
@@ -48,9 +49,13 @@ Choose your preferred installation method:
 
 #### Option 1: Persistent Installation (Recommended)
 
-Install once and use everywhere:
+Install once and use everywhere. Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
 
 ```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
 ```
 
@@ -72,7 +77,7 @@ 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
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@vX.Y.Z
 ```
 
 #### Option 2: One-time Usage
@@ -80,13 +85,13 @@ uv tool install specify-cli --force --from git+https://github.com/github/spec-ki
 Run directly without installing:
 
 ```bash
-# Create new project
-uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
+# Create new project (pinned to a stable release — 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 initialize in existing project
-uvx --from git+https://github.com/github/spec-kit.git specify init . --ai claude
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init . --ai claude
 # or
-uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai claude
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here --ai claude
 ```
 
 **Benefits of persistent installation:**
@@ -96,9 +101,13 @@ uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai c
 - 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. The `/speckit.*` commands are available in the assistant.
+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.
 
 Use the **`/speckit.constitution`** command to create your project's governing principles and development guidelines that will guide all subsequent development.
 
@@ -158,6 +167,10 @@ See Spec-Driven Development in action across different scenarios with these comm
 
 - **[Brownfield Java runtime extension](https://github.com/mnriem/spec-kit-java-brownfield-demo)** — Extends an existing open-source Jakarta EE runtime (Piranha, ~420,000 lines of Java, XML, JSP, HTML, and config files across 180 Maven modules) with a password-protected Server Admin Console, demonstrating spec-kit on a large multi-module Java project with no prior specs or constitution.
 
+- **[Brownfield Go / React dashboard demo](https://github.com/mnriem/spec-kit-go-brownfield-demo)** — Demonstrates spec-kit driven entirely from the **terminal using GitHub Copilot CLI**. Extends NASA's open-source Hermes ground support system (Go) with a lightweight React-based web telemetry dashboard, showing that the full constitution → specify → plan → tasks → implement workflow works from the terminal.
+
+- **[Greenfield Spring Boot MVC with a custom preset](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo)** — Builds a Spring Boot MVC application from scratch using a custom pirate-speak preset, demonstrating how presets can reshape the entire spec-kit experience: specifications become "Voyage Manifests," plans become "Battle Plans," and tasks become "Crew Assignments" — all generated in full pirate vernacular without changing any tooling.
+
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |
@@ -168,7 +181,7 @@ 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)                                         | ✅      |                                                                                                                                           |
+| [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>`. |
 | [Cursor](https://cursor.sh/)                                                         | ✅      |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | ✅      |                                                                                                                                           |
 | [GitHub Copilot](https://code.visualstudio.com/)                                     | ✅      |                                                                                                                                           |
@@ -176,14 +189,18 @@ 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                                                 |
 
 ## 🔧 Specify CLI Reference
@@ -192,27 +209,28 @@ The `specify` command supports the following options:
 
 ### Commands
 
-| Command | Description                                                                                                                                             |
-| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `init`  | Initialize a new Specify project from the latest template                                                                                               |
-| `check` | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`, `kiro-cli`, `shai`, `qodercli`, `vibe`, `kimi`) |
+| Command | Description                                                                                                                                                                                                                                                                              |
+| ------- |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `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.) |
 
 ### `specify init` Arguments & Options
 
-| Argument/Option        | Type     | Description                                                                                                                                                                                  |
-| ---------------------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory)                                                                                           |
-| `--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/`)                                                                                                  |
-| `--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                                                                                                                                              |
-| `--no-git`             | Flag     | Skip git repository initialization                                                                                                                                                           |
-| `--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)                                                                                                             |
-| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                  |
-| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                             |
-| `--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`)                                                                                          |
+| Argument/Option        | Type     | Description                                                                                                                                                                                                                                                                                                                                                                               |
+| ---------------------- | -------- |-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `<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-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)                                                                                                                                                                                                                                                                                                                               |
+| `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                                                                                                                                                                                                                                                                                                                                           |
+| `--no-git`             | Flag     | Skip git repository initialization                                                                                                                                                                                                                                                                                                                                                        |
+| `--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)                                                                                                                                                                                                                                                                                                          |
+| `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                                                                                                                                                                                                               |
+| `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                                                                                                                                                                                                                          |
+| `--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`)                                                                                                                                                                                                                                                                                       |
+| `--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
 
@@ -247,6 +265,12 @@ 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
 
@@ -281,13 +305,18 @@ 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
 
@@ -317,6 +346,68 @@ 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:
@@ -411,11 +502,11 @@ specify init <project_name> --ai copilot
 
 # Or in current directory:
 specify init . --ai claude
-specify init . --ai codex
+specify init . --ai codex --ai-skills
 
 # or use --here flag
 specify init --here --ai claude
-specify init --here --ai codex
+specify init --here --ai codex --ai-skills
 
 # Force merge into a non-empty current directory
 specify init . --force --ai claude
@@ -424,7 +515,7 @@ 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, 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, 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:
 
 ```bash
 specify init <project_name> --ai claude --ignore-agent-tools

SUPPORT.md

@@ -1,18 +1,17 @@
 # Support
 
-## How to file issues and get help
+## How to get help
 
-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.
+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.
 
-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
 - Review the [README](./README.md) for getting started instructions and troubleshooting tips
+- 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
+- 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 in a timely manner.
+**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.
 
 ## GitHub Support Policy
 

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) or [Gemini CLI](https://github.com/google-gemini/gemini-cli)
+- 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)
 - [uv](https://docs.astral.sh/uv/) for package management
 - [Python 3.11+](https://www.python.org/downloads/)
 - [Git](https://git-scm.com/downloads)
@@ -12,18 +12,22 @@
 
 ### Initialize a New Project
 
-The easiest way to get started is to 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):
 
 ```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 specify init .
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init .
 # or use the --here flag
-uvx --from git+https://github.com/github/spec-kit.git specify init --here
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here
 ```
 
 ### Specify AI Agent
@@ -31,10 +35,11 @@ uvx --from git+https://github.com/github/spec-kit.git specify init --here
 You can proactively specify your AI agent during initialization:
 
 ```bash
-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 specify init <project_name> --ai gemini
-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 specify init <project_name> --ai codebuddy
+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@vX.Y.Z 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@vX.Y.Z 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)
@@ -50,8 +55,8 @@ Auto behavior:
 Force a specific script type:
 
 ```bash
-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 specify init <project_name> --script ps
+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@vX.Y.Z specify init <project_name> --script ps
 ```
 
 ### Ignore Agent Tools Check
@@ -59,7 +64,7 @@ uvx --from git+https://github.com/github/spec-kit.git specify init <project_name
 If you prefer to get the templates without checking for the right tools:
 
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git specify init <project_name> --ai claude --ignore-agent-tools
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <project_name> --ai claude --ignore-agent-tools
 ```
 
 ## Verification
@@ -74,6 +79,52 @@ 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:

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` | 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@vX.Y.Z` | 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 |
 
@@ -20,16 +20,18 @@ 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
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@vX.Y.Z
 ```
 
 ### If you use one-shot `uvx` commands
 
-No upgrade needed—`uvx` always fetches the latest version. Just run your commands as normal:
+Specify the desired release tag:
 
 ```bash
-uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai copilot
+uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init --here --ai copilot
 ```
 
 ### Verify the upgrade
@@ -289,8 +291,9 @@ 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 .cursor/commands/       # Cursor
+   ls -la .gemini/commands/      # Gemini
+   ls -la .cursor/commands/      # Cursor
+   ls -la .pi/prompts/           # Pi Coding Agent
    ```
 
 3. **Check agent-specific setup:**
@@ -398,7 +401,7 @@ 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/`, 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/`, `.pi/prompts/`, etc.). Your AI assistant reads these command files directly—no need to run `specify` again.
 
 **If your agent isn't recognizing slash commands:**
 
@@ -410,6 +413,9 @@ 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)

extensions/EXTENSION-API-REFERENCE.md

@@ -53,7 +53,7 @@ provides:
       required: boolean  # Default: false
 
 hooks:                   # Optional, event hooks
-  event_name:            # e.g., "after_tasks", "after_implement"
+  event_name:            # e.g., "after_specify", "after_plan", "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_tasks`, `after_implement`, `before_commit`)
+- **Keys**: Event names (e.g., `after_specify`, `after_plan`, `after_tasks`, `after_implement`, `before_commit`)
 - **Description**: Hooks that execute at lifecycle events
 - **Events**: Defined by core spec-kit commands
 
@@ -551,10 +551,16 @@ 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
-- `after_commit` - After git commit
+- `before_commit` - Before git commit *(planned - not yet wired into core templates)*
+- `after_commit` - After git commit *(planned - not yet wired into core templates)*
 
 ### Hook Configuration
 

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -209,9 +209,22 @@ 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 | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
+| Your Extension Name | Brief description of what it does | `<category>` | <effect> | [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

extensions/EXTENSION-USER-GUIDE.md

@@ -387,6 +387,9 @@ 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

extensions/README.md

@@ -70,20 +70,34 @@ 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):
 
-| Extension | Purpose | URL |
-|-----------|---------|-----|
-| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
-| Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
-| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
-| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
-| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
-| Ralph Loop | Autonomous implementation loop using AI agent CLI | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
-| Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
-| Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| 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) |
-| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | [understanding](https://github.com/Testimonial/understanding) |
-| 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) |
-| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
+**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
+
+**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
+
+| Extension | Purpose | Category | Effect | URL |
+|-----------|---------|----------|--------|-----|
+| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [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 | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
+| Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| 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) |
+| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
+| 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

extensions/RFC-EXTENSION-SYSTEM.md

@@ -359,12 +359,15 @@ specify extension add jira
       "installed_at": "2026-01-28T14:30:00Z",
       "source": "catalog",
       "manifest_hash": "sha256:abc123...",
-      "enabled": true
+      "enabled": true,
+      "priority": 10
     }
   }
 }
 ```
 
+**Priority Field**: Extensions are ordered by `priority` (lower = higher precedence). Default is 10. Used for template resolution when multiple extensions provide the same template.
+
 ### 3. Configuration
 
 ```bash
@@ -1084,11 +1087,15 @@ List installed extensions in current project.
 $ specify extension list
 
 Installed Extensions:
-  ✓ jira (v1.0.0) - Jira Integration
-    Commands: 3 | Hooks: 2 | Status: Enabled
+  ✓ Jira Integration (v1.0.0)
+     jira
+     Create Jira issues from spec-kit artifacts
+     Commands: 3 | Hooks: 2 | Priority: 10 | Status: Enabled
 
-  ✓ linear (v0.9.0) - Linear Integration
-    Commands: 1 | Hooks: 1 | Status: Enabled
+  ✓ Linear Integration (v0.9.0)
+     linear
+     Create Linear issues from spec-kit artifacts
+     Commands: 1 | Hooks: 1 | Priority: 10 | Status: Enabled
 ```
 
 **Options:**
@@ -1196,10 +1203,9 @@ Next steps:
 
 **Options:**
 
-- `--from URL`: Install from custom URL or Git repo
-- `--version VERSION`: Install specific version
-- `--dev PATH`: Install from local path (development mode)
-- `--no-register`: Skip command registration (manual setup)
+- `--from URL`: Install from a remote URL (archive). Does not accept Git repositories directly.
+- `--dev`: Install from a local path in development mode (the PATH is the positional `extension` argument).
+- `--priority NUMBER`: Set resolution priority (lower = higher precedence, default 10)
 
