Add modular extension system (#1551)

* Add modular extension system for Spec Kit

Implement a complete extension system that allows third-party developers
to extend Spec Kit functionality through plugins.

## Core Features
- Extension discovery and loading from local and global directories
- YAML-based extension manifest (extension.yml) with metadata and capabilities
- Command extensions: custom slash commands with markdown templates
- Hook system: pre/post hooks for generate, task, and sync operations
- Extension catalog for discovering and installing community extensions
- SPECKIT_CATALOG_URL environment variable for catalog URL override

## Installation Methods
- Catalog install: `specify extension add <name>`
- URL install: `specify extension add <name> --from <url>`
- Dev install: `specify extension add --dev <path>`

## Implementation
- ExtensionManager class for lifecycle management (load, enable, disable)
- Support for extension dependencies and version constraints
- Configuration layering (global → project → extension)
- Hook conditions for conditional execution

## Documentation
- RFC with design rationale and architecture decisions
- API reference for extension developers
- Development guide with examples
- User guide for installing and managing extensions
- Publishing guide for the extension catalog

## Included
- Extension template for bootstrapping new extensions
- Comprehensive test suite
- Example catalog.json structure

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Update Jira extension to v2.1.0 in catalog

Adds 2-level mode support (Epic → Stories only).

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Address PR review feedback

- Fix Zip Slip vulnerability in ZIP extraction with path validation
- Fix keep_config option to actually preserve config files on removal
- Add URL validation for SPECKIT_CATALOG_URL (HTTPS required, localhost exception)
- Add security warning when installing from custom URLs (--from flag)
- Empty catalog.json so organizations can ship their own catalogs
- Fix markdown linter errors (MD040: add language to code blocks)
- Remove redundant import and fix unused variables in tests
- Add comment explaining empty except clause for backwards compatibility

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add comprehensive organization catalog customization docs

- Explain why default catalog is empty (org control)
- Document how to create and host custom catalogs
- Add catalog JSON schema reference
- Include use cases: private extensions, curated catalogs, air-gapped environments
- Add examples for combining catalog with direct installation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix test assertions for extension system data structures

- Update test_config_backup_on_remove to use new subdirectory structure
  (.backup/test-ext/file.yml instead of .backup/test-ext-file.yml)
- Update test_full_install_and_remove_workflow to handle registered_commands
  being a dict keyed by agent name instead of a flat list

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Address Copilot review feedback

- Fix localhost URL check to use parsed.hostname instead of netloc.startswith()
  This correctly handles URLs with ports like localhost:8080
- Fix YAML indentation error in config-template.yml (line 57)
- Fix double space typo in example.md (line 172)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add catalog.example.json as reference for organizations

The main catalog.json is intentionally empty so organizations can ship
their own curated catalogs. This example file shows the expected schema
and structure for creating organization-specific catalogs.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Address remaining Copilot security and logic review feedback

- Fix Zip Slip vulnerability by using relative_to() for safe path validation
- Add HTTPS validation for extension download URLs
- Backup both *-config.yml and *-config.local.yml files on remove
- Normalize boolean values to lowercase for hook condition comparisons
- Show non-default catalog warning only once per instance

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Ignoring linter for extensions directory

---------

Co-authored-by: iamaeroplane <michal.bachorik@gmail.com>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-authored-by: Manfred Riem <manfred.riem@microsoft.com>

.github/workflows/lint.yml

@@ -17,4 +17,6 @@ jobs:
       - name: Run markdownlint-cli2
         uses: DavidAnson/markdownlint-cli2-action@v19
         with:
-          globs: '**/*.md'
+          globs: |
+            '**/*.md'
+            !extensions/**/*.md

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

@@ -40,9 +40,15 @@ gh release create "$VERSION" \
   .genreleases/spec-kit-template-roo-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-codebuddy-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-codebuddy-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-qoder-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-qoder-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-amp-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-amp-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-shai-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-shai-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-q-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-q-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-bob-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-bob-ps-"$VERSION".zip \
   --title "Spec Kit Templates - $VERSION_NO_V" \
   --notes-file release_notes.md

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

@@ -0,0 +1,424 @@
+#!/usr/bin/env pwsh
+#requires -Version 7.0
+
+<#
+.SYNOPSIS
+    Build Spec Kit template release archives for each supported AI assistant and script type.
+
+.DESCRIPTION
+    create-release-packages.ps1 (workflow-local)
+    Build Spec Kit template release archives for each supported AI assistant and script type.
+    
+.PARAMETER Version
+    Version string with leading 'v' (e.g., v0.2.0)
+
+.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, q, bob, qoder
+
+.PARAMETER Scripts
+    Comma or space separated subset of script types to build (default: both)
+    Valid scripts: sh, ps
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0 -Agents claude,copilot -Scripts sh
+
+.EXAMPLE
+    .\create-release-packages.ps1 -Version v0.2.0 -Agents claude -Scripts ps
+#>
+
+param(
+    [Parameter(Mandatory=$true, Position=0)]
+    [string]$Version,
+    
+    [Parameter(Mandatory=$false)]
+    [string]$Agents = "",
+    
+    [Parameter(Mandatory=$false)]
+    [string]$Scripts = ""
+)
+
+$ErrorActionPreference = "Stop"
+
+# Validate version format
+if ($Version -notmatch '^v\d+\.\d+\.\d+$') {
+    Write-Error "Version must look like v0.0.0"
+    exit 1
+}
+
+Write-Host "Building release packages for $Version"
+
+# Create and use .genreleases directory for all build artifacts
+$GenReleasesDir = ".genreleases"
+if (Test-Path $GenReleasesDir) {
+    Remove-Item -Path $GenReleasesDir -Recurse -Force -ErrorAction SilentlyContinue
+}
+New-Item -ItemType Directory -Path $GenReleasesDir -Force | Out-Null
+
+function Rewrite-Paths {
+    param([string]$Content)
+    
+    $Content = $Content -replace '(/?)\bmemory/', '.specify/memory/'
+    $Content = $Content -replace '(/?)\bscripts/', '.specify/scripts/'
+    $Content = $Content -replace '(/?)\btemplates/', '.specify/templates/'
+    return $Content
+}
+
+function Generate-Commands {
+    param(
+        [string]$Agent,
+        [string]$Extension,
+        [string]$ArgFormat,
+        [string]$OutputDir,
+        [string]$ScriptVariant
+    )
+    
+    New-Item -ItemType Directory -Path $OutputDir -Force | Out-Null
+    
+    $templates = Get-ChildItem -Path "templates/commands/*.md" -File -ErrorAction SilentlyContinue
+    
+    foreach ($template in $templates) {
+        $name = [System.IO.Path]::GetFileNameWithoutExtension($template.Name)
+        
+        # Read file content and normalize line endings
+        $fileContent = (Get-Content -Path $template.FullName -Raw) -replace "`r`n", "`n"
+        
+        # Extract description from YAML frontmatter
+        $description = ""
+        if ($fileContent -match '(?m)^description:\s*(.+)$') {
+            $description = $matches[1]
+        }
+        
+        # Extract script command from YAML frontmatter
+        $scriptCommand = ""
+        if ($fileContent -match "(?m)^\s*${ScriptVariant}:\s*(.+)$") {
+            $scriptCommand = $matches[1]
+        }
+        
+        if ([string]::IsNullOrEmpty($scriptCommand)) {
+            Write-Warning "No script command found for $ScriptVariant in $($template.Name)"
+            $scriptCommand = "(Missing script command for $ScriptVariant)"
+        }
+        
+        # Extract agent_script command from YAML frontmatter if present
+        $agentScriptCommand = ""
+        if ($fileContent -match "(?ms)agent_scripts:.*?^\s*${ScriptVariant}:\s*(.+?)$") {
+            $agentScriptCommand = $matches[1].Trim()
+        }
+        
+        # Replace {SCRIPT} placeholder with the script command
+        $body = $fileContent -replace '\{SCRIPT\}', $scriptCommand
+        
+        # Replace {AGENT_SCRIPT} placeholder with the agent script command if found
+        if (-not [string]::IsNullOrEmpty($agentScriptCommand)) {
+            $body = $body -replace '\{AGENT_SCRIPT\}', $agentScriptCommand
+        }
+        
+        # Remove the scripts: and agent_scripts: sections from frontmatter
+        $lines = $body -split "`n"
+        $outputLines = @()
+        $inFrontmatter = $false
+        $skipScripts = $false
+        $dashCount = 0
+        
+        foreach ($line in $lines) {
+            if ($line -match '^---$') {
+                $outputLines += $line
+                $dashCount++
+                if ($dashCount -eq 1) {
+                    $inFrontmatter = $true
+                } else {
+                    $inFrontmatter = $false
+                }
+                continue
+            }
+            
+            if ($inFrontmatter) {
+                if ($line -match '^(scripts|agent_scripts):$') {
+                    $skipScripts = $true
+                    continue
+                }
+                if ($line -match '^[a-zA-Z].*:' -and $skipScripts) {
+                    $skipScripts = $false
+                }
+                if ($skipScripts -and $line -match '^\s+') {
+                    continue
+                }
+            }
+            
+            $outputLines += $line
+        }
+        
+        $body = $outputLines -join "`n"
+        
+        # Apply other substitutions
+        $body = $body -replace '\{ARGS\}', $ArgFormat
+        $body = $body -replace '__AGENT__', $Agent
+        $body = Rewrite-Paths -Content $body
+        
+        # Generate output file based on extension
+        $outputFile = Join-Path $OutputDir "speckit.$name.$Extension"
+        
+        switch ($Extension) {
+            'toml' {
+                $body = $body -replace '\\', '\\'
+                $output = "description = `"$description`"`n`nprompt = `"`"`"`n$body`n`"`"`""
+                Set-Content -Path $outputFile -Value $output -NoNewline
+            }
+            'md' {
+                Set-Content -Path $outputFile -Value $body -NoNewline
+            }
+            'agent.md' {
+                Set-Content -Path $outputFile -Value $body -NoNewline
+            }
+        }
+    }
+}
+
+function Generate-CopilotPrompts {
+    param(
+        [string]$AgentsDir,
+        [string]$PromptsDir
+    )
+    
+    New-Item -ItemType Directory -Path $PromptsDir -Force | Out-Null
+    
+    $agentFiles = Get-ChildItem -Path "$AgentsDir/speckit.*.agent.md" -File -ErrorAction SilentlyContinue
+    
+    foreach ($agentFile in $agentFiles) {
+        $basename = $agentFile.Name -replace '\.agent\.md$', ''
+        $promptFile = Join-Path $PromptsDir "$basename.prompt.md"
+        
+        $content = @"
+---
+agent: $basename
+---
+"@
+        Set-Content -Path $promptFile -Value $content
+    }
+}
+
+function Build-Variant {
+    param(
+        [string]$Agent,
+        [string]$Script
+    )
+    
+    $baseDir = Join-Path $GenReleasesDir "sdd-${Agent}-package-${Script}"
+    Write-Host "Building $Agent ($Script) package..."
+    New-Item -ItemType Directory -Path $baseDir -Force | Out-Null
+    
+    # Copy base structure but filter scripts by variant
+    $specDir = Join-Path $baseDir ".specify"
+    New-Item -ItemType Directory -Path $specDir -Force | Out-Null
+    
+    # Copy memory directory
+    if (Test-Path "memory") {
+        Copy-Item -Path "memory" -Destination $specDir -Recurse -Force
+        Write-Host "Copied memory -> .specify"
+    }
+    
+    # Only copy the relevant script variant directory
+    if (Test-Path "scripts") {
+        $scriptsDestDir = Join-Path $specDir "scripts"
+        New-Item -ItemType Directory -Path $scriptsDestDir -Force | Out-Null
+        
+        switch ($Script) {
+            'sh' {
+                if (Test-Path "scripts/bash") {
+                    Copy-Item -Path "scripts/bash" -Destination $scriptsDestDir -Recurse -Force
+                    Write-Host "Copied scripts/bash -> .specify/scripts"
+                }
+            }
+            'ps' {
+                if (Test-Path "scripts/powershell") {
+                    Copy-Item -Path "scripts/powershell" -Destination $scriptsDestDir -Recurse -Force
+                    Write-Host "Copied scripts/powershell -> .specify/scripts"
+                }
+            }
+        }
+        
+        # Copy any script files that aren't in variant-specific directories
+        Get-ChildItem -Path "scripts" -File -ErrorAction SilentlyContinue | ForEach-Object {
+            Copy-Item -Path $_.FullName -Destination $scriptsDestDir -Force
+        }
+    }
+    
+    # Copy templates (excluding commands directory and vscode-settings.json)
+    if (Test-Path "templates") {
+        $templatesDestDir = Join-Path $specDir "templates"
+        New-Item -ItemType Directory -Path $templatesDestDir -Force | Out-Null
+        
+        Get-ChildItem -Path "templates" -Recurse -File | Where-Object {
+            $_.FullName -notmatch 'templates[/\\]commands[/\\]' -and $_.Name -ne 'vscode-settings.json'
+        } | ForEach-Object {
+            $relativePath = $_.FullName.Substring((Resolve-Path "templates").Path.Length + 1)
+            $destFile = Join-Path $templatesDestDir $relativePath
+            $destFileDir = Split-Path $destFile -Parent
+            New-Item -ItemType Directory -Path $destFileDir -Force | Out-Null
+            Copy-Item -Path $_.FullName -Destination $destFile -Force
+        }
+        Write-Host "Copied templates -> .specify/templates"
+    }
+    
+    # Generate agent-specific command files
+    switch ($Agent) {
+        'claude' {
+            $cmdDir = Join-Path $baseDir ".claude/commands"
+            Generate-Commands -Agent 'claude' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'gemini' {
+            $cmdDir = Join-Path $baseDir ".gemini/commands"
+            Generate-Commands -Agent 'gemini' -Extension 'toml' -ArgFormat '{{args}}' -OutputDir $cmdDir -ScriptVariant $Script
+            if (Test-Path "agent_templates/gemini/GEMINI.md") {
+                Copy-Item -Path "agent_templates/gemini/GEMINI.md" -Destination (Join-Path $baseDir "GEMINI.md")
+            }
+        }
+        'copilot' {
+            $agentsDir = Join-Path $baseDir ".github/agents"
+            Generate-Commands -Agent 'copilot' -Extension 'agent.md' -ArgFormat '$ARGUMENTS' -OutputDir $agentsDir -ScriptVariant $Script
+            
+            # Generate companion prompt files
+            $promptsDir = Join-Path $baseDir ".github/prompts"
+            Generate-CopilotPrompts -AgentsDir $agentsDir -PromptsDir $promptsDir
+            
+            # Create VS Code workspace settings
+            $vscodeDir = Join-Path $baseDir ".vscode"
+            New-Item -ItemType Directory -Path $vscodeDir -Force | Out-Null
+            if (Test-Path "templates/vscode-settings.json") {
+                Copy-Item -Path "templates/vscode-settings.json" -Destination (Join-Path $vscodeDir "settings.json")
+            }
+        }
+        'cursor-agent' {
+            $cmdDir = Join-Path $baseDir ".cursor/commands"
+            Generate-Commands -Agent 'cursor-agent' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'qwen' {
+            $cmdDir = Join-Path $baseDir ".qwen/commands"
+            Generate-Commands -Agent 'qwen' -Extension 'toml' -ArgFormat '{{args}}' -OutputDir $cmdDir -ScriptVariant $Script
+            if (Test-Path "agent_templates/qwen/QWEN.md") {
+                Copy-Item -Path "agent_templates/qwen/QWEN.md" -Destination (Join-Path $baseDir "QWEN.md")
+            }
+        }
+        'opencode' {
+            $cmdDir = Join-Path $baseDir ".opencode/command"
+            Generate-Commands -Agent 'opencode' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'windsurf' {
+            $cmdDir = Join-Path $baseDir ".windsurf/workflows"
+            Generate-Commands -Agent 'windsurf' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'codex' {
+            $cmdDir = Join-Path $baseDir ".codex/prompts"
+            Generate-Commands -Agent 'codex' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'kilocode' {
+            $cmdDir = Join-Path $baseDir ".kilocode/workflows"
+            Generate-Commands -Agent 'kilocode' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'auggie' {
+            $cmdDir = Join-Path $baseDir ".augment/commands"
+            Generate-Commands -Agent 'auggie' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'roo' {
+            $cmdDir = Join-Path $baseDir ".roo/commands"
+            Generate-Commands -Agent 'roo' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'codebuddy' {
+            $cmdDir = Join-Path $baseDir ".codebuddy/commands"
+            Generate-Commands -Agent 'codebuddy' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'amp' {
+            $cmdDir = Join-Path $baseDir ".agents/commands"
+            Generate-Commands -Agent 'amp' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'q' {
+            $cmdDir = Join-Path $baseDir ".amazonq/prompts"
+            Generate-Commands -Agent 'q' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'bob' {
+            $cmdDir = Join-Path $baseDir ".bob/commands"
+            Generate-Commands -Agent 'bob' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+        'qoder' {
+            $cmdDir = Join-Path $baseDir ".qoder/commands"
+            Generate-Commands -Agent 'qoder' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+        }
+    }
+    
+    # Create zip archive
+    $zipFile = Join-Path $GenReleasesDir "spec-kit-template-${Agent}-${Script}-${Version}.zip"
+    Compress-Archive -Path "$baseDir/*" -DestinationPath $zipFile -Force
+    Write-Host "Created $zipFile"
+}
+
+# Define all agents and scripts
+$AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode', 'windsurf', 'codex', 'kilocode', 'auggie', 'roo', 'codebuddy', 'amp', 'q', 'bob', 'qoder')
+$AllScripts = @('sh', 'ps')
+
+function Normalize-List {
+    param([string]$Input)
+    
+    if ([string]::IsNullOrEmpty($Input)) {
+        return @()
+    }
+    
+    # Split by comma or space and remove duplicates while preserving order
+    $items = $Input -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
+    return $items
+}
+
+function Validate-Subset {
+    param(
+        [string]$Type,
+        [string[]]$Allowed,
+        [string[]]$Items
+    )
+    
+    $ok = $true
+    foreach ($item in $Items) {
+        if ($item -notin $Allowed) {
+            Write-Error "Unknown $Type '$item' (allowed: $($Allowed -join ', '))"
+            $ok = $false
+        }
+    }
+    return $ok
+}
+
+# Determine agent list
+if (-not [string]::IsNullOrEmpty($Agents)) {
+    $AgentList = Normalize-List -Input $Agents
+    if (-not (Validate-Subset -Type 'agent' -Allowed $AllAgents -Items $AgentList)) {
+        exit 1
+    }
+} else {
+    $AgentList = $AllAgents
+}
+
+# Determine script list
+if (-not [string]::IsNullOrEmpty($Scripts)) {
+    $ScriptList = Normalize-List -Input $Scripts
+    if (-not (Validate-Subset -Type 'script' -Allowed $AllScripts -Items $ScriptList)) {
+        exit 1
+    }
+} else {
+    $ScriptList = $AllScripts
+}
+
+Write-Host "Agents: $($AgentList -join ', ')"
+Write-Host "Scripts: $($ScriptList -join ', ')"
+
+# Build all variants
+foreach ($agent in $AgentList) {
+    foreach ($script in $ScriptList) {
+        Build-Variant -Agent $agent -Script $script
+    }
+}
+
+Write-Host "`nArchives in ${GenReleasesDir}:"
+Get-ChildItem -Path $GenReleasesDir -Filter "spec-kit-template-*-${Version}.zip" | ForEach-Object {
+    Write-Host "  $($_.Name)"
+}

.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 amp (default: all)
+#     AGENTS  : space or comma separated subset of: claude gemini copilot cursor-agent qwen opencode windsurf codex amp shai bob (default: all)
 #     SCRIPTS : space or comma separated subset of: sh ps (default: both)
 #   Examples:
 #     AGENTS=claude SCRIPTS=sh $0 v0.2.0
@@ -34,7 +34,8 @@ rewrite_paths() {
   sed -E \
     -e 's@(/?)memory/@.specify/memory/@g' \
     -e 's@(/?)scripts/@.specify/scripts/@g' \
-    -e 's@(/?)templates/@.specify/templates/@g'
+    -e 's@(/?)templates/@.specify/templates/@g' \
+    -e 's@\.specify\.specify/@.specify/@g'
 }
 
 generate_commands() {
@@ -95,21 +96,21 @@ generate_commands() {
         { echo "description = \"$description\""; echo; echo "prompt = \"\"\""; echo "$body"; echo "\"\"\""; } > "$output_dir/speckit.$name.$ext" ;;
       md)
         echo "$body" > "$output_dir/speckit.$name.$ext" ;;
-      chatmode.md)
+      agent.md)
         echo "$body" > "$output_dir/speckit.$name.$ext" ;;
     esac
   done
 }
 
 generate_copilot_prompts() {
-  local chatmodes_dir=$1 prompts_dir=$2
+  local agents_dir=$1 prompts_dir=$2
   mkdir -p "$prompts_dir"
   
-  # Generate a .prompt.md file for each .chatmode.md file
+  # Generate a .prompt.md file for each .agent.md file
-  for chatmode_file in "$chatmodes_dir"/speckit.*.chatmode.md; do
+  for agent_file in "$agents_dir"/speckit.*.agent.md; do
-    [[ -f "$chatmode_file" ]] || continue
+    [[ -f "$agent_file" ]] || continue
     
-    local basename=$(basename "$chatmode_file" .chatmode.md)
+    local basename=$(basename "$agent_file" .agent.md)
     local prompt_file="$prompts_dir/${basename}.prompt.md"
     
     # Create prompt file with agent frontmatter
@@ -166,10 +167,10 @@ build_variant() {
       generate_commands gemini toml "{{args}}" "$base_dir/.gemini/commands" "$script"
       [[ -f agent_templates/gemini/GEMINI.md ]] && cp agent_templates/gemini/GEMINI.md "$base_dir/GEMINI.md" ;;
     copilot)
-      mkdir -p "$base_dir/.github/chatmodes"
+      mkdir -p "$base_dir/.github/agents"
-      generate_commands copilot chatmode.md "\$ARGUMENTS" "$base_dir/.github/chatmodes" "$script"
+      generate_commands copilot agent.md "\$ARGUMENTS" "$base_dir/.github/agents" "$script"
       # Generate companion prompt files
-      generate_copilot_prompts "$base_dir/.github/chatmodes" "$base_dir/.github/prompts"
+      generate_copilot_prompts "$base_dir/.github/agents" "$base_dir/.github/prompts"
       # Create VS Code workspace settings
       mkdir -p "$base_dir/.vscode"
       [[ -f templates/vscode-settings.json ]] && cp templates/vscode-settings.json "$base_dir/.vscode/settings.json"
@@ -202,38 +203,47 @@ build_variant() {
     codebuddy)
       mkdir -p "$base_dir/.codebuddy/commands"
       generate_commands codebuddy md "\$ARGUMENTS" "$base_dir/.codebuddy/commands" "$script" ;;
+    qoder)
+      mkdir -p "$base_dir/.qoder/commands"
+      generate_commands qoder md "\$ARGUMENTS" "$base_dir/.qoder/commands" "$script" ;;
     amp)
       mkdir -p "$base_dir/.agents/commands"
       generate_commands amp md "\$ARGUMENTS" "$base_dir/.agents/commands" "$script" ;;
+    shai)
+      mkdir -p "$base_dir/.shai/commands"
+      generate_commands shai md "\$ARGUMENTS" "$base_dir/.shai/commands" "$script" ;;
     q)
       mkdir -p "$base_dir/.amazonq/prompts"
       generate_commands q md "\$ARGUMENTS" "$base_dir/.amazonq/prompts" "$script" ;;
+    bob)
+      mkdir -p "$base_dir/.bob/commands"
+      generate_commands bob md "\$ARGUMENTS" "$base_dir/.bob/commands" "$script" ;;
   esac
   ( cd "$base_dir" && zip -r "../spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip" . )
   echo "Created $GENRELEASES_DIR/spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip"
 }
 
 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp q)
+ALL_AGENTS=(claude gemini copilot cursor-agent qwen opencode windsurf codex kilocode auggie roo codebuddy amp shai q bob qoder)
 ALL_SCRIPTS=(sh ps)
 
 norm_list() {
-  # convert comma+space separated -> space separated unique while preserving order of first occurrence
+  # convert comma+space separated -> line separated unique while preserving order of first occurrence
-  tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?" ":"") $i)}}}END{printf("\n")}'
+  tr ',\n' '  ' | awk '{for(i=1;i<=NF;i++){if(!seen[$i]++){printf((out?"\n":"") $i);out=1}}}END{printf("\n")}'
 }
 
 validate_subset() {
   local type=$1; shift; local -n allowed=$1; shift; local items=("$@")
-  local ok=1
+  local invalid=0
   for it in "${items[@]}"; do
     local found=0
     for a in "${allowed[@]}"; do [[ $it == "$a" ]] && { found=1; break; }; done
     if [[ $found -eq 0 ]]; then
       echo "Error: unknown $type '$it' (allowed: ${allowed[*]})" >&2
-      ok=0
+      invalid=1
     fi
   done
-  return $ok
+  return $invalid
 }
 
 if [[ -n ${AGENTS:-} ]]; then

.gitignore

@@ -32,6 +32,7 @@ env/
 *.swp
 *.swo
 .DS_Store
+*.tmp
 
 # Project specific
 *.log
@@ -43,3 +44,10 @@ env/
 .genreleases/
 *.zip
 sdd-*/
+
+docs/dev
+
+# Extension system
+.specify/extensions/.cache/
+.specify/extensions/.backup/
+.specify/extensions/*/local-config.yml

.markdownlint-cli2.jsonc

@@ -19,7 +19,9 @@
     },
     "MD050": {
       "style": "asterisk"
-    }
+    },
+    "MD036": false,
+    "MD060": false
   },
   "ignores": [
     ".genreleases/"

AGENTS.md

@@ -30,10 +30,10 @@ Specify supports multiple AI agents by generating agent-specific command files a
 ### Current Supported Agents
 
 | Agent                      | Directory              | Format   | CLI Tool        | Description                 |
-|-------|-----------|---------|----------|-------------|
+| -------------------------- | ---------------------- | -------- | --------------- | --------------------------- |
 | **Claude Code**            | `.claude/commands/`    | Markdown | `claude`        | Anthropic's Claude Code CLI |
 | **Gemini CLI**             | `.gemini/commands/`    | TOML     | `gemini`        | Google's Gemini CLI         |
-| **GitHub Copilot** | `.github/chatmodes/` | Markdown | N/A (IDE-based) | GitHub Copilot in VS Code |
+| **GitHub Copilot**         | `.github/agents/`      | Markdown | N/A (IDE-based) | GitHub Copilot in VS Code   |
 | **Cursor**                 | `.cursor/commands/`    | Markdown | `cursor-agent`  | Cursor CLI                  |
 | **Qwen Code**              | `.qwen/commands/`      | TOML     | `qwen`          | Alibaba's Qwen Code CLI     |
 | **opencode**               | `.opencode/command/`   | Markdown | `opencode`      | opencode CLI                |
@@ -43,8 +43,11 @@ Specify supports multiple AI agents by generating agent-specific command files a
 | **Auggie CLI**             | `.augment/rules/`      | Markdown | `auggie`        | Auggie CLI                  |
 | **Roo Code**               | `.roo/rules/`          | Markdown | N/A (IDE-based) | Roo Code IDE                |
 | **CodeBuddy CLI**          | `.codebuddy/commands/` | Markdown | `codebuddy`     | CodeBuddy CLI               |
+| **Qoder CLI**              | `.qoder/commands/`     | Markdown | `qoder`         | Qoder CLI                   |
 | **Amazon Q Developer CLI** | `.amazonq/prompts/`    | Markdown | `q`             | Amazon Q Developer CLI      |
 | **Amp**                    | `.agents/commands/`    | Markdown | `amp`           | Amp CLI                     |
+| **SHAI**                   | `.shai/commands/`      | Markdown | `shai`          | SHAI CLI                    |
+| **IBM Bob**                | `.bob/commands/`       | Markdown | N/A (IDE-based) | IBM Bob IDE                 |
 
 ### Step-by-Step Integration Guide
 
@@ -310,7 +313,9 @@ Require a command-line tool to be installed:
 - **opencode**: `opencode` CLI
 - **Amazon Q Developer CLI**: `q` CLI
 - **CodeBuddy CLI**: `codebuddy` CLI
+- **Qoder CLI**: `qoder` CLI
 - **Amp**: `amp` CLI
+- **SHAI**: `shai` CLI
 
 ### IDE-Based Agents
 
@@ -318,12 +323,13 @@ Work within integrated development environments:
 
 - **GitHub Copilot**: Built into VS Code/compatible editors
 - **Windsurf**: Built into Windsurf IDE
+- **IBM Bob**: Built into IBM Bob IDE
 
 ## Command File Formats
 
 ### Markdown Format
 
-Used by: Claude, Cursor, opencode, Windsurf, Amazon Q Developer, Amp
+Used by: Claude, Cursor, opencode, Windsurf, Amazon Q Developer, Amp, SHAI, IBM Bob
 
 **Standard format:**
 
@@ -362,7 +368,7 @@ Command content with {SCRIPT} and {{args}} placeholders.
 