 #### `specify extension remove NAME`
 
@@ -1280,6 +1286,29 @@ $ specify extension disable jira
 To re-enable: specify extension enable jira
 ```
 
+#### `specify extension set-priority NAME PRIORITY`
+
+Change the resolution priority of an installed extension.
+
+```bash
+$ specify extension set-priority jira 5
+
+✓ Extension 'Jira Integration' priority changed: 10 → 5
+
+Lower priority = higher precedence in template resolution
+```
+
+**Priority Values:**
+
+- Lower numbers = higher precedence (checked first in resolution)
+- Default priority is 10
+- Must be a positive integer (1 or higher)
+
+**Use Cases:**
+
+- Ensure a critical extension's templates take precedence
+- Override default resolution order when multiple extensions provide similar templates
+
 ---
 
 ## Compatibility & Versioning

extensions/catalog.community.json

@@ -1,8 +1,39 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-13T12:00:00Z",
+  "updated_at": "2026-03-19T12:08:20Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
+    "archive": {
+      "name": "Archive Extension",
+      "id": "archive",
+      "description": "Archive merged features into main project memory, resolving gaps and conflicts.",
+      "author": "Stanislav Deviatov",
+      "version": "1.0.0",
+      "download_url": "https://github.com/stn1slv/spec-kit-archive/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/stn1slv/spec-kit-archive",
+      "homepage": "https://github.com/stn1slv/spec-kit-archive",
+      "documentation": "https://github.com/stn1slv/spec-kit-archive/blob/main/README.md",
+      "changelog": "https://github.com/stn1slv/spec-kit-archive/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "archive",
+        "memory",
+        "merge",
+        "changelog"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-14T00:00:00Z",
+      "updated_at": "2026-03-14T00:00:00Z"
+    },
     "azure-devops": {
       "name": "Azure DevOps Integration",
       "id": "azure-devops",
@@ -74,6 +105,122 @@
       "created_at": "2026-02-22T00:00:00Z",
       "updated_at": "2026-02-22T00:00:00Z"
     },
+    "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",
+      "author": "Testimonial",
+      "version": "0.1.0",
+      "download_url": "https://github.com/Testimonial/cognitive-squad/archive/refs/tags/v0.1.0.zip",
+      "repository": "https://github.com/Testimonial/cognitive-squad",
+      "homepage": "https://github.com/Testimonial/cognitive-squad",
+      "documentation": "https://github.com/Testimonial/cognitive-squad/blob/main/README.md",
+      "changelog": "https://github.com/Testimonial/cognitive-squad/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0",
+        "tools": [
+          {
+            "name": "understanding",
+            "version": ">=3.4.0",
+            "required": false
+          },
+          {
+            "name": "spec-kit-reverse-eng",
+            "version": ">=1.0.0",
+            "required": false
+          }
+        ]
+      },
+      "provides": {
+        "commands": 10,
+        "hooks": 1
+      },
+      "tags": [
+        "ai-agents",
+        "cognitive",
+        "full-lifecycle",
+        "verification",
+        "multi-agent"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-18T00:00:00Z"
+    },
+    "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.",
+      "author": "raccioly",
+      "version": "0.9.11",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.9.11/spec-kit-docguard-v0.9.11.zip",
+      "repository": "https://github.com/raccioly/docguard",
+      "homepage": "https://www.npmjs.com/package/docguard-cli",
+      "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
+      "changelog": "https://github.com/raccioly/docguard/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "node",
+            "version": ">=18.0.0",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 6,
+        "hooks": 3
+      },
+      "tags": [
+        "documentation",
+        "validation",
+        "quality",
+        "cdd",
+        "traceability",
+        "ai-agents",
+        "enforcement",
+        "spec-kit"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-13T00:00:00Z",
+      "updated_at": "2026-03-18T18:53:31Z"
+    },
     "doctor": {
       "name": "Project Health Check",
       "id": "doctor",
@@ -124,13 +271,48 @@
         "commands": 2,
         "hooks": 1
       },
-      "tags": ["orchestration", "workflow", "human-in-the-loop", "parallel"],
+      "tags": [
+        "orchestration",
+        "workflow",
+        "human-in-the-loop",
+        "parallel"
+      ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "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",
@@ -191,13 +373,49 @@
         "commands": 2,
         "hooks": 1
       },
-      "tags": ["implementation", "automation", "loop", "copilot"],
+      "tags": [
+        "implementation",
+        "automation",
+        "loop",
+        "copilot"
+      ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-09T00:00:00Z",
       "updated_at": "2026-03-09T00:00:00Z"
     },
+    "reconcile": {
+      "name": "Reconcile Extension",
+      "id": "reconcile",
+      "description": "Reconcile implementation drift by surgically updating the feature's own spec, plan, and tasks.",
+      "author": "Stanislav Deviatov",
+      "version": "1.0.0",
+      "download_url": "https://github.com/stn1slv/spec-kit-reconcile/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/stn1slv/spec-kit-reconcile",
+      "homepage": "https://github.com/stn1slv/spec-kit-reconcile",
+      "documentation": "https://github.com/stn1slv/spec-kit-reconcile/blob/main/README.md",
+      "changelog": "https://github.com/stn1slv/spec-kit-reconcile/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "reconcile",
+        "drift",
+        "tasks",
+        "remediation"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-14T00:00:00Z",
+      "updated_at": "2026-03-14T00:00:00Z"
+    },
     "retrospective": {
       "name": "Retrospective Extension",
       "id": "retrospective",
@@ -249,13 +467,53 @@
         "commands": 7,
         "hooks": 1
       },
-      "tags": ["code-review", "quality", "review", "testing", "error-handling", "type-design", "simplification"],
+      "tags": [
+        "code-review",
+        "quality",
+        "review",
+        "testing",
+        "error-handling",
+        "type-design",
+        "simplification"
+      ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "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",
@@ -291,7 +549,7 @@
     "understanding": {
       "name": "Understanding",
       "id": "understanding",
-      "description": "Automated requirements quality analysis — validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
+      "description": "Automated requirements quality analysis \u2014 validates specs against IEEE/ISO standards using 31 deterministic metrics. Catches ambiguity, missing testability, and structural issues before they reach implementation. Includes experimental energy-based ambiguity detection using local LM token perplexity.",
       "author": "Ladislav Bihari",
       "version": "3.4.0",
       "download_url": "https://github.com/Testimonial/understanding/archive/refs/tags/v3.4.0.zip",
@@ -329,6 +587,38 @@
       "created_at": "2026-03-07T00:00:00Z",
       "updated_at": "2026-03-07T00:00:00Z"
     },
+    "status": {
+      "name": "Project Status",
+      "id": "status",
+      "description": "Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "status",
+        "workflow",
+        "progress",
+        "feature-tracking",
+        "task-progress"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-16T00:00:00Z"
+    },
     "v-model": {
       "name": "V-Model Extension Pack",
       "id": "v-model",
@@ -361,6 +651,37 @@
       "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",
@@ -392,6 +713,37 @@
       "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"
     }
   }
 }

presets/ARCHITECTURE.md

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

presets/PUBLISHING.md

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

presets/README.md

@@ -0,0 +1,117 @@
+# Presets
+
+Presets are stackable, priority-ordered collections of template and command overrides for Spec Kit. They let you customize both the artifacts produced by the Spec-Driven Development workflow (specs, plans, tasks, checklists, constitutions) and the commands that guide the LLM in creating them — without forking or modifying core files.
+
+## How It Works
+
+When Spec Kit needs a template (e.g. `spec-template`), it walks a resolution stack:
+
+1. `.specify/templates/overrides/` — project-local one-off overrides
+2. `.specify/presets/<preset-id>/templates/` — installed presets (sorted by priority)
+3. `.specify/extensions/<ext-id>/templates/` — extension-provided templates
+4. `.specify/templates/` — core templates shipped with Spec Kit
+
+If no preset is installed, core templates are used — exactly the same behavior as before presets existed.
+
+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.
+
+## Quick Start
+
+```bash
+# Search available presets
+specify preset search
+
+# Install a preset from the catalog
+specify preset add healthcare-compliance
+
+# Install from a local directory (for development)
+specify preset add --dev ./my-preset
+
+# Install with a specific priority (lower = higher precedence)
+specify preset add healthcare-compliance --priority 5
+
+# List installed presets
+specify preset list
+
+# See which template a name resolves to
+specify preset resolve spec-template
+
+# Get detailed info about a preset
+specify preset info healthcare-compliance
+
+# Remove a preset
+specify preset remove healthcare-compliance
+```
+
+## Stacking Presets
+
+Multiple presets can be installed simultaneously. The `--priority` flag controls which one wins when two presets provide the same template (lower number = higher precedence):
+
+```bash
+specify preset add enterprise-safe --priority 10      # base layer
+specify preset add healthcare-compliance --priority 5  # overrides enterprise-safe
+specify preset add pm-workflow --priority 1            # overrides everything
+```
+
+Presets **override**, they don't merge. If two presets both provide `spec-template`, the one with the lowest priority number wins entirely.
+
+## Catalog Management
+
+Presets are discovered through catalogs. By default, Spec Kit uses the official and community catalogs:
+
+```bash
+# List active catalogs
+specify preset catalog list
+
+# Add a custom catalog
+specify preset catalog add https://example.com/catalog.json --name my-org --install-allowed
+
+# Remove a catalog
+specify preset catalog remove my-org
+```
+
+## Creating a Preset
+
+See [scaffold/](scaffold/) for a scaffold you can copy to create your own preset.
+
+1. Copy `scaffold/` to a new directory
+2. Edit `preset.yml` with your preset's metadata
+3. Add or replace templates in `templates/`
+4. Test locally with `specify preset add --dev .`
+5. Verify with `specify preset resolve spec-template`
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `SPECKIT_PRESET_CATALOG_URL` | Override the catalog URL (replaces all defaults) |
+
+## Configuration Files
+
+| File | Scope | Description |
+|------|-------|-------------|
+| `.specify/preset-catalogs.yml` | Project | Custom catalog stack for this project |
+| `~/.specify/preset-catalogs.yml` | User | Custom catalog stack for all projects |
+
+## Future Considerations
+
+The following enhancements are under consideration for future releases:
+
+- **Composition strategies** — Allow presets to declare a `strategy` per template instead of the default `replace`:
+
+  | Type | `replace` | `prepend` | `append` | `wrap` |
+  |------|-----------|-----------|----------|--------|
+  | **template** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **command** | ✓ (default) | ✓ | ✓ | ✓ |
+  | **script** | ✓ (default) | — | — | ✓ |
+
+  For artifacts and commands (which are LLM directives), `wrap` would inject preset content before and after the core template using a `{CORE_TEMPLATE}` placeholder. For scripts, `wrap` would run custom logic before/after the core script via a `$CORE_SCRIPT` variable.
+- **Script overrides** — Enable presets to provide alternative versions of core scripts (e.g. `create-new-feature.sh`) for workflow customization. A `strategy: "wrap"` option could allow presets to run custom logic before/after the core script without fully replacing it.

presets/catalog.community.json

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

presets/catalog.json

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

presets/scaffold/README.md

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

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

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

presets/scaffold/commands/speckit.specify.md

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

presets/scaffold/preset.yml

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

presets/scaffold/templates/myext-template.md

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

presets/scaffold/templates/spec-template.md

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

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

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

presets/self-test/preset.yml

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

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

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

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

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

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

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

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

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

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

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

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

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

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.2.1"
+version = "0.3.2"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -14,6 +14,7 @@ dependencies = [
     "pyyaml>=6.0",
     "packaging>=23.0",
     "pathspec>=0.12.0",
+    "json5>=0.13.0",
 ]
 
 [project.scripts]
@@ -26,6 +27,25 @@ 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"
+# Official agent packs (embedded in wheel for zero-config offline operation)
+"src/specify_cli/core_pack/agents" = "specify_cli/core_pack/agents"
+
 [project.optional-dependencies]
 test = [
     "pytest>=7.0",

scripts/bash/check-prerequisites.sh

@@ -168,7 +168,7 @@ if $JSON_MODE; then
         if [[ ${#docs[@]} -eq 0 ]]; then
             json_docs="[]"
         else
-            json_docs=$(printf '"%s",' "${docs[@]}")
+            json_docs=$(for d in "${docs[@]}"; do printf '"%s",' "$(json_escape "$d")"; done)
             json_docs="[${json_docs%,}]"
         fi
         printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"

scripts/bash/common.sh

@@ -33,16 +33,27 @@ 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 [[ "$dirname" =~ ^([0-9]{3})- ]]; then
+                if [[ "$dirname" =~ ^([0-9]{8}-[0-9]{6})- ]]; 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
-                        latest_feature=$dirname
+                        # Only update if no timestamp branch found yet
+                        if [[ -z "$latest_timestamp" ]]; then
+                            latest_feature=$dirname
+                        fi
                     fi
                 fi
             fi
@@ -72,9 +83,9 @@ check_feature_branch() {
         return 0
     fi
 
-    if [[ ! "$branch" =~ ^[0-9]{3}- ]]; then
+    if [[ ! "$branch" =~ ^[0-9]{3}- ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
         echo "ERROR: Not on a feature branch. Current branch: $branch" >&2
-        echo "Feature branches should be named like: 001-feature-name" >&2
+        echo "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name" >&2
         return 1
     fi
 
@@ -90,15 +101,18 @@ find_feature_dir_by_prefix() {
     local branch_name="$2"
     local specs_dir="$repo_root/specs"
 
-    # Extract numeric prefix from branch (e.g., "004" from "004-whatever")
-    if [[ ! "$branch_name" =~ ^([0-9]{3})- ]]; then
-        # If branch doesn't have numeric prefix, fall back to exact match
+    # Extract prefix from branch (e.g., "004" from "004-whatever" or "20260319-143022" from timestamp branches)
+    local prefix=""
+    if [[ "$branch_name" =~ ^([0-9]{8}-[0-9]{6})- ]]; then
+        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
@@ -119,7 +133,7 @@ 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 numeric prefix." >&2
+        echo "Please ensure only one spec directory exists per prefix." >&2
         return 1
     fi
 }
@@ -161,7 +175,7 @@ has_jq() {
 }
 
 # Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
-# Handles backslash, double-quote, and control characters (newline, tab, carriage return).
+# Handles backslash, double-quote, and JSON-required control character escapes (RFC 8259).
 json_escape() {
     local s="$1"
     s="${s//\\/\\\\}"
@@ -169,9 +183,107 @@ json_escape() {
     s="${s//$'\n'/\\n}"
     s="${s//$'\t'/\\t}"
     s="${s//$'\r'/\\r}"
-    printf '%s' "$s"
+    s="${s//$'\b'/\\b}"
+    s="${s//$'\f'/\\f}"
+    # Escape any remaining U+0001-U+001F control characters as \uXXXX.
+    # (U+0000/NUL cannot appear in bash strings and is excluded.)
+    # LC_ALL=C ensures ${#s} counts bytes and ${s:$i:1} yields single bytes,
+    # 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"; }
 check_dir() { [[ -d "$1" && -n $(ls -A "$1" 2>/dev/null) ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 
+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+resolve_template() {
+    local template_name="$1"
+    local repo_root="$2"
+    local base="$repo_root/.specify/templates"
+
+    # Priority 1: Project overrides
+    local override="$base/overrides/${template_name}.md"
+    [ -f "$override" ] && echo "$override" && return 0
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    local presets_dir="$repo_root/.specify/presets"
+    if [ -d "$presets_dir" ]; then
+        local registry_file="$presets_dir/.registry"
+        if [ -f "$registry_file" ] && command -v python3 >/dev/null 2>&1; then
+            # Read preset IDs sorted by priority (lower number = higher precedence).
+            # The python3 call is wrapped in an if-condition so that set -e does not
+            # abort the function when python3 exits non-zero (e.g. invalid JSON).
+            local sorted_presets=""
+            if sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
+import json, sys, os
+try:
+    with open(os.environ['SPECKIT_REGISTRY']) as f:
+        data = json.load(f)
+    presets = data.get('presets', {})
+    for pid, meta in sorted(presets.items(), key=lambda x: x[1].get('priority', 10)):
+        print(pid)
+except Exception:
+    sys.exit(1)
+" 2>/dev/null); then
+                if [ -n "$sorted_presets" ]; then
+                    # python3 succeeded and returned preset IDs — search in priority order
+                    while IFS= read -r preset_id; do
+                        local candidate="$presets_dir/$preset_id/templates/${template_name}.md"
+                        [ -f "$candidate" ] && echo "$candidate" && return 0
+                    done <<< "$sorted_presets"
+                fi
+                # python3 succeeded but registry has no presets — nothing to search
+            else
+                # python3 failed (missing, or registry parse error) — fall back to unordered directory scan
+                for preset in "$presets_dir"/*/; do
+                    [ -d "$preset" ] || continue
+                    local candidate="$preset/templates/${template_name}.md"
+                    [ -f "$candidate" ] && echo "$candidate" && return 0
+                done
+            fi
+        else
+            # Fallback: alphabetical directory order (no python3 available)
+            for preset in "$presets_dir"/*/; do
+                [ -d "$preset" ] || continue
+                local candidate="$preset/templates/${template_name}.md"
+                [ -f "$candidate" ] && echo "$candidate" && return 0
+            done
+        fi
+    fi
+
+    # Priority 3: Extension-provided templates
+    local ext_dir="$repo_root/.specify/extensions"
+    if [ -d "$ext_dir" ]; then
+        for ext in "$ext_dir"/*/; do
+            [ -d "$ext" ] || continue
+            # Skip hidden directories (e.g. .backup, .cache)
+            case "$(basename "$ext")" in .*) continue;; esac
+            local candidate="$ext/templates/${template_name}.md"
+            [ -f "$candidate" ] && echo "$candidate" && return 0
+        done
+    fi
+
+    # Priority 4: Core templates
+    local core="$base/${template_name}.md"
+    [ -f "$core" ] && echo "$core" && return 0
+
+    # Template not found in any location.
+    # Return 1 so callers can distinguish "not found" from "found".
+    # Callers running under set -e should use: TEMPLATE=$(resolve_template ...) || true
+    return 1
+}
+

scripts/bash/create-new-feature.sh

@@ -5,13 +5,14 @@ set -e
 JSON_MODE=false
 SHORT_NAME=""
 BRANCH_NUMBER=""
+USE_TIMESTAMP=false
 ARGS=()
 i=1
 while [ $i -le $# ]; do
     arg="${!i}"
     case "$arg" in
-        --json) 
-            JSON_MODE=true 
+        --json)
+            JSON_MODE=true
             ;;
         --short-name)
             if [ $((i + 1)) -gt $# ]; then
@@ -40,22 +41,27 @@ while [ $i -le $# ]; do
             fi
             BRANCH_NUMBER="$next_arg"
             ;;
-        --help|-h) 
-            echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>"
+        --timestamp)
+            USE_TIMESTAMP=true
+            ;;
+        --help|-h)
+            echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
             echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
             echo "  --number N          Specify branch number manually (overrides auto-detection)"
+            echo "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
             echo "  --help, -h          Show this help message"
             echo ""
             echo "Examples:"
             echo "  $0 'Add user authentication system' --short-name 'user-auth'"
             echo "  $0 'Implement OAuth2 integration for API' --number 5"
+            echo "  $0 --timestamp --short-name 'user-auth' 'Add user authentication'"
             exit 0
             ;;
-        *) 
-            ARGS+=("$arg") 
+        *)
+            ARGS+=("$arg")
             ;;
     esac
     i=$((i + 1))
@@ -63,7 +69,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
     exit 1
 fi
 
@@ -96,10 +102,13 @@ get_highest_from_specs() {
         for dir in "$specs_dir"/*; do
             [ -d "$dir" ] || continue
             dirname=$(basename "$dir")
-            number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
-            number=$((10#$number))
-            if [ "$number" -gt "$highest" ]; then
-                highest=$number
+            # Only match sequential prefixes (###-*), skip timestamp dirs
+            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
+                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
+                number=$((10#$number))
+                if [ "$number" -gt "$highest" ]; then
+                    highest=$number
+                fi
             fi
         done
     fi
@@ -138,7 +147,7 @@ check_existing_branches() {
     local specs_dir="$1"
 
     # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    git fetch --all --prune 2>/dev/null || true
+    git fetch --all --prune >/dev/null 2>&1 || true
 
     # Get highest number from ALL branches (not just matching short name)
     local highest_branch=$(get_highest_from_branches)
@@ -162,21 +171,11 @@ clean_branch_name() {
     echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }
 
-# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
-json_escape() {
-    local s="$1"
-    s="${s//\\/\\\\}"
-    s="${s//\"/\\\"}"
-    s="${s//$'\n'/\\n}"
-    s="${s//$'\t'/\\t}"
-    s="${s//$'\r'/\\r}"
-    printf '%s' "$s"
-}
-
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/common.sh"
 
 if git rev-parse --show-toplevel >/dev/null 2>&1; then
     REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -252,29 +251,42 @@ else
     BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
 fi
 
-# 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=$((HIGHEST + 1))
-    fi
+# Warn if --number and --timestamp are both specified
+if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
+    >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
+    BRANCH_NUMBER=""
 fi
 
-# 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}-${BRANCH_SUFFIX}"
+# Determine branch prefix
+if [ "$USE_TIMESTAMP" = true ]; then
+    FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
+    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+else
+    # Determine branch number
+    if [ -z "$BRANCH_NUMBER" ]; then
+        if [ "$HAS_GIT" = true ]; then
+            # Check existing branches on remotes
+            BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
+        else
+            # Fall back to local directory check
+            HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
+            BRANCH_NUMBER=$((HIGHEST + 1))
+        fi
+    fi
+
+    # Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
+    FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
+    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+fi
 
 # GitHub enforces a 244-byte limit on branch names
 # Validate and truncate if necessary
 MAX_BRANCH_LENGTH=244
 if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
     # Calculate how much we need to trim from suffix
-    # Account for: feature number (3) + hyphen (1) = 4 chars
-    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - 4))
+    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
+    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
+    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
     
     # Truncate suffix at word boundary if possible
     TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
@@ -293,7 +305,11 @@ if [ "$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
-            >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
+            if [ "$USE_TIMESTAMP" = true ]; then
+                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Rerun to get a new timestamp or use a different --short-name."
+            else
+                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
+            fi
             exit 1
         else
             >&2 echo "Error: Failed to create git branch '$BRANCH_NAME'. Please check your git configuration and try again."
@@ -307,9 +323,14 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
-TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
+TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
+if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
+    cp "$TEMPLATE" "$SPEC_FILE"
+else
+    echo "Warning: Spec template not found; created empty spec file" >&2
+    touch "$SPEC_FILE"
+fi
 
 # Inform the user how to persist the feature variable in their own shell
 printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2

scripts/bash/setup-plan.sh

@@ -39,12 +39,12 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 mkdir -p "$FEATURE_DIR"
 
 # Copy plan template if it exists
-TEMPLATE="$REPO_ROOT/.specify/templates/plan-template.md"
-if [[ -f "$TEMPLATE" ]]; then
+TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