 - **CLI agents**: Usually `.<agent-name>/commands/`
 - **IDE agents**: Follow IDE-specific patterns:
-  - Copilot: `.github/chatmodes/`
+  - Copilot: `.github/agents/`
   - Cursor: `.cursor/commands/`
   - Windsurf: `.windsurf/workflows/`
 

CHANGELOG.md

@@ -7,6 +7,128 @@ All notable changes to the Specify CLI and templates are documented here.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.0] - 2026-01-28
+
+### Added
+
+- **Extension System**: Introduced modular extension architecture for Spec Kit
+  - Extensions are self-contained packages that add commands and functionality without bloating core
+  - Extension manifest schema (`extension.yml`) with validation
+  - Extension registry (`.specify/extensions/.registry`) for tracking installed extensions
+  - Extension manager module (`src/specify_cli/extensions.py`) for installation/removal
+  - New CLI commands:
+    - `specify extension list` - List installed extensions
+    - `specify extension add` - Install extension from local directory or URL
+    - `specify extension remove` - Uninstall extension
+    - `specify extension search` - Search extension catalog
+    - `specify extension info` - Show detailed extension information
+  - Semantic versioning compatibility checks
+  - Support for extension configuration files
+  - Command registration system for AI agents (Claude support initially)
+  - Added dependencies: `pyyaml>=6.0`, `packaging>=23.0`
+
+- **Extension Catalog**: Extension discovery and distribution system
+  - Central catalog (`extensions/catalog.json`) for published extensions
+  - Extension catalog manager (`ExtensionCatalog` class) with:
+    - Catalog fetching from GitHub
+    - 1-hour local caching for performance
+    - Search by query, tag, author, or verification status
+    - Extension info retrieval
+  - Catalog cache stored in `.specify/extensions/.cache/`
+  - Search and info commands with rich console output
+  - Added 9 catalog-specific unit tests (100% pass rate)
+
+- **Jira Extension**: First official extension for Jira integration
+  - Extension ID: `jira`
+  - Version: 1.0.0
+  - Commands:
+    - `/speckit.jira.specstoissues` - Create Jira hierarchy from spec and tasks
+    - `/speckit.jira.discover-fields` - Discover Jira custom fields
+    - `/speckit.jira.sync-status` - Sync task completion status
+  - Comprehensive documentation (README, usage guide, examples)
+  - MIT licensed
+
+- **Hook System**: Extension lifecycle hooks for automation
+  - `HookExecutor` class for managing extension hooks
+  - Hooks registered in `.specify/extensions.yml`
+  - Hook registration during extension installation
+  - Hook unregistration during extension removal
+  - Support for optional and mandatory hooks
+  - Hook execution messages for AI agent integration
+  - Condition support for conditional hook execution (placeholder)
+
+- **Extension Management**: Advanced extension management commands
+  - `specify extension update` - Check and update extensions to latest version
+  - `specify extension enable` - Enable a disabled extension
+  - `specify extension disable` - Disable extension without removing it
+  - Version comparison with catalog
+  - Update notifications
+  - Preserve configuration during updates
+
+- **Multi-Agent Support**: Extensions now work with all supported AI agents (Phase 6)
+  - Automatic detection and registration for all agents in project
+  - Support for 16+ AI agents (Claude, Gemini, Copilot, Cursor, Qwen, and more)
+  - Agent-specific command formats (Markdown and TOML)
+  - Automatic argument placeholder conversion ($ARGUMENTS → {{args}})
+  - Commands registered for all detected agents during installation
+  - Multi-agent command unregistration on extension removal
+  - `CommandRegistrar.register_commands_for_agent()` method
+  - `CommandRegistrar.register_commands_for_all_agents()` method
+
+- **Configuration Layers**: Full configuration cascade system (Phase 6)
+  - **Layer 1**: Defaults from extension manifest (`extension.yml`)
+  - **Layer 2**: Project config (`.specify/extensions/{ext-id}/{ext-id}-config.yml`)
+  - **Layer 3**: Local config (`.specify/extensions/{ext-id}/local-config.yml`, gitignored)
+  - **Layer 4**: Environment variables (`SPECKIT_{EXT_ID}_{KEY}` pattern)
+  - Recursive config merging with proper precedence
+  - `ConfigManager` class for programmatic config access
+  - `get_config()`, `get_value()`, `has_value()` methods
+  - Support for nested configuration paths with dot-notation
+
+- **Hook Condition Evaluation**: Smart hook execution based on runtime conditions (Phase 6)
+  - Config conditions: `config.key.path is set`, `config.key == 'value'`, `config.key != 'value'`
+  - Environment conditions: `env.VAR is set`, `env.VAR == 'value'`, `env.VAR != 'value'`
+  - Automatic filtering of hooks based on condition evaluation
+  - Safe fallback behavior on evaluation errors
+  - Case-insensitive pattern matching
+
+- **Hook Integration**: Agent-level hook checking and execution (Phase 6)
+  - `check_hooks_for_event()` method for AI agents to query hooks after core commands
+  - Condition-aware hook filtering before execution
+  - `enable_hooks()` and `disable_hooks()` methods per extension
+  - Formatted hook messages for agent display
+  - `execute_hook()` method for hook execution information
+
+- **Documentation Suite**: Comprehensive documentation for users and developers
+  - **EXTENSION-USER-GUIDE.md**: Complete user guide with installation, usage, configuration, and troubleshooting
+  - **EXTENSION-API-REFERENCE.md**: Technical API reference with manifest schema, Python API, and CLI commands
+  - **EXTENSION-PUBLISHING-GUIDE.md**: Publishing guide for extension authors
+  - **RFC-EXTENSION-SYSTEM.md**: Extension architecture design document
+
+- **Extension Template**: Starter template in `extensions/template/` for creating new extensions
+  - Fully commented `extension.yml` manifest template
+  - Example command file with detailed explanations
+  - Configuration template with all options
+  - Complete project structure (README, LICENSE, CHANGELOG, .gitignore)
+  - EXAMPLE-README.md showing final documentation format
+
+- **Unit Tests**: Comprehensive test suite with 39 tests covering all extension system components
+  - Test coverage: 83% of extension module code
+  - Test dependencies: `pytest>=7.0`, `pytest-cov>=4.0`
+  - Configured pytest in `pyproject.toml`
+
+### Changed
+
+- Version bumped to 0.1.0 (minor release for new feature)
+
+## [0.0.22] - 2025-11-07
+
+- Support for VS Code/Copilot agents, and moving away from prompts to proper agents with hand-offs.
+- Move to use `AGENTS.md` for Copilot workloads, since it's already supported out-of-the-box.
+- Adds support for the version command. ([#486](https://github.com/github/spec-kit/issues/486))
+- Fixes potential bug with the `create-new-feature.ps1` script that ignores existing feature branches when determining next feature number ([#975](https://github.com/github/spec-kit/issues/975))
+- Add graceful fallback and logging for GitHub API rate-limiting during template fetch ([#970](https://github.com/github/spec-kit/issues/970))
+
 ## [0.0.21] - 2025-10-21
 
 - Fixes [#975](https://github.com/github/spec-kit/issues/975) (thank you [@fgalarraga](https://github.com/fgalarraga)).

CODE_OF_CONDUCT.md

@@ -23,7 +23,7 @@ include:
 Examples of unacceptable behavior by participants include:
 
 - The use of sexualized language or imagery and unwelcome sexual attention or
-advances
+  advances
 - Trolling, insulting/derogatory comments, and personal or political attacks
 - Public or private harassment
 - Publishing others' private information, such as a physical or electronic

CONTRIBUTING.md

@@ -32,8 +32,8 @@ On [GitHub Codespaces](https://github.com/features/codespaces) it's even simpler
 
 ## Submitting a pull request
 
->[!NOTE]
+> [!NOTE]
->If your pull request introduces a large change that materially impacts the work of the CLI or the rest of the repository (e.g., you're introducing new templates, arguments, or otherwise major changes), make sure that it was **discussed and agreed upon** by the project maintainers. Pull requests with large changes that did not have a prior conversation and agreement will be closed.
+> If your pull request introduces a large change that materially impacts the work of the CLI or the rest of the repository (e.g., you're introducing new templates, arguments, or otherwise major changes), make sure that it was **discussed and agreed upon** by the project maintainers. Pull requests with large changes that did not have a prior conversation and agreement will be closed.
 
 1. Fork and clone the repository
 1. Configure and install the dependencies: `uv sync`
@@ -71,13 +71,13 @@ To test your templates, commands, and other changes locally, follow these steps:
 
    Run the following command to generate the local packages:
 
-   ```
+   ```bash
    ./.github/workflows/scripts/create-release-packages.sh v1.0.0
    ```
 
 2. **Copy the relevant package to your test project**
 
-   ```
+   ```bash
    cp -r .genreleases/sdd-copilot-package-sh/. <path-to-test-project>/
    ```
 

README.md

@@ -1,5 +1,5 @@
 <div align="center">
-    <img src="./media/logo_small.webp" alt="Spec Kit Logo"/>
+    <img src="./media/logo_large.webp" alt="Spec Kit Logo" width="200" height="200"/>
     <h1>🌱 Spec Kit</h1>
     <h3><em>Build high-quality software faster.</em></h3>
 </div>
@@ -57,11 +57,19 @@ uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 Then use the tool directly:
 
 ```bash
+# Create new project
 specify init <PROJECT_NAME>
+
+# Or initialize in existing project
+specify init . --ai claude
+# or
+specify init --here --ai claude
+
+# Check installed tools
 specify check
 ```
 
-To upgrade specify run:
+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
@@ -135,21 +143,25 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |
-|-----------------------------------------------------------|---------|---------------------------------------------------|
+| ------------------------------------------------------------------------------------ | ------- | ----------------------------------------------------------------------------------------------------------------------------------------- |
-| [Claude Code](https://www.anthropic.com/claude-code)      | ✅ |                                                   |
+| [Qoder CLI](https://qoder.com/cli)                                                   | ✅      |                                                                                                                                           |
-| [GitHub Copilot](https://code.visualstudio.com/)          | ✅ |                                                   |
-| [Gemini CLI](https://github.com/google-gemini/gemini-cli) | ✅ |                                                   |
-| [Cursor](https://cursor.sh/)                              | ✅ |                                                   |
-| [Qwen Code](https://github.com/QwenLM/qwen-code)          | ✅ |                                                   |
-| [opencode](https://opencode.ai/)                          | ✅ |                                                   |
-| [Windsurf](https://windsurf.com/)                         | ✅ |                                                   |
-| [Kilo Code](https://github.com/Kilo-Org/kilocode)         | ✅ |                                                   |
-| [Auggie CLI](https://docs.augmentcode.com/cli/overview)   | ✅ |                                                   |
-| [CodeBuddy CLI](https://www.codebuddy.ai/cli)             | ✅ |                                                   |
-| [Roo Code](https://roocode.com/)                          | ✅ |                                                   |
-| [Codex CLI](https://github.com/openai/codex)              | ✅ |                                                   |
 | [Amazon Q Developer CLI](https://aws.amazon.com/developer/learning/q-developer-cli/) | ⚠️      | Amazon Q Developer CLI [does not support](https://github.com/aws/amazon-q-developer-cli/issues/3064) custom arguments for slash commands. |
 | [Amp](https://ampcode.com/)                                                          | ✅      |                                                                                                                                           |
+| [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)                                         | ✅      |                                                                                                                                           |
+| [Cursor](https://cursor.sh/)                                                         | ✅      |                                                                                                                                           |
+| [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | ✅      |                                                                                                                                           |
+| [GitHub Copilot](https://code.visualstudio.com/)                                     | ✅      |                                                                                                                                           |
+| [IBM Bob](https://www.ibm.com/products/bob)                                          | ✅      | IDE-based agent with slash command support                                                                                                |
+| [Jules](https://jules.google.com/)                                                   | ✅      |                                                                                                                                           |
+| [Kilo Code](https://github.com/Kilo-Org/kilocode)                                    | ✅      |                                                                                                                                           |
+| [opencode](https://opencode.ai/)                                                     | ✅      |                                                                                                                                           |
+| [Qwen Code](https://github.com/QwenLM/qwen-code)                                     | ✅      |                                                                                                                                           |
+| [Roo Code](https://roocode.com/)                                                     | ✅      |                                                                                                                                           |
+| [SHAI (OVHcloud)](https://github.com/ovh/shai)                                       | ✅      |                                                                                                                                           |
+| [Windsurf](https://windsurf.com/)                                                    | ✅      |                                                                                                                                           |
 
 ## 🔧 Specify CLI Reference
 
@@ -158,16 +170,16 @@ 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`) |
+| `check` | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`, `shai`, `qoder`) |
 
 ### `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`, or `q` |
+| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, `shai`, `q`, `bob`, or `qoder` |
 | `--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                                                                                                                                                           |
@@ -189,12 +201,21 @@ specify init my-project --ai claude
 # Initialize with Cursor support
 specify init my-project --ai cursor-agent
 
+# Initialize with Qoder support
+specify init my-project --ai qoder
+
 # Initialize with Windsurf support
 specify init my-project --ai windsurf
 
 # Initialize with Amp support
 specify init my-project --ai amp
 
+# Initialize with SHAI support
+specify init my-project --ai shai
+
+# Initialize with IBM Bob support
+specify init my-project --ai bob
+
 # Initialize with PowerShell scripts (Windows/cross-platform)
 specify init my-project --ai copilot --script ps
 
@@ -230,7 +251,7 @@ After running `specify init`, your AI coding agent will have access to these sla
 Essential commands for the Spec-Driven Development workflow:
 
 | Command                 | Description                                                              |
-|--------------------------|-----------------------------------------------------------------------|
+| ----------------------- | ------------------------------------------------------------------------ |
 | `/speckit.constitution` | Create or update project governing principles and development guidelines |
 | `/speckit.specify`      | Define what you want to build (requirements and user stories)            |
 | `/speckit.plan`         | Create technical implementation plans with your chosen tech stack        |
@@ -242,7 +263,7 @@ Essential commands for the Spec-Driven Development workflow:
 Additional commands for enhanced quality and validation:
 
 | Command              | Description                                                                                                                          |
-|----------------------|-----------------------------------------------------------------------|
+| -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
 | `/speckit.clarify`   | Clarify underspecified areas (recommended before `/speckit.plan`; formerly `/quizme`)                                                |
 | `/speckit.analyze`   | Cross-artifact consistency & coverage analysis (run after `/speckit.tasks`, before `/speckit.implement`)                             |
 | `/speckit.checklist` | Generate custom quality checklists that validate requirements completeness, clarity, and consistency (like "unit tests for English") |
@@ -250,8 +271,8 @@ Additional commands for enhanced quality and validation:
 ### Environment Variables
 
 | Variable          | Description                                                                                                                                                                                                                                                                                            |
-|------------------|------------------------------------------------------------------------------------------------|
+| ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `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. |
+| `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. |
 
 ## 📚 Core Philosophy
 
@@ -265,7 +286,7 @@ Spec-Driven Development is a structured process that emphasizes:
 ## 🌟 Development Phases
 
 | Phase                                    | Focus                    | Key Activities                                                                                                                                                     |
-|-------|-------|----------------|
+| ---------------------------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | **0-to-1 Development** ("Greenfield")    | Generate from scratch    | <ul><li>Start with high-level requirements</li><li>Generate specifications</li><li>Plan implementation steps</li><li>Build production-ready applications</li></ul> |
 | **Creative Exploration**                 | Parallel implementations | <ul><li>Explore diverse solutions</li><li>Support multiple technology stacks & architectures</li><li>Experiment with UX patterns</li></ul>                         |
 | **Iterative Enhancement** ("Brownfield") | Brownfield modernization | <ul><li>Add features iteratively</li><li>Modernize legacy systems</li><li>Adapt processes</li></ul>                                                                |
@@ -360,7 +381,7 @@ 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, or Amazon Q Developer CLI 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, or Amazon Q Developer CLI 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
@@ -386,8 +407,8 @@ This step creates or updates the `.specify/memory/constitution.md` file with you
 
 With your project principles established, you can now create the functional specifications. Use the `/speckit.specify` command and then provide the concrete requirements for the project you want to develop.
 
->[!IMPORTANT]
+> [!IMPORTANT]
->Be as explicit as possible about *what* you are trying to build and *why*. **Do not focus on the tech stack at this point**.
+> Be as explicit as possible about *what* you are trying to build and *why*. **Do not focus on the tech stack at this point**.
 
 An example prompt:
 
@@ -530,8 +551,8 @@ researching .NET Aspire in general and I don't think that's gonna do much for us
 That's way too untargeted research. The research needs to help you solve a specific targeted question.
 ```
 
->[!NOTE]
+> [!NOTE]
->Claude Code might be over-eager and add components that you did not ask for. Ask it to clarify the rationale and the source of the change.
+> Claude Code might be over-eager and add components that you did not ask for. Ask it to clarify the rationale and the source of the change.
 
 ### **STEP 5:** Have Claude Code validate the plan
 
@@ -549,8 +570,8 @@ This helps refine the implementation plan and helps you avoid potential blind sp
 
 You can also ask Claude Code (if you have the [GitHub CLI](https://docs.github.com/en/github-cli/github-cli) installed) to go ahead and create a pull request from your current branch to `main` with a detailed description, to make sure that the effort is properly tracked.
 
->[!NOTE]
+> [!NOTE]
->Before you have the agent implement it, it's also worth prompting Claude Code to cross-check the details to see if there are any over-engineered pieces (remember - it can be over-eager). If over-engineered components or decisions exist, you can ask Claude Code to resolve them. Ensure that Claude Code follows the [constitution](base/memory/constitution.md) as the foundational piece that it must adhere to when establishing the plan.
+> Before you have the agent implement it, it's also worth prompting Claude Code to cross-check the details to see if there are any over-engineered pieces (remember - it can be over-eager). If over-engineered components or decisions exist, you can ask Claude Code to resolve them. Ensure that Claude Code follows the [constitution](base/memory/constitution.md) as the foundational piece that it must adhere to when establishing the plan.
 
 ### **STEP 6:** Generate task breakdown with /speckit.tasks
 
@@ -587,8 +608,8 @@ The `/speckit.implement` command will:
 - Follow the TDD approach defined in your task plan
 - Provide progress updates and handle errors appropriately
 
->[!IMPORTANT]
+> [!IMPORTANT]
->The AI agent will execute local CLI commands (such as `dotnet`, `npm`, etc.) - make sure you have the required tools installed on your machine.
+> The AI agent will execute local CLI commands (such as `dotnet`, `npm`, etc.) - make sure you have the required tools installed on your machine.
 
 Once the implementation is complete, test the application and resolve any runtime errors that may not be visible in CLI logs (e.g., browser console errors). You can copy and paste such errors back to your AI agent for resolution.
 

docs/index.md

@@ -12,6 +12,7 @@ Spec-Driven Development **flips the script** on traditional software development
 
 - [Installation Guide](installation.md)
 - [Quick Start Guide](quickstart.md)
+- [Upgrade Guide](upgrade.md)
 - [Local Development](local-development.md)
 
 ## Core Philosophy

docs/quickstart.md

@@ -2,16 +2,24 @@
 
 This guide will help you get started with Spec-Driven Development using Spec Kit.
 
-> NEW: All automation scripts now provide both Bash (`.sh`) and PowerShell (`.ps1`) variants. The `specify` CLI auto-selects based on OS unless you pass `--script sh|ps`.
+> [!NOTE]
+> All automation scripts now provide both Bash (`.sh`) and PowerShell (`.ps1`) variants. The `specify` CLI auto-selects based on OS unless you pass `--script sh|ps`.
 
-## The 4-Step Process
+## The 6-Step Process
 
-### 1. Install Specify
+> [!TIP]
+> **Context Awareness**: Spec Kit commands automatically detect the active feature based on your current Git branch (e.g., `001-feature-name`). To switch between different specifications, simply switch Git branches.
 
-Initialize your project depending on the coding agent you're using:
+### Step 1: Install Specify
+
+**In your terminal**, run the `specify` CLI command to initialize your project:
 
 ```bash
+# Create a new project directory
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
+
+# OR initialize in the current directory
+uvx --from git+https://github.com/github/spec-kit.git specify init .
 ```
 
 Pick script type explicitly (optional):
@@ -21,31 +29,71 @@ uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME> --script sh  # Force POSIX shell
 ```
 
-### 2. Create the Spec
+### Step 2: Define Your Constitution
 
-Use the `/speckit.specify` command to describe what you want to build. Focus on the **what** and **why**, not the tech stack.
+**In your AI Agent's chat interface**, use the `/speckit.constitution` slash command to establish the core rules and principles for your project. You should provide your project's specific principles as arguments.
 
-```bash
+```markdown
+/speckit.constitution This project follows a "Library-First" approach. All features must be implemented as standalone libraries first. We use TDD strictly. We prefer functional programming patterns.
+```
+
+### Step 3: Create the Spec
+
+**In the chat**, use the `/speckit.specify` slash command to describe what you want to build. Focus on the **what** and **why**, not the tech stack.
+
+```markdown
 /speckit.specify Build an application that can help me organize my photos in separate photo albums. Albums are grouped by date and can be re-organized by dragging and dropping on the main page. Albums are never in other nested albums. Within each album, photos are previewed in a tile-like interface.
 ```
 
-### 3. Create a Technical Implementation Plan
+### Step 4: Refine the Spec
 
-Use the `/speckit.plan` command to provide your tech stack and architecture choices.
+**In the chat**, use the `/speckit.clarify` slash command to identify and resolve ambiguities in your specification. You can provide specific focus areas as arguments.
 
 ```bash
+/speckit.clarify Focus on security and performance requirements.
+```
+
+### Step 5: Create a Technical Implementation Plan
+
+**In the chat**, use the `/speckit.plan` slash command to provide your tech stack and architecture choices.
+
+```markdown
 /speckit.plan The application uses Vite with minimal number of libraries. Use vanilla HTML, CSS, and JavaScript as much as possible. Images are not uploaded anywhere and metadata is stored in a local SQLite database.
 ```
 
-### 4. Break Down and Implement
+### Step 6: Break Down and Implement
 
-Use `/speckit.tasks` to create an actionable task list, then ask your agent to implement the feature.
+**In the chat**, use the `/speckit.tasks` slash command to create an actionable task list.
+
+```markdown
+/speckit.tasks
+```
+
+Optionally, validate the plan with `/speckit.analyze`:
+
+```markdown
+/speckit.analyze
+```
+
+Then, use the `/speckit.implement` slash command to execute the plan.
+
+```markdown
+/speckit.implement
+```
 
 ## Detailed Example: Building Taskify
 
 Here's a complete example of building a team productivity platform:
 
-### Step 1: Define Requirements with `/speckit.specify`
+### Step 1: Define Constitution
+
+Initialize the project's constitution to set ground rules:
+
+```markdown
+/speckit.constitution Taskify is a "Security-First" application. All user inputs must be validated. We use a microservices architecture. Code must be fully documented.
+```
+
+### Step 2: Define Requirements with `/speckit.specify`
 
 ```text
 Develop Taskify, a team productivity platform. It should allow users to create projects, add team members,
@@ -54,58 +102,51 @@ let's call it "Create Taskify," let's have multiple users but the users will be
 I want five users in two different categories, one product manager and four engineers. Let's create three
 different sample projects. Let's have the standard Kanban columns for the status of each task, such as "To Do,"
 "In Progress," "In Review," and "Done." There will be no login for this application as this is just the very
-first testing thing to ensure that our basic features are set up. For each task in the UI for a task card,
+first testing thing to ensure that our basic features are set up.
-you should be able to change the current status of the task between the different columns in the Kanban work board.
-You should be able to leave an unlimited number of comments for a particular card. You should be able to, from that task
-card, assign one of the valid users. When you first launch Taskify, it's going to give you a list of the five users to pick
-from. There will be no password required. When you click on a user, you go into the main view, which displays the list of
-projects. When you click on a project, you open the Kanban board for that project. You're going to see the columns.
-You'll be able to drag and drop cards back and forth between different columns. You will see any cards that are
-assigned to you, the currently logged in user, in a different color from all the other ones, so you can quickly
-see yours. You can edit any comments that you make, but you can't edit comments that other people made. You can
-delete any comments that you made, but you can't delete comments anybody else made.
 ```
 
-### Step 2: Refine the Specification
+### Step 3: Refine the Specification
 
-After the initial specification is created, clarify any missing requirements:
+Use the `/speckit.clarify` command to interactively resolve any ambiguities in your specification. You can also provide specific details you want to ensure are included.
 
-```text
+```bash
-For each sample project or project that you create there should be a variable number of tasks between 5 and 15
+/speckit.clarify I want to clarify the task card details. For each task in the UI for a task card, you should be able to change the current status of the task between the different columns in the Kanban work board. You should be able to leave an unlimited number of comments for a particular card. You should be able to, from that task card, assign one of the valid users.
-tasks for each one randomly distributed into different states of completion. Make sure that there's at least
-one task in each stage of completion.
 ```
 
-Also validate the specification checklist:
+You can continue to refine the spec with more details using `/speckit.clarify`:
 
-```text
+```bash
-Read the review and acceptance checklist, and check off each item in the checklist if the feature spec meets the criteria. Leave it empty if it does not.
+/speckit.clarify When you first launch Taskify, it's going to give you a list of the five users to pick from. There will be no password required. When you click on a user, you go into the main view, which displays the list of projects. When you click on a project, you open the Kanban board for that project. You're going to see the columns. You'll be able to drag and drop cards back and forth between different columns. You will see any cards that are assigned to you, the currently logged in user, in a different color from all the other ones, so you can quickly see yours. You can edit any comments that you make, but you can't edit comments that other people made. You can delete any comments that you made, but you can't delete comments anybody else made.
 ```
 
-### Step 3: Generate Technical Plan with `/speckit.plan`
+### Step 4: Validate the Spec
+
+Validate the specification checklist using the `/speckit.checklist` command:
+
+```bash
+/speckit.checklist
+```
+
+### Step 5: Generate Technical Plan with `/speckit.plan`
 
 Be specific about your tech stack and technical requirements:
 
-```text
+```bash
-We are going to generate this using .NET Aspire, using Postgres as the database. The frontend should use
+/speckit.plan We are going to generate this using .NET Aspire, using Postgres as the database. The frontend should use Blazor server with drag-and-drop task boards, real-time updates. There should be a REST API created with a projects API, tasks API, and a notifications API.
-Blazor server with drag-and-drop task boards, real-time updates. There should be a REST API created with a projects API,
-tasks API, and a notifications API.
 ```
 
-### Step 4: Validate and Implement
+### Step 6: Validate and Implement
 
-Have your AI agent audit the implementation plan:
+Have your AI agent audit the implementation plan using `/speckit.analyze`:
 
-```text
+```bash
-Now I want you to go and audit the implementation plan and the implementation detail files.
+/speckit.analyze
-Read through it with an eye on determining whether or not there is a sequence of tasks that you need
-to be doing that are obvious from reading this. Because I don't know if there's enough here.
 ```
 
 Finally, implement the solution:
 
-```text
+```bash
-implement specs/002-create-taskify/plan.md
+/speckit.implement
 ```
 