+if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
     cp "$TEMPLATE" "$IMPL_PLAN"
     echo "Copied plan template to $IMPL_PLAN"
 else
-    echo "Warning: Plan template not found at $TEMPLATE"
+    echo "Warning: Plan template not found"
     # Create a basic plan file if template doesn't exist
     touch "$IMPL_PLAN"
 fi

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, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Tabnine CLI, Kiro CLI, Mistral Vibe, Kimi Code, Antigravity or Generic
+#    - 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
 #    - 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|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic
+# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic
 # Leave empty to update all existing agent files
 
 set -e
@@ -68,12 +68,13 @@ 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, and IBM Bob all share AGENTS.md — use AGENTS_FILE to avoid
+# Amp, Kiro CLI, IBM Bob, and Pi 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"
@@ -83,6 +84,8 @@ AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
 BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
+TRAE_FILE="$REPO_ROOT/.trae/rules/AGENTS.md"
+IFLOW_FILE="$REPO_ROOT/IFLOW.md"
 
 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -636,6 +639,9 @@ update_specific_agent() {
         windsurf)
             update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
             ;;
+        junie)
+            update_agent_file "$JUNIE_FILE" "Junie" || return 1
+            ;;
         kilocode)
             update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
             ;;
@@ -675,67 +681,90 @@ update_specific_agent() {
         kimi)
             update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
             ;;
+        trae)
+            update_agent_file "$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|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic"
+            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic"
             exit 1
             ;;
     esac
 }
 
+# Helper: skip non-existent files and files already updated (dedup by
+# realpath so that variables pointing to the same file — e.g. AMP_FILE,
+# KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
+# Uses a linear array instead of associative array for bash 3.2 compatibility.
+# Note: defined at top level because bash 3.2 does not support true
+# nested/local functions. _updated_paths, _found_agent, and _all_ok are
+# initialised exclusively inside update_all_existing_agents so that
+# sourcing this script has no side effects on the caller's environment.
+
+_update_if_new() {
+    local file="$1" name="$2"
+    [[ -f "$file" ]] || return 0
+    local real_path
+    real_path=$(realpath "$file" 2>/dev/null || echo "$file")
+    local p
+    if [[ ${#_updated_paths[@]} -gt 0 ]]; then
+        for p in "${_updated_paths[@]}"; do
+            [[ "$p" == "$real_path" ]] && return 0
+        done
+    fi
+    # Record the file as seen before attempting the update so that:
+    # (a) aliases pointing to the same path are not retried on failure
+    # (b) _found_agent reflects file existence, not update success
+    _updated_paths+=("$real_path")
+    _found_agent=true
+    update_agent_file "$file" "$name"
+}
+
 update_all_existing_agents() {
-    local found_agent=false
-    local _updated_paths=()
+    _found_agent=false
+    _updated_paths=()
+    local _all_ok=true
 
-    # Helper: skip non-existent files and files already updated (dedup by
-    # realpath so that variables pointing to the same file — e.g. AMP_FILE,
-    # KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
-    # Uses a linear array instead of associative array for bash 3.2 compatibility.
-    update_if_new() {
-        local file="$1" name="$2"
-        [[ -f "$file" ]] || return 0
-        local real_path
-        real_path=$(realpath "$file" 2>/dev/null || echo "$file")
-        local p
-        if [[ ${#_updated_paths[@]} -gt 0 ]]; then
-            for p in "${_updated_paths[@]}"; do
-                [[ "$p" == "$real_path" ]] && return 0
-            done
-        fi
-        update_agent_file "$file" "$name" || return 1
-        _updated_paths+=("$real_path")
-        found_agent=true
-    }
-
-    update_if_new "$CLAUDE_FILE" "Claude Code"
-    update_if_new "$GEMINI_FILE" "Gemini CLI"
-    update_if_new "$COPILOT_FILE" "GitHub Copilot"
-    update_if_new "$CURSOR_FILE" "Cursor IDE"
-    update_if_new "$QWEN_FILE" "Qwen Code"
-    update_if_new "$AGENTS_FILE" "Codex/opencode"
-    update_if_new "$AMP_FILE" "Amp"
-    update_if_new "$KIRO_FILE" "Kiro CLI"
-    update_if_new "$BOB_FILE" "IBM Bob"
-    update_if_new "$WINDSURF_FILE" "Windsurf"
-    update_if_new "$KILOCODE_FILE" "Kilo Code"
-    update_if_new "$AUGGIE_FILE" "Auggie CLI"
-    update_if_new "$ROO_FILE" "Roo Code"
-    update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"
-    update_if_new "$SHAI_FILE" "SHAI"
-    update_if_new "$TABNINE_FILE" "Tabnine CLI"
-    update_if_new "$QODER_FILE" "Qoder CLI"
-    update_if_new "$AGY_FILE" "Antigravity"
-    update_if_new "$VIBE_FILE" "Mistral Vibe"
-    update_if_new "$KIMI_FILE" "Kimi Code"
+    _update_if_new "$CLAUDE_FILE" "Claude Code"           || _all_ok=false
+    _update_if_new "$GEMINI_FILE" "Gemini CLI"             || _all_ok=false
+    _update_if_new "$COPILOT_FILE" "GitHub Copilot"        || _all_ok=false
+    _update_if_new "$CURSOR_FILE" "Cursor IDE"             || _all_ok=false
+    _update_if_new "$QWEN_FILE" "Qwen Code"                || _all_ok=false
+    _update_if_new "$AGENTS_FILE" "Codex/opencode"         || _all_ok=false
+    _update_if_new "$AMP_FILE" "Amp"                       || _all_ok=false
+    _update_if_new "$KIRO_FILE" "Kiro CLI"                 || _all_ok=false
+    _update_if_new "$BOB_FILE" "IBM Bob"                   || _all_ok=false
+    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
+    _update_if_new "$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 "$ROO_FILE" "Roo Code"                  || _all_ok=false
+    _update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"       || _all_ok=false
+    _update_if_new "$SHAI_FILE" "SHAI"                     || _all_ok=false
+    _update_if_new "$TABNINE_FILE" "Tabnine CLI"           || _all_ok=false
+    _update_if_new "$QODER_FILE" "Qoder CLI"               || _all_ok=false
+    _update_if_new "$AGY_FILE" "Antigravity"               || _all_ok=false
+    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
+    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
+    _update_if_new "$TRAE_FILE" "Trae"                     || _all_ok=false
+    _update_if_new "$IFLOW_FILE" "iFlow CLI"               || _all_ok=false
 
     # If no agent files exist, create a default Claude file
-    if [[ "$found_agent" == false ]]; then
+    if [[ "$_found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
         update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
     fi
+
+    [[ "$_all_ok" == true ]]
 }
 print_summary() {
     echo
@@ -754,7 +783,7 @@ print_summary() {
     fi
     
     echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic]"
 }
 
 #==============================================================================

scripts/powershell/common.ps1

@@ -38,17 +38,28 @@ function Get-CurrentBranch {
     if (Test-Path $specsDir) {
         $latestFeature = ""
         $highest = 0
-        
+        $latestTimestamp = ""
+
         Get-ChildItem -Path $specsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{3})-') {
+            if ($_.Name -match '^(\d{8}-\d{6})-') {
+                # 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
-                    $latestFeature = $_.Name
+                    # Only update if no timestamp branch found yet
+                    if (-not $latestTimestamp) {
+                        $latestFeature = $_.Name
+                    }
                 }
             }
         }
-        
+
         if ($latestFeature) {
             return $latestFeature
         }
@@ -79,9 +90,9 @@ function Test-FeatureBranch {
         return $true
     }
     
-    if ($Branch -notmatch '^[0-9]{3}-') {
+    if ($Branch -notmatch '^[0-9]{3}-' -and $Branch -notmatch '^\d{8}-\d{6}-') {
         Write-Output "ERROR: Not on a feature branch. Current branch: $Branch"
-        Write-Output "Feature branches should be named like: 001-feature-name"
+        Write-Output "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name"
         return $false
     }
     return $true
@@ -135,3 +146,70 @@ function Test-DirHasFiles {
     }
 }
 
+# Resolve a template name to a file path using the priority stack:
+#   1. .specify/templates/overrides/
+#   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
+#   3. .specify/extensions/<ext-id>/templates/
+#   4. .specify/templates/ (core)
+function Resolve-Template {
+    param(
+        [Parameter(Mandatory=$true)][string]$TemplateName,
+        [Parameter(Mandatory=$true)][string]$RepoRoot
+    )
+
+    $base = Join-Path $RepoRoot '.specify/templates'
+
+    # Priority 1: Project overrides
+    $override = Join-Path $base "overrides/$TemplateName.md"
+    if (Test-Path $override) { return $override }
+
+    # Priority 2: Installed presets (sorted by priority from .registry)
+    $presetsDir = Join-Path $RepoRoot '.specify/presets'
+    if (Test-Path $presetsDir) {
+        $registryFile = Join-Path $presetsDir '.registry'
+        $sortedPresets = @()
+        if (Test-Path $registryFile) {
+            try {
+                $registryData = Get-Content $registryFile -Raw | ConvertFrom-Json
+                $presets = $registryData.presets
+                if ($presets) {
+                    $sortedPresets = $presets.PSObject.Properties |
+                        Sort-Object { if ($null -ne $_.Value.priority) { $_.Value.priority } else { 10 } } |
+                        ForEach-Object { $_.Name }
+                }
+            } catch {
+                # Fallback: alphabetical directory order
+                $sortedPresets = @()
+            }
+        }
+
+        if ($sortedPresets.Count -gt 0) {
+            foreach ($presetId in $sortedPresets) {
+                $candidate = Join-Path $presetsDir "$presetId/templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        } else {
+            # Fallback: alphabetical directory order
+            foreach ($preset in Get-ChildItem -Path $presetsDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' }) {
+                $candidate = Join-Path $preset.FullName "templates/$TemplateName.md"
+                if (Test-Path $candidate) { return $candidate }
+            }
+        }
+    }
+
+    # Priority 3: Extension-provided templates
+    $extDir = Join-Path $RepoRoot '.specify/extensions'
+    if (Test-Path $extDir) {
+        foreach ($ext in Get-ChildItem -Path $extDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' } | Sort-Object Name) {
+            $candidate = Join-Path $ext.FullName "templates/$TemplateName.md"
+            if (Test-Path $candidate) { return $candidate }
+        }
+    }
+
+    # Priority 4: Core templates
+    $core = Join-Path $base "$TemplateName.md"
+    if (Test-Path $core) { return $core }
+
+    return $null
+}
+

scripts/powershell/create-new-feature.ps1

@@ -4,32 +4,36 @@
 param(
     [switch]$Json,
     [string]$ShortName,
+    [Parameter()]
     [int]$Number = 0,
+    [switch]$Timestamp,
     [switch]$Help,
-    [Parameter(ValueFromRemainingArguments = $true)]
+    [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
     [string[]]$FeatureDescription
 )
 $ErrorActionPreference = 'Stop'
 
 # Show help if requested
 if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] <feature description>"
+    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
     Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
+    Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
     Write-Host "  -Help               Show this help message"
     Write-Host ""
     Write-Host "Examples:"
     Write-Host "  ./create-new-feature.ps1 'Add user authentication system' -ShortName 'user-auth'"
     Write-Host "  ./create-new-feature.ps1 'Implement OAuth2 integration for API'"
+    Write-Host "  ./create-new-feature.ps1 -Timestamp -ShortName 'user-auth' 'Add user authentication'"
     exit 0
 }
 
 # Check if feature description provided
 if (-not $FeatureDescription -or $FeatureDescription.Count -eq 0) {
-    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] <feature description>"
+    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     exit 1
 }
 
@@ -71,7 +75,7 @@ function Get-HighestNumberFromSpecs {
     $highest = 0
     if (Test-Path $SpecsDir) {
         Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d+)') {
+            if ($_.Name -match '^(\d{3})-') {
                 $num = [int]$matches[1]
                 if ($num -gt $highest) { $highest = $num }
             }
@@ -92,7 +96,7 @@ function Get-HighestNumberFromBranches {
                 $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
                 
                 # Extract feature number if branch matches pattern ###-*
-                if ($cleanBranch -match '^(\d+)-') {
+                if ($cleanBranch -match '^(\d{3})-') {
                     $num = [int]$matches[1]
                     if ($num -gt $highest) { $highest = $num }
                 }
@@ -141,6 +145,9 @@ if (-not $fallbackRoot) {
     exit 1
 }
 
+# Load common functions (includes Resolve-Template)
+. "$PSScriptRoot/common.ps1"
+
 try {
     $repoRoot = git rev-parse --show-toplevel 2>$null
     if ($LASTEXITCODE -eq 0) {
@@ -212,27 +219,40 @@ if ($ShortName) {
     $branchSuffix = Get-BranchName -Description $featureDesc
 }
 
-# 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 $specsDir) + 1
-    }