 ## Key Principles
@@ -118,6 +159,6 @@ implement specs/002-create-taskify/plan.md
 
 ## Next Steps
 
-- Read the complete methodology for in-depth guidance
+- Read the [complete methodology](../spec-driven.md) for in-depth guidance
-- Check out more examples in the repository
+- Check out [more examples](../templates) in the repository
-- Explore the source code on GitHub
+- Explore the [source code on GitHub](https://github.com/github/spec-kit)

docs/toc.yml

@@ -9,10 +9,11 @@
       href: installation.md
     - name: Quick Start
       href: quickstart.md
+    - name: Upgrade
+      href: upgrade.md
 
 # Development workflows
 - name: Development
   items:
     - name: Local Development
       href: local-development.md
-

docs/upgrade.md

@@ -0,0 +1,444 @@
+# Upgrade Guide
+
+> You have Spec Kit installed and want to upgrade to the latest version to get new features, bug fixes, or updated slash commands. This guide covers both upgrading the CLI tool and updating your project files.
+
+---
+
+## Quick Reference
+
+| 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 |
+| **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 |
+
+---
+
+## Part 1: Upgrade the CLI Tool
+
+The CLI tool (`specify`) is separate from your project files. Upgrade it to get the latest features and bug fixes.
+
+### If you installed with `uv tool install`
+
+```bash
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+```
+
+### If you use one-shot `uvx` commands
+
+No upgrade needed—`uvx` always fetches the latest version. Just run your commands as normal:
+
+```bash
+uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai copilot
+```
+
+### Verify the upgrade
+
+```bash
+specify check
+```
+
+This shows installed tools and confirms the CLI is working.
+
+---
+
+## Part 2: Updating Project Files
+
+When Spec Kit releases new features (like new slash commands or updated templates), you need to refresh your project's Spec Kit files.
+
+### What gets updated?
+
+Running `specify init --here --force` will update:
+
+- ✅ **Slash command files** (`.claude/commands/`, `.github/prompts/`, etc.)
+- ✅ **Script files** (`.specify/scripts/`)
+- ✅ **Template files** (`.specify/templates/`)
+- ✅ **Shared memory files** (`.specify/memory/`) - **⚠️ See warnings below**
+
+### What stays safe?
+
+These files are **never touched** by the upgrade—the template packages don't even contain them:
+
+- ✅ **Your specifications** (`specs/001-my-feature/spec.md`, etc.) - **CONFIRMED SAFE**
+- ✅ **Your implementation plans** (`specs/001-my-feature/plan.md`, `tasks.md`, etc.) - **CONFIRMED SAFE**
+- ✅ **Your source code** - **CONFIRMED SAFE**
+- ✅ **Your git history** - **CONFIRMED SAFE**
+
+The `specs/` directory is completely excluded from template packages and will never be modified during upgrades.
+
+### Update command
+
+Run this inside your project directory:
+
+```bash
+specify init --here --force --ai <your-agent>
+```
+
+Replace `<your-agent>` with your AI assistant. Refer to this list of [Supported AI Agents](../README.md#-supported-ai-agents)
+
+**Example:**
+
+```bash
+specify init --here --force --ai copilot
+```
+
+### Understanding the `--force` flag
+
+Without `--force`, the CLI warns you and asks for confirmation:
+
+```text
+Warning: Current directory is not empty (25 items)
+Template files will be merged with existing content and may overwrite existing files
+Proceed? [y/N]
+```
+
+With `--force`, it skips the confirmation and proceeds immediately.
+
+**Important: Your `specs/` directory is always safe.** The `--force` flag only affects template files (commands, scripts, templates, memory). Your feature specifications, plans, and tasks in `specs/` are never included in upgrade packages and cannot be overwritten.
+
+---
+
+## ⚠️ Important Warnings
+
+### 1. Constitution file will be overwritten
+
+**Known issue:** `specify init --here --force` currently overwrites `.specify/memory/constitution.md` with the default template, erasing any customizations you made.
+
+**Workaround:**
+
+```bash
+# 1. Back up your constitution before upgrading
+cp .specify/memory/constitution.md .specify/memory/constitution-backup.md
+
+# 2. Run the upgrade
+specify init --here --force --ai copilot
+
+# 3. Restore your customized constitution
+mv .specify/memory/constitution-backup.md .specify/memory/constitution.md
+```
+
+Or use git to restore it:
+
+```bash
+# After upgrade, restore from git history
+git restore .specify/memory/constitution.md
+```
+
+### 2. Custom template modifications
+
+If you customized any templates in `.specify/templates/`, the upgrade will overwrite them. Back them up first:
+
+```bash
+# Back up custom templates
+cp -r .specify/templates .specify/templates-backup
+
+# After upgrade, merge your changes back manually
+```
+
+### 3. Duplicate slash commands (IDE-based agents)
+
+Some IDE-based agents (like Kilo Code, Windsurf) may show **duplicate slash commands** after upgrading—both old and new versions appear.
+
+**Solution:** Manually delete the old command files from your agent's folder.
+
+**Example for Kilo Code:**
+
+```bash
+# Navigate to the agent's commands folder
+cd .kilocode/rules/
+
+# List files and identify duplicates
+ls -la
+
+# Delete old versions (example filenames - yours may differ)
+rm speckit.specify-old.md
+rm speckit.plan-v1.md
+```
+
+Restart your IDE to refresh the command list.
+
+---
+
+## Common Scenarios
+
+### Scenario 1: "I just want new slash commands"
+
+```bash
+# Upgrade CLI (if using persistent install)
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+
+# Update project files to get new commands
+specify init --here --force --ai copilot
+
+# Restore your constitution if customized
+git restore .specify/memory/constitution.md
+```
+
+### Scenario 2: "I customized templates and constitution"
+
+```bash
+# 1. Back up customizations
+cp .specify/memory/constitution.md /tmp/constitution-backup.md
+cp -r .specify/templates /tmp/templates-backup
+
+# 2. Upgrade CLI
+uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git
+
+# 3. Update project
+specify init --here --force --ai copilot
+
+# 4. Restore customizations
+mv /tmp/constitution-backup.md .specify/memory/constitution.md
+# Manually merge template changes if needed
+```
+
+### Scenario 3: "I see duplicate slash commands in my IDE"
+
+This happens with IDE-based agents (Kilo Code, Windsurf, Roo Code, etc.).
+
+```bash
+# Find the agent folder (example: .kilocode/rules/)
+cd .kilocode/rules/
+
+# List all files
+ls -la
+
+# Delete old command files
+rm speckit.old-command-name.md
+
+# Restart your IDE
+```
+
+### Scenario 4: "I'm working on a project without Git"
+
+If you initialized your project with `--no-git`, you can still upgrade:
+
+```bash
+# Manually back up files you customized
+cp .specify/memory/constitution.md /tmp/constitution-backup.md
+
+# Run upgrade
+specify init --here --force --ai copilot --no-git
+
+# Restore customizations
+mv /tmp/constitution-backup.md .specify/memory/constitution.md
+```
+
+The `--no-git` flag skips git initialization but doesn't affect file updates.
+
+---
+
+## Using `--no-git` Flag
+
+The `--no-git` flag tells Spec Kit to **skip git repository initialization**. This is useful when:
+
+- You manage version control differently (Mercurial, SVN, etc.)
+- Your project is part of a larger monorepo with existing git setup
+- You're experimenting and don't want version control yet
+
+**During initial setup:**
+
+```bash
+specify init my-project --ai copilot --no-git
+```
+
+**During upgrade:**
+
+```bash
+specify init --here --force --ai copilot --no-git
+```
+
+### What `--no-git` does NOT do
+
+❌ Does NOT prevent file updates
+❌ Does NOT skip slash command installation
+❌ Does NOT affect template merging
+
+It **only** skips running `git init` and creating the initial commit.
+
+### Working without Git
+
+If you use `--no-git`, you'll need to manage feature directories manually:
+
+**Set the `SPECIFY_FEATURE` environment variable** before using planning commands:
+
+```bash
+# Bash/Zsh
+export SPECIFY_FEATURE="001-my-feature"
+
+# PowerShell
+$env:SPECIFY_FEATURE = "001-my-feature"
+```
+
+This tells Spec Kit which feature directory to use when creating specs, plans, and tasks.
+
+**Why this matters:** Without git, Spec Kit can't detect your current branch name to determine the active feature. The environment variable provides that context manually.
+
+---
+
+## Troubleshooting
+
+### "Slash commands not showing up after upgrade"
+
+**Cause:** Agent didn't reload the command files.
+
+**Fix:**
+
+1. **Restart your IDE/editor** completely (not just reload window)
+2. **For CLI-based agents**, verify files exist:
+
+   ```bash
+   ls -la .claude/commands/      # Claude Code
+   ls -la .gemini/commands/       # Gemini
+   ls -la .cursor/commands/       # Cursor
+   ```
+
+3. **Check agent-specific setup:**
+   - Codex requires `CODEX_HOME` environment variable
+   - Some agents need workspace restart or cache clearing
+
+### "I lost my constitution customizations"
+
+**Fix:** Restore from git or backup:
+
+```bash
+# If you committed before upgrading
+git restore .specify/memory/constitution.md
+
+# If you backed up manually
+cp /tmp/constitution-backup.md .specify/memory/constitution.md
+```
+
+**Prevention:** Always commit or back up `constitution.md` before upgrading.
+
+### "Warning: Current directory is not empty"
+
+**Full warning message:**
+
+```text
+Warning: Current directory is not empty (25 items)
+Template files will be merged with existing content and may overwrite existing files
+Do you want to continue? [y/N]
+```
+
+**What this means:**
+
+This warning appears when you run `specify init --here` (or `specify init .`) in a directory that already has files. It's telling you:
+
+1. **The directory has existing content** - In the example, 25 files/folders
+2. **Files will be merged** - New template files will be added alongside your existing files
+3. **Some files may be overwritten** - If you already have Spec Kit files (`.claude/`, `.specify/`, etc.), they'll be replaced with the new versions
+
+**What gets overwritten:**
+
+Only Spec Kit infrastructure files:
+
+- Agent command files (`.claude/commands/`, `.github/prompts/`, etc.)
+- Scripts in `.specify/scripts/`
+- Templates in `.specify/templates/`
+- Memory files in `.specify/memory/` (including constitution)
+
+**What stays untouched:**
+
+- Your `specs/` directory (specifications, plans, tasks)
+- Your source code files
+- Your `.git/` directory and git history
+- Any other files not part of Spec Kit templates
+
+**How to respond:**
+
+- **Type `y` and press Enter** - Proceed with the merge (recommended if upgrading)
+- **Type `n` and press Enter** - Cancel the operation
+- **Use `--force` flag** - Skip this confirmation entirely:
+
+  ```bash
+  specify init --here --force --ai copilot
+  ```
+
+**When you see this warning:**
+
+- ✅ **Expected** when upgrading an existing Spec Kit project
+- ✅ **Expected** when adding Spec Kit to an existing codebase
+- ⚠️ **Unexpected** if you thought you were creating a new project in an empty directory
+
+**Prevention tip:** Before upgrading, commit or back up your `.specify/memory/constitution.md` if you customized it.
+
+### "CLI upgrade doesn't seem to work"
+
+Verify the installation:
+
+```bash
+# Check installed tools
+uv tool list
+
+# Should show specify-cli
+
+# Verify path
+which specify
+
+# Should point to the uv tool installation directory
+```
+
+If not found, reinstall:
+
+```bash
+uv tool uninstall specify-cli
+uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
+```
+
+### "Do I need to run specify every time I open my project?"
+
+**Short answer:** No, you only run `specify init` once per project (or when upgrading).
+
+**Explanation:**
+
+The `specify` CLI tool is used for:
+
+- **Initial setup:** `specify init` to bootstrap Spec Kit in your project
+- **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.
+
+**If your agent isn't recognizing slash commands:**
+
+1. **Verify command files exist:**
+
+   ```bash
+   # For GitHub Copilot
+   ls -la .github/prompts/
+
+   # For Claude
+   ls -la .claude/commands/
+   ```
+
+2. **Restart your IDE/editor completely** (not just reload window)
+
+3. **Check you're in the correct directory** where you ran `specify init`
+
+4. **For some agents**, you may need to reload the workspace or clear cache
+
+**Related issue:** If Copilot can't open local files or uses PowerShell commands unexpectedly, this is typically an IDE context issue, not related to `specify`. Try:
+
+- Restarting VS Code
+- Checking file permissions
+- Ensuring the workspace folder is properly opened
+
+---
+
+## Version Compatibility
+
+Spec Kit follows semantic versioning for major releases. The CLI and project files are designed to be compatible within the same major version.
+
+**Best practice:** Keep both CLI and project files in sync by upgrading both together during major version changes.
+
+---
+
+## Next Steps
+
+After upgrading:
+
+- **Test new slash commands:** Run `/speckit.constitution` or another command to verify everything works
+- **Review release notes:** Check [GitHub Releases](https://github.com/github/spec-kit/releases) for new features and breaking changes
+- **Update workflows:** If new commands were added, update your team's development workflows
+- **Check documentation:** Visit [github.io/spec-kit](https://github.github.io/spec-kit/) for updated guides

extensions/EXTENSION-API-REFERENCE.md

@@ -0,0 +1,714 @@
+# Extension API Reference
+
+Technical reference for Spec Kit extension system APIs and manifest schema.
+
+## Table of Contents
+
+1. [Extension Manifest](#extension-manifest)
+2. [Python API](#python-api)
+3. [Command File Format](#command-file-format)
+4. [Configuration Schema](#configuration-schema)
+5. [Hook System](#hook-system)
+6. [CLI Commands](#cli-commands)
+
+---
+
+## Extension Manifest
+
+### Schema Version 1.0
+
+File: `extension.yml`
+
+```yaml
+schema_version: "1.0"  # Required
+
+extension:
+  id: string           # Required, pattern: ^[a-z0-9-]+$
+  name: string         # Required, human-readable name
+  version: string      # Required, semantic version (X.Y.Z)
+  description: string  # Required, brief description (<200 chars)
+  author: string       # Required
+  repository: string   # Required, valid URL
+  license: string      # Required (e.g., "MIT", "Apache-2.0")
+  homepage: string     # Optional, valid URL
+
+requires:
+  speckit_version: string  # Required, version specifier (>=X.Y.Z)
+  tools:                   # Optional, array of tool requirements
+    - name: string         # Tool name
+      version: string      # Optional, version specifier
+      required: boolean    # Optional, default: false
+
+provides:
+  commands:              # Required, at least one command
+    - name: string       # Required, pattern: ^speckit\.[a-z0-9-]+\.[a-z0-9-]+$
+      file: string       # Required, relative path to command file
+      description: string # Required
+      aliases: [string]  # Optional, array of alternate names
+
+  config:                # Optional, array of config files
+    - name: string       # Config file name
+      template: string   # Template file path
+      description: string
+      required: boolean  # Default: false
+
+hooks:                   # Optional, event hooks
+  event_name:            # e.g., "after_tasks", "after_implement"
+    command: string      # Command to execute
+    optional: boolean    # Default: true
+    prompt: string       # Prompt text for optional hooks
+    description: string  # Hook description
+    condition: string    # Optional, condition expression
+
+tags:                    # Optional, array of tags (2-10 recommended)
+  - string
+
+defaults:                # Optional, default configuration values
+  key: value             # Any YAML structure
+```
+
+### Field Specifications
+
+#### `extension.id`
+
+- **Type**: string
+- **Pattern**: `^[a-z0-9-]+$`
+- **Description**: Unique extension identifier
+- **Examples**: `jira`, `linear`, `azure-devops`
+- **Invalid**: `Jira`, `my_extension`, `extension.id`
+
+#### `extension.version`
+
+- **Type**: string
+- **Format**: Semantic versioning (X.Y.Z)
+- **Description**: Extension version
+- **Examples**: `1.0.0`, `0.9.5`, `2.1.3`
+- **Invalid**: `v1.0`, `1.0`, `1.0.0-beta`
+
+#### `requires.speckit_version`
+
+- **Type**: string
+- **Format**: Version specifier
+- **Description**: Required spec-kit version range
+- **Examples**:
+  - `>=0.1.0` - Any version 0.1.0 or higher
+  - `>=0.1.0,<2.0.0` - Version 0.1.x or 1.x
+  - `==0.1.0` - Exactly 0.1.0
+- **Invalid**: `0.1.0`, `>= 0.1.0` (space), `latest`
+
+#### `provides.commands[].name`
+
+- **Type**: string
+- **Pattern**: `^speckit\.[a-z0-9-]+\.[a-z0-9-]+$`
+- **Description**: Namespaced command name
+- **Format**:  `speckit.{extension-id}.{command-name}`
+- **Examples**: `speckit.jira.specstoissues`, `speckit.linear.sync`
+- **Invalid**: `jira.specstoissues`, `speckit.command`, `speckit.jira.CreateIssues`
+
+#### `hooks`
+
+- **Type**: object
+- **Keys**: Event names (e.g., `after_tasks`, `after_implement`, `before_commit`)
+- **Description**: Hooks that execute at lifecycle events
+- **Events**: Defined by core spec-kit commands
+
+---
+
+## Python API
+
+### ExtensionManifest
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionManifest
+
+manifest = ExtensionManifest(Path("extension.yml"))
+```
+
+**Properties**:
+
+```python
+manifest.id                        # str: Extension ID
+manifest.name                      # str: Extension name
+manifest.version                   # str: Version
+manifest.description               # str: Description
+manifest.requires_speckit_version  # str: Required spec-kit version
+manifest.commands                  # List[Dict]: Command definitions
+manifest.hooks                     # Dict: Hook definitions
+```
+
+**Methods**:
+
+```python
+manifest.get_hash()  # str: SHA256 hash of manifest file
+```
+
+**Exceptions**:
+
+```python
+ValidationError       # Invalid manifest structure
+CompatibilityError    # Incompatible with current spec-kit version
+```
+
+### ExtensionRegistry
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionRegistry
+
+registry = ExtensionRegistry(extensions_dir)
+```
+
+**Methods**:
+
+```python
+# Add extension to registry
+registry.add(extension_id: str, metadata: dict)
+
+# Remove extension from registry
+registry.remove(extension_id: str)
+
+# Get extension metadata
+metadata = registry.get(extension_id: str)  # Optional[dict]
+
+# List all extensions
+extensions = registry.list()  # Dict[str, dict]
+
+# Check if installed
+is_installed = registry.is_installed(extension_id: str)  # bool
+```
+
+**Registry Format**:
+
+```json
+{
+  "schema_version": "1.0",
+  "extensions": {
+    "jira": {
+      "version": "1.0.0",
+      "source": "catalog",
+      "manifest_hash": "sha256...",
+      "enabled": true,
+      "registered_commands": ["speckit.jira.specstoissues", ...],
+      "installed_at": "2026-01-28T..."
+    }
+  }
+}
+```
+
+### ExtensionManager
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionManager
+
+manager = ExtensionManager(project_root)
+```
+
+**Methods**:
+
+```python
+# Install from directory
+manifest = manager.install_from_directory(
+    source_dir: Path,
+    speckit_version: str,
+    register_commands: bool = True
+)  # Returns: ExtensionManifest
+
+# Install from ZIP
+manifest = manager.install_from_zip(
+    zip_path: Path,
+    speckit_version: str
+)  # Returns: ExtensionManifest
+
+# Remove extension
+success = manager.remove(
+    extension_id: str,
+    keep_config: bool = False
+)  # Returns: bool
+
+# List installed extensions
+extensions = manager.list_installed()  # List[Dict]
+
+# Get extension manifest
+manifest = manager.get_extension(extension_id: str)  # Optional[ExtensionManifest]
+
+# Check compatibility
+manager.check_compatibility(
+    manifest: ExtensionManifest,
+    speckit_version: str
+)  # Raises: CompatibilityError if incompatible
+```
+
+### ExtensionCatalog
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import ExtensionCatalog
+
+catalog = ExtensionCatalog(project_root)
+```
+
+**Methods**:
+
+```python
+# Fetch catalog
+catalog_data = catalog.fetch_catalog(force_refresh: bool = False)  # Dict
+
+# Search extensions
+results = catalog.search(
+    query: Optional[str] = None,
+    tag: Optional[str] = None,
+    author: Optional[str] = None,
+    verified_only: bool = False
+)  # Returns: List[Dict]
+
+# Get extension info
+ext_info = catalog.get_extension_info(extension_id: str)  # Optional[Dict]
+
+# Check cache validity
+is_valid = catalog.is_cache_valid()  # bool
+
+# Clear cache
+catalog.clear_cache()
+```
+
+### HookExecutor
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import HookExecutor
+
+hook_executor = HookExecutor(project_root)
+```
+
+**Methods**:
+
+```python
+# Get project config
+config = hook_executor.get_project_config()  # Dict
+
+# Save project config
+hook_executor.save_project_config(config: Dict)
+
+# Register hooks
+hook_executor.register_hooks(manifest: ExtensionManifest)
+
+# Unregister hooks
+hook_executor.unregister_hooks(extension_id: str)
+
+# Get hooks for event
+hooks = hook_executor.get_hooks_for_event(event_name: str)  # List[Dict]
+
+# Check if hook should execute
+should_run = hook_executor.should_execute_hook(hook: Dict)  # bool
+
+# Format hook message
+message = hook_executor.format_hook_message(
+    event_name: str,
+    hooks: List[Dict]
+)  # str
+```
+
+### CommandRegistrar
+
+**Module**: `specify_cli.extensions`
+
+```python
+from specify_cli.extensions import CommandRegistrar
+
+registrar = CommandRegistrar()
+```
+
+**Methods**:
+
+```python
+# Register commands for Claude Code
+registered = registrar.register_commands_for_claude(
+    manifest: ExtensionManifest,
+    extension_dir: Path,
+    project_root: Path
+)  # Returns: List[str] (command names)
+
+# Parse frontmatter
+frontmatter, body = registrar.parse_frontmatter(content: str)
+
+# Render frontmatter
+yaml_text = registrar.render_frontmatter(frontmatter: Dict)  # str
+```
+
+---
+
+## Command File Format
+
+### Universal Command Format
+
+**File**: `commands/{command-name}.md`
+
+```markdown
+---
+description: "Command description"
+tools:
+  - 'mcp-server/tool_name'
+  - 'other-mcp-server/other_tool'
+---
+
+# Command Title
+
+Command documentation in Markdown.
+
+## Prerequisites
+
+1. Requirement 1
+2. Requirement 2
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+### Step 1: Description
+
+Instruction text...
+
+\`\`\`bash
+# Shell commands
+\`\`\`
+
+### Step 2: Another Step
+
+More instructions...
+
+## Configuration Reference
+
+Information about configuration options.
+
+## Notes
+
+Additional notes and tips.
+```
+
+### Frontmatter Fields
+
+```yaml
+description: string   # Required, brief command description
+tools: [string]       # Optional, MCP tools required
+```
+
+### Special Variables
+
+- `$ARGUMENTS` - Placeholder for user-provided arguments
+- Extension context automatically injected:
+
+  ```markdown
+  <!-- Extension: {extension-id} -->
+  <!-- Config: .specify/extensions/{extension-id}/ -->
+  ```
+
+---
+
+## Configuration Schema
+
+### Extension Config File
+
+**File**: `.specify/extensions/{extension-id}/{extension-id}-config.yml`
+
+Extensions define their own config schema. Common patterns:
+
+```yaml
+# Connection settings
+connection:
+  url: string
+  api_key: string
+
+# Project settings
+project:
+  key: string
+  workspace: string
+
+# Feature flags
+features:
+  enabled: boolean
+  auto_sync: boolean
+
+# Defaults
+defaults:
+  labels: [string]
+  assignee: string
+
+# Custom fields
+field_mappings:
+  internal_name: "external_field_id"
+```
+
+### Config Layers
+
+1. **Extension Defaults** (from `extension.yml` `defaults` section)
+2. **Project Config** (`{extension-id}-config.yml`)
+3. **Local Override** (`{extension-id}-config.local.yml`, gitignored)
+4. **Environment Variables** (`SPECKIT_{EXTENSION}_*`)
+
+### Environment Variable Pattern
+
+Format: `SPECKIT_{EXTENSION}_{KEY}`
+
+Examples:
+
+- `SPECKIT_JIRA_PROJECT_KEY`
+- `SPECKIT_LINEAR_API_KEY`
+- `SPECKIT_GITHUB_TOKEN`
+
+---
+
+## Hook System
+
+### Hook Definition
+
+**In extension.yml**:
+
+```yaml
+hooks:
+  after_tasks:
+    command: "speckit.jira.specstoissues"
+    optional: true
+    prompt: "Create Jira issues from tasks?"
+    description: "Automatically create Jira hierarchy"
+    condition: null
+```
+
+### Hook Events
+
+Standard events (defined by core):
+
+- `after_tasks` - After task generation
+- `after_implement` - After implementation
+- `before_commit` - Before git commit
+- `after_commit` - After git commit
+
+### Hook Configuration
+
+**In `.specify/extensions.yml`**:
+
+```yaml
+hooks:
+  after_tasks:
+    - extension: jira
+      command: speckit.jira.specstoissues
+      enabled: true
+      optional: true
+      prompt: "Create Jira issues from tasks?"
+      description: "..."
+      condition: null
+```
+
+### Hook Message Format
+
+```markdown
+## Extension Hooks
+
+**Optional Hook**: {extension}
+Command: `/{command}`
+Description: {description}
+
+Prompt: {prompt}
+To execute: `/{command}`
+```
+
+Or for mandatory hooks:
+
+```markdown
+**Automatic Hook**: {extension}
+Executing: `/{command}`
+EXECUTE_COMMAND: {command}
+```
+
+---
+
+## CLI Commands
+
+### extension list
+
+**Usage**: `specify extension list [OPTIONS]`
+
+**Options**:
+
+- `--available` - Show available extensions from catalog
+- `--all` - Show both installed and available
+
+**Output**: List of installed extensions with metadata
+
+### extension add
+
+**Usage**: `specify extension add EXTENSION [OPTIONS]`
+
+**Options**:
+
+- `--from URL` - Install from custom URL
+- `--dev PATH` - Install from local directory
+- `--version VERSION` - Install specific version
+- `--no-register` - Skip command registration
+
+**Arguments**:
+
+- `EXTENSION` - Extension name or URL
+
+### extension remove
+
+**Usage**: `specify extension remove EXTENSION [OPTIONS]`
+
+**Options**:
+
+- `--keep-config` - Preserve config files
+- `--force` - Skip confirmation
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension search
+
+**Usage**: `specify extension search [QUERY] [OPTIONS]`
+
+**Options**:
+
+- `--tag TAG` - Filter by tag
+- `--author AUTHOR` - Filter by author
+- `--verified` - Show only verified extensions
+
+**Arguments**:
+
+- `QUERY` - Optional search query
+
+### extension info
+
+**Usage**: `specify extension info EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension update
+
+**Usage**: `specify extension update [EXTENSION]`
+
+**Arguments**:
+
+- `EXTENSION` - Optional, extension ID (default: all)
+
+### extension enable
+
+**Usage**: `specify extension enable EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+### extension disable
+
+**Usage**: `specify extension disable EXTENSION`
+
+**Arguments**:
+
+- `EXTENSION` - Extension ID
+
+---
+
+## Exceptions
+
+### ValidationError
+
+Raised when extension manifest validation fails.
+
+```python
+from specify_cli.extensions import ValidationError
+
+try:
+    manifest = ExtensionManifest(path)
+except ValidationError as e:
+    print(f"Invalid manifest: {e}")
+```
+
+### CompatibilityError
+
+Raised when extension is incompatible with current spec-kit version.
+
+```python
+from specify_cli.extensions import CompatibilityError
+
+try:
+    manager.check_compatibility(manifest, "0.1.0")
+except CompatibilityError as e:
+    print(f"Incompatible: {e}")
+```
+
+### ExtensionError
+
+Base exception for all extension-related errors.
+
+```python
+from specify_cli.extensions import ExtensionError
+
+try:
+    manager.install_from_directory(path, "0.1.0")
+except ExtensionError as e:
+    print(f"Extension error: {e}")
+```
+
+---
+
+## Version Functions
+
+### version_satisfies
+
+Check if a version satisfies a specifier.
+
+```python
+from specify_cli.extensions import version_satisfies
+
+# True if 1.2.3 satisfies >=1.0.0,<2.0.0
+satisfied = version_satisfies("1.2.3", ">=1.0.0,<2.0.0")  # bool
+```
+
+---
+
+## File System Layout
+
+```text
+.specify/
+├── extensions/
+│   ├── .registry               # Extension registry (JSON)
+│   ├── .cache/                 # Catalog cache
+│   │   ├── catalog.json
+│   │   └── catalog-metadata.json
+│   ├── .backup/                # Config backups
+│   │   └── {ext}-{config}.yml
+│   ├── {extension-id}/         # Extension directory
+│   │   ├── extension.yml       # Manifest
+│   │   ├── {ext}-config.yml    # User config
+│   │   ├── {ext}-config.local.yml  # Local overrides (gitignored)
+│   │   ├── {ext}-config.template.yml  # Template
+│   │   ├── commands/           # Command files
+│   │   │   └── *.md
+│   │   ├── scripts/            # Helper scripts
+│   │   │   └── *.sh
+│   │   ├── docs/               # Documentation
+│   │   └── README.md
+│   └── extensions.yml          # Project extension config
+└── scripts/                    # (existing spec-kit)
+
+.claude/
+└── commands/
+    └── speckit.{ext}.{cmd}.md  # Registered commands
+```
+
+---
+
+*Last Updated: 2026-01-28*
+*API Version: 1.0*
+*Spec Kit Version: 0.1.0*

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -0,0 +1,649 @@
+# Extension Development Guide
+
+A guide for creating Spec Kit extensions.
+
+---
+
+## Quick Start
+
+### 1. Create Extension Directory
+
+```bash
+mkdir my-extension
+cd my-extension
+```
+
+### 2. Create `extension.yml` Manifest
+
+```yaml
+schema_version: "1.0"
+
+extension:
+  id: "my-ext"                          # Lowercase, alphanumeric + hyphens only
+  name: "My Extension"
+  version: "1.0.0"                      # Semantic versioning
+  description: "My custom extension"
+  author: "Your Name"
+  repository: "https://github.com/you/spec-kit-my-ext"
+  license: "MIT"
+
+requires:
+  speckit_version: ">=0.1.0"            # Minimum spec-kit version
+  tools:                                # Optional: External tools required
+    - name: "my-tool"
+      required: true
+      version: ">=1.0.0"
+  commands:                             # Optional: Core commands needed
+    - "speckit.tasks"
+
+provides:
+  commands:
+    - name: "speckit.my-ext.hello"      # Must follow pattern: speckit.{ext-id}.{cmd}
+      file: "commands/hello.md"
+      description: "Say hello"
+      aliases: ["speckit.hello"]        # Optional aliases
+
+  config:                               # Optional: Config files
+    - name: "my-ext-config.yml"
+      template: "my-ext-config.template.yml"
+      description: "Extension configuration"
+      required: false
+
+hooks:                                  # Optional: Integration hooks
+  after_tasks:
+    command: "speckit.my-ext.hello"
+    optional: true
+    prompt: "Run hello command?"
+
+tags:                                   # Optional: For catalog search
+  - "example"
+  - "utility"
+```
+
+### 3. Create Commands Directory
+
+```bash
+mkdir commands
+```
+
+### 4. Create Command File
+
+**File**: `commands/hello.md`
+
+```markdown
+---
+description: "Say hello command"
+tools:                              # Optional: AI tools this command uses
+  - 'some-tool/function'
+scripts:                            # Optional: Helper scripts
+  sh: ../../scripts/bash/helper.sh
+  ps: ../../scripts/powershell/helper.ps1
+---
+
+# Hello Command
+
+This command says hello!
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+1. Greet the user
+2. Show extension is working
+
+```bash
+echo "Hello from my extension!"
+echo "Arguments: $ARGUMENTS"
+```
+
+## Extension Configuration
+
+Load extension config from `.specify/extensions/my-ext/my-ext-config.yml`.
+
+### 5. Test Locally
+
+```bash
+cd /path/to/spec-kit-project
+specify extension add --dev /path/to/my-extension
+```
+
+### 6. Verify Installation
+
+```bash
+specify extension list
+
+# Should show:
+#  ✓ My Extension (v1.0.0)
+#     My custom extension
+#     Commands: 1 | Hooks: 1 | Status: Enabled
+```
+
+### 7. Test Command
+
+If using Claude:
+
+```bash
+claude
+> /speckit.my-ext.hello world
+```
+
+The command will be available in `.claude/commands/speckit.my-ext.hello.md`.
+
+---
+
+## Manifest Schema Reference
+
+### Required Fields
+
+#### `schema_version`
+
+Extension manifest schema version. Currently: `"1.0"`
+
+#### `extension`
+
+Extension metadata block.
+
+**Required sub-fields**:
+
+- `id`: Extension identifier (lowercase, alphanumeric, hyphens)
+- `name`: Human-readable name
+- `version`: Semantic version (e.g., "1.0.0")
+- `description`: Short description
+
+**Optional sub-fields**:
+
+- `author`: Extension author
+- `repository`: Source code URL
+- `license`: SPDX license identifier
+- `homepage`: Extension homepage URL
+
+#### `requires`
+
+Compatibility requirements.
+
+**Required sub-fields**:
+
+- `speckit_version`: Semantic version specifier (e.g., ">=0.1.0,<2.0.0")
+
+**Optional sub-fields**:
+
+- `tools`: External tools required (array of tool objects)
+- `commands`: Core spec-kit commands needed (array of command names)
+- `scripts`: Core scripts required (array of script names)
+
+#### `provides`
+
+What the extension provides.
+
+**Required sub-fields**:
+
+- `commands`: Array of command objects (must have at least one)
+
+**Command object**:
+
+- `name`: Command name (must match `speckit.{ext-id}.{command}`)
+- `file`: Path to command file (relative to extension root)
+- `description`: Command description (optional)
+- `aliases`: Alternative command names (optional, array)
+
+### Optional Fields
+
+#### `hooks`
+
+Integration hooks for automatic execution.
+
+Available hook points:
+
+- `after_tasks`: After `/speckit.tasks` completes
+- `after_implement`: After `/speckit.implement` completes (future)
+
+Hook object:
+
+- `command`: Command to execute (must be in `provides.commands`)
+- `optional`: If true, prompt user before executing
+- `prompt`: Prompt text for optional hooks
+- `description`: Hook description
+- `condition`: Execution condition (future)
+
+#### `tags`
+
+Array of tags for catalog discovery.
+
+#### `defaults`
+
+Default extension configuration values.
+
+#### `config_schema`
+
+JSON Schema for validating extension configuration.
+
+---
+
+## Command File Format
+
+### Frontmatter (YAML)
+
+```yaml
+---
+description: "Command description"          # Required
+tools:                                      # Optional
+  - 'tool-name/function'
+scripts:                                    # Optional
+  sh: ../../scripts/bash/helper.sh
+  ps: ../../scripts/powershell/helper.ps1
+---
+```
+
+### Body (Markdown)
+
+Use standard Markdown with special placeholders:
+
+- `$ARGUMENTS`: User-provided arguments
+- `{SCRIPT}`: Replaced with script path during registration
+
+**Example**:
+
+````markdown
+## Steps
+
+1. Parse arguments
+2. Execute logic
+
+```bash
+args="$ARGUMENTS"
+echo "Running with args: $args"
+```
+````
+
+### Script Path Rewriting
+
+Extension commands use relative paths that get rewritten during registration:
+
+**In extension**:
+
+```yaml
+scripts:
+  sh: ../../scripts/bash/helper.sh
+```
+
+**After registration**:
+
+```yaml
+scripts:
+  sh: .specify/scripts/bash/helper.sh
+```
+
+This allows scripts to reference core spec-kit scripts.
+
+---
+
+## Configuration Files
+
+### Config Template
+
+**File**: `my-ext-config.template.yml`
+
+```yaml
+# My Extension Configuration
+# Copy this to my-ext-config.yml and customize
+
+# Example configuration
+api:
+  endpoint: "https://api.example.com"
+  timeout: 30
+
+features:
+  feature_a: true
+  feature_b: false
+
+credentials:
+  # DO NOT commit credentials!
+  # Use environment variables instead
+  api_key: "${MY_EXT_API_KEY}"
+```
+
+### Config Loading
+
+In your command, load config with layered precedence:
+
+1. Extension defaults (`extension.yml` → `defaults`)
+2. Project config (`.specify/extensions/my-ext/my-ext-config.yml`)
+3. Local overrides (`.specify/extensions/my-ext/my-ext-config.local.yml` - gitignored)
+4. Environment variables (`SPECKIT_MY_EXT_*`)
+
+**Example loading script**:
+
+```bash
+#!/usr/bin/env bash
+EXT_DIR=".specify/extensions/my-ext"
+
+# Load and merge config
+config=$(yq eval '.' "$EXT_DIR/my-ext-config.yml" -o=json)
+
+# Apply env overrides
+if [ -n "${SPECKIT_MY_EXT_API_KEY:-}" ]; then
+  config=$(echo "$config" | jq ".api.api_key = \"$SPECKIT_MY_EXT_API_KEY\"")
+fi
+
+echo "$config"
+```
+
+---
+
+## Validation Rules
+
+### Extension ID
+
+- **Pattern**: `^[a-z0-9-]+$`
+- **Valid**: `my-ext`, `tool-123`, `awesome-plugin`
+- **Invalid**: `MyExt` (uppercase), `my_ext` (underscore), `my ext` (space)
+
+### Extension Version
+
+- **Format**: Semantic versioning (MAJOR.MINOR.PATCH)
+- **Valid**: `1.0.0`, `0.1.0`, `2.5.3`
+- **Invalid**: `1.0`, `v1.0.0`, `1.0.0-beta`
+
+### Command Name
+
+- **Pattern**: `^speckit\.[a-z0-9-]+\.[a-z0-9-]+$`
+- **Valid**: `speckit.my-ext.hello`, `speckit.tool.cmd`
+- **Invalid**: `my-ext.hello` (missing prefix), `speckit.hello` (no extension namespace)
+
+### Command File Path
+
+- **Must be** relative to extension root
+- **Valid**: `commands/hello.md`, `commands/subdir/cmd.md`
+- **Invalid**: `/absolute/path.md`, `../outside.md`
+
+---
+
+## Testing Extensions
+
+### Manual Testing
+
+1. **Create test extension**
+2. **Install locally**:
+
+   ```bash
+   specify extension add --dev /path/to/extension
+   ```
+
+3. **Verify installation**:
+
+   ```bash
+   specify extension list
+   ```
+
+4. **Test commands** with your AI agent
+5. **Check command registration**:
+
+   ```bash
+   ls .claude/commands/speckit.my-ext.*
+   ```
+
+6. **Remove extension**:
+
+   ```bash
+   specify extension remove my-ext
+   ```
+
+### Automated Testing
+
+Create tests for your extension:
+
+```python
+# tests/test_my_extension.py
+import pytest
+from pathlib import Path
+from specify_cli.extensions import ExtensionManifest
+
+def test_manifest_valid():
+    """Test extension manifest is valid."""
+    manifest = ExtensionManifest(Path("extension.yml"))
+    assert manifest.id == "my-ext"
+    assert len(manifest.commands) >= 1
+
+def test_command_files_exist():
+    """Test all command files exist."""
+    manifest = ExtensionManifest(Path("extension.yml"))
+    for cmd in manifest.commands:
+        cmd_file = Path(cmd["file"])
+        assert cmd_file.exists(), f"Command file not found: {cmd_file}"
+```
+
+---
+
+## Distribution
+
+### Option 1: GitHub Repository
+
+1. **Create repository**: `spec-kit-my-ext`
+2. **Add files**:
+
+   ```text
+   spec-kit-my-ext/
+   ├── extension.yml
+   ├── commands/
+   ├── scripts/
+   ├── docs/
+   ├── README.md
+   ├── LICENSE
+   └── CHANGELOG.md
+   ```
+
+3. **Create release**: Tag with version (e.g., `v1.0.0`)
+4. **Install from repo**:
+
+   ```bash
+   git clone https://github.com/you/spec-kit-my-ext
+   specify extension add --dev spec-kit-my-ext/
+   ```
+
+### Option 2: ZIP Archive (Future)
+
+Create ZIP archive and host on GitHub Releases:
+
+```bash
+zip -r spec-kit-my-ext-1.0.0.zip extension.yml commands/ scripts/ docs/
+```
+
+Users install with:
+
+```bash
+specify extension add --from https://github.com/.../spec-kit-my-ext-1.0.0.zip
+```
+
+### Option 3: Extension Catalog (Future)
+
+Submit to official catalog:
+
+1. **Fork** spec-kit repository
+2. **Add entry** to `extensions/catalog.json`
+3. **Create PR**
+4. **After merge**, users can install with:
+
+   ```bash
+   specify extension add my-ext  # No URL needed!
+   ```
+
+---
+
+## Best Practices
+
+### Naming Conventions
+
+- **Extension ID**: Use descriptive, hyphenated names (`jira-integration`, not `ji`)
+- **Commands**: Use verb-noun pattern (`create-issue`, `sync-status`)
+- **Config files**: Match extension ID (`jira-config.yml`)
+
+### Documentation
+
+- **README.md**: Overview, installation, usage
+- **CHANGELOG.md**: Version history
+- **docs/**: Detailed guides
+- **Command descriptions**: Clear, concise
+
+### Versioning
+
+- **Follow SemVer**: `MAJOR.MINOR.PATCH`
+- **MAJOR**: Breaking changes
+- **MINOR**: New features
+- **PATCH**: Bug fixes
+
+### Security
+
+- **Never commit secrets**: Use environment variables
+- **Validate input**: Sanitize user arguments
+- **Document permissions**: What files/APIs are accessed
+
+### Compatibility
+
+- **Specify version range**: Don't require exact version
+- **Test with multiple versions**: Ensure compatibility
+- **Graceful degradation**: Handle missing features
+
+---
+
+## Example Extensions
+
+### Minimal Extension
+
+Smallest possible extension:
+
+```yaml
+# extension.yml
+schema_version: "1.0"
+extension:
+  id: "minimal"
+  name: "Minimal Extension"
+  version: "1.0.0"
+  description: "Minimal example"
+requires:
+  speckit_version: ">=0.1.0"
+provides:
+  commands:
+    - name: "speckit.minimal.hello"
+      file: "commands/hello.md"
+```
+
+````markdown
+<!-- commands/hello.md -->
+---
+description: "Hello command"
+---
+
+# Hello World
+
+```bash
+echo "Hello, $ARGUMENTS!"
+```
+````
+
+### Extension with Config
+
+Extension using configuration:
+
+```yaml
+# extension.yml
+# ... metadata ...
+provides:
+  config:
+    - name: "tool-config.yml"
+      template: "tool-config.template.yml"
+      required: true
+```
+
+```yaml
+# tool-config.template.yml
+api_endpoint: "https://api.example.com"
+timeout: 30
+```
+
+````markdown
+<!-- commands/use-config.md -->
+# Use Config
+
+Load config:
+```bash
+config_file=".specify/extensions/tool/tool-config.yml"
+endpoint=$(yq eval '.api_endpoint' "$config_file")
+echo "Using endpoint: $endpoint"
+```
+````
+
+### Extension with Hooks
+
+Extension that runs automatically:
+
+```yaml
+# extension.yml
+hooks:
+  after_tasks:
+    command: "speckit.auto.analyze"
+    optional: false  # Always run
+    description: "Analyze tasks after generation"
+```
+
+---
+
+## Troubleshooting
+
+### Extension won't install
+
+**Error**: `Invalid extension ID`
+
+- **Fix**: Use lowercase, alphanumeric + hyphens only
+
+**Error**: `Extension requires spec-kit >=0.2.0`
+
+- **Fix**: Update spec-kit with `uv tool install specify-cli --force`
+
+**Error**: `Command file not found`
+
+- **Fix**: Ensure command files exist at paths specified in manifest
+
+### Commands not registered
+
+**Symptom**: Commands don't appear in AI agent
+
+**Check**:
+
+1. `.claude/commands/` directory exists
+2. Extension installed successfully
+3. Commands registered in registry:
+
+   ```bash
+   cat .specify/extensions/.registry
+   ```
+
+**Fix**: Reinstall extension to trigger registration
+
+### Config not loading
+
+**Check**:
+
+1. Config file exists: `.specify/extensions/{ext-id}/{ext-id}-config.yml`
+2. YAML syntax is valid: `yq eval '.' config.yml`
+3. Environment variables set correctly
+
+---
+
+## Getting Help
+
+- **Issues**: Report bugs at GitHub repository
+- **Discussions**: Ask questions in GitHub Discussions
+- **Examples**: See `spec-kit-jira` for full-featured example (Phase B)
+
+---
+
+## Next Steps
+
+1. **Create your extension** following this guide
+2. **Test locally** with `--dev` flag
+3. **Share with community** (GitHub, catalog)
+4. **Iterate** based on feedback
+
+Happy extending! 🚀

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -0,0 +1,530 @@
+# Extension Publishing Guide
+
+This guide explains how to publish your extension to the Spec Kit extension catalog, making it discoverable by `specify extension search`.
+
+## Table of Contents
+
+1. [Prerequisites](#prerequisites)
+2. [Prepare Your Extension](#prepare-your-extension)
+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 an extension, ensure you have:
+
+1. **Valid Extension**: A working extension with a valid `extension.yml` manifest
+2. **Git Repository**: Extension hosted on GitHub (or other public git hosting)
+3. **Documentation**: README.md with installation 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**: Extension tested on real projects
+
+---
+
+## Prepare Your Extension
+
+### 1. Extension Structure
+
+Ensure your extension follows the standard structure:
+
+```text
+your-extension/
+├── extension.yml              # Required: Extension manifest
+├── README.md                  # Required: Documentation
+├── LICENSE                    # Required: License file
+├── CHANGELOG.md               # Recommended: Version history
+├── .gitignore                 # Recommended: Git ignore rules
+│
+├── commands/                  # Extension commands
+│   ├── command1.md
+│   └── command2.md
+│
+├── config-template.yml        # Config template (if needed)
+│
+└── docs/                      # Additional documentation
+    ├── usage.md
+    └── examples/
+```
+
+### 2. extension.yml Validation
+
+Verify your manifest is valid:
+
+```yaml
+schema_version: "1.0"
+
+extension:
+  id: "your-extension"           # Unique lowercase-hyphenated ID
+  name: "Your Extension 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-your-extension"
+  license: "MIT"
+  homepage: "https://github.com/your-org/spec-kit-your-extension"
+
+requires:
+  speckit_version: ">=0.1.0"    # Required spec-kit version
+
+provides:
+  commands:                       # List all commands
+    - name: "speckit.your-extension.command"
+      file: "commands/command.md"
+      description: "Command description"
+
+tags:                             # 2-5 relevant tags
+  - "category"
+  - "tool-name"
+```
+
+**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 100 characters)
+- ✅ `repository` URL is valid and public
+- ✅ All command files exist in the extension directory
+- ✅ Tags are lowercase and descriptive
+
+### 3. Create GitHub Release
+
+Create a GitHub release for your extension version:
+
+```bash
+# Tag the release
+git tag v1.0.0
+git push origin v1.0.0
+
+# Create release on GitHub
+# Go to: https://github.com/your-org/spec-kit-your-extension/releases/new
+# - Tag: v1.0.0
+# - Title: v1.0.0 - Release Name
+# - Description: Changelog/release notes
+```
+
+The release archive URL will be:
+
+```text
+https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+```
+
+### 4. Test Installation
+
+Test that users can install from your release:
+
+```bash
+# Test dev installation
+specify extension add --dev /path/to/your-extension
+
+# Test from GitHub archive
+specify extension add --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
+```
+
+---
+
+## Submit to Catalog
+
+### 1. Fork the spec-kit Repository
+
+```bash
+# Fork on GitHub
+# https://github.com/statsperform/spec-kit/fork
+
+# Clone your fork
+git clone https://github.com/YOUR-USERNAME/spec-kit.git
+cd spec-kit
+```
+
+### 2. Add Extension to Catalog
+
+Edit `extensions/catalog.json` and add your extension:
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-01-28T15:54:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/statsperform/spec-kit/main/extensions/catalog.json",
+  "extensions": {
+    "your-extension": {
+      "name": "Your Extension Name",
+      "id": "your-extension",
+      "description": "Brief description of your extension",
+      "author": "Your Name",
+      "version": "1.0.0",
+      "download_url": "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-your-extension",
+      "homepage": "https://github.com/your-org/spec-kit-your-extension",
+      "documentation": "https://github.com/your-org/spec-kit-your-extension/blob/main/docs/",
+      "changelog": "https://github.com/your-org/spec-kit-your-extension/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "required-mcp-tool",
+            "version": ">=1.0.0",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": [
+        "category",
+        "tool-name",
+        "feature"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-01-28T00:00:00Z",
+      "updated_at": "2026-01-28T00:00:00Z"
+    }
+  }
+}
+```
+
+**Important**:
+
+- Set `verified: false` (maintainers will verify)
+- Set `downloads: 0` and `stars: 0` (auto-updated later)
+- Use current timestamp for `created_at` and `updated_at`
+- Update the top-level `updated_at` to current time
+
+### 3. Submit Pull Request
+
+```bash
+# Create a branch
+git checkout -b add-your-extension
+
+# Commit your changes
+git add extensions/catalog.json
+git commit -m "Add your-extension to catalog
+
+- Extension ID: your-extension
+- Version: 1.0.0
+- Author: Your Name
+- Description: Brief description
+"
+
+# Push to your fork
+git push origin add-your-extension
+
+# Create Pull Request on GitHub
+# https://github.com/statsperform/spec-kit/compare
+```
+
+**Pull Request Template**:
+
+```markdown
+## Extension Submission
+
+**Extension Name**: Your Extension Name
+**Extension ID**: your-extension
+**Version**: 1.0.0
+**Author**: Your Name
+**Repository**: https://github.com/your-org/spec-kit-your-extension
+
+### Description
+Brief description of what your extension does.
+
+### Checklist
+- [x] Valid extension.yml manifest
+- [x] README.md with installation and usage docs
+- [x] LICENSE file included
+- [x] GitHub release created (v1.0.0)
+- [x] Extension tested on real project
+- [x] All commands working
+- [x] No security vulnerabilities
+
+### Testing
+Tested on:
+- macOS 13.0+ with spec-kit 0.1.0
+- Project: [Your test project]
+
+### Additional Notes
+Any additional context or notes for reviewers.
+```
+
+---
+
+## Verification Process
+
+### What Happens After Submission
+
+1. **Automated Checks** (if available):
+   - Manifest validation
+   - Download URL accessibility
+   - Repository existence
+   - License file presence
+
+2. **Manual Review**:
+   - Code quality review
+   - Security audit
+   - Functionality testing
+   - Documentation review
+
+3. **Verification**:
+   - If approved, `verified: true` is set
+   - Extension appears in `specify extension search --verified`
+
+### Verification Criteria
+
+To be verified, your extension must:
+
+✅ **Functionality**:
+
+- Works as described in documentation
+- All commands execute without errors
+- No breaking changes to user workflows
+
+✅ **Security**:
+
+- No known vulnerabilities
+- No malicious code
+- Safe handling of user data
+- Proper validation of inputs
+
+✅ **Code Quality**:
+
+- Clean, readable code
+- Follows extension best practices
+- Proper error handling
+- Helpful error messages
+
+✅ **Documentation**:
+
+- Clear installation instructions
+- Usage examples
+- Troubleshooting section
+- Accurate description
+
+✅ **Maintenance**:
+
+- Active repository
+- Responsive to issues
+- Regular updates
+- Semantic versioning followed
+
+### Typical Review Timeline
+
+- **Automated checks**: Immediate (if implemented)
+- **Manual review**: 3-7 business days
+- **Verification**: After successful review
+
+---
+
+## Release Workflow
+
+### Publishing New Versions
+
+When releasing a new version:
+
+1. **Update version** in `extension.yml`:
+
+   ```yaml
+   extension:
+     version: "1.1.0"  # Updated version
+   ```
+
+2. **Update CHANGELOG.md**:
+
+   ```markdown
+   ## [1.1.0] - 2026-02-15
+
+   ### Added
+   - New feature X
+
+   ### Fixed
+   - Bug fix Y
+   ```
+
+3. **Create GitHub release**:
+
+   ```bash
+   git tag v1.1.0
+   git push origin v1.1.0
+   # Create release on GitHub
+   ```
+
+4. **Update catalog**:
+
+   ```bash
+   # Fork spec-kit repo (or update existing fork)
+   cd spec-kit
+
+   # Update extensions/catalog.json
+   jq '.extensions["your-extension"].version = "1.1.0"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.extensions["your-extension"].download_url = "https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.1.0.zip"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.extensions["your-extension"].updated_at = "2026-02-15T00:00:00Z"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+   jq '.updated_at = "2026-02-15T00:00:00Z"' extensions/catalog.json > tmp.json && mv tmp.json extensions/catalog.json
+
+   # Submit PR
+   git checkout -b update-your-extension-v1.1.0
+   git add extensions/catalog.json
+   git commit -m "Update your-extension to v1.1.0"
+   git push origin update-your-extension-v1.1.0
+   ```
+
+5. **Submit update PR** with changelog in description
+
+---
+
+## Best Practices
+
+### Extension Design
+
+1. **Single Responsibility**: Each extension should focus on one tool/integration
+2. **Clear Naming**: Use descriptive, unambiguous names
+3. **Minimal Dependencies**: Avoid unnecessary dependencies
+4. **Backward Compatibility**: Follow semantic versioning strictly
+
+### Documentation
+
+1. **README.md Structure**:
+   - Overview and features
+   - Installation instructions
+   - Configuration guide
+   - Usage examples
+   - Troubleshooting
+   - Contributing guidelines
+
+2. **Command Documentation**:
+   - Clear description
+   - Prerequisites listed
+   - Step-by-step instructions
+   - Error handling guidance
+   - Examples
+
+3. **Configuration**:
+   - Provide template file
+   - Document all options
+   - Include examples
+   - Explain defaults
+
+### Security
+
+1. **Input Validation**: Validate all user inputs
+2. **No Hardcoded Secrets**: Never include credentials
+3. **Safe Dependencies**: Only use trusted dependencies
+4. **Audit Regularly**: Check for vulnerabilities
+
+### Maintenance
+
+1. **Respond to Issues**: Address issues within 1-2 weeks
+2. **Regular Updates**: Keep dependencies updated
+3. **Changelog**: Maintain detailed changelog
+4. **Deprecation**: Give advance notice for breaking changes
+
+### Community
+
+1. **License**: Use permissive open-source license (MIT, Apache 2.0)
+2. **Contributing**: Welcome contributions
+3. **Code of Conduct**: Be respectful and inclusive
+4. **Support**: Provide ways to get help (issues, discussions, email)
+
+---
+
+## FAQ
+
+### Q: Can I publish private/proprietary extensions?
+
+A: The main catalog is for public extensions only. For private extensions:
+
+- Host your own catalog.json file
+- Users add your catalog: `specify extension add-catalog https://your-domain.com/catalog.json`
+- Not yet implemented - coming in Phase 4
+
+### Q: How long does verification take?
+
+A: Typically 3-7 business days for initial review. Updates to verified extensions are usually faster.
+
+### Q: What if my extension is rejected?
+
+A: You'll receive feedback on what needs to be fixed. Make the changes and resubmit.
+
+### Q: Can I update my extension anytime?
+
+A: Yes, submit a PR to update the catalog with your new version. Verified status may be re-evaluated for major changes.
+
+### Q: Do I need to be verified to be in the catalog?
+
+A: No, unverified extensions are still searchable. Verification just adds trust and visibility.
+
+### Q: Can extensions have paid features?
+
+A: Extensions should be free and open-source. Commercial support/services are allowed, but core functionality must be free.
+
+---
+
+## Support
+
+- **Catalog Issues**: <https://github.com/statsperform/spec-kit/issues>
+- **Extension Template**: <https://github.com/statsperform/spec-kit-extension-template> (coming soon)
+- **Development Guide**: See EXTENSION-DEVELOPMENT-GUIDE.md
+- **Community**: Discussions and Q&A
+
+---
+
+## Appendix: Catalog Schema
+
+### Complete Catalog Entry Schema
+
+```json
+{
+  "name": "string (required)",
+  "id": "string (required, unique)",
+  "description": "string (required, <200 chars)",
+  "author": "string (required)",
+  "version": "string (required, semver)",
+  "download_url": "string (required, valid URL)",
+  "repository": "string (required, valid URL)",
+  "homepage": "string (optional, valid URL)",
+  "documentation": "string (optional, valid URL)",
+  "changelog": "string (optional, valid URL)",
+  "license": "string (required)",
+  "requires": {
+    "speckit_version": "string (required, version specifier)",
+    "tools": [
+      {
+        "name": "string (required)",
+        "version": "string (optional, version specifier)",
+        "required": "boolean (default: false)"
+      }
+    ]
+  },
+  "provides": {
+    "commands": "integer (optional)",
+    "hooks": "integer (optional)"
+  },
+  "tags": ["array of strings (2-10 tags)"],
+  "verified": "boolean (default: false)",
+  "downloads": "integer (auto-updated)",
+  "stars": "integer (auto-updated)",
+  "created_at": "string (ISO 8601 datetime)",
+  "updated_at": "string (ISO 8601 datetime)"
+}
+```
+
+### Valid Tags
+
+Recommended tag categories:
+
+- **Integration**: jira, linear, github, gitlab, azure-devops
+- **Category**: issue-tracking, vcs, ci-cd, documentation, testing
+- **Platform**: atlassian, microsoft, google
+- **Feature**: automation, reporting, deployment, monitoring
+
+Use 2-5 tags that best describe your extension.
+
+---
+
+*Last Updated: 2026-01-28*
+*Catalog Format Version: 1.0*