+# Warn if -Number and -Timestamp are both specified
+if ($Timestamp -and $Number -ne 0) {
+    Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
+    $Number = 0
 }
 
-$featureNum = ('{0:000}' -f $Number)
-$branchName = "$featureNum-$branchSuffix"
+# Determine branch prefix
+if ($Timestamp) {
+    $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
+    $branchName = "$featureNum-$branchSuffix"
+} else {
+    # Determine branch number
+    if ($Number -eq 0) {
+        if ($hasGit) {
+            # Check existing branches on remotes
+            $Number = Get-NextBranchNumber -SpecsDir $specsDir
+        } else {
+            # Fall back to local directory check
+            $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
+        }
+    }
+
+    $featureNum = ('{0:000}' -f $Number)
+    $branchName = "$featureNum-$branchSuffix"
+}
 
 # GitHub enforces a 244-byte limit on branch names
 # Validate and truncate if necessary
 $maxBranchLength = 244
 if ($branchName.Length -gt $maxBranchLength) {
     # Calculate how much we need to trim from suffix
-    # Account for: feature number (3) + hyphen (1) = 4 chars
-    $maxSuffixLength = $maxBranchLength - 4
+    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
+    $prefixLength = $featureNum.Length + 1
+    $maxSuffixLength = $maxBranchLength - $prefixLength
     
     # Truncate suffix
     $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
@@ -262,7 +282,11 @@ if ($hasGit) {
         # Check if branch already exists
         $existingBranch = git branch --list $branchName 2>$null
         if ($existingBranch) {
-            Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
+            if ($Timestamp) {
+                Write-Error "Error: Branch '$branchName' already exists. Rerun to get a new timestamp or use a different -ShortName."
+            } else {
+                Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
+            }
             exit 1
         } else {
             Write-Error "Error: Failed to create git branch '$branchName'. Please check your git configuration and try again."
@@ -276,9 +300,9 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
 
-$template = Join-Path $repoRoot '.specify/templates/spec-template.md'
+$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
 $specFile = Join-Path $featureDir 'spec.md'
-if (Test-Path $template) { 
+if ($template -and (Test-Path $template)) { 
     Copy-Item $template $specFile -Force 
 } else { 
     New-Item -ItemType File -Path $specFile | Out-Null 

scripts/powershell/setup-plan.ps1

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

scripts/powershell/update-agent-context.ps1

@@ -9,7 +9,7 @@ Mirrors the behavior of scripts/bash/update-agent-context.sh:
  2. Plan Data Extraction
  3. Agent File Management (create from template or update existing)
  4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, generic)
+ 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, junie, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, pi, iflow, generic)
 
 .PARAMETER AgentType
 Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
@@ -25,7 +25,7 @@ Relies on common helper functions in common.ps1
 #>
 param(
     [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','generic')]
+    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','junie','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','qodercli','vibe','kimi','trae','pi','iflow','generic')]
     [string]$AgentType
 )
 
@@ -51,6 +51,7 @@ $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'
@@ -64,6 +65,8 @@ $AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
 $BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 $VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
 $KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
+$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/AGENTS.md'
+$IFLOW_FILE    = Join-Path $REPO_ROOT 'IFLOW.md'
 
 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
 
@@ -395,6 +398,7 @@ 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' }
@@ -408,8 +412,11 @@ function Update-SpecificAgent {
         'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
         'vibe'     { Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe' }
         'kimi'     { Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code' }
+        'trae'     { Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae' }
+        '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|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|generic'; return $false }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|generic'; return $false }
     }
 }
 
@@ -423,6 +430,7 @@ 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 }
@@ -435,6 +443,8 @@ function Update-AllExistingAgents {
     if (Test-Path $BOB_FILE)      { if (-not (Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob')) { $ok = $false }; $found = $true }
     if (Test-Path $VIBE_FILE)     { if (-not (Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe')) { $ok = $false }; $found = $true }
     if (Test-Path $KIMI_FILE)     { if (-not (Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code')) { $ok = $false }; $found = $true }
+    if (Test-Path $TRAE_FILE)     { if (-not (Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae')) { $ok = $false }; $found = $true }
+    if (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 = $false }
@@ -449,7 +459,7 @@ function Print-Summary {
     if ($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|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|generic]'
+    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]'
 }
 
 function Main {

src/specify_cli/agent_pack.py

@@ -0,0 +1,849 @@
+"""
+Agent Pack Manager for Spec Kit
+
+Implements self-bootstrapping agent packs with declarative manifests
+(speckit-agent.yml) and Python bootstrap modules (bootstrap.py).
+
+Agent packs resolve by priority:
+  1. User-level   (~/.specify/agents/<id>/)
+  2. Project-level (.specify/agents/<id>/)
+  3. Catalog-installed (downloaded via `specify agent add`)
+  4. Embedded in wheel (official packs under core_pack/agents/)
+
+The embedded packs ship inside the pip wheel so that
+`pip install specify-cli && specify init --ai claude` works offline.
+"""
+
+import hashlib
+import importlib.util
+import json
+import shutil
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+import yaml
+from platformdirs import user_data_path
+
+
+# ---------------------------------------------------------------------------
+# Manifest schema
+# ---------------------------------------------------------------------------
+
+MANIFEST_FILENAME = "speckit-agent.yml"
+BOOTSTRAP_FILENAME = "bootstrap.py"
+
+MANIFEST_SCHEMA_VERSION = "1.0"
+
+# Required top-level keys
+_REQUIRED_TOP_KEYS = {"schema_version", "agent"}
+
+# Required keys within the ``agent`` block
+_REQUIRED_AGENT_KEYS = {"id", "name", "version"}
+
+
+class AgentPackError(Exception):
+    """Base exception for agent-pack operations."""
+
+
+class ManifestValidationError(AgentPackError):
+    """Raised when a speckit-agent.yml file is invalid."""
+
+
+class PackResolutionError(AgentPackError):
+    """Raised when no pack can be found for the requested agent id."""
+
+
+class AgentFileModifiedError(AgentPackError):
+    """Raised when teardown finds user-modified files and ``--force`` is not set."""
+
+
+# ---------------------------------------------------------------------------
+# Manifest
+# ---------------------------------------------------------------------------
+
+@dataclass
+class AgentManifest:
+    """Parsed and validated representation of a speckit-agent.yml file."""
+
+    # identity
+    id: str
+    name: str
+    version: str
+    description: str = ""
+    author: str = ""
+    license: str = ""
+
+    # runtime
+    requires_cli: bool = False
+    install_url: Optional[str] = None
+    cli_tool: Optional[str] = None
+
+    # compatibility
+    speckit_version: str = ">=0.1.0"
+
+    # discovery
+    tags: List[str] = field(default_factory=list)
+
+    # command registration metadata (used by CommandRegistrar / extensions)
+    commands_dir: str = ""
+    command_format: str = "markdown"
+    arg_placeholder: str = "$ARGUMENTS"
+    file_extension: str = ".md"
+
+    # raw data for anything else
+    raw: Dict[str, Any] = field(default_factory=dict, repr=False)
+
+    # filesystem path to the pack directory that produced this manifest
+    pack_path: Optional[Path] = field(default=None, repr=False)
+
+    @classmethod
+    def from_yaml(cls, path: Path) -> "AgentManifest":
+        """Load and validate a manifest from *path*.
+
+        Raises ``ManifestValidationError`` on structural problems.
+        """
+        try:
+            text = path.read_text(encoding="utf-8")
+            data = yaml.safe_load(text) or {}
+        except yaml.YAMLError as exc:
+            raise ManifestValidationError(f"Invalid YAML in {path}: {exc}")
+        except FileNotFoundError:
+            raise ManifestValidationError(f"Manifest not found: {path}")
+
+        return cls.from_dict(data, pack_path=path.parent)
+
+    @classmethod
+    def from_dict(cls, data: dict, *, pack_path: Optional[Path] = None) -> "AgentManifest":
+        """Build a manifest from a raw dictionary."""
+        if not isinstance(data, dict):
+            raise ManifestValidationError("Manifest must be a YAML mapping")
+
+        missing_top = _REQUIRED_TOP_KEYS - set(data)
+        if missing_top:
+            raise ManifestValidationError(
+                f"Missing required top-level key(s): {', '.join(sorted(missing_top))}"
+            )
+
+        if data.get("schema_version") != MANIFEST_SCHEMA_VERSION:
+            raise ManifestValidationError(
+                f"Unsupported schema_version: {data.get('schema_version')!r} "
+                f"(expected {MANIFEST_SCHEMA_VERSION!r})"
+            )
+
+        agent_block = data.get("agent")
+        if not isinstance(agent_block, dict):
+            raise ManifestValidationError("'agent' must be a mapping")
+
+        missing_agent = _REQUIRED_AGENT_KEYS - set(agent_block)
+        if missing_agent:
+            raise ManifestValidationError(
+                f"Missing required agent key(s): {', '.join(sorted(missing_agent))}"
+            )
+
+        runtime = data.get("runtime") or {}
+        requires = data.get("requires") or {}
+        tags = data.get("tags") or []
+        cmd_reg = data.get("command_registration") or {}
+
+        return cls(
+            id=str(agent_block["id"]),
+            name=str(agent_block["name"]),
+            version=str(agent_block["version"]),
+            description=str(agent_block.get("description", "")),
+            author=str(agent_block.get("author", "")),
+            license=str(agent_block.get("license", "")),
+            requires_cli=bool(runtime.get("requires_cli", False)),
+            install_url=runtime.get("install_url"),
+            cli_tool=runtime.get("cli_tool"),
+            speckit_version=str(requires.get("speckit_version", ">=0.1.0")),
+            tags=[str(t) for t in tags] if isinstance(tags, list) else [],
+            commands_dir=str(cmd_reg.get("commands_dir", "")),
+            command_format=str(cmd_reg.get("format", "markdown")),
+            arg_placeholder=str(cmd_reg.get("arg_placeholder", "$ARGUMENTS")),
+            file_extension=str(cmd_reg.get("file_extension", ".md")),
+            raw=data,
+            pack_path=pack_path,
+        )
+
+
+# ---------------------------------------------------------------------------
+# Bootstrap base class
+# ---------------------------------------------------------------------------
+
+class AgentBootstrap:
+    """Base class that every agent pack's ``bootstrap.py`` must subclass.
+
+    Subclasses override :meth:`setup` and :meth:`teardown` to define
+    agent-specific lifecycle operations.
+    """
+
+    def __init__(self, manifest: AgentManifest):
+        self.manifest = manifest
+        self.pack_path = manifest.pack_path
+
+    # -- lifecycle -----------------------------------------------------------
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install agent files into *project_path*.
+
+        This is invoked by ``specify init --ai <agent>`` and
+        ``specify agent switch <agent>``.
+
+        Implementations **must** return every file they create so that the
+        CLI can record both agent-installed files and extension-installed
+        files in a single install manifest.
+
+        Args:
+            project_path: Target project directory.
+            script_type: ``"sh"`` or ``"ps"``.
+            options: Arbitrary key/value options forwarded from the CLI.
+
+        Returns:
+            List of absolute paths of files created during setup.
+        """
+        raise NotImplementedError
+
+    def teardown(
+        self,
+        project_path: Path,
+        *,
+        force: bool = False,
+        files: Optional[Dict[str, str]] = None,
+    ) -> List[str]:
+        """Remove agent-specific files from *project_path*.
+
+        Invoked by ``specify agent switch`` (for the *old* agent) and
+        ``specify agent remove`` when the user explicitly uninstalls.
+        Must preserve shared infrastructure (specs, plans, tasks, etc.).
+
+        Only individual files are removed — directories are **never**
+        deleted.
+
+        The caller (CLI) is expected to check for user-modified files
+        **before** invoking teardown and prompt for confirmation.  If
+        *files* is provided, exactly those files are removed (values are
+        ignored but kept for forward compatibility).  Otherwise the
+        install manifest is read.
+
+        Args:
+            project_path: Project directory to clean up.
+            force: When ``True``, remove files even if they were modified
+                after installation.