extensions/EXTENSION-USER-GUIDE.md

@@ -0,0 +1,885 @@
+# Extension User Guide
+
+Complete guide for using Spec Kit extensions to enhance your workflow.
+
+## Table of Contents
+
+1. [Introduction](#introduction)
+2. [Getting Started](#getting-started)
+3. [Finding Extensions](#finding-extensions)
+4. [Installing Extensions](#installing-extensions)
+5. [Using Extensions](#using-extensions)
+6. [Managing Extensions](#managing-extensions)
+7. [Configuration](#configuration)
+8. [Troubleshooting](#troubleshooting)
+9. [Best Practices](#best-practices)
+
+---
+
+## Introduction
+
+### What are Extensions?
+
+Extensions are modular packages that add new commands and functionality to Spec Kit without bloating the core framework. They allow you to:
+
+- **Integrate** with external tools (Jira, Linear, GitHub, etc.)
+- **Automate** repetitive tasks with hooks
+- **Customize** workflows for your team
+- **Share** solutions across projects
+
+### Why Use Extensions?
+
+- **Clean Core**: Keeps spec-kit lightweight and focused
+- **Optional Features**: Only install what you need
+- **Community Driven**: Anyone can create and share extensions
+- **Version Controlled**: Extensions are versioned independently
+
+---
+
+## Getting Started
+
+### Prerequisites
+
+- Spec Kit version 0.1.0 or higher
+- A spec-kit project (directory with `.specify/` folder)
+
+### Check Your Version
+
+```bash
+specify --version
+# Should show 0.1.0 or higher
+```
+
+### First Extension
+
+Let's install the Jira extension as an example:
+
+```bash
+# 1. Search for the extension
+specify extension search jira
+
+# 2. Get detailed information
+specify extension info jira
+
+# 3. Install it
+specify extension add jira
+
+# 4. Configure it
+vim .specify/extensions/jira/jira-config.yml
+
+# 5. Use it
+# (Commands are now available in Claude Code)
+/speckit.jira.specstoissues
+```
+
+---
+
+## Finding Extensions
+
+### Browse All Extensions
+
+```bash
+specify extension search
+```
+
+Shows all available extensions in the catalog.
+
+### Search by Keyword
+
+```bash
+# Search for "jira"
+specify extension search jira
+
+# Search for "issue tracking"
+specify extension search issue
+```
+
+### Filter by Tag
+
+```bash
+# Find all issue-tracking extensions
+specify extension search --tag issue-tracking
+
+# Find all Atlassian tools
+specify extension search --tag atlassian
+```
+
+### Filter by Author
+
+```bash
+# Extensions by Stats Perform
+specify extension search --author "Stats Perform"
+```
+
+### Show Verified Only
+
+```bash
+# Only show verified extensions
+specify extension search --verified
+```
+
+### Get Extension Details
+
+```bash
+# Detailed information
+specify extension info jira
+```
+
+Shows:
+
+- Description
+- Requirements
+- Commands provided
+- Hooks available
+- Links (documentation, repository, changelog)
+- Installation status
+
+---
+
+## Installing Extensions
+
+### Install from Catalog
+
+```bash
+# By name (from catalog)
+specify extension add jira
+```
+
+This will:
+
+1. Download the extension from GitHub
+2. Validate the manifest
+3. Check compatibility with your spec-kit version
+4. Install to `.specify/extensions/jira/`
+5. Register commands with your AI agent
+6. Create config template
+
+### Install from URL
+
+```bash
+# From GitHub release
+specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/tags/v1.0.0.zip
+```
+
+### Install from Local Directory (Development)
+
+```bash
+# For testing or development
+specify extension add --dev /path/to/extension
+```
+
+### Installation Output
+
+```text
+✓ Extension installed successfully!
+
+Jira Integration (v1.0.0)
+  Create Jira Epics, Stories, and Issues from spec-kit artifacts
+
+Provided commands:
+  • speckit.jira.specstoissues - Create Jira hierarchy from spec and tasks
+  • speckit.jira.discover-fields - Discover Jira custom fields for configuration
+  • speckit.jira.sync-status - Sync task completion status to Jira
+
+⚠  Configuration may be required
+   Check: .specify/extensions/jira/
+```
+
+---
+
+## Using Extensions
+
+### Using Extension Commands
+
+Extensions add commands that appear in your AI agent (Claude Code):
+
+```text
+# In Claude Code
+> /speckit.jira.specstoissues
+
+# Or use short alias (if provided)
+> /speckit.specstoissues
+```
+
+### Extension Configuration
+
+Most extensions require configuration:
+
+```bash
+# 1. Find the config file
+ls .specify/extensions/jira/
+
+# 2. Copy template to config
+cp .specify/extensions/jira/jira-config.template.yml \
+   .specify/extensions/jira/jira-config.yml
+
+# 3. Edit configuration
+vim .specify/extensions/jira/jira-config.yml
+
+# 4. Use the extension
+# (Commands will now work with your config)
+```
+
+### Extension Hooks
+
+Some extensions provide hooks that execute after core commands:
+
+**Example**: Jira extension hooks into `/speckit.tasks`
+
+```text
+# Run core command
+> /speckit.tasks
+
+# Output includes:
+## Extension Hooks
+
+**Optional Hook**: jira
+Command: `/speckit.jira.specstoissues`
+Description: Automatically create Jira hierarchy after task generation
+
+Prompt: Create Jira issues from tasks?
+To execute: `/speckit.jira.specstoissues`
+```
+
+You can then choose to run the hook or skip it.
+
+---
+
+## Managing Extensions
+
+### List Installed Extensions
+
+```bash
+specify extension list
+```
+
+Output:
+
+```text
+Installed Extensions:
+
+  ✓ Jira Integration (v1.0.0)
+     Create Jira Epics, Stories, and Issues from spec-kit artifacts
+     Commands: 3 | Hooks: 1 | Status: Enabled
+```
+
+### Update Extensions
+
+```bash
+# Check for updates (all extensions)
+specify extension update
+
+# Update specific extension
+specify extension update jira
+```
+
+Output:
+
+```text
+🔄 Checking for updates...
+
+Updates available:
+
+  • jira: 1.0.0 → 1.1.0
+
+Update these extensions? [y/N]:
+```
+
+### Disable Extension Temporarily
+
+```bash
+# Disable without removing
+specify extension disable jira
+
+✓ Extension 'jira' disabled
+
+Commands will no longer be available. Hooks will not execute.
+To re-enable: specify extension enable jira
+```
+
+### Re-enable Extension
+
+```bash
+specify extension enable jira
+
+✓ Extension 'jira' enabled
+```
+
+### Remove Extension
+
+```bash
+# Remove extension (with confirmation)
+specify extension remove jira
+
+# Keep configuration when removing
+specify extension remove jira --keep-config
+
+# Force removal (no confirmation)
+specify extension remove jira --force
+```
+
+---
+
+## Configuration
+
+### Configuration Files
+
+Extensions can have multiple configuration files:
+
+```text
+.specify/extensions/jira/
+├── jira-config.yml           # Main config (version controlled)
+├── jira-config.local.yml     # Local overrides (gitignored)
+└── jira-config.template.yml  # Template (reference)
+```
+
+### Configuration Layers
+
+Configuration is merged in this order (highest priority last):
+
+1. **Extension defaults** (from `extension.yml`)
+2. **Project config** (`jira-config.yml`)
+3. **Local overrides** (`jira-config.local.yml`)
+4. **Environment variables** (`SPECKIT_JIRA_*`)
+
+### Example: Jira Configuration
+
+**Project config** (`.specify/extensions/jira/jira-config.yml`):
+
+```yaml
+project:
+  key: "MSATS"
+
+defaults:
+  epic:
+    labels: ["spec-driven"]
+```
+
+**Local override** (`.specify/extensions/jira/jira-config.local.yml`):
+
+```yaml
+project:
+  key: "MYTEST"  # Override for local development
+```
+
+**Environment variable**:
+
+```bash
+export SPECKIT_JIRA_PROJECT_KEY="DEVTEST"
+```
+
+Final resolved config uses `DEVTEST` from environment variable.
+
+### Project-Wide Extension Settings
+
+File: `.specify/extensions.yml`
+
+```yaml
+# Extensions installed in this project
+installed:
+  - jira
+  - linear
+
+# Global settings
+settings:
+  auto_execute_hooks: true
+
+# Hook configuration
+hooks:
+  after_tasks:
+    - extension: jira
+      command: speckit.jira.specstoissues
+      enabled: true
+      optional: true
+      prompt: "Create Jira issues from tasks?"
+```
+
+### Core Environment Variables
+
+In addition to extension-specific environment variables (`SPECKIT_{EXT_ID}_*`), spec-kit supports core environment variables:
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `SPECKIT_CATALOG_URL`       | Override the extension catalog URL | GitHub-hosted catalog |
+| `GH_TOKEN` / `GITHUB_TOKEN` | GitHub API token for downloads     | None                  |
+
+#### Example: Using a custom catalog for testing
+
+```bash
+# Point to a local or alternative catalog
+export SPECKIT_CATALOG_URL="http://localhost:8000/catalog.json"
+
+# Or use a staging catalog
+export SPECKIT_CATALOG_URL="https://example.com/staging/catalog.json"
+```
+
+---
+
+## Organization Catalog Customization
+
+### Why the Default Catalog is Empty
+
+The default spec-kit catalog ships empty by design. This allows organizations to:
+
+- **Control available extensions** - Curate which extensions your team can install
+- **Host private extensions** - Internal tools that shouldn't be public
+- **Customize for compliance** - Meet security/audit requirements
+- **Support air-gapped environments** - Work without internet access
+
+### Setting Up a Custom Catalog
+
+#### 1. Create Your Catalog File
+
+Create a `catalog.json` file with your extensions:
+
+```json
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-03T00:00:00Z",
+  "catalog_url": "https://your-org.com/spec-kit/catalog.json",
+  "extensions": {
+    "jira": {
+      "name": "Jira Integration",
+      "id": "jira",
+      "description": "Create Jira issues from spec-kit artifacts",
+      "author": "Your Organization",
+      "version": "2.1.0",
+      "download_url": "https://github.com/your-org/spec-kit-jira/archive/refs/tags/v2.1.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-jira",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {"name": "atlassian-mcp-server", "required": true}
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": ["jira", "atlassian", "issue-tracking"],
+      "verified": true
+    },
+    "internal-tool": {
+      "name": "Internal Tool Integration",
+      "id": "internal-tool",
+      "description": "Connect to internal company systems",
+      "author": "Your Organization",
+      "version": "1.0.0",
+      "download_url": "https://internal.your-org.com/extensions/internal-tool-1.0.0.zip",
+      "repository": "https://github.internal.your-org.com/spec-kit-internal",
+      "license": "Proprietary",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 2
+      },
+      "tags": ["internal", "proprietary"],
+      "verified": true
+    }
+  }
+}
+```
+
+#### 2. Host the Catalog
+
+Options for hosting your catalog:
+
+| Method | URL Example | Use Case |
+| ------ | ----------- | -------- |
+| GitHub Pages | `https://your-org.github.io/spec-kit-catalog/catalog.json` | Public or org-visible |
+| Internal web server | `https://internal.company.com/spec-kit/catalog.json` | Corporate network |
+| S3/Cloud storage | `https://s3.amazonaws.com/your-bucket/catalog.json` | Cloud-hosted teams |
+| Local file server | `http://localhost:8000/catalog.json` | Development/testing |
+
+**Security requirement**: URLs must use HTTPS (except `localhost` for testing).
+
+#### 3. Configure Your Environment
+
+##### Option A: Environment variable (recommended for CI/CD)
+
+```bash
+# In ~/.bashrc, ~/.zshrc, or CI pipeline
+export SPECKIT_CATALOG_URL="https://your-org.com/spec-kit/catalog.json"
+```
+
+##### Option B: Per-project configuration
+
+Create `.env` or set in your shell before running spec-kit commands:
+
+```bash
+SPECKIT_CATALOG_URL="https://your-org.com/spec-kit/catalog.json" specify extension search
+```
+
+#### 4. Verify Configuration
+
+```bash
+# Search should now show your catalog's extensions
+specify extension search
+
+# Install from your catalog
+specify extension add jira
+```
+
+### Catalog JSON Schema
+
+Required fields for each extension entry:
+
+| Field | Type | Required | Description |
+| ----- | ---- | -------- | ----------- |
+| `name` | string | Yes | Human-readable name |
+| `id` | string | Yes | Unique identifier (lowercase, hyphens) |
+| `version` | string | Yes | Semantic version (X.Y.Z) |
+| `download_url` | string | Yes | URL to ZIP archive |
+| `repository` | string | Yes | Source code URL |
+| `description` | string | No | Brief description |
+| `author` | string | No | Author/organization |
+| `license` | string | No | SPDX license identifier |
+| `requires.speckit_version` | string | No | Version constraint |
+| `requires.tools` | array | No | Required external tools |
+| `provides.commands` | number | No | Number of commands |
+| `provides.hooks` | number | No | Number of hooks |
+| `tags` | array | No | Search tags |
+| `verified` | boolean | No | Verification status |
+
+### Use Cases
+
+#### Private/Internal Extensions
+
+Host proprietary extensions that integrate with internal systems:
+
+```json
+{
+  "internal-auth": {
+    "name": "Internal SSO Integration",
+    "download_url": "https://artifactory.company.com/spec-kit/internal-auth-1.0.0.zip",
+    "verified": true
+  }
+}
+```
+
+#### Curated Team Catalog
+
+Limit which extensions your team can install:
+
+```json
+{
+  "extensions": {
+    "jira": { "..." },
+    "github": { "..." }
+  }
+}
+```
+
+Only `jira` and `github` will appear in `specify extension search`.
+
+#### Air-Gapped Environments
+
+For networks without internet access:
+
+1. Download extension ZIPs to internal file server
+2. Create catalog pointing to internal URLs
+3. Host catalog on internal web server
+
+```json
+{
+  "jira": {
+    "download_url": "https://files.internal/spec-kit/jira-2.1.0.zip"
+  }
+}
+```
+
+#### Development/Testing
+
+Test new extensions before publishing:
+
+```bash
+# Start local server
+python -m http.server 8000 --directory ./my-catalog/
+
+# Point spec-kit to local catalog
+export SPECKIT_CATALOG_URL="http://localhost:8000/catalog.json"
+
+# Test installation
+specify extension add my-new-extension
+```
+
+### Combining with Direct Installation
+
+You can still install extensions not in your catalog using `--from`:
+
+```bash
+# From catalog
+specify extension add jira
+
+# Direct URL (bypasses catalog)
+specify extension add --from https://github.com/someone/spec-kit-ext/archive/v1.0.0.zip
+
+# Local development
+specify extension add --dev /path/to/extension
+```
+
+**Note**: Direct URL installation shows a security warning since the extension isn't from your configured catalog.
+
+---
+
+## Troubleshooting
+
+### Extension Not Found
+
+**Error**: `Extension 'jira' not found in catalog
+
+**Solutions**:
+
+1. Check spelling: `specify extension search jira`
+2. Refresh catalog: `specify extension search --help`
+3. Check internet connection
+4. Extension may not be published yet
+
+### Configuration Not Found
+
+**Error**: `Jira configuration not found`
+
+**Solutions**:
+
+1. Check if extension is installed: `specify extension list`
+2. Create config from template:
+
+   ```bash
+   cp .specify/extensions/jira/jira-config.template.yml \
+      .specify/extensions/jira/jira-config.yml
+   ```
+
+3. Reinstall extension: `specify extension remove jira && specify extension add jira`
+
+### Command Not Available
+
+**Issue**: Extension command not appearing in AI agent
+
+**Solutions**:
+
+1. Check extension is enabled: `specify extension list`
+2. Restart AI agent (Claude Code)
+3. Check command file exists:
+
+   ```bash
+   ls .claude/commands/speckit.jira.*.md
+   ```
+
+4. Reinstall extension
+
+### Incompatible Version
+
+**Error**: `Extension requires spec-kit >=0.2.0, but you have 0.1.0`
+
+**Solutions**:
+
+1. Upgrade spec-kit:
+
+   ```bash
+   uv tool upgrade specify-cli
+   ```
+
+2. Install older version of extension:
+
+   ```bash
+   specify extension add --from https://github.com/org/ext/archive/v1.0.0.zip
+   ```
+
+### MCP Tool Not Available
+
+**Error**: `Tool 'jira-mcp-server/epic_create' not found`
+
+**Solutions**:
+
+1. Check MCP server is installed
+2. Check AI agent MCP configuration
+3. Restart AI agent
+4. Check extension requirements: `specify extension info jira`
+
+### Permission Denied
+
+**Error**: `Permission denied` when accessing Jira
+
+**Solutions**:
+
+1. Check Jira credentials in MCP server config
+2. Verify project permissions in Jira
+3. Test MCP server connection independently
+
+---
+
+## Best Practices
+
+### 1. Version Control
+
+**Do commit**:
+
+- `.specify/extensions.yml` (project extension config)
+- `.specify/extensions/*/jira-config.yml` (project config)
+
+**Don't commit**:
+
+- `.specify/extensions/.cache/` (catalog cache)
+- `.specify/extensions/.backup/` (config backups)
+- `.specify/extensions/*/*.local.yml` (local overrides)
+- `.specify/extensions/.registry` (installation state)
+
+Add to `.gitignore`:
+
+```gitignore
+.specify/extensions/.cache/
+.specify/extensions/.backup/
+.specify/extensions/*/*.local.yml
+.specify/extensions/.registry
+```
+
+### 2. Team Workflows
+
+**For teams**:
+
+1. Agree on which extensions to use
+2. Commit extension configuration
+3. Document extension usage in README
+4. Keep extensions updated together
+
+**Example README section**:
+
+```markdown
+## Extensions
+
+This project uses:
+- **jira** (v1.0.0) - Jira integration
+  - Config: `.specify/extensions/jira/jira-config.yml`
+  - Requires: jira-mcp-server
+
+To install: `specify extension add jira`
+```
+
+### 3. Local Development
+
+Use local config for development:
+
+```yaml
+# .specify/extensions/jira/jira-config.local.yml
+project:
+  key: "DEVTEST"  # Your test project
+
+defaults:
+  task:
+    custom_fields:
+      customfield_10002: 1  # Lower story points for testing
+```
+
+### 4. Environment-Specific Config
+
+Use environment variables for CI/CD:
+
+```bash
+# .github/workflows/deploy.yml
+env:
+  SPECKIT_JIRA_PROJECT_KEY: ${{ secrets.JIRA_PROJECT }}
+
+- name: Create Jira Issues
+  run: specify extension add jira && ...
+```
+
+### 5. Extension Updates
+
+**Check for updates regularly**:
+
+```bash
+# Weekly or before major releases
+specify extension update
+```
+
+**Pin versions for stability**:
+
+```yaml
+# .specify/extensions.yml
+installed:
+  - id: jira
+    version: "1.0.0"  # Pin to specific version
+```
+
+### 6. Minimal Extensions
+
+Only install extensions you actively use:
+
+- Reduces complexity
+- Faster command loading
+- Less configuration
+
+### 7. Documentation
+
+Document extension usage in your project:
+
+```markdown
+# PROJECT.md
+
+## Working with Jira
+
+After creating tasks, sync to Jira:
+1. Run `/speckit.tasks` to generate tasks
+2. Run `/speckit.jira.specstoissues` to create Jira issues
+3. Run `/speckit.jira.sync-status` to update status
+```
+
+---
+
+## FAQ
+
+### Q: Can I use multiple extensions at once?
+
+**A**: Yes! Extensions are designed to work together. Install as many as you need.
+
+### Q: Do extensions slow down spec-kit?
+
+**A**: No. Extensions are loaded on-demand and only when their commands are used.
+
+### Q: Can I create private extensions?
+
+**A**: Yes. Install with `--dev` or `--from` and keep private. Public catalog submission is optional.
+
+### Q: How do I know if an extension is safe?
+
+**A**: Look for the ✓ Verified badge. Verified extensions are reviewed by maintainers. Always review extension code before installing.
+
+### Q: Can extensions modify spec-kit core?
+
+**A**: No. Extensions can only add commands and hooks. They cannot modify core functionality.
+
+### Q: What happens if two extensions have the same command name?
+
+**A**: Extensions use namespaced commands (`speckit.{extension}.{command}`), so conflicts are very rare. The extension system will warn you if conflicts occur.
+
+### Q: Can I contribute to existing extensions?
+
+**A**: Yes! Most extensions are open source. Check the repository link in `specify extension info {extension}`.
+
+### Q: How do I report extension bugs?
+
+**A**: Go to the extension's repository (shown in `specify extension info`) and create an issue.
+
+### Q: Can extensions work offline?
+
+**A**: Once installed, extensions work offline. However, some extensions may require internet for their functionality (e.g., Jira requires Jira API access).
+
+### Q: How do I backup my extension configuration?
+
+**A**: Extension configs are in `.specify/extensions/{extension}/`. Back up this directory or commit configs to git.
+
+---
+
+## Support
+
+- **Extension Issues**: Report to extension repository (see `specify extension info`)
+- **Spec Kit Issues**: <https://github.com/statsperform/spec-kit/issues>
+- **Extension Catalog**: <https://github.com/statsperform/spec-kit/tree/main/extensions>
+- **Documentation**: See EXTENSION-DEVELOPMENT-GUIDE.md and EXTENSION-PUBLISHING-GUIDE.md
+
+---
+
+*Last Updated: 2026-01-28*
+*Spec Kit Version: 0.1.0*

extensions/catalog.example.json

@@ -0,0 +1,60 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-03T00:00:00Z",
+  "catalog_url": "https://your-org.example.com/speckit/catalog.json",
+  "extensions": {
+    "jira": {
+      "name": "Jira Integration",
+      "id": "jira",
+      "description": "Create Jira Epics, Stories, and Issues from spec-kit artifacts",
+      "author": "Your Organization",
+      "version": "2.1.0",
+      "download_url": "https://github.com/your-org/spec-kit-jira/archive/refs/tags/v2.1.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-jira",
+      "homepage": "https://github.com/your-org/spec-kit-jira",
+      "documentation": "https://github.com/your-org/spec-kit-jira/blob/main/README.md",
+      "changelog": "https://github.com/your-org/spec-kit-jira/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          {
+            "name": "atlassian",
+            "version": ">=1.0.0",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": ["jira", "atlassian", "issue-tracking"],
+      "verified": true,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-01-28T00:00:00Z",
+      "updated_at": "2026-02-03T00:00:00Z"
+    },
+    "linear": {
+      "name": "Linear Integration",
+      "id": "linear",
+      "description": "Sync specs and tasks with Linear issues",
+      "author": "Your Organization",
+      "version": "1.0.0",
+      "download_url": "https://github.com/your-org/spec-kit-linear/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/your-org/spec-kit-linear",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 2
+      },
+      "tags": ["linear", "issue-tracking"],
+      "verified": false,
+      "created_at": "2026-01-30T00:00:00Z",
+      "updated_at": "2026-01-30T00:00:00Z"
+    }
+  }
+}

extensions/catalog.json

@@ -0,0 +1,6 @@
+{
+  "schema_version": "1.0",
+  "updated_at": "2026-02-03T00:00:00Z",
+  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.json",
+  "extensions": {}
+}

extensions/template/.gitignore

@@ -0,0 +1,39 @@
+# Local configuration overrides
+*-config.local.yml
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log
+
+# Build artifacts
+dist/
+build/
+*.egg-info/
+
+# Temporary files
+*.tmp
+.cache/

extensions/template/CHANGELOG.md

@@ -0,0 +1,39 @@
+# Changelog
+
+All notable changes to this extension will be documented in this file.
+
+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).
+
+## [Unreleased]
+
+### Planned
+
+- Feature ideas for future versions
+- Enhancements
+- Bug fixes
+
+## [1.0.0] - YYYY-MM-DD
+
+### Added
+
+- Initial release of extension
+- Command: `/speckit.my-extension.example` - Example command functionality
+- Configuration system with template
+- Documentation and examples
+
+### Features
+
+- Feature 1 description
+- Feature 2 description
+- Feature 3 description
+
+### Requirements
+
+- Spec Kit: >=0.1.0
+- External dependencies (if any)
+
+---
+
+[Unreleased]: https://github.com/your-org/spec-kit-my-extension/compare/v1.0.0...HEAD
+[1.0.0]: https://github.com/your-org/spec-kit-my-extension/releases/tag/v1.0.0

extensions/template/EXAMPLE-README.md

@@ -0,0 +1,158 @@
+# EXAMPLE: Extension README
+
+This is an example of what your extension README should look like after customization.
+**Delete this file and replace README.md with content similar to this.**
+
+---
+
+# My Extension
+
+<!-- CUSTOMIZE: Replace with your extension description -->
+
+Brief description of what your extension does and why it's useful.
+
+## Features
+
+<!-- CUSTOMIZE: List key features -->
+
+- Feature 1: Description
+- Feature 2: Description
+- Feature 3: Description
+
+## Installation
+
+```bash
+# Install from catalog
+specify extension add my-extension
+
+# Or install from local development directory
+specify extension add --dev /path/to/my-extension
+```
+
+## Configuration
+
+1. Create configuration file:
+
+   ```bash
+   cp .specify/extensions/my-extension/config-template.yml \
+      .specify/extensions/my-extension/my-extension-config.yml
+   ```
+
+2. Edit configuration:
+
+   ```bash
+   vim .specify/extensions/my-extension/my-extension-config.yml
+   ```
+
+3. Set required values:
+   <!-- CUSTOMIZE: List required configuration -->
+   ```yaml
+   connection:
+     url: "https://api.example.com"
+     api_key: "your-api-key"
+
+   project:
+     id: "your-project-id"
+   ```
+
+## Usage
+
+<!-- CUSTOMIZE: Add usage examples -->
+
+### Command: example
+
+Description of what this command does.
+
+```bash
+# In Claude Code
+> /speckit.my-extension.example
+```
+
+**Prerequisites**:
+
+- Prerequisite 1
+- Prerequisite 2
+
+**Output**:
+
+- What this command produces
+- Where results are saved
+
+## Configuration Reference
+
+<!-- CUSTOMIZE: Document all configuration options -->
+
+### Connection Settings
+
+| Setting | Type | Required | Description |
+|---------|------|----------|-------------|
+| `connection.url` | string | Yes | API endpoint URL |
+| `connection.api_key` | string | Yes | API authentication key |
+
+### Project Settings
+
+| Setting | Type | Required | Description |
+|---------|------|----------|-------------|
+| `project.id` | string | Yes | Project identifier |
+| `project.workspace` | string | No | Workspace or organization |
+
+## Environment Variables
+
+Override configuration with environment variables:
+
+```bash
+# Override connection settings
+export SPECKIT_MY_EXTENSION_CONNECTION_URL="https://custom-api.com"
+export SPECKIT_MY_EXTENSION_CONNECTION_API_KEY="custom-key"
+```
+
+## Examples
+
+<!-- CUSTOMIZE: Add real-world examples -->
+
+### Example 1: Basic Workflow
+
+```bash
+# Step 1: Create specification
+> /speckit.spec
+
+# Step 2: Generate tasks
+> /speckit.tasks
+
+# Step 3: Use extension
+> /speckit.my-extension.example
+```
+
+## Troubleshooting
+
+<!-- CUSTOMIZE: Add common issues -->
+
+### Issue: Configuration not found
+
+**Solution**: Create config from template (see Configuration section)
+
+### Issue: Command not available
+
+**Solutions**:
+
+1. Check extension is installed: `specify extension list`
+2. Restart AI agent
+3. Reinstall extension
+
+## License
+
+MIT License - see LICENSE file
+
+## Support
+
+- **Issues**: <https://github.com/your-org/spec-kit-my-extension/issues>
+- **Spec Kit Docs**: <https://github.com/statsperform/spec-kit>
+
+## Changelog
+
+See [CHANGELOG.md](CHANGELOG.md) for version history.
+
+---
+
+*Extension Version: 1.0.0*
+*Spec Kit: >=0.1.0*

extensions/template/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 [Your Name or Organization]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/template/README.md