+            files: Mapping of project-relative path → SHA-256 hash.
+                When supplied, only these files are removed and the
+                install manifest is not consulted.
+
+        Returns:
+            List of project-relative paths that were actually deleted.
+        """
+        raise NotImplementedError
+
+    # -- helpers available to subclasses ------------------------------------
+
+    def agent_dir(self, project_path: Path) -> Path:
+        """Return the agent's top-level directory inside the project."""
+        return project_path / self.manifest.commands_dir.split("/")[0]
+
+    def collect_installed_files(self, project_path: Path) -> List[Path]:
+        """Return every file under the agent's directory tree.
+
+        Subclasses should call this at the end of :meth:`setup` to build
+        the return list.  Any files present in the agent directory at
+        that point — whether created by ``setup()`` itself, by the
+        scaffold pipeline, or by a preceding step — are reported.
+        """
+        root = self.agent_dir(project_path)
+        if not root.is_dir():
+            return []
+        return sorted(p for p in root.rglob("*") if p.is_file())
+
+    def _scaffold_project(
+        self,
+        project_path: Path,
+        script_type: str,
+        is_current_dir: bool = False,
+    ) -> List[Path]:
+        """Run the shared scaffolding pipeline and return new files.
+
+        Calls ``scaffold_from_core_pack`` for this agent and then
+        collects every file that was created.  Subclasses should call
+        this from :meth:`setup` when they want to use the shared
+        scaffolding rather than creating files manually.
+
+        Returns:
+            List of absolute paths of **all** files created by the
+            scaffold (agent-specific commands, shared scripts,
+            templates, etc.).
+        """
+        # Lazy import to avoid circular dependency (agent_pack is
+        # imported by specify_cli.__init__).
+        from specify_cli import scaffold_from_core_pack
+
+        # Snapshot existing files
+        before: set[Path] = set()
+        if project_path.exists():
+            before = {p for p in project_path.rglob("*") if p.is_file()}
+
+        ok = scaffold_from_core_pack(
+            project_path, self.manifest.id, script_type, is_current_dir,
+        )
+        if not ok:
+            raise AgentPackError(
+                f"Scaffolding failed for agent '{self.manifest.id}'")
+
+        # Collect every new file
+        after = {p for p in project_path.rglob("*") if p.is_file()}
+        return sorted(after - before)
+
+    def finalize_setup(
+        self,
+        project_path: Path,
+        agent_files: Optional[List[Path]] = None,
+        extension_files: Optional[List[Path]] = None,
+    ) -> None:
+        """Record installed files for tracked teardown.
+
+        This must be called **after** the full init pipeline has finished
+        writing files (commands, context files, extensions) into the
+        project.  It combines the files reported by :meth:`setup` with
+        any extra files (e.g. from extension registration), scans the
+        agent's directory tree for anything additional, and writes the
+        install manifest.
+
+        ``setup()`` may return *all* files created by the shared
+        scaffolding (including shared project files in ``.specify/``).
+        Only files under the agent's own directory tree are recorded as
+        ``agent_files`` — shared project infrastructure is not tracked
+        per-agent and will not be removed during teardown.
+
+        Args:
+            agent_files: Files reported by :meth:`setup`.
+            extension_files: Files created by extension registration.
+        """
+        all_extension = list(extension_files or [])
+
+        # Filter agent_files: only keep files under the agent's directory
+        # tree.  setup() returns *all* scaffolded files (including shared
+        # project infrastructure in .specify/) but only agent-owned files
+        # should be tracked per-agent — shared files are not removed
+        # during teardown/switch.
+        agent_root = self.agent_dir(project_path)
+        agent_root_resolved = agent_root.resolve()
+        all_agent: List[Path] = []
+        for p in (agent_files or []):
+            try:
+                p.resolve().relative_to(agent_root_resolved)
+                all_agent.append(p)
+            except ValueError:
+                pass
+
+        # Scan the agent's directory tree for files created by later
+        # init pipeline steps (skills, presets, extensions) that
+        # setup() did not report.  We scan the agent root directory
+        # (e.g. .claude/) so we catch both commands and skills
+        # directories (skills-migrated agents replace the commands
+        # directory with a sibling skills directory during init).
+        if self.manifest.commands_dir:
+            agent_root = self.agent_dir(project_path)
+            if agent_root.is_dir():
+                agent_set = {p.resolve() for p in all_agent}
+                for p in agent_root.rglob("*"):
+                    if p.is_file() and p.resolve() not in agent_set:
+                        all_agent.append(p)
+                        agent_set.add(p.resolve())
+
+        record_installed_files(
+            project_path,
+            self.manifest.id,
+            agent_files=all_agent,
+            extension_files=all_extension,
+        )
+
+
+# ---------------------------------------------------------------------------
+# Installed-file tracking
+# ---------------------------------------------------------------------------
+
+def _manifest_path(project_path: Path, agent_id: str) -> Path:
+    """Return the path to the install manifest for *agent_id*."""
+    return project_path / ".specify" / f"agent-manifest-{agent_id}.json"
+
+
+def _sha256(path: Path) -> str:
+    """Return the hex SHA-256 of a file."""
+    h = hashlib.sha256()
+    with open(path, "rb") as f:
+        for chunk in iter(lambda: f.read(8192), b""):
+            h.update(chunk)
+    return h.hexdigest()
+
+
+def _hash_file_list(
+    project_path: Path,
+    files: List[Path],
+) -> Dict[str, str]:
+    """Build a {relative_path: sha256} dict from a list of file paths."""
+    entries: Dict[str, str] = {}
+    for file_path in files:
+        abs_path = project_path / file_path if not file_path.is_absolute() else file_path
+        if abs_path.is_file():
+            rel = str(abs_path.relative_to(project_path))
+            entries[rel] = _sha256(abs_path)
+    return entries
+
+
+def record_installed_files(
+    project_path: Path,
+    agent_id: str,
+    agent_files: Optional[List[Path]] = None,
+    extension_files: Optional[List[Path]] = None,
+) -> Path:
+    """Record the installed files and their SHA-256 hashes.
+
+    Writes ``.specify/agent-manifest-<agent_id>.json`` containing
+    categorised mappings of project-relative paths to SHA-256 digests.
+
+    Args:
+        project_path: Project root directory.
+        agent_id: Agent identifier.
+        agent_files: Files created by the agent's ``setup()`` and the
+            init pipeline (core commands / templates).
+        extension_files: Files created by extension registration.
+
+    Returns:
+        Path to the written manifest file.
+    """
+    agent_entries = _hash_file_list(project_path, agent_files or [])
+    extension_entries = _hash_file_list(project_path, extension_files or [])
+
+    manifest_file = _manifest_path(project_path, agent_id)
+    manifest_file.parent.mkdir(parents=True, exist_ok=True)
+    manifest_file.write_text(
+        json.dumps(
+            {
+                "agent_id": agent_id,
+                "agent_files": agent_entries,
+                "extension_files": extension_entries,
+            },
+            indent=2,
+        ),
+        encoding="utf-8",
+    )
+    return manifest_file
+
+
+def _all_tracked_entries(data: dict) -> Dict[str, str]:
+    """Return the combined file → hash mapping from a manifest dict.
+
+    Supports both the new categorised layout (``agent_files`` +
+    ``extension_files``) and the legacy flat ``files`` key.
+    """
+    combined: Dict[str, str] = {}
+    # Legacy flat format
+    if "files" in data and isinstance(data["files"], dict):
+        combined.update(data["files"])
+    # New categorised format
+    if "agent_files" in data and isinstance(data["agent_files"], dict):
+        combined.update(data["agent_files"])
+    if "extension_files" in data and isinstance(data["extension_files"], dict):
+        combined.update(data["extension_files"])
+    return combined
+
+
+def get_tracked_files(
+    project_path: Path,
+    agent_id: str,
+) -> tuple[Dict[str, str], Dict[str, str]]:
+    """Return the tracked file hashes split by source.
+
+    Returns:
+        A tuple ``(agent_files, extension_files)`` where each is a
+        ``{relative_path: sha256}`` dict.  Returns two empty dicts
+        when no install manifest exists.
+    """
+    manifest_file = _manifest_path(project_path, agent_id)
+    if not manifest_file.is_file():
+        return {}, {}
+
+    try:
+        data = json.loads(manifest_file.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError):
+        return {}, {}
+
+    # Support legacy flat format
+    if "files" in data and "agent_files" not in data:
+        return dict(data["files"]), {}
+
+    agent_entries = data.get("agent_files", {})
+    ext_entries = data.get("extension_files", {})
+    return dict(agent_entries), dict(ext_entries)
+
+
+def check_modified_files(
+    project_path: Path,
+    agent_id: str,
+) -> List[str]:
+    """Return project-relative paths of files modified since installation.
+
+    Returns an empty list when no install manifest exists or when every
+    tracked file still has its original hash.
+    """
+    manifest_file = _manifest_path(project_path, agent_id)
+    if not manifest_file.is_file():
+        return []
+
+    try:
+        data = json.loads(manifest_file.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError):
+        return []
+
+    entries = _all_tracked_entries(data)
+
+    modified: List[str] = []
+    for rel_path, original_hash in entries.items():
+        abs_path = project_path / rel_path
+        if abs_path.is_file():
+            if _sha256(abs_path) != original_hash:
+                modified.append(rel_path)
+        # If the file was deleted by the user, treat it as not needing
+        # removal — skip rather than flag as modified.
+
+    return modified
+
+
+def remove_tracked_files(
+    project_path: Path,
+    agent_id: str,
+    *,
+    force: bool = False,
+    files: Optional[Dict[str, str]] = None,
+) -> List[str]:
+    """Remove individual tracked files.
+
+    If *files* is provided, exactly those files are removed (the values
+    are ignored but accepted for forward compatibility).  Otherwise the
+    install manifest for *agent_id* is read.
+
+    Raises :class:`AgentFileModifiedError` if any tracked file was
+    modified and *force* is ``False`` (only when reading from the
+    manifest — callers that pass *files* are expected to have already
+    prompted the user).
+
+    Directories are **never** deleted — only individual files.
+
+    Args:
+        project_path: Project root directory.
+        agent_id: Agent identifier.
+        force: When ``True``, delete even modified files.
+        files: Explicit mapping of project-relative path → hash.  When
+            supplied, the install manifest is not consulted.
+
+    Returns:
+        List of project-relative paths that were removed.
+    """
+    manifest_file = _manifest_path(project_path, agent_id)
+
+    if files is not None:
+        entries = files
+    else:
+        if not manifest_file.is_file():
+            return []
+        try:
+            data = json.loads(manifest_file.read_text(encoding="utf-8"))
+        except (json.JSONDecodeError, OSError):
+            return []
+
+        entries = _all_tracked_entries(data)
+        if not entries:
+            manifest_file.unlink(missing_ok=True)
+            return []
+
+        if not force:
+            modified = check_modified_files(project_path, agent_id)
+            if modified:
+                raise AgentFileModifiedError(
+                    f"The following agent files have been modified since installation:\n"
+                    + "\n".join(f"  {p}" for p in modified)
+                    + "\nUse --force to remove them anyway."
+                )
+
+    removed: List[str] = []
+    for rel_path in entries:
+        abs_path = project_path / rel_path
+        if abs_path.is_file():
+            abs_path.unlink()
+            removed.append(rel_path)
+
+    # Clean up the install manifest itself
+    if manifest_file.is_file():
+        manifest_file.unlink(missing_ok=True)
+    return removed
+
+
+# ---------------------------------------------------------------------------
+# Pack resolution
+# ---------------------------------------------------------------------------
+
+def _embedded_agents_dir() -> Path:
+    """Return the path to the embedded agent packs inside the wheel."""
+    return Path(__file__).parent / "core_pack" / "agents"
+
+
+def _user_agents_dir() -> Path:
+    """Return the user-level agent overrides directory."""
+    return user_data_path("specify", "github") / "agents"
+
+
+def _project_agents_dir(project_path: Path) -> Path:
+    """Return the project-level agent overrides directory."""
+    return project_path / ".specify" / "agents"
+
+
+def _catalog_agents_dir() -> Path:
+    """Return the catalog-installed agent cache directory."""
+    return user_data_path("specify", "github") / "agent-cache"
+
+
+@dataclass
+class ResolvedPack:
+    """Result of resolving an agent pack through the priority stack."""