@@ -0,0 +1,79 @@
+# Extension Template
+
+Starter template for creating a Spec Kit extension.
+
+## Quick Start
+
+1. **Copy this template**:
+
+   ```bash
+   cp -r extensions/template my-extension
+   cd my-extension
+   ```
+
+2. **Customize `extension.yml`**:
+   - Change extension ID, name, description
+   - Update author and repository
+   - Define your commands
+
+3. **Create commands**:
+   - Add command files in `commands/` directory
+   - Use Markdown format with YAML frontmatter
+
+4. **Create config template**:
+   - Define configuration options
+   - Document all settings
+
+5. **Write documentation**:
+   - Update README.md with usage instructions
+   - Add examples
+
+6. **Test locally**:
+
+   ```bash
+   cd /path/to/spec-kit-project
+   specify extension add --dev /path/to/my-extension
+   ```
+
+7. **Publish** (optional):
+   - Create GitHub repository
+   - Create release
+   - Submit to catalog (see EXTENSION-PUBLISHING-GUIDE.md)
+
+## Files in This Template
+
+- `extension.yml` - Extension manifest (CUSTOMIZE THIS)
+- `config-template.yml` - Configuration template (CUSTOMIZE THIS)
+- `commands/example.md` - Example command (REPLACE THIS)
+- `README.md` - Extension documentation (REPLACE THIS)
+- `LICENSE` - MIT License (REVIEW THIS)
+- `CHANGELOG.md` - Version history (UPDATE THIS)
+- `.gitignore` - Git ignore rules
+
+## Customization Checklist
+
+- [ ] Update `extension.yml` with your extension details
+- [ ] Change extension ID to your extension name
+- [ ] Update author information
+- [ ] Define your commands
+- [ ] Create command files in `commands/`
+- [ ] Update config template
+- [ ] Write README with usage instructions
+- [ ] Add examples
+- [ ] Update LICENSE if needed
+- [ ] Test extension locally
+- [ ] Create git repository
+- [ ] Create first release
+
+## Need Help?
+
+- **Development Guide**: See EXTENSION-DEVELOPMENT-GUIDE.md
+- **API Reference**: See EXTENSION-API-REFERENCE.md
+- **Publishing Guide**: See EXTENSION-PUBLISHING-GUIDE.md
+- **User Guide**: See EXTENSION-USER-GUIDE.md
+
+## Template Version
+
+- Version: 1.0.0
+- Last Updated: 2026-01-28
+- Compatible with Spec Kit: >=0.1.0

extensions/template/commands/example.md

@@ -0,0 +1,210 @@
+---
+description: "Example command that demonstrates extension functionality"
+# CUSTOMIZE: List MCP tools this command uses
+tools:
+  - 'example-mcp-server/example_tool'
+---
+
+# Example Command
+
+<!-- CUSTOMIZE: Replace this entire file with your command documentation -->
+
+This is an example command that demonstrates how to create commands for Spec Kit extensions.
+
+## Purpose
+
+Describe what this command does and when to use it.
+
+## Prerequisites
+
+List requirements before using this command:
+
+1. Prerequisite 1 (e.g., "MCP server configured")
+2. Prerequisite 2 (e.g., "Configuration file exists")
+3. Prerequisite 3 (e.g., "Valid API credentials")
+
+## User Input
+
+$ARGUMENTS
+
+## Steps
+
+### Step 1: Load Configuration
+
+<!-- CUSTOMIZE: Replace with your actual steps -->
+
+Load extension configuration from the project:
+
+``bash
+config_file=".specify/extensions/my-extension/my-extension-config.yml"
+
+if [ ! -f "$config_file" ]; then
+  echo "❌ Error: Configuration not found at $config_file"
+  echo "Run 'specify extension add my-extension' to install and configure"
+  exit 1
+fi
+
+# Read configuration values
+
+setting_value=$(yq eval '.settings.key' "$config_file")
+
+# Apply environment variable overrides
+
+setting_value="${SPECKIT_MY_EXTENSION_KEY:-$setting_value}"
+
+# Validate configuration
+
+if [ -z "$setting_value" ]; then
+  echo "❌ Error: Configuration value not set"
+  echo "Edit $config_file and set 'settings.key'"
+  exit 1
+fi
+
+echo "📋 Configuration loaded: $setting_value"
+``
+
+### Step 2: Perform Main Action
+
+<!-- CUSTOMIZE: Replace with your command logic -->
+
+Describe what this step does:
+
+``markdown
+Use MCP tools to perform the main action:
+
+- Tool: example-mcp-server example_tool
+- Parameters: { "key": "$setting_value" }
+
+This calls the MCP server tool to execute the operation.
+``
+
+### Step 3: Process Results
+
+<!-- CUSTOMIZE: Add more steps as needed -->
+
+Process the results and provide output:
+
+`` bash
+echo ""
+echo "✅ Command completed successfully!"
+echo ""
+echo "Results:"
+echo "  • Item 1: Value"
+echo "  • Item 2: Value"
+echo ""
+``
+
+### Step 4: Save Output (Optional)
+
+Save results to a file if needed:
+
+``bash
+output_file=".specify/my-extension-output.json"
+
+cat > "$output_file" <<EOF
+{
+  "timestamp": "$(date -u +"%Y-%m-%dT%H:%M:%SZ")",
+  "setting": "$setting_value",
+  "results": []
+}
+EOF
+
+echo "💾 Output saved to $output_file"
+``
+
+## Configuration Reference
+
+<!-- CUSTOMIZE: Document configuration options -->
+
+This command uses the following configuration from `my-extension-config.yml`:
+
+- **settings.key**: Description of what this setting does
+  - Type: string
+  - Required: Yes
+  - Example: `"example-value"`
+
+- **settings.another_key**: Description of another setting
+  - Type: boolean
+  - Required: No
+  - Default: `false`
+  - Example: `true`
+
+## Environment Variables
+
+<!-- CUSTOMIZE: Document environment variable overrides -->
+
+Configuration can be overridden with environment variables:
+
+- `SPECKIT_MY_EXTENSION_KEY` - Overrides `settings.key`
+- `SPECKIT_MY_EXTENSION_ANOTHER_KEY` - Overrides `settings.another_key`
+
+Example:
+``bash
+export SPECKIT_MY_EXTENSION_KEY="override-value"
+``
+
+## Troubleshooting
+
+<!-- CUSTOMIZE: Add common issues and solutions -->
+
+### "Configuration not found"
+
+**Solution**: Install the extension and create configuration:
+``bash
+specify extension add my-extension
+cp .specify/extensions/my-extension/config-template.yml \
+   .specify/extensions/my-extension/my-extension-config.yml
+``
+
+### "MCP tool not available"
+
+**Solution**: Ensure MCP server is configured in your AI agent settings.
+
+### "Permission denied"
+
+**Solution**: Check credentials and permissions in the external service.
+
+## Notes
+
+<!-- CUSTOMIZE: Add helpful notes and tips -->
+
+- This command requires an active connection to the external service
+- Results are cached for performance
+- Re-run the command to refresh data
+
+## Examples
+
+<!-- CUSTOMIZE: Add usage examples -->
+
+### Example 1: Basic Usage
+
+``bash
+
+# Run with default configuration
+>
+> /speckit.my-extension.example
+``
+
+### Example 2: With Environment Override
+
+``bash
+
+# Override configuration with environment variable
+
+export SPECKIT_MY_EXTENSION_KEY="custom-value"
+> /speckit.my-extension.example
+``
+
+### Example 3: After Core Command
+
+``bash
+
+# Use as part of a workflow
+>
+> /speckit.tasks
+> /speckit.my-extension.example
+``
+
+---
+
+*For more information, see the extension README or run `specify extension info my-extension`*

extensions/template/config-template.yml

@@ -0,0 +1,75 @@
+# Extension Configuration Template
+# Copy this to my-extension-config.yml and customize for your project
+
+# CUSTOMIZE: Add your configuration sections below
+
+# Example: Connection settings
+connection:
+  # URL to external service
+  url: ""  # REQUIRED: e.g., "https://api.example.com"
+
+  # API key or token
+  api_key: ""  # REQUIRED: Your API key
+
+# Example: Project settings
+project:
+  # Project identifier
+  id: ""  # REQUIRED: e.g., "my-project"
+
+  # Workspace or organization
+  workspace: ""  # OPTIONAL: e.g., "my-org"
+
+# Example: Feature flags
+features:
+  # Enable/disable main functionality
+  enabled: true
+
+  # Automatic synchronization
+  auto_sync: false
+
+  # Verbose logging
+  verbose: false
+
+# Example: Default values
+defaults:
+  # Labels to apply
+  labels: []  # e.g., ["automated", "spec-kit"]
+
+  # Priority level
+  priority: "medium"  # Options: "low", "medium", "high"
+
+  # Assignee
+  assignee: ""  # OPTIONAL: Default assignee
+
+# Example: Field mappings
+# Map internal names to external field IDs
+field_mappings:
+  # Example mappings
+  # internal_field: "external_field_id"
+  # status: "customfield_10001"
+
+# Example: Advanced settings
+advanced:
+  # Timeout in seconds
+  timeout: 30
+
+  # Retry attempts
+  retry_count: 3
+
+  # Cache duration in seconds
+  cache_duration: 3600
+
+# Environment Variable Overrides:
+# You can override any setting with environment variables  using this pattern:
+# SPECKIT_MY_EXTENSION_{SECTION}_{KEY}
+#
+# Examples:
+# - SPECKIT_MY_EXTENSION_CONNECTION_API_KEY: Override connection.api_key
+# - SPECKIT_MY_EXTENSION_PROJECT_ID: Override project.id
+# - SPECKIT_MY_EXTENSION_FEATURES_ENABLED: Override features.enabled
+#
+# Note: Use uppercase and replace dots with underscores
+
+# Local Overrides:
+# For local development, create my-extension-config.local.yml (gitignored)
+# to override settings without affecting the team configuration

extensions/template/extension.yml

@@ -0,0 +1,97 @@
+schema_version: "1.0"
+
+extension:
+  # CUSTOMIZE: Change 'my-extension' to your extension ID (lowercase, hyphen-separated)
+  id: "my-extension"
+
+  # CUSTOMIZE: Human-readable name for your extension
+  name: "My Extension"
+
+  # 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 extension does"
+
+  # CUSTOMIZE: Your name or organization name
+  author: "Your Name"
+
+  # CUSTOMIZE: GitHub repository URL (create before publishing)
+  repository: "https://github.com/your-org/spec-kit-my-extension"
+
+  # REVIEW: License (MIT is recommended for open source)
+  license: "MIT"
+
+  # CUSTOMIZE: Extension homepage (can be same as repository)
+  homepage: "https://github.com/your-org/spec-kit-my-extension"
+
+# Requirements for this extension
+requires:
+  # CUSTOMIZE: Minimum spec-kit version required
+  # Use >=X.Y.Z for minimum version
+  # Use >=X.Y.Z,<Y.0.0 for version range
+  speckit_version: ">=0.1.0"
+
+  # CUSTOMIZE: Add MCP tools or other dependencies
+  # Remove if no external tools required
+  tools:
+    - name: "example-mcp-server"
+      version: ">=1.0.0"
+      required: true
+
+# Commands provided by this extension
+provides:
+  commands:
+    # CUSTOMIZE: Define your commands
+    # Pattern: speckit.{extension-id}.{command-name}
+    - name: "speckit.my-extension.example"
+      file: "commands/example.md"
+      description: "Example command that demonstrates functionality"
+      # Optional: Add aliases for shorter command names
+      aliases: ["speckit.example"]
+
+    # ADD MORE COMMANDS: Copy this block for each command
+    # - name: "speckit.my-extension.another-command"
+    #   file: "commands/another-command.md"
+    #   description: "Another command"
+
+  # CUSTOMIZE: Define configuration files
+  config:
+    - name: "my-extension-config.yml"
+      template: "config-template.yml"
+      description: "Extension configuration"
+      required: true # Set to false if config is optional
+
+# CUSTOMIZE: Define hooks (optional)
+# Remove if no hooks needed
+hooks:
+  # Hook that runs after /speckit.tasks
+  after_tasks:
+    command: "speckit.my-extension.example"
+    optional: true # User will be prompted
+    prompt: "Run example command?"
+    description: "Demonstrates hook functionality"
+    condition: null # Future: conditional execution
+
+  # ADD MORE HOOKS: Copy this block for other events
+  # after_implement:
+  #   command: "speckit.my-extension.another"
+  #   optional: false  # Auto-execute without prompting
+  #   description: "Runs automatically after implementation"
+
+# CUSTOMIZE: Add relevant tags (2-5 recommended)
+# Used for discovery in catalog
+tags:
+  - "example"
+  - "template"
+  # ADD MORE: "category", "tool-name", etc.
+
+# CUSTOMIZE: Default configuration values (optional)
+# These are merged with user config
+defaults:
+  # Example default values
+  feature:
+    enabled: true
+    auto_sync: false
+
+  # ADD MORE: Any default settings for your extension

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.0.21"
+version = "0.1.0"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -10,6 +10,8 @@ dependencies = [
     "platformdirs",
     "readchar",
     "truststore>=0.10.4",
+    "pyyaml>=6.0",
+    "packaging>=23.0",
 ]
 
 [project.scripts]
@@ -22,3 +24,30 @@ build-backend = "hatchling.build"
 [tool.hatch.build.targets.wheel]
 packages = ["src/specify_cli"]
 
+[project.optional-dependencies]
+test = [
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--strict-markers",
+    "--tb=short",
+]
+
+[tool.coverage.run]
+source = ["src"]
+omit = ["*/tests/*", "*/__pycache__/*"]
+
+[tool.coverage.report]
+precision = 2
+show_missing = true
+skip_covered = false
+
+

scripts/bash/check-prerequisites.sh

@@ -75,7 +75,7 @@ EOF
 done
 
 # Source common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths and validate branch

scripts/bash/common.sh

@@ -7,7 +7,7 @@ get_repo_root() {
         git rev-parse --show-toplevel
     else
         # Fall back to script location for non-git repos
-        local script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+        local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
         (cd "$script_dir/../../.." && pwd)
     fi
 }

scripts/bash/create-new-feature.sh

@@ -4,6 +4,7 @@ set -e
 
 JSON_MODE=false
 SHORT_NAME=""
+BRANCH_NUMBER=""
 ARGS=()
 i=1
 while [ $i -le $# ]; do
@@ -26,17 +27,31 @@ while [ $i -le $# ]; do
             fi
             SHORT_NAME="$next_arg"
             ;;
+        --number)
+            if [ $((i + 1)) -gt $# ]; then
+                echo 'Error: --number requires a value' >&2
+                exit 1
+            fi
+            i=$((i + 1))
+            next_arg="${!i}"
+            if [[ "$next_arg" == --* ]]; then
+                echo 'Error: --number requires a value' >&2
+                exit 1
+            fi
+            BRANCH_NUMBER="$next_arg"
+            ;;
         --help|-h) 
-            echo "Usage: $0 [--json] [--short-name <name>] <feature_description>"
+            echo "Usage: $0 [--json] [--short-name <name>] [--number N] <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 "  --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'"
+            echo "  $0 'Implement OAuth2 integration for API' --number 5"
             exit 0
             ;;
         *) 
@@ -48,7 +63,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--short-name <name>] [--number N] <feature_description>" >&2
     exit 1
 fi
 
@@ -65,10 +80,85 @@ find_repo_root() {
     return 1
 }
 
+# Function to get highest number from specs directory
+get_highest_from_specs() {
+    local specs_dir="$1"
+    local highest=0
+    
+    if [ -d "$specs_dir" ]; then
+        for dir in "$specs_dir"/*; do
+            [ -d "$dir" ] || continue
+            dirname=$(basename "$dir")
+            number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
+            number=$((10#$number))
+            if [ "$number" -gt "$highest" ]; then
+                highest=$number
+            fi
+        done
+    fi
+    
+    echo "$highest"
+}
+
+# Function to get highest number from git branches
+get_highest_from_branches() {
+    local highest=0
+    
+    # Get all branches (local and remote)
+    branches=$(git branch -a 2>/dev/null || echo "")
+    
+    if [ -n "$branches" ]; then
+        while IFS= read -r branch; do
+            # Clean branch name: remove leading markers and remote prefixes
+            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
+            
+            # Extract feature number if branch matches pattern ###-*
+            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
+                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
+                number=$((10#$number))
+                if [ "$number" -gt "$highest" ]; then
+                    highest=$number
+                fi
+            fi
+        done <<< "$branches"
+    fi
+    
+    echo "$highest"
+}
+
+# Function to check existing branches (local and remote) and return next available number
+check_existing_branches() {
+    local specs_dir="$1"
+
+    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
+    git fetch --all --prune 2>/dev/null || true
+
+    # Get highest number from ALL branches (not just matching short name)
+    local highest_branch=$(get_highest_from_branches)
+
+    # Get highest number from ALL specs (not just matching short name)
+    local highest_spec=$(get_highest_from_specs "$specs_dir")
+
+    # Take the maximum of both
+    local max_num=$highest_branch
+    if [ "$highest_spec" -gt "$max_num" ]; then
+        max_num=$highest_spec
+    fi
+
+    # Return next number
+    echo $((max_num + 1))
+}
+
+# Function to clean and format a branch name
+clean_branch_name() {
+    local name="$1"
+    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
+}
+
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 if git rev-parse --show-toplevel >/dev/null 2>&1; then
     REPO_ROOT=$(git rev-parse --show-toplevel)
@@ -87,48 +177,6 @@ cd "$REPO_ROOT"
 SPECS_DIR="$REPO_ROOT/specs"
 mkdir -p "$SPECS_DIR"
 
-# Get highest number from specs directory
-HIGHEST_FROM_SPECS=0
-if [ -d "$SPECS_DIR" ]; then
-    for dir in "$SPECS_DIR"/*; do
-        [ -d "$dir" ] || continue
-        dirname=$(basename "$dir")
-        number=$(echo "$dirname" | grep -o '^[0-9]\+' || echo "0")
-        number=$((10#$number))
-        if [ "$number" -gt "$HIGHEST_FROM_SPECS" ]; then HIGHEST_FROM_SPECS=$number; fi
-    done
-fi
-
-# Get highest number from branch names (both local and remote)
-HIGHEST_FROM_BRANCHES=0
-if [ "$HAS_GIT" = true ]; then
-    # Get all branches (local and remote)
-    branches=$(git branch -a 2>/dev/null || echo "")
-    
-    if [ -n "$branches" ]; then
-        while IFS= read -r branch; do
-            # Clean branch name: remove leading markers and remote prefixes
-            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
-            
-            # Extract feature number if branch matches pattern ###-*
-            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
-                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
-                number=$((10#$number))
-                if [ "$number" -gt "$HIGHEST_FROM_BRANCHES" ]; then HIGHEST_FROM_BRANCHES=$number; fi
-            fi
-        done <<< "$branches"
-    fi
-fi
-
-# Use the highest number from either source
-HIGHEST=$HIGHEST_FROM_SPECS
-if [ "$HIGHEST_FROM_BRANCHES" -gt "$HIGHEST" ]; then
-    HIGHEST=$HIGHEST_FROM_BRANCHES
-fi
-
-NEXT=$((HIGHEST + 1))
-FEATURE_NUM=$(printf "%03d" "$NEXT")
-
 # Function to generate branch name with stop word filtering and length filtering
 generate_branch_name() {
     local description="$1"
@@ -172,19 +220,34 @@ generate_branch_name() {
         echo "$result"
     else
         # Fallback to original logic if no meaningful words found
-        echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//' | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
+        local cleaned=$(clean_branch_name "$description")
+        echo "$cleaned" | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
     fi
 }
 
 # Generate branch name
 if [ -n "$SHORT_NAME" ]; then
     # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(echo "$SHORT_NAME" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//')
+    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
 else
     # Generate from description with smart filtering
     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=$((HIGHEST + 1))
+    fi
+fi
+
+# Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
+FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
 BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
 
 # GitHub enforces a 244-byte limit on branch names

scripts/bash/setup-plan.sh

@@ -24,7 +24,7 @@ for arg in "$@"; do
 done
 
 # Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions

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, Amp, or Amazon Q Developer CLI
+#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, or Amazon Q Developer CLI
 #    - 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|q
+# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|shai|q|bob|qoder
 # Leave empty to update all existing agent files
 
 set -e
@@ -49,7 +49,7 @@ set -o pipefail
 #==============================================================================
 
 # Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
@@ -61,7 +61,7 @@ AGENT_TYPE="${1:-}"
 # Agent-specific file paths  
 CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
 GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/chatmodes/copilot-instructions.md"
+COPILOT_FILE="$REPO_ROOT/.github/agents/copilot-instructions.md"
 CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
 QWEN_FILE="$REPO_ROOT/QWEN.md"
 AGENTS_FILE="$REPO_ROOT/AGENTS.md"
@@ -70,8 +70,11 @@ 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="$REPO_ROOT/QODER.md"
 AMP_FILE="$REPO_ROOT/AGENTS.md"
+SHAI_FILE="$REPO_ROOT/SHAI.md"
 Q_FILE="$REPO_ROOT/AGENTS.md"
+BOB_FILE="$REPO_ROOT/AGENTS.md"
 
 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -615,15 +618,24 @@ update_specific_agent() {
         codebuddy)
             update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
             ;;
+        qoder)
+            update_agent_file "$QODER_FILE" "Qoder CLI"
+            ;;
         amp)
             update_agent_file "$AMP_FILE" "Amp"
             ;;
+        shai)
+            update_agent_file "$SHAI_FILE" "SHAI"
+            ;;
         q)
             update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
             ;;
+        bob)
+            update_agent_file "$BOB_FILE" "IBM Bob"
+            ;;
         *)
             log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|amp|q"
+            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|amp|shai|q|bob|qoder"
             exit 1
             ;;
     esac
@@ -688,11 +700,26 @@ update_all_existing_agents() {
         found_agent=true
     fi
 
+    if [[ -f "$SHAI_FILE" ]]; then
+        update_agent_file "$SHAI_FILE" "SHAI"
+        found_agent=true
+    fi
+
+    if [[ -f "$QODER_FILE" ]]; then
+        update_agent_file "$QODER_FILE" "Qoder CLI"
+        found_agent=true
+    fi
+
     if [[ -f "$Q_FILE" ]]; then
         update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
         found_agent=true
     fi
     
+    if [[ -f "$BOB_FILE" ]]; then
+        update_agent_file "$BOB_FILE" "IBM Bob"
+        found_agent=true
+    fi
+    
     # If no agent files exist, create a default Claude file
     if [[ "$found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
@@ -717,7 +744,7 @@ print_summary() {
     
     echo
 
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|codebuddy|q]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|codebuddy|shai|q|bob|qoder]"
 }
 
 #==============================================================================

scripts/powershell/create-new-feature.ps1

@@ -4,6 +4,7 @@
 param(
     [switch]$Json,
     [string]$ShortName,
+    [int]$Number = 0,
     [switch]$Help,
     [Parameter(ValueFromRemainingArguments = $true)]
     [string[]]$FeatureDescription
@@ -12,11 +13,12 @@ $ErrorActionPreference = 'Stop'
 
 # Show help if requested
 if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] <feature description>"
+    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] <feature description>"
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
+    Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
     Write-Host "  -Help               Show this help message"
     Write-Host ""
     Write-Host "Examples:"
@@ -56,6 +58,77 @@ function Find-RepositoryRoot {
         $current = $parent
     }
 }
+
+function Get-HighestNumberFromSpecs {
+    param([string]$SpecsDir)
+    
+    $highest = 0
+    if (Test-Path $SpecsDir) {
+        Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
+            if ($_.Name -match '^(\d+)') {
+                $num = [int]$matches[1]
+                if ($num -gt $highest) { $highest = $num }
+            }
+        }
+    }
+    return $highest
+}
+
+function Get-HighestNumberFromBranches {
+    param()
+    
+    $highest = 0
+    try {
+        $branches = git branch -a 2>$null
+        if ($LASTEXITCODE -eq 0) {
+            foreach ($branch in $branches) {
+                # Clean branch name: remove leading markers and remote prefixes
+                $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
+                
+                # Extract feature number if branch matches pattern ###-*
+                if ($cleanBranch -match '^(\d+)-') {
+                    $num = [int]$matches[1]
+                    if ($num -gt $highest) { $highest = $num }
+                }
+            }
+        }
+    } catch {
+        # If git command fails, return 0
+        Write-Verbose "Could not check Git branches: $_"
+    }
+    return $highest
+}
+
+function Get-NextBranchNumber {
+    param(
+        [string]$SpecsDir
+    )
+
+    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
+    try {
+        git fetch --all --prune 2>$null | Out-Null
+    } catch {
+        # Ignore fetch errors
+    }
+
+    # Get highest number from ALL branches (not just matching short name)
+    $highestBranch = Get-HighestNumberFromBranches
+
+    # Get highest number from ALL specs (not just matching short name)
+    $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
+
+    # Take the maximum of both
+    $maxNum = [Math]::Max($highestBranch, $highestSpec)
+
+    # Return next number
+    return $maxNum + 1
+}
+
+function ConvertTo-CleanBranchName {
+    param([string]$Name)
+    
+    return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+}
 $fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
 if (-not $fallbackRoot) {
     Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
@@ -79,43 +152,6 @@ Set-Location $repoRoot
 $specsDir = Join-Path $repoRoot 'specs'
 New-Item -ItemType Directory -Path $specsDir -Force | Out-Null
 
-# Get highest number from specs directory
-$highestFromSpecs = 0
-if (Test-Path $specsDir) {
-    Get-ChildItem -Path $specsDir -Directory | ForEach-Object {
-        if ($_.Name -match '^(\d{3})') {
-            $num = [int]$matches[1]
-            if ($num -gt $highestFromSpecs) { $highestFromSpecs = $num }
-        }
-    }
-}
-
-# Get highest number from branch names (both local and remote)
-$highestFromBranches = 0
-try {
-    $branches = git branch -a 2>$null
-    if ($LASTEXITCODE -eq 0) {
-        foreach ($branch in $branches) {
-            # Clean branch name: remove leading markers and remote prefixes
-            $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
-            
-            # Extract feature number if branch matches pattern ###-*
-            if ($cleanBranch -match '^(\d{3})-') {
-                $num = [int]$matches[1]
-                if ($num -gt $highestFromBranches) { $highestFromBranches = $num }
-            }
-        }
-    }
-} catch {
-    # If git command fails, just continue with specs-only check
-    Write-Verbose "Could not check Git branches: $_"
-}
-
-# Use the highest number from either source
-$highest = [Math]::Max($highestFromSpecs, $highestFromBranches)
-$next = $highest + 1
-$featureNum = ('{0:000}' -f $next)
-
 # Function to generate branch name with stop word filtering and length filtering
 function Get-BranchName {
     param([string]$Description)
@@ -155,7 +191,7 @@ function Get-BranchName {
         return $result
     } else {
         # Fallback to original logic if no meaningful words found
-        $result = $Description.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+        $result = ConvertTo-CleanBranchName -Name $Description
         $fallbackWords = ($result -split '-') | Where-Object { $_ } | Select-Object -First 3
         return [string]::Join('-', $fallbackWords)
     }
@@ -164,12 +200,24 @@ function Get-BranchName {
 # Generate branch name
 if ($ShortName) {
     # Use provided short name, just clean it up
-    $branchSuffix = $ShortName.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
+    $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
 } else {
     # Generate from description with smart filtering
     $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 $specsDir) + 1
+    }
+}
+
+$featureNum = ('{0:000}' -f $Number)
 $branchName = "$featureNum-$branchSuffix"
 
 # GitHub enforces a 244-byte limit on branch names

scripts/powershell/setup-plan.ps1

@@ -59,4 +59,3 @@ if ($Json) {
     Write-Output "BRANCH: $($paths.CURRENT_BRANCH)"
     Write-Output "HAS_GIT: $($paths.HAS_GIT)"
 }
-

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, amp, q)
+ 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, roo, codebuddy, amp, shai, q, bob, qoder)
 
 .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','q')]
+    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','kilocode','auggie','roo','codebuddy','amp','shai','q','bob','qoder')]
     [string]$AgentType
 )
 
@@ -46,7 +46,7 @@ $NEW_PLAN = $IMPL_PLAN
 # Agent file paths
 $CLAUDE_FILE   = Join-Path $REPO_ROOT 'CLAUDE.md'
 $GEMINI_FILE   = Join-Path $REPO_ROOT 'GEMINI.md'
-$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/chatmodes/copilot-instructions.md'
+$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/agents/copilot-instructions.md'
 $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'
@@ -55,8 +55,11 @@ $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'
 $CODEBUDDY_FILE = Join-Path $REPO_ROOT 'CODEBUDDY.md'
+$QODER_FILE    = Join-Path $REPO_ROOT 'QODER.md'
 $AMP_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
+$SHAI_FILE     = Join-Path $REPO_ROOT 'SHAI.md'
 $Q_FILE        = Join-Path $REPO_ROOT 'AGENTS.md'
+$BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 
 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
 
@@ -380,9 +383,12 @@ function Update-SpecificAgent {
         'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
         'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
         'codebuddy' { Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI' }
+        'qoder'    { Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI' }
         'amp'      { Update-AgentFile -TargetFile $AMP_FILE      -AgentName 'Amp' }
+        'shai'     { Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI' }
         'q'        { Update-AgentFile -TargetFile $Q_FILE        -AgentName 'Amazon Q Developer CLI' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|q'; return $false }
+        'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|bob|qoder'; return $false }
     }
 }
 
@@ -400,7 +406,10 @@ function Update-AllExistingAgents {
     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 }
     if (Test-Path $CODEBUDDY_FILE) { if (-not (Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $QODER_FILE)    { if (-not (Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $SHAI_FILE)     { if (-not (Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI')) { $ok = $false }; $found = $true }
     if (Test-Path $Q_FILE)        { if (-not (Update-AgentFile -TargetFile $Q_FILE        -AgentName 'Amazon Q Developer CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $BOB_FILE)      { if (-not (Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob')) { $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 = $false }
@@ -415,7 +424,7 @@ function Print-Summary {
     if ($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|q]'
+    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|codebuddy|amp|shai|q|bob|qoder]'
 }
 
 function Main {

spec-driven.md

@@ -195,6 +195,7 @@ The templates include comprehensive checklists that act as "unit tests" for the
 
 ```markdown
 ### Requirement Completeness
+
 - [ ] No [NEEDS CLARIFICATION] markers remain
 - [ ] Requirements are testable and unambiguous
 - [ ] Success criteria are measurable
@@ -208,10 +209,14 @@ The implementation plan template enforces architectural principles through phase
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
+
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 ```
@@ -347,15 +352,19 @@ The implementation plan template operationalizes these articles through concrete
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
 
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 
 #### Integration-First Gate (Article IX)
+
 - [ ] Contracts defined?
 - [ ] Contract tests written?
 ```

spec-kit.code-workspace

@@ -0,0 +1,8 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}

src/specify_cli/__init__.py

@@ -190,6 +190,12 @@ AGENT_CONFIG = {
         "install_url": "https://www.codebuddy.ai/cli",
         "requires_cli": True,
     },
+    "qoder": {
+        "name": "Qoder CLI",
+        "folder": ".qoder/",
+        "install_url": "https://qoder.com/cli",
+        "requires_cli": True,
+    },
     "roo": {
         "name": "Roo Code",
         "folder": ".roo/",
@@ -208,6 +214,18 @@ AGENT_CONFIG = {
         "install_url": "https://ampcode.com/manual#install",
         "requires_cli": True,
     },
+    "shai": {
+        "name": "SHAI",
+        "folder": ".shai/",
+        "install_url": "https://github.com/ovh/shai",
+        "requires_cli": True,
+    },
+    "bob": {
+        "name": "IBM Bob",
+        "folder": ".bob/",
+        "install_url": None,  # IDE-based
+        "requires_cli": False,
+    },
 }
 
 SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
@@ -924,10 +942,45 @@ def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None =
             for f in failures:
                 console.print(f"  - {f}")
 
+def ensure_constitution_from_template(project_path: Path, tracker: StepTracker | None = None) -> None:
+    """Copy constitution template to memory if it doesn't exist (preserves existing constitution on reinitialization)."""
+    memory_constitution = project_path / ".specify" / "memory" / "constitution.md"
+    template_constitution = project_path / ".specify" / "templates" / "constitution-template.md"
+
+    # If constitution already exists in memory, preserve it
+    if memory_constitution.exists():
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.skip("constitution", "existing file preserved")
+        return
+
+    # If template doesn't exist, something went wrong with extraction
+    if not template_constitution.exists():
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.error("constitution", "template not found")
+        return
+
+    # Copy template to memory directory
+    try:
+        memory_constitution.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copy2(template_constitution, memory_constitution)
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.complete("constitution", "copied from template")
+        else:
+            console.print(f"[cyan]Initialized constitution from template[/cyan]")
+    except Exception as e:
+        if tracker:
+            tracker.add("constitution", "Constitution setup")
+            tracker.error("constitution", str(e))
+        else:
+            console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")
+
 @app.command()
 def init(
     project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
-    ai_assistant: str = typer.Option(None, "--ai", help="AI assistant to use: claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, codebuddy, amp, or q"),
+    ai_assistant: str = typer.Option(None, "--ai", help="AI assistant to use: claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, codebuddy, amp, shai, q, bob, or qoder "),
     script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
     ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for AI agent tools like Claude Code"),
     no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
@@ -1090,6 +1143,7 @@ def init(
         ("zip-list", "Archive contents"),
         ("extracted-summary", "Extraction summary"),
         ("chmod", "Ensure scripts executable"),
+        ("constitution", "Constitution setup"),
         ("cleanup", "Cleanup"),
         ("git", "Initialize git repository"),
         ("final", "Finalize")
@@ -1110,6 +1164,8 @@ def init(
 
             ensure_executable_scripts(project_path, tracker=tracker)
 
+            ensure_constitution_from_template(project_path, tracker=tracker)
+
             if not no_git:
                 tracker.start("git")
                 if is_git_repo(project_path):
@@ -1328,7 +1384,7 @@ def version():
     info_table.add_row("Template Version", template_version)
     info_table.add_row("Released", release_date)
     info_table.add_row("", "")
-    info_table.add_row("Python", f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}")
+    info_table.add_row("Python", platform.python_version())
     info_table.add_row("Platform", platform.system())
     info_table.add_row("Architecture", platform.machine())
     info_table.add_row("OS Version", platform.version())
@@ -1343,6 +1399,641 @@ def version():
     console.print(panel)
     console.print()
 
+
+# ===== Extension Commands =====
+
+extension_app = typer.Typer(
+    name="extension",
+    help="Manage spec-kit extensions",
+    add_completion=False,
+)
+app.add_typer(extension_app, name="extension")
+
+
+def get_speckit_version() -> str:
+    """Get current spec-kit version."""
+    import importlib.metadata
+    try:
+        return importlib.metadata.version("specify-cli")
+    except Exception:
+        # Fallback: try reading from pyproject.toml
+        try:
+            import tomllib
+            pyproject_path = Path(__file__).parent.parent.parent / "pyproject.toml"
+            if pyproject_path.exists():
+                with open(pyproject_path, "rb") as f:
+                    data = tomllib.load(f)
+                    return data.get("project", {}).get("version", "unknown")
+        except Exception:
+            # Intentionally ignore any errors while reading/parsing pyproject.toml.
+            # If this lookup fails for any reason, we fall back to returning "unknown" below.
+            pass
+    return "unknown"
+
+
+@extension_app.command("list")
+def extension_list(
+    available: bool = typer.Option(False, "--available", help="Show available extensions from catalog"),
+    all_extensions: bool = typer.Option(False, "--all", help="Show both installed and available"),
+):
+    """List installed extensions."""
+    from .extensions import ExtensionManager
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+    installed = manager.list_installed()
+
+    if not installed and not (available or all_extensions):
+        console.print("[yellow]No extensions installed.[/yellow]")
+        console.print("\nInstall an extension with:")
+        console.print("  specify extension add <extension-name>")
+        return
+
+    if installed:
+        console.print("\n[bold cyan]Installed Extensions:[/bold cyan]\n")
+
+        for ext in installed:
+            status_icon = "✓" if ext["enabled"] else "✗"
+            status_color = "green" if ext["enabled"] else "red"
+
+            console.print(f"  [{status_color}]{status_icon}[/{status_color}] [bold]{ext['name']}[/bold] (v{ext['version']})")
+            console.print(f"     {ext['description']}")
+            console.print(f"     Commands: {ext['command_count']} | Hooks: {ext['hook_count']} | Status: {'Enabled' if ext['enabled'] else 'Disabled'}")
+            console.print()
+
+    if available or all_extensions:
+        console.print("\nInstall an extension:")
+        console.print("  [cyan]specify extension add <name>[/cyan]")
+
+
+@extension_app.command("add")
+def extension_add(
+    extension: str = typer.Argument(help="Extension name or path"),
+    dev: bool = typer.Option(False, "--dev", help="Install from local directory"),
+    from_url: Optional[str] = typer.Option(None, "--from", help="Install from custom URL"),
+):
+    """Install an extension."""
+    from .extensions import ExtensionManager, ExtensionCatalog, ExtensionError, ValidationError, CompatibilityError
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+    speckit_version = get_speckit_version()
+
+    try:
+        with console.status(f"[cyan]Installing extension: {extension}[/cyan]"):
+            if dev:
+                # Install from local directory
+                source_path = Path(extension).expanduser().resolve()
+                if not source_path.exists():
+                    console.print(f"[red]Error:[/red] Directory not found: {source_path}")
+                    raise typer.Exit(1)
+
+                if not (source_path / "extension.yml").exists():
+                    console.print(f"[red]Error:[/red] No extension.yml found in {source_path}")
+                    raise typer.Exit(1)
+
+                manifest = manager.install_from_directory(source_path, speckit_version)
+
+            elif from_url:
+                # Install from URL (ZIP file)
+                import urllib.request
+                import urllib.error
+                from urllib.parse import urlparse
+
+                # Validate URL
+                parsed = urlparse(from_url)
+                is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+
+                if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
+                    console.print("[red]Error:[/red] URL must use HTTPS for security.")
+                    console.print("HTTP is only allowed for localhost URLs.")
+                    raise typer.Exit(1)
+
+                # Warn about untrusted sources
+                console.print("[yellow]Warning:[/yellow] Installing from external URL.")
+                console.print("Only install extensions from sources you trust.\n")
+                console.print(f"Downloading from {from_url}...")
+
+                # Download ZIP to temp location
+                download_dir = project_root / ".specify" / "extensions" / ".cache" / "downloads"
+                download_dir.mkdir(parents=True, exist_ok=True)
+                zip_path = download_dir / f"{extension}-url-download.zip"
+
+                try:
+                    with urllib.request.urlopen(from_url, timeout=60) as response:
+                        zip_data = response.read()
+                    zip_path.write_bytes(zip_data)
+
+                    # Install from downloaded ZIP
+                    manifest = manager.install_from_zip(zip_path, speckit_version)
+                except urllib.error.URLError as e:
+                    console.print(f"[red]Error:[/red] Failed to download from {from_url}: {e}")
+                    raise typer.Exit(1)
+                finally:
+                    # Clean up downloaded ZIP
+                    if zip_path.exists():
+                        zip_path.unlink()
+
+            else:
+                # Install from catalog
+                catalog = ExtensionCatalog(project_root)
+
+                # Check if extension exists in catalog
+                ext_info = catalog.get_extension_info(extension)
+                if not ext_info:
+                    console.print(f"[red]Error:[/red] Extension '{extension}' not found in catalog")
+                    console.print("\nSearch available extensions:")
+                    console.print("  specify extension search")
+                    raise typer.Exit(1)
+
+                # Download extension ZIP
+                console.print(f"Downloading {ext_info['name']} v{ext_info.get('version', 'unknown')}...")
+                zip_path = catalog.download_extension(extension)
+
+                try:
+                    # Install from downloaded ZIP
+                    manifest = manager.install_from_zip(zip_path, speckit_version)
+                finally:
+                    # Clean up downloaded ZIP
+                    if zip_path.exists():
+                        zip_path.unlink()
+
+        console.print(f"\n[green]✓[/green] Extension installed successfully!")
+        console.print(f"\n[bold]{manifest.name}[/bold] (v{manifest.version})")
+        console.print(f"  {manifest.description}")
+        console.print(f"\n[bold cyan]Provided commands:[/bold cyan]")
+        for cmd in manifest.commands:
+            console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
+
+        console.print(f"\n[yellow]⚠[/yellow]  Configuration may be required")
+        console.print(f"   Check: .specify/extensions/{manifest.id}/")
+
+    except ValidationError as e:
+        console.print(f"\n[red]Validation Error:[/red] {e}")
+        raise typer.Exit(1)
+    except CompatibilityError as e:
+        console.print(f"\n[red]Compatibility Error:[/red] {e}")
+        raise typer.Exit(1)
+    except ExtensionError as e:
+        console.print(f"\n[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+
+@extension_app.command("remove")
+def extension_remove(
+    extension: str = typer.Argument(help="Extension ID to remove"),
+    keep_config: bool = typer.Option(False, "--keep-config", help="Don't remove config files"),
+    force: bool = typer.Option(False, "--force", help="Skip confirmation"),
+):
+    """Uninstall an extension."""
+    from .extensions import ExtensionManager
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+
+    # Check if extension is installed
+    if not manager.registry.is_installed(extension):
+        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
+        raise typer.Exit(1)
+
+    # Get extension info
+    ext_manifest = manager.get_extension(extension)
+    if ext_manifest:
+        ext_name = ext_manifest.name
+        cmd_count = len(ext_manifest.commands)
+    else:
+        ext_name = extension
+        cmd_count = 0
+
+    # Confirm removal
+    if not force:
+        console.print(f"\n[yellow]⚠  This will remove:[/yellow]")
+        console.print(f"   • {cmd_count} commands from AI agent")
+        console.print(f"   • Extension directory: .specify/extensions/{extension}/")
+        if not keep_config:
+            console.print(f"   • Config files (will be backed up)")
+        console.print()
+
+        confirm = typer.confirm("Continue?")
+        if not confirm:
+            console.print("Cancelled")
+            raise typer.Exit(0)
+
+    # Remove extension
+    success = manager.remove(extension, keep_config=keep_config)
+
+    if success:
+        console.print(f"\n[green]✓[/green] Extension '{ext_name}' removed successfully")
+        if keep_config:
+            console.print(f"\nConfig files preserved in .specify/extensions/{extension}/")
+        else:
+            console.print(f"\nConfig files backed up to .specify/extensions/.backup/{extension}/")
+        console.print(f"\nTo reinstall: specify extension add {extension}")
+    else:
+        console.print(f"[red]Error:[/red] Failed to remove extension")
+        raise typer.Exit(1)
+
+
+@extension_app.command("search")
+def extension_search(
+    query: str = typer.Argument(None, help="Search query (optional)"),
+    tag: Optional[str] = typer.Option(None, "--tag", help="Filter by tag"),
+    author: Optional[str] = typer.Option(None, "--author", help="Filter by author"),
+    verified: bool = typer.Option(False, "--verified", help="Show only verified extensions"),
+):
+    """Search for available extensions in catalog."""
+    from .extensions import ExtensionCatalog, ExtensionError
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    catalog = ExtensionCatalog(project_root)
+
+    try:
+        console.print("🔍 Searching extension catalog...")
+        results = catalog.search(query=query, tag=tag, author=author, verified_only=verified)
+
+        if not results:
+            console.print("\n[yellow]No extensions found matching criteria[/yellow]")
+            if query or tag or author or verified:
+                console.print("\nTry:")
+                console.print("  • Broader search terms")
+                console.print("  • Remove filters")
+                console.print("  • specify extension search (show all)")
+            raise typer.Exit(0)
+
+        console.print(f"\n[green]Found {len(results)} extension(s):[/green]\n")
+
+        for ext in results:
+            # Extension header
+            verified_badge = " [green]✓ Verified[/green]" if ext.get("verified") else ""
+            console.print(f"[bold]{ext['name']}[/bold] (v{ext['version']}){verified_badge}")
+            console.print(f"  {ext['description']}")
+
+            # Metadata
+            console.print(f"\n  [dim]Author:[/dim] {ext.get('author', 'Unknown')}")
+            if ext.get('tags'):
+                tags_str = ", ".join(ext['tags'])
+                console.print(f"  [dim]Tags:[/dim] {tags_str}")
+
+            # Stats
+            stats = []
+            if ext.get('downloads') is not None:
+                stats.append(f"Downloads: {ext['downloads']:,}")
+            if ext.get('stars') is not None:
+                stats.append(f"Stars: {ext['stars']}")
+            if stats:
+                console.print(f"  [dim]{' | '.join(stats)}[/dim]")
+
+            # Links
+            if ext.get('repository'):
+                console.print(f"  [dim]Repository:[/dim] {ext['repository']}")
+
+            # Install command
+            console.print(f"\n  [cyan]Install:[/cyan] specify extension add {ext['id']}")
+            console.print()
+
+    except ExtensionError as e:
+        console.print(f"\n[red]Error:[/red] {e}")
+        console.print("\nTip: The catalog may be temporarily unavailable. Try again later.")
+        raise typer.Exit(1)
+
+
+@extension_app.command("info")
+def extension_info(
+    extension: str = typer.Argument(help="Extension ID or name"),
+):
+    """Show detailed information about an extension."""
+    from .extensions import ExtensionCatalog, ExtensionManager, ExtensionError
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    catalog = ExtensionCatalog(project_root)
+    manager = ExtensionManager(project_root)
+
+    try:
+        ext_info = catalog.get_extension_info(extension)
+
+        if not ext_info:
+            console.print(f"[red]Error:[/red] Extension '{extension}' not found in catalog")
+            console.print("\nTry: specify extension search")
+            raise typer.Exit(1)
+
+        # Header
+        verified_badge = " [green]✓ Verified[/green]" if ext_info.get("verified") else ""
+        console.print(f"\n[bold]{ext_info['name']}[/bold] (v{ext_info['version']}){verified_badge}")
+        console.print(f"ID: {ext_info['id']}")
+        console.print()
+
+        # Description
+        console.print(f"{ext_info['description']}")
+        console.print()
+
+        # Author and License
+        console.print(f"[dim]Author:[/dim] {ext_info.get('author', 'Unknown')}")
+        console.print(f"[dim]License:[/dim] {ext_info.get('license', 'Unknown')}")
+        console.print()
+
+        # Requirements
+        if ext_info.get('requires'):
+            console.print("[bold]Requirements:[/bold]")
+            reqs = ext_info['requires']
+            if reqs.get('speckit_version'):
+                console.print(f"  • Spec Kit: {reqs['speckit_version']}")
+            if reqs.get('tools'):
+                for tool in reqs['tools']:
+                    tool_name = tool['name']
+                    tool_version = tool.get('version', 'any')
+                    required = " (required)" if tool.get('required') else " (optional)"
+                    console.print(f"  • {tool_name}: {tool_version}{required}")
+            console.print()
+
+        # Provides
+        if ext_info.get('provides'):
+            console.print("[bold]Provides:[/bold]")
+            provides = ext_info['provides']
+            if provides.get('commands'):
+                console.print(f"  • Commands: {provides['commands']}")
+            if provides.get('hooks'):
+                console.print(f"  • Hooks: {provides['hooks']}")
+            console.print()
+
+        # Tags
+        if ext_info.get('tags'):
+            tags_str = ", ".join(ext_info['tags'])
+            console.print(f"[bold]Tags:[/bold] {tags_str}")
+            console.print()
+
+        # Statistics
+        stats = []
+        if ext_info.get('downloads') is not None:
+            stats.append(f"Downloads: {ext_info['downloads']:,}")
+        if ext_info.get('stars') is not None:
+            stats.append(f"Stars: {ext_info['stars']}")
+        if stats:
+            console.print(f"[bold]Statistics:[/bold] {' | '.join(stats)}")
+            console.print()
+
+        # Links
+        console.print("[bold]Links:[/bold]")
+        if ext_info.get('repository'):
+            console.print(f"  • Repository: {ext_info['repository']}")
+        if ext_info.get('homepage'):
+            console.print(f"  • Homepage: {ext_info['homepage']}")
+        if ext_info.get('documentation'):
+            console.print(f"  • Documentation: {ext_info['documentation']}")
+        if ext_info.get('changelog'):
+            console.print(f"  • Changelog: {ext_info['changelog']}")
+        console.print()
+
+        # Installation status and command
+        is_installed = manager.registry.is_installed(ext_info['id'])
+        if is_installed:
+            console.print("[green]✓ Installed[/green]")
+            console.print(f"\nTo remove: specify extension remove {ext_info['id']}")
+        else:
+            console.print("[yellow]Not installed[/yellow]")
+            console.print(f"\n[cyan]Install:[/cyan] specify extension add {ext_info['id']}")
+
+    except ExtensionError as e:
+        console.print(f"\n[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+
+@extension_app.command("update")
+def extension_update(
+    extension: str = typer.Argument(None, help="Extension ID to update (or all)"),
+):
+    """Update extension(s) to latest version."""
+    from .extensions import ExtensionManager, ExtensionCatalog, ExtensionError
+    from packaging import version as pkg_version
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+    catalog = ExtensionCatalog(project_root)
+
+    try:
+        # Get list of extensions to update
+        if extension:
+            # Update specific extension
+            if not manager.registry.is_installed(extension):
+                console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
+                raise typer.Exit(1)
+            extensions_to_update = [extension]
+        else:
+            # Update all extensions
+            installed = manager.list_installed()
+            extensions_to_update = [ext["id"] for ext in installed]
+
+        if not extensions_to_update:
+            console.print("[yellow]No extensions installed[/yellow]")
+            raise typer.Exit(0)
+
+        console.print("🔄 Checking for updates...\n")
+
+        updates_available = []
+
+        for ext_id in extensions_to_update:
+            # Get installed version
+            metadata = manager.registry.get(ext_id)
+            installed_version = pkg_version.Version(metadata["version"])
+
+            # Get catalog info
+            ext_info = catalog.get_extension_info(ext_id)
+            if not ext_info:
+                console.print(f"⚠  {ext_id}: Not found in catalog (skipping)")
+                continue
+
+            catalog_version = pkg_version.Version(ext_info["version"])
+
+            if catalog_version > installed_version:
+                updates_available.append(
+                    {
+                        "id": ext_id,
+                        "installed": str(installed_version),
+                        "available": str(catalog_version),
+                        "download_url": ext_info.get("download_url"),
+                    }
+                )
+            else:
+                console.print(f"✓ {ext_id}: Up to date (v{installed_version})")
+
+        if not updates_available:
+            console.print("\n[green]All extensions are up to date![/green]")
+            raise typer.Exit(0)
+
+        # Show available updates
+        console.print("\n[bold]Updates available:[/bold]\n")
+        for update in updates_available:
+            console.print(
+                f"  • {update['id']}: {update['installed']} → {update['available']}"
+            )
+
+        console.print()
+        confirm = typer.confirm("Update these extensions?")
+        if not confirm:
+            console.print("Cancelled")
+            raise typer.Exit(0)
+
+        # Perform updates
+        console.print()
+        for update in updates_available:
+            ext_id = update["id"]
+            console.print(f"📦 Updating {ext_id}...")
+
+            # TODO: Implement download and reinstall from URL
+            # For now, just show  message
+            console.print(
+                f"[yellow]Note:[/yellow] Automatic update not yet implemented. "
+                f"Please update manually:"
+            )
+            console.print(f"  specify extension remove {ext_id} --keep-config")
+            console.print(f"  specify extension add {ext_id}")
+
+        console.print(
+            "\n[cyan]Tip:[/cyan] Automatic updates will be available in a future version"
+        )
+
+    except ExtensionError as e:
+        console.print(f"\n[red]Error:[/red] {e}")
+        raise typer.Exit(1)
+
+
+@extension_app.command("enable")
+def extension_enable(
+    extension: str = typer.Argument(help="Extension ID to enable"),
+):
+    """Enable a disabled extension."""
+    from .extensions import ExtensionManager, HookExecutor
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+    hook_executor = HookExecutor(project_root)
+
+    if not manager.registry.is_installed(extension):
+        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
+        raise typer.Exit(1)
+
+    # Update registry
+    metadata = manager.registry.get(extension)
+    if metadata.get("enabled", True):
+        console.print(f"[yellow]Extension '{extension}' is already enabled[/yellow]")
+        raise typer.Exit(0)
+
+    metadata["enabled"] = True
+    manager.registry.add(extension, metadata)
+
+    # Enable hooks in extensions.yml
+    config = hook_executor.get_project_config()
+    if "hooks" in config:
+        for hook_name in config["hooks"]:
+            for hook in config["hooks"][hook_name]:
+                if hook.get("extension") == extension:
+                    hook["enabled"] = True
+        hook_executor.save_project_config(config)
+
+    console.print(f"[green]✓[/green] Extension '{extension}' enabled")
+
+
+@extension_app.command("disable")
+def extension_disable(
+    extension: str = typer.Argument(help="Extension ID to disable"),
+):
+    """Disable an extension without removing it."""
+    from .extensions import ExtensionManager, HookExecutor
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = ExtensionManager(project_root)
+    hook_executor = HookExecutor(project_root)
+
+    if not manager.registry.is_installed(extension):
+        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
+        raise typer.Exit(1)
+
+    # Update registry
+    metadata = manager.registry.get(extension)
+    if not metadata.get("enabled", True):
+        console.print(f"[yellow]Extension '{extension}' is already disabled[/yellow]")
+        raise typer.Exit(0)
+
+    metadata["enabled"] = False
+    manager.registry.add(extension, metadata)
+
+    # Disable hooks in extensions.yml
+    config = hook_executor.get_project_config()
+    if "hooks" in config:
+        for hook_name in config["hooks"]:
+            for hook in config["hooks"][hook_name]:
+                if hook.get("extension") == extension:
+                    hook["enabled"] = False
+        hook_executor.save_project_config(config)
+
+    console.print(f"[green]✓[/green] Extension '{extension}' disabled")
+    console.print(f"\nCommands will no longer be available. Hooks will not execute.")
+    console.print(f"To re-enable: specify extension enable {extension}")
+
+
 def main():
     app()
 

templates/commands/constitution.md

@@ -16,11 +16,13 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 ## Outline
 
-You are updating the project constitution at `/memory/constitution.md`. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. `[PROJECT_NAME]`, `[PRINCIPLE_1_NAME]`). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.
+You are updating the project constitution at `.specify/memory/constitution.md`. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. `[PROJECT_NAME]`, `[PRINCIPLE_1_NAME]`). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.
+
+**Note**: If `.specify/memory/constitution.md` does not exist yet, it should have been initialized from `.specify/templates/constitution-template.md` during project setup. If it's missing, copy the template first.
 