+    manifest: AgentManifest
+    source: str          # "user", "project", "catalog", "embedded"
+    path: Path
+    overrides: Optional[str] = None  # version of the pack being overridden
+
+
+def resolve_agent_pack(
+    agent_id: str,
+    project_path: Optional[Path] = None,
+) -> ResolvedPack:
+    """Resolve an agent pack through the priority stack.
+
+    Priority (highest first):
+      1. User-level     ``~/.specify/agents/<id>/``
+      2. Project-level  ``.specify/agents/<id>/``
+      3. Catalog-installed cache
+      4. Embedded in wheel
+
+    Raises ``PackResolutionError`` when no pack is found at any level.
+    """
+    candidates: List[tuple[str, Path]] = []
+
+    # Priority 1 — user level
+    user_dir = _user_agents_dir() / agent_id
+    candidates.append(("user", user_dir))
+
+    # Priority 2 — project level
+    if project_path is not None:
+        proj_dir = _project_agents_dir(project_path) / agent_id
+        candidates.append(("project", proj_dir))
+
+    # Priority 3 — catalog cache
+    catalog_dir = _catalog_agents_dir() / agent_id
+    candidates.append(("catalog", catalog_dir))
+
+    # Priority 4 — embedded
+    embedded_dir = _embedded_agents_dir() / agent_id
+    candidates.append(("embedded", embedded_dir))
+
+    embedded_manifest: Optional[AgentManifest] = None
+
+    for source, pack_dir in candidates:
+        manifest_file = pack_dir / MANIFEST_FILENAME
+        if manifest_file.is_file():
+            manifest = AgentManifest.from_yaml(manifest_file)
+            if source == "embedded":
+                embedded_manifest = manifest
+
+            overrides = None
+            if source != "embedded" and embedded_manifest is None:
+                # Try loading embedded to record what it overrides
+                emb_file = _embedded_agents_dir() / agent_id / MANIFEST_FILENAME
+                if emb_file.is_file():
+                    try:
+                        emb = AgentManifest.from_yaml(emb_file)
+                        overrides = f"embedded v{emb.version}"
+                    except AgentPackError:
+                        pass
+
+            return ResolvedPack(
+                manifest=manifest,
+                source=source,
+                path=pack_dir,
+                overrides=overrides,
+            )
+
+    raise PackResolutionError(
+        f"Agent '{agent_id}' not found locally or in any active catalog.\n"
+        f"Run 'specify agent search' to browse available agents, or\n"
+        f"'specify agent add {agent_id} --from <path>' for offline install."
+    )
+
+
+# ---------------------------------------------------------------------------
+# Pack discovery helpers
+# ---------------------------------------------------------------------------
+
+def list_embedded_agents() -> List[AgentManifest]:
+    """Return manifests for all agent packs embedded in the wheel."""
+    agents_dir = _embedded_agents_dir()
+    if not agents_dir.is_dir():
+        return []
+
+    manifests: List[AgentManifest] = []
+    for child in sorted(agents_dir.iterdir()):
+        manifest_file = child / MANIFEST_FILENAME
+        if child.is_dir() and manifest_file.is_file():
+            try:
+                manifests.append(AgentManifest.from_yaml(manifest_file))
+            except AgentPackError:
+                continue
+    return manifests
+
+
+def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
+    """List all available agents, resolved through the priority stack.
+
+    Each agent id appears at most once, at its highest-priority source.
+    """
+    seen: dict[str, ResolvedPack] = {}
+
+    # Start from lowest priority (embedded) so higher priorities overwrite
+    for manifest in list_embedded_agents():
+        seen[manifest.id] = ResolvedPack(
+            manifest=manifest,
+            source="embedded",
+            path=manifest.pack_path or _embedded_agents_dir() / manifest.id,
+        )
+
+    # Catalog cache
+    catalog_dir = _catalog_agents_dir()
+    if catalog_dir.is_dir():
+        for child in sorted(catalog_dir.iterdir()):
+            mf = child / MANIFEST_FILENAME
+            if child.is_dir() and mf.is_file():
+                try:
+                    m = AgentManifest.from_yaml(mf)
+                    overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
+                    seen[m.id] = ResolvedPack(manifest=m, source="catalog", path=child, overrides=overrides)
+                except AgentPackError:
+                    continue
+
+    # Project-level
+    if project_path is not None:
+        proj_dir = _project_agents_dir(project_path)
+        if proj_dir.is_dir():
+            for child in sorted(proj_dir.iterdir()):
+                mf = child / MANIFEST_FILENAME
+                if child.is_dir() and mf.is_file():
+                    try:
+                        m = AgentManifest.from_yaml(mf)
+                        overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
+                        seen[m.id] = ResolvedPack(manifest=m, source="project", path=child, overrides=overrides)
+                    except AgentPackError:
+                        continue
+
+    # User-level
+    user_dir = _user_agents_dir()
+    if user_dir.is_dir():
+        for child in sorted(user_dir.iterdir()):
+            mf = child / MANIFEST_FILENAME
+            if child.is_dir() and mf.is_file():
+                try:
+                    m = AgentManifest.from_yaml(mf)
+                    overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
+                    seen[m.id] = ResolvedPack(manifest=m, source="user", path=child, overrides=overrides)
+                except AgentPackError:
+                    continue
+
+    return sorted(seen.values(), key=lambda r: r.manifest.id)
+
+
+def load_bootstrap(pack_path: Path, manifest: AgentManifest) -> AgentBootstrap:
+    """Import ``bootstrap.py`` from *pack_path* and return the bootstrap instance.
+
+    The bootstrap module must define exactly one public subclass of
+    ``AgentBootstrap``.  That class is instantiated with *manifest* and
+    returned.
+    """
+    bootstrap_file = pack_path / BOOTSTRAP_FILENAME
+    if not bootstrap_file.is_file():
+        raise AgentPackError(
+            f"Bootstrap module not found: {bootstrap_file}"
+        )
+
+    spec = importlib.util.spec_from_file_location(
+        f"speckit_agent_{manifest.id}_bootstrap", bootstrap_file
+    )
+    if spec is None or spec.loader is None:
+        raise AgentPackError(f"Cannot load bootstrap module: {bootstrap_file}")
+
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+
+    # Find the AgentBootstrap subclass
+    candidates = [
+        obj
+        for name, obj in vars(module).items()
+        if (
+            isinstance(obj, type)
+            and issubclass(obj, AgentBootstrap)
+            and obj is not AgentBootstrap
+            and not name.startswith("_")
+        )
+    ]
+    if not candidates:
+        raise AgentPackError(
+            f"No AgentBootstrap subclass found in {bootstrap_file}"
+        )
+    if len(candidates) > 1:
+        raise AgentPackError(
+            f"Multiple AgentBootstrap subclasses in {bootstrap_file}: "
+            f"{[c.__name__ for c in candidates]}"
+        )
+
+    return candidates[0](manifest)
+
+
+def validate_pack(pack_path: Path) -> List[str]:
+    """Validate a pack directory structure and return a list of warnings.
+
+    Returns an empty list when the pack is fully valid.
+    Raises ``ManifestValidationError`` on hard errors.
+    """
+    warnings: List[str] = []
+    manifest_file = pack_path / MANIFEST_FILENAME
+
+    if not manifest_file.is_file():
+        raise ManifestValidationError(
+            f"Missing {MANIFEST_FILENAME} in {pack_path}"
+        )
+
+    manifest = AgentManifest.from_yaml(manifest_file)
+
+    bootstrap_file = pack_path / BOOTSTRAP_FILENAME
+    if not bootstrap_file.is_file():
+        warnings.append(f"Missing {BOOTSTRAP_FILENAME} (pack cannot be bootstrapped)")
+
+    if not manifest.commands_dir:
+        warnings.append("command_registration.commands_dir not set in manifest")
+
+    if not manifest.description:
+        warnings.append("agent.description is empty")
+
+    if not manifest.tags:
+        warnings.append("No tags specified (reduces discoverability)")
+
+    return warnings
+
+
+def export_pack(agent_id: str, dest: Path, project_path: Optional[Path] = None) -> Path:
+    """Export the active pack for *agent_id* to *dest*.
+
+    Returns the path to the exported pack directory.
+    """
+    resolved = resolve_agent_pack(agent_id, project_path=project_path)
+    dest.mkdir(parents=True, exist_ok=True)
+    shutil.copytree(resolved.path, dest, dirs_exist_ok=True)
+    return dest

src/specify_cli/agents.py

@@ -0,0 +1,573 @@
+"""
+Agent Command Registrar for Spec Kit
+
+Shared infrastructure for registering commands with AI agents.
+Used by both the extension system and the preset system to write
+command files into agent-specific directories in the correct format.
+"""
+
+from pathlib import Path
+from typing import Dict, List, Any
+
+import platform
+import yaml
+
+
+class CommandRegistrar:
+    """Handles registration of commands with AI agents.
+
+    Supports writing command files in Markdown or TOML format to the
+    appropriate agent directory, with correct argument placeholders
+    and companion files (e.g. Copilot .prompt.md).
+    """
+
+    # Agent configurations with directory, format, and argument placeholder
+    AGENT_CONFIGS = {
+        "claude": {
+            "dir": ".claude/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "gemini": {
+            "dir": ".gemini/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "copilot": {
+            "dir": ".github/agents",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".agent.md"
+        },
+        "cursor": {
+            "dir": ".cursor/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qwen": {
+            "dir": ".qwen/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "opencode": {
+            "dir": ".opencode/command",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codex": {
+            "dir": ".agents/skills",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": "/SKILL.md",
+        },
+        "windsurf": {
+            "dir": ".windsurf/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "junie": {
+            "dir": ".junie/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kilocode": {
+            "dir": ".kilocode/workflows",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "auggie": {
+            "dir": ".augment/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "roo": {
+            "dir": ".roo/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "codebuddy": {
+            "dir": ".codebuddy/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "qodercli": {
+            "dir": ".qoder/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kiro-cli": {
+            "dir": ".kiro/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "pi": {
+            "dir": ".pi/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "amp": {
+            "dir": ".agents/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "shai": {
+            "dir": ".shai/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "tabnine": {
+            "dir": ".tabnine/agent/commands",
+            "format": "toml",
+            "args": "{{args}}",
+            "extension": ".toml"
+        },
+        "bob": {
+            "dir": ".bob/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "kimi": {
+            "dir": ".kimi/skills",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": "/SKILL.md",
+        },
+        "trae": {
+            "dir": ".trae/rules",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        },
+        "iflow": {
+            "dir": ".iflow/commands",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
+        }
+    }
+
+    @staticmethod
+    def parse_frontmatter(content: str) -> tuple[dict, str]:
+        """Parse YAML frontmatter from Markdown content.
+
+        Args:
+            content: Markdown content with YAML frontmatter
+
+        Returns:
+            Tuple of (frontmatter_dict, body_content)
+        """
+        if not content.startswith("---"):
+            return {}, content
+
+        # Find second ---
+        end_marker = content.find("---", 3)
+        if end_marker == -1:
+            return {}, content
+
+        frontmatter_str = content[3:end_marker].strip()
+        body = content[end_marker + 3:].strip()
+
+        try:
+            frontmatter = yaml.safe_load(frontmatter_str) or {}
+        except yaml.YAMLError:
+            frontmatter = {}
+
+        if not isinstance(frontmatter, dict):
+            frontmatter = {}
+
+        return frontmatter, body
+
+    @staticmethod
+    def render_frontmatter(fm: dict) -> str:
+        """Render frontmatter dictionary as YAML.
+
+        Args:
+            fm: Frontmatter dictionary
+
+        Returns:
+            YAML-formatted frontmatter with delimiters
+        """
+        if not fm:
+            return ""
+
+        yaml_str = yaml.dump(fm, default_flow_style=False, sort_keys=False)
+        return f"---\n{yaml_str}---\n"
+
+    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+        """Adjust script paths from extension-relative to repo-relative.
+
+        Args:
+            frontmatter: Frontmatter dictionary
+
+        Returns:
+            Modified frontmatter with adjusted paths
+        """
+        for script_key in ("scripts", "agent_scripts"):
+            scripts = frontmatter.get(script_key)
+            if not isinstance(scripts, dict):
+                continue
+
+            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(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str,
+        context_note: str = None