 Follow this execution flow:
 
-1. Load the existing constitution template at `/memory/constitution.md`.
+1. Load the existing constitution at `.specify/memory/constitution.md`.
    - Identify every placeholder token of the form `[ALL_CAPS_IDENTIFIER]`.
    **IMPORTANT**: The user might require less or more principles than the ones used in the template. If a number is specified, respect that - follow the general template. You will update the doc accordingly.
 
@@ -41,10 +43,10 @@ Follow this execution flow:
    - Ensure Governance section lists amendment procedure, versioning policy, and compliance review expectations.
 
 4. Consistency propagation checklist (convert prior checklist into active validations):
-   - Read `/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
+   - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
-   - Read `/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
+   - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
-   - Read `/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
+   - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
-   - Read each command file in `/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
+   - Read each command file in `.specify/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
    - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
 
 5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):
@@ -61,7 +63,7 @@ Follow this execution flow:
    - Dates ISO format YYYY-MM-DD.
    - Principles are declarative, testable, and free of vague language ("should" → replace with MUST/SHOULD rationale where appropriate).
 
-7. Write the completed constitution back to `/memory/constitution.md` (overwrite).
+7. Write the completed constitution back to `.specify/memory/constitution.md` (overwrite).
 
 8. Output a final summary to the user with:
    - New version and bump rationale.
@@ -79,4 +81,4 @@ If the user supplies partial updates (e.g., only one principle revision), still
 
 If critical info missing (e.g., ratification date truly unknown), insert `TODO(<FIELD_NAME>): explanation` and include in the Sync Impact Report under deferred items.
 
-Do not create a new template; always operate on the existing `/memory/constitution.md` file.
+Do not create a new template; always operate on the existing `.specify/memory/constitution.md` file.

templates/commands/implement.md

@@ -67,7 +67,8 @@ You **MUST** consider the user input before proceeding (if not empty).
      ```
 
    - Check if Dockerfile* exists or Docker in plan.md → create/verify .dockerignore
-   - Check if .eslintrc*or eslint.config.* exists → create/verify .eslintignore
+   - Check if .eslintrc* exists → create/verify .eslintignore
+   - Check if eslint.config.* exists → ensure the config's `ignores` entries cover required patterns
    - Check if .prettierrc* exists → create/verify .prettierignore
    - Check if .npmrc or package.json exists → create/verify .npmignore (if publishing)
    - Check if terraform files (*.tf) exist → create/verify .terraformignore

templates/commands/specify.md

@@ -39,16 +39,37 @@ Given that feature description, do this:
      - "Create a dashboard for analytics" → "analytics-dashboard"
      - "Fix payment processing timeout bug" → "fix-payment-timeout"
 
-2. Run the script `{SCRIPT}` from repo root **with the short-name argument** and parse its JSON output for BRANCH_NAME and SPEC_FILE. All file paths must be absolute.
+2. **Check for existing branches before creating new one**:
+
+   a. First, fetch all remote branches to ensure we have the latest information:
+
+      ```bash
+      git fetch --all --prune
+      ```
+
+   b. Find the highest feature number across all sources for the short-name:
+      - Remote branches: `git ls-remote --heads origin | grep -E 'refs/heads/[0-9]+-<short-name>$'`
+      - Local branches: `git branch | grep -E '^[* ]*[0-9]+-<short-name>$'`
+      - Specs directories: Check for directories matching `specs/[0-9]+-<short-name>`
+
+   c. Determine the next available number:
+      - Extract all numbers from all three sources
+      - Find the highest number N
+      - Use N+1 for the new branch number
+
+   d. Run the script `{SCRIPT}` with the calculated number and short-name:
+      - Pass `--number N+1` and `--short-name "your-short-name"` along with the feature description
+      - Bash example: `{SCRIPT} --json --number 5 --short-name "user-auth" "Add user authentication"`
+      - PowerShell example: `{SCRIPT} -Json -Number 5 -ShortName "user-auth" "Add user authentication"`
 
    **IMPORTANT**:
-
+   - Check all three sources (remote branches, local branches, specs directories) to find the highest number
-   - Append the short-name argument to the `{SCRIPT}` command with the 2-4 word short name you created in step 1. Keep the feature description as the final argument.
+   - Only match branches/directories with the exact short-name pattern
-   - Bash example: `--short-name "your-generated-short-name" "Feature description here"`
+   - If no existing branches/directories found with this short-name, start with number 1
-   - PowerShell example: `-ShortName "your-generated-short-name" "Feature description here"`
+   - You must only ever run this script once per feature
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
-   - You must only ever run this script once
    - The JSON is provided in the terminal as output - always refer to it to get the actual content you're looking for
+   - The JSON output will contain BRANCH_NAME and SPEC_FILE paths
+   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
 
 3. Load `templates/spec-template.md` to understand required sections.
 

templates/commands/tasks.md

@@ -42,7 +42,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Create parallel execution examples per user story
    - Validate task completeness (each user story has all needed tasks, independently testable)
 
-4. **Generate tasks.md**: Use `.specify/templates/tasks-template.md` as structure, fill with:
+4. **Generate tasks.md**: Use `templates/tasks-template.md` as structure, fill with:
    - Correct feature name from plan.md
    - Phase 1: Setup tasks (project initialization)
    - Phase 2: Foundational tasks (blocking prerequisites for all user stories)

templates/commands/taskstoissues.md

@@ -1,6 +1,6 @@
 ---
-description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
+description: Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts.
-tools: ['github/github-mcp-server/create_issue']
+tools: ['github/github-mcp-server/issue_write']
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
@@ -24,8 +24,10 @@ You **MUST** consider the user input before proceeding (if not empty).
 git config --get remote.origin.url
 ```
 
-**ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL**
+> [!CAUTION]
+> ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL
 
 1. For each task in the list, use the GitHub MCP server to create a new issue in the repository that is representative of the Git remote.
 
-**UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL**
+> [!CAUTION]
+> UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL

tests/__init__.py

@@ -0,0 +1 @@
+"""Unit tests for Spec Kit."""

tests/test_extensions.py

@@ -0,0 +1,989 @@
+"""
+Unit tests for the extension system.
+
+Tests cover:
+- Extension manifest validation
+- Extension registry operations
+- Extension manager installation/removal
+- Command registration
+"""
+
+import pytest
+import json
+import tempfile
+import shutil
+from pathlib import Path
+from datetime import datetime, timezone
+
+from specify_cli.extensions import (
+    ExtensionManifest,
+    ExtensionRegistry,
+    ExtensionManager,
+    CommandRegistrar,
+    ExtensionCatalog,
+    ExtensionError,
+    ValidationError,
+    CompatibilityError,
+    version_satisfies,
+)
+
+
+# ===== Fixtures =====
+
+@pytest.fixture
+def temp_dir():
+    """Create a temporary directory for tests."""
+    tmpdir = tempfile.mkdtemp()
+    yield Path(tmpdir)
+    shutil.rmtree(tmpdir)
+
+
+@pytest.fixture
+def valid_manifest_data():
+    """Valid extension manifest data."""
+    return {
+        "schema_version": "1.0",
+        "extension": {
+            "id": "test-ext",
+            "name": "Test Extension",
+            "version": "1.0.0",
+            "description": "A test extension",
+            "author": "Test Author",
+            "repository": "https://github.com/test/test-ext",
+            "license": "MIT",
+        },
+        "requires": {
+            "speckit_version": ">=0.1.0",
+            "commands": ["speckit.tasks"],
+        },
+        "provides": {
+            "commands": [
+                {
+                    "name": "speckit.test.hello",
+                    "file": "commands/hello.md",
+                    "description": "Test command",
+                }
+            ]
+        },
+        "hooks": {
+            "after_tasks": {
+                "command": "speckit.test.hello",
+                "optional": True,
+                "prompt": "Run test?",
+            }
+        },
+        "tags": ["testing", "example"],
+    }
+
+
+@pytest.fixture
+def extension_dir(temp_dir, valid_manifest_data):
+    """Create a complete extension directory structure."""
+    ext_dir = temp_dir / "test-ext"
+    ext_dir.mkdir()
+
+    # Write manifest
+    import yaml
+    manifest_path = ext_dir / "extension.yml"
+    with open(manifest_path, 'w') as f:
+        yaml.dump(valid_manifest_data, f)
+
+    # Create commands directory
+    commands_dir = ext_dir / "commands"
+    commands_dir.mkdir()
+
+    # Write command file
+    cmd_file = commands_dir / "hello.md"
+    cmd_file.write_text("""---
+description: "Test hello command"
+---
+
+# Test Hello Command
+
+$ARGUMENTS
+""")
+
+    return ext_dir
+
+
+@pytest.fixture
+def project_dir(temp_dir):
+    """Create a mock spec-kit project directory."""
+    proj_dir = temp_dir / "project"
+    proj_dir.mkdir()
+
+    # Create .specify directory
+    specify_dir = proj_dir / ".specify"
+    specify_dir.mkdir()
+
+    return proj_dir
+
+
+# ===== ExtensionManifest Tests =====
+
+class TestExtensionManifest:
+    """Test ExtensionManifest validation and parsing."""
+
+    def test_valid_manifest(self, extension_dir):
+        """Test loading a valid manifest."""
+        manifest_path = extension_dir / "extension.yml"
+        manifest = ExtensionManifest(manifest_path)
+
+        assert manifest.id == "test-ext"
+        assert manifest.name == "Test Extension"
+        assert manifest.version == "1.0.0"
+        assert manifest.description == "A test extension"
+        assert len(manifest.commands) == 1
+        assert manifest.commands[0]["name"] == "speckit.test.hello"
+
+    def test_missing_required_field(self, temp_dir):
+        """Test manifest missing required field."""
+        import yaml
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump({"schema_version": "1.0"}, f)  # Missing 'extension'
+
+        with pytest.raises(ValidationError, match="Missing required field"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_extension_id(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid extension ID format."""
+        import yaml
+
+        valid_manifest_data["extension"]["id"] = "Invalid_ID"  # Uppercase not allowed
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid extension ID"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_version(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid semantic version."""
+        import yaml
+
+        valid_manifest_data["extension"]["version"] = "invalid"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid version"):
+            ExtensionManifest(manifest_path)
+
+    def test_invalid_command_name(self, temp_dir, valid_manifest_data):
+        """Test manifest with invalid command name format."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"][0]["name"] = "invalid-name"
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="Invalid command name"):
+            ExtensionManifest(manifest_path)
+
+    def test_no_commands(self, temp_dir, valid_manifest_data):
+        """Test manifest with no commands provided."""
+        import yaml
+
+        valid_manifest_data["provides"]["commands"] = []
+
+        manifest_path = temp_dir / "extension.yml"
+        with open(manifest_path, 'w') as f:
+            yaml.dump(valid_manifest_data, f)
+
+        with pytest.raises(ValidationError, match="must provide at least one command"):
+            ExtensionManifest(manifest_path)
+
+    def test_manifest_hash(self, extension_dir):
+        """Test manifest hash calculation."""
+        manifest_path = extension_dir / "extension.yml"
+        manifest = ExtensionManifest(manifest_path)
+
+        hash_value = manifest.get_hash()
+        assert hash_value.startswith("sha256:")
+        assert len(hash_value) > 10
+
+
+# ===== ExtensionRegistry Tests =====
+
+class TestExtensionRegistry:
+    """Test ExtensionRegistry operations."""
+
+    def test_empty_registry(self, temp_dir):
+        """Test creating a new empty registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        assert registry.data["schema_version"] == "1.0"
+        assert registry.data["extensions"] == {}
+        assert len(registry.list()) == 0
+
+    def test_add_extension(self, temp_dir):
+        """Test adding an extension to registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        metadata = {
+            "version": "1.0.0",
+            "source": "local",
+            "enabled": True,
+        }
+        registry.add("test-ext", metadata)
+
+        assert registry.is_installed("test-ext")
+        ext_data = registry.get("test-ext")
+        assert ext_data["version"] == "1.0.0"
+        assert "installed_at" in ext_data
+
+    def test_remove_extension(self, temp_dir):
+        """Test removing an extension from registry."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("test-ext", {"version": "1.0.0"})
+
+        assert registry.is_installed("test-ext")
+
+        registry.remove("test-ext")
+
+        assert not registry.is_installed("test-ext")
+        assert registry.get("test-ext") is None
+
+    def test_registry_persistence(self, temp_dir):
+        """Test that registry persists to disk."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        # Create registry and add extension
+        registry1 = ExtensionRegistry(extensions_dir)
+        registry1.add("test-ext", {"version": "1.0.0"})
+
+        # Load new registry instance
+        registry2 = ExtensionRegistry(extensions_dir)
+
+        # Should still have the extension
+        assert registry2.is_installed("test-ext")
+        assert registry2.get("test-ext")["version"] == "1.0.0"
+
+
+# ===== ExtensionManager Tests =====
+
+class TestExtensionManager:
+    """Test ExtensionManager installation and removal."""
+
+    def test_check_compatibility_valid(self, extension_dir, project_dir):
+        """Test compatibility check with valid version."""
+        manager = ExtensionManager(project_dir)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        # Should not raise
+        result = manager.check_compatibility(manifest, "0.1.0")
+        assert result is True
+
+    def test_check_compatibility_invalid(self, extension_dir, project_dir):
+        """Test compatibility check with invalid version."""
+        manager = ExtensionManager(project_dir)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        # Requires >=0.1.0, but we have 0.0.1
+        with pytest.raises(CompatibilityError, match="Extension requires spec-kit"):
+            manager.check_compatibility(manifest, "0.0.1")
+
+    def test_install_from_directory(self, extension_dir, project_dir):
+        """Test installing extension from directory."""
+        manager = ExtensionManager(project_dir)
+
+        manifest = manager.install_from_directory(
+            extension_dir,
+            "0.1.0",
+            register_commands=False  # Skip command registration for now
+        )
+
+        assert manifest.id == "test-ext"
+        assert manager.registry.is_installed("test-ext")
+
+        # Check extension directory was copied
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        assert ext_dir.exists()
+        assert (ext_dir / "extension.yml").exists()
+        assert (ext_dir / "commands" / "hello.md").exists()
+
+    def test_install_duplicate(self, extension_dir, project_dir):
+        """Test installing already installed extension."""
+        manager = ExtensionManager(project_dir)
+
+        # Install once
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Try to install again
+        with pytest.raises(ExtensionError, match="already installed"):
+            manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+    def test_remove_extension(self, extension_dir, project_dir):
+        """Test removing an installed extension."""
+        manager = ExtensionManager(project_dir)
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        assert ext_dir.exists()
+
+        # Remove extension
+        result = manager.remove("test-ext", keep_config=False)
+
+        assert result is True
+        assert not manager.registry.is_installed("test-ext")
+        assert not ext_dir.exists()
+
+    def test_remove_nonexistent(self, project_dir):
+        """Test removing non-existent extension."""
+        manager = ExtensionManager(project_dir)
+
+        result = manager.remove("nonexistent")
+        assert result is False
+
+    def test_list_installed(self, extension_dir, project_dir):
+        """Test listing installed extensions."""
+        manager = ExtensionManager(project_dir)
+
+        # Initially empty
+        assert len(manager.list_installed()) == 0
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Should have one extension
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "test-ext"
+        assert installed[0]["name"] == "Test Extension"
+        assert installed[0]["version"] == "1.0.0"
+        assert installed[0]["command_count"] == 1
+        assert installed[0]["hook_count"] == 1
+
+    def test_config_backup_on_remove(self, extension_dir, project_dir):
+        """Test that config files are backed up on removal."""
+        manager = ExtensionManager(project_dir)
+
+        # Install extension
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # Create a config file
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        config_file = ext_dir / "test-ext-config.yml"
+        config_file.write_text("test: config")
+
+        # Remove extension (without keep_config)
+        manager.remove("test-ext", keep_config=False)
+
+        # Check backup was created (now in subdirectory per extension)
+        backup_dir = project_dir / ".specify" / "extensions" / ".backup" / "test-ext"
+        backup_file = backup_dir / "test-ext-config.yml"
+        assert backup_file.exists()
+        assert backup_file.read_text() == "test: config"
+
+
+# ===== CommandRegistrar Tests =====
+
+class TestCommandRegistrar:
+    """Test CommandRegistrar command registration."""
+
+    def test_parse_frontmatter_valid(self):
+        """Test parsing valid YAML frontmatter."""
+        content = """---
+description: "Test command"
+tools:
+  - tool1
+  - tool2
+---
+
+# Command body
+$ARGUMENTS
+"""
+        registrar = CommandRegistrar()
+        frontmatter, body = registrar.parse_frontmatter(content)
+
+        assert frontmatter["description"] == "Test command"
+        assert frontmatter["tools"] == ["tool1", "tool2"]
+        assert "Command body" in body
+        assert "$ARGUMENTS" in body
+
+    def test_parse_frontmatter_no_frontmatter(self):
+        """Test parsing content without frontmatter."""
+        content = "# Just a command\n$ARGUMENTS"
+
+        registrar = CommandRegistrar()
+        frontmatter, body = registrar.parse_frontmatter(content)
+
+        assert frontmatter == {}
+        assert body == content
+
+    def test_render_frontmatter(self):
+        """Test rendering frontmatter to YAML."""
+        frontmatter = {
+            "description": "Test command",
+            "tools": ["tool1", "tool2"]
+        }
+
+        registrar = CommandRegistrar()
+        output = registrar.render_frontmatter(frontmatter)
+
+        assert output.startswith("---\n")
+        assert output.endswith("---\n")
+        assert "description: Test command" in output
+
+    def test_register_commands_for_claude(self, extension_dir, project_dir):
+        """Test registering commands for Claude agent."""
+        # Create .claude directory
+        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir.mkdir(parents=True)
+
+        ExtensionManager(project_dir)  # Initialize manager (side effects only)
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_claude(
+            manifest,
+            extension_dir,
+            project_dir
+        )
+
+        assert len(registered) == 1
+        assert "speckit.test.hello" in registered
+
+        # Check command file was created
+        cmd_file = claude_dir / "speckit.test.hello.md"
+        assert cmd_file.exists()
+
+        content = cmd_file.read_text()
+        assert "description: Test hello command" in content
+        assert "<!-- Extension: test-ext -->" in content
+        assert "<!-- Config: .specify/extensions/test-ext/ -->" in content
+
+    def test_command_with_aliases(self, project_dir, temp_dir):
+        """Test registering a command with aliases."""
+        import yaml
+
+        # Create extension with command alias
+        ext_dir = temp_dir / "ext-alias"
+        ext_dir.mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-alias",
+                "name": "Extension with Alias",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {
+                "speckit_version": ">=0.1.0",
+            },
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.alias.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shortcut"],
+                    }
+                ]
+            },
+        }
+
+        with open(ext_dir / "extension.yml", 'w') as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nTest")
+
+        claude_dir = project_dir / ".claude" / "commands"
+        claude_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_claude(manifest, ext_dir, project_dir)
+
+        assert len(registered) == 2
+        assert "speckit.alias.cmd" in registered
+        assert "speckit.shortcut" in registered
+        assert (claude_dir / "speckit.alias.cmd.md").exists()
+        assert (claude_dir / "speckit.shortcut.md").exists()
+
+
+# ===== Utility Function Tests =====
+
+class TestVersionSatisfies:
+    """Test version_satisfies utility function."""
+
+    def test_version_satisfies_simple(self):
+        """Test simple version comparison."""
+        assert version_satisfies("1.0.0", ">=1.0.0")
+        assert version_satisfies("1.0.1", ">=1.0.0")
+        assert not version_satisfies("0.9.9", ">=1.0.0")
+
+    def test_version_satisfies_range(self):
+        """Test version range."""
+        assert version_satisfies("1.5.0", ">=1.0.0,<2.0.0")
+        assert not version_satisfies("2.0.0", ">=1.0.0,<2.0.0")
+        assert not version_satisfies("0.9.0", ">=1.0.0,<2.0.0")
+
+    def test_version_satisfies_complex(self):
+        """Test complex version specifier."""
+        assert version_satisfies("1.0.5", ">=1.0.0,!=1.0.3")
+        assert not version_satisfies("1.0.3", ">=1.0.0,!=1.0.3")
+
+    def test_version_satisfies_invalid(self):
+        """Test invalid version strings."""
+        assert not version_satisfies("invalid", ">=1.0.0")
+        assert not version_satisfies("1.0.0", "invalid specifier")
+
+
+# ===== Integration Tests =====
+
+class TestIntegration:
+    """Integration tests for complete workflows."""
+
+    def test_full_install_and_remove_workflow(self, extension_dir, project_dir):
+        """Test complete installation and removal workflow."""
+        # Create Claude directory
+        (project_dir / ".claude" / "commands").mkdir(parents=True)
+
+        manager = ExtensionManager(project_dir)
+
+        # Install
+        manager.install_from_directory(
+            extension_dir,
+            "0.1.0",
+            register_commands=True
+        )
+
+        # Verify installation
+        assert manager.registry.is_installed("test-ext")
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "test-ext"
+
+        # Verify command registered
+        cmd_file = project_dir / ".claude" / "commands" / "speckit.test.hello.md"
+        assert cmd_file.exists()
+
+        # Verify registry has registered commands (now a dict keyed by agent)
+        metadata = manager.registry.get("test-ext")
+        registered_commands = metadata["registered_commands"]
+        # Check that the command is registered for at least one agent
+        assert any(
+            "speckit.test.hello" in cmds
+            for cmds in registered_commands.values()
+        )
+
+        # Remove
+        result = manager.remove("test-ext")
+        assert result is True
+
+        # Verify removal
+        assert not manager.registry.is_installed("test-ext")
+        assert not cmd_file.exists()
+        assert len(manager.list_installed()) == 0
+
+    def test_multiple_extensions(self, temp_dir, project_dir):
+        """Test installing multiple extensions."""
+        import yaml
+
+        # Create two extensions
+        for i in range(1, 3):
+            ext_dir = temp_dir / f"ext{i}"
+            ext_dir.mkdir()
+
+            manifest_data = {
+                "schema_version": "1.0",
+                "extension": {
+                    "id": f"ext{i}",
+                    "name": f"Extension {i}",
+                    "version": "1.0.0",
+                    "description": f"Extension {i}",
+                },
+                "requires": {"speckit_version": ">=0.1.0"},
+                "provides": {
+                    "commands": [
+                        {
+                            "name": f"speckit.ext{i}.cmd",
+                            "file": "commands/cmd.md",
+                        }
+                    ]
+                },
+            }
+
+            with open(ext_dir / "extension.yml", 'w') as f:
+                yaml.dump(manifest_data, f)
+
+            (ext_dir / "commands").mkdir()
+            (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\nTest")
+
+        manager = ExtensionManager(project_dir)
+
+        # Install both
+        manager.install_from_directory(temp_dir / "ext1", "0.1.0", register_commands=False)
+        manager.install_from_directory(temp_dir / "ext2", "0.1.0", register_commands=False)
+
+        # Verify both installed
+        installed = manager.list_installed()
+        assert len(installed) == 2
+        assert {ext["id"] for ext in installed} == {"ext1", "ext2"}
+
+        # Remove first
+        manager.remove("ext1")
+
+        # Verify only second remains
+        installed = manager.list_installed()
+        assert len(installed) == 1
+        assert installed[0]["id"] == "ext2"
+
+
+# ===== Extension Catalog Tests =====
+
+
+class TestExtensionCatalog:
+    """Test extension catalog functionality."""
+
+    def test_catalog_initialization(self, temp_dir):
+        """Test catalog initialization."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        assert catalog.project_root == project_dir
+        assert catalog.cache_dir == project_dir / ".specify" / "extensions" / ".cache"
+
+    def test_cache_directory_creation(self, temp_dir):
+        """Test catalog cache directory is created when fetching."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog data
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "test-ext": {
+                    "name": "Test Extension",
+                    "id": "test-ext",
+                    "version": "1.0.0",
+                    "description": "Test",
+                }
+            },
+        }
+
+        # Manually save to cache to test cache reading
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com/catalog.json",
+                }
+            )
+        )
+
+        # Should use cache
+        result = catalog.fetch_catalog()
+        assert result == catalog_data
+
+    def test_cache_expiration(self, temp_dir):
+        """Test that expired cache is not used."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create expired cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog_data = {"schema_version": "1.0", "extensions": {}}
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+
+        # Set cache time to 2 hours ago (expired)
+        expired_time = datetime.now(timezone.utc).timestamp() - 7200
+        expired_datetime = datetime.fromtimestamp(expired_time, tz=timezone.utc)
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": expired_datetime.isoformat(),
+                    "catalog_url": "http://test.com/catalog.json",
+                }
+            )
+        )
+
+        # Cache should be invalid
+        assert not catalog.is_cache_valid()
+
+    def test_search_all_extensions(self, temp_dir):
+        """Test searching all extensions without filters."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira integration",
+                    "author": "Stats Perform",
+                    "tags": ["issue-tracking", "jira"],
+                    "verified": True,
+                },
+                "linear": {
+                    "name": "Linear Integration",
+                    "id": "linear",
+                    "version": "0.9.0",
+                    "description": "Linear integration",
+                    "author": "Community",
+                    "tags": ["issue-tracking"],
+                    "verified": False,
+                },
+            },
+        }
+
+        # Save to cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search without filters
+        results = catalog.search()
+        assert len(results) == 2
+
+    def test_search_by_query(self, temp_dir):
+        """Test searching by query text."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira issue tracking",
+                    "tags": ["jira"],
+                },
+                "linear": {
+                    "name": "Linear Integration",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear project management",
+                    "tags": ["linear"],
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search for "jira"
+        results = catalog.search(query="jira")
+        assert len(results) == 1
+        assert results[0]["id"] == "jira"
+
+    def test_search_by_tag(self, temp_dir):
+        """Test searching by tag."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira",
+                    "tags": ["issue-tracking", "jira"],
+                },
+                "linear": {
+                    "name": "Linear",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear",
+                    "tags": ["issue-tracking", "linear"],
+                },
+                "github": {
+                    "name": "GitHub",
+                    "id": "github",
+                    "version": "1.0.0",
+                    "description": "GitHub",
+                    "tags": ["vcs", "github"],
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search by tag "issue-tracking"
+        results = catalog.search(tag="issue-tracking")
+        assert len(results) == 2
+        assert {r["id"] for r in results} == {"jira", "linear"}
+
+    def test_search_verified_only(self, temp_dir):
+        """Test searching verified extensions only."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira",
+                    "verified": True,
+                },
+                "linear": {
+                    "name": "Linear",
+                    "id": "linear",
+                    "version": "1.0.0",
+                    "description": "Linear",
+                    "verified": False,
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Search verified only
+        results = catalog.search(verified_only=True)
+        assert len(results) == 1
+        assert results[0]["id"] == "jira"
+
+    def test_get_extension_info(self, temp_dir):
+        """Test getting specific extension info."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create mock catalog
+        catalog_data = {
+            "schema_version": "1.0",
+            "extensions": {
+                "jira": {
+                    "name": "Jira Integration",
+                    "id": "jira",
+                    "version": "1.0.0",
+                    "description": "Jira integration",
+                    "author": "Stats Perform",
+                },
+            },
+        }
+
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text(json.dumps(catalog_data))
+        catalog.cache_metadata_file.write_text(
+            json.dumps(
+                {
+                    "cached_at": datetime.now(timezone.utc).isoformat(),
+                    "catalog_url": "http://test.com",
+                }
+            )
+        )
+
+        # Get extension info
+        info = catalog.get_extension_info("jira")
+        assert info is not None
+        assert info["id"] == "jira"
+        assert info["name"] == "Jira Integration"
+
+        # Non-existent extension
+        info = catalog.get_extension_info("nonexistent")
+        assert info is None
+
+    def test_clear_cache(self, temp_dir):
+        """Test clearing catalog cache."""
+        project_dir = temp_dir / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        catalog = ExtensionCatalog(project_dir)
+
+        # Create cache
+        catalog.cache_dir.mkdir(parents=True, exist_ok=True)
+        catalog.cache_file.write_text("{}")
+        catalog.cache_metadata_file.write_text("{}")
+
+        assert catalog.cache_file.exists()
+        assert catalog.cache_metadata_file.exists()
+
+        # Clear cache
+        catalog.clear_cache()
+
+        assert not catalog.cache_file.exists()
+        assert not catalog.cache_metadata_file.exists()