+    ) -> str:
+        """Render command in Markdown format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+            context_note: Custom context comment (default: <!-- Source: {source_id} -->)
+
+        Returns:
+            Formatted Markdown command file content
+        """
+        if context_note is None:
+            context_note = f"\n<!-- Source: {source_id} -->\n"
+        return self.render_frontmatter(frontmatter) + "\n" + context_note + body
+
+    def render_toml_command(
+        self,
+        frontmatter: dict,
+        body: str,
+        source_id: str
+    ) -> str:
+        """Render command in TOML format.
+
+        Args:
+            frontmatter: Command frontmatter
+            body: Command body content
+            source_id: Source identifier (extension or preset ID)
+
+        Returns:
+            Formatted TOML command file content
+        """
+        toml_lines = []
+
+        if "description" in frontmatter:
+            desc = frontmatter["description"].replace('"', '\\"')
+            toml_lines.append(f'description = "{desc}"')
+            toml_lines.append("")
+
+        toml_lines.append(f"# Source: {source_id}")
+        toml_lines.append("")
+
+        toml_lines.append('prompt = """')
+        toml_lines.append(body)
+        toml_lines.append('"""')
+
+        return "\n".join(toml_lines)
+
+    def 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.
+
+        Args:
+            content: Command content
+            from_placeholder: Source placeholder (e.g., "$ARGUMENTS")
+            to_placeholder: Target placeholder (e.g., "{{args}}")
+
+        Returns:
+            Content with converted placeholders
+        """
+        return content.replace(from_placeholder, to_placeholder)
+
+    @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,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> List[str]:
+        """Register commands for a specific agent.
+
+        Args:
+            agent_name: Agent name (claude, gemini, copilot, etc.)
+            commands: List of command info dicts with 'name', 'file', and optional 'aliases'
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            List of registered command names
+
+        Raises:
+            ValueError: If agent is not supported
+        """
+        if agent_name not in self.AGENT_CONFIGS:
+            raise ValueError(f"Unsupported agent: {agent_name}")
+
+        agent_config = self.AGENT_CONFIGS[agent_name]
+        commands_dir = project_root / agent_config["dir"]
+        commands_dir.mkdir(parents=True, exist_ok=True)
+
+        registered = []
+
+        for cmd_info in commands:
+            cmd_name = cmd_info["name"]
+            cmd_file = cmd_info["file"]
+
+            source_file = source_dir / cmd_file
+            if not source_file.exists():
+                continue
+
+            content = source_file.read_text(encoding="utf-8")
+            frontmatter, body = self.parse_frontmatter(content)
+
+            frontmatter = self._adjust_script_paths(frontmatter)
+
+            body = self._convert_argument_placeholder(
+                body, "$ARGUMENTS", agent_config["args"]
+            )
+
+            output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+
+            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.parent.mkdir(parents=True, exist_ok=True)
+            dest_file.write_text(output, encoding="utf-8")
+
+            if agent_name == "copilot":
+                self.write_copilot_prompt(project_root, cmd_name)
+
+            registered.append(cmd_name)
+
+            for alias in cmd_info.get("aliases", []):
+                alias_output_name = self._compute_output_name(agent_name, alias, agent_config)
+                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")
+                if agent_name == "copilot":
+                    self.write_copilot_prompt(project_root, alias)
+                registered.append(alias)
+
+        return registered
+
+    @staticmethod
+    def write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
+        """Generate a companion .prompt.md file for a Copilot agent command.
+
+        Args:
+            project_root: Path to project root
+            cmd_name: Command name (e.g. 'speckit.my-ext.example')
+        """
+        prompts_dir = project_root / ".github" / "prompts"
+        prompts_dir.mkdir(parents=True, exist_ok=True)
+        prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
+        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n", encoding="utf-8")
+
+    def register_commands_for_all_agents(
+        self,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+        project_root: Path,
+        context_note: str = None
+    ) -> Dict[str, List[str]]:
+        """Register commands for all detected agents in the project.
+
+        Args:
+            commands: List of command info dicts
+            source_id: Identifier of the source (extension or preset ID)
+            source_dir: Directory containing command source files
+            project_root: Path to project root
+            context_note: Custom context comment for markdown output
+
+        Returns:
+            Dictionary mapping agent names to list of registered commands
+        """
+        results = {}
+
+        for agent_name, agent_config in self.AGENT_CONFIGS.items():
+            agent_dir = project_root / agent_config["dir"]
+
+            if agent_dir.exists():
+                try:
+                    registered = self.register_commands(
+                        agent_name, commands, source_id, source_dir, project_root,
+                        context_note=context_note
+                    )
+                    if registered:
+                        results[agent_name] = registered
+                except ValueError:
+                    continue
+
+        return results
+
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories.
+
+        Args:
+            registered_commands: Dict mapping agent names to command name lists
+            project_root: Path to project root
+        """
+        for agent_name, cmd_names in registered_commands.items():
+            if agent_name not in self.AGENT_CONFIGS:
+                continue
+
+            agent_config = self.AGENT_CONFIGS[agent_name]
+            commands_dir = project_root / agent_config["dir"]
+
+            for cmd_name in cmd_names:
+                output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+                cmd_file = commands_dir / f"{output_name}{agent_config['extension']}"
+                if cmd_file.exists():
+                    cmd_file.unlink()
+
+                if agent_name == "copilot":
+                    prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
+                    if prompt_file.exists():
+                        prompt_file.unlink()

src/specify_cli/core_pack/agents/agy/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Antigravity agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Agy(AgentBootstrap):
+    """Bootstrap for Antigravity."""
+
+    AGENT_DIR = ".agent"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Antigravity agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Antigravity agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/amp/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Amp agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Amp(AgentBootstrap):
+    """Bootstrap for Amp."""
+
+    AGENT_DIR = ".agents"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Amp agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Amp agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/auggie/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Auggie CLI agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Auggie(AgentBootstrap):
+    """Bootstrap for Auggie CLI."""
+
+    AGENT_DIR = ".augment"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Auggie CLI agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Auggie CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/bob/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for IBM Bob agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Bob(AgentBootstrap):
+    """Bootstrap for IBM Bob."""
+
+    AGENT_DIR = ".bob"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install IBM Bob agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove IBM Bob agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/claude/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Claude Code agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Claude(AgentBootstrap):
+    """Bootstrap for Claude Code."""
+
+    AGENT_DIR = ".claude"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Claude Code agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Claude Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/codebuddy/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for CodeBuddy agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Codebuddy(AgentBootstrap):
+    """Bootstrap for CodeBuddy."""
+
+    AGENT_DIR = ".codebuddy"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install CodeBuddy agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove CodeBuddy agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/codex/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Codex CLI agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Codex(AgentBootstrap):
+    """Bootstrap for Codex CLI."""
+
+    AGENT_DIR = ".agents"
+    COMMANDS_SUBDIR = "skills"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Codex CLI agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Codex CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/copilot/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for GitHub Copilot agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Copilot(AgentBootstrap):
+    """Bootstrap for GitHub Copilot."""
+
+    AGENT_DIR = ".github"
+    COMMANDS_SUBDIR = "agents"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install GitHub Copilot agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove GitHub Copilot agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/cursor-agent/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Cursor agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class CursorAgent(AgentBootstrap):
+    """Bootstrap for Cursor."""
+
+    AGENT_DIR = ".cursor"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Cursor agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Cursor agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/gemini/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Gemini CLI agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Gemini(AgentBootstrap):
+    """Bootstrap for Gemini CLI."""
+
+    AGENT_DIR = ".gemini"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Gemini CLI agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Gemini CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/iflow/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for iFlow CLI agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Iflow(AgentBootstrap):
+    """Bootstrap for iFlow CLI."""
+
+    AGENT_DIR = ".iflow"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install iFlow CLI agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove iFlow CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/junie/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Junie agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Junie(AgentBootstrap):
+    """Bootstrap for Junie."""
+
+    AGENT_DIR = ".junie"
+    COMMANDS_SUBDIR = "commands"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Junie agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Junie agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/kilocode/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Kilo Code agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Kilocode(AgentBootstrap):
+    """Bootstrap for Kilo Code."""
+
+    AGENT_DIR = ".kilocode"
+    COMMANDS_SUBDIR = "workflows"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Kilo Code agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Kilo Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/kimi/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Kimi Code agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class Kimi(AgentBootstrap):
+    """Bootstrap for Kimi Code."""
+
+    AGENT_DIR = ".kimi"
+    COMMANDS_SUBDIR = "skills"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Kimi Code agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Kimi Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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

src/specify_cli/core_pack/agents/kiro-cli/bootstrap.py

@@ -0,0 +1,30 @@
+"""Bootstrap module for Kiro CLI agent pack."""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
+
+
+class KiroCli(AgentBootstrap):
+    """Bootstrap for Kiro CLI."""
+
+    AGENT_DIR = ".kiro"
+    COMMANDS_SUBDIR = "prompts"
+
+    def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -> List[Path]:
+        """Install Kiro CLI agent files into the project."""
+        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        return self._scaffold_project(project_path, script_type)
+
+    def teardown(self, project_path: Path, *, force: bool = False, files: Optional[Dict[str, str]] = None) -> List[str]:
+        """Remove Kiro CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  When *files* is provided, exactly those files are
+        removed.  Otherwise the install manifest is consulted and
+        ``AgentFileModifiedError`` is raised if any tracked file was
+        modified and *force* is ``False``.
+        """
+        return remove_tracked_files(project_path, self.manifest.id, force=force, files=files)

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

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