fix: update docs script to count all commands recursively

- Modified countCommands() to recursively scan subdirectories
- Updated updateCommandCatalog() to properly categorize commands
- Fixed command count from 14 to 22 (includes subdirectories)
- Regenerated COMMAND_CATALOG.md with proper categorization

🤖 Generated with [Claude Code](https://claude.ai/code)

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

Author: rmurphey

README.md

@@ -3,7 +3,7 @@
 **A living reference implementation of professional Claude Code commands and workflows**
 
 [![Version](https://img.shields.io/badge/version-2.0.0-blue)](https://github.com/rmurphey/claude-setup)
-[![Commands](https://img.shields.io/badge/commands-37-green)](.claude/commands/)
+[![Commands](https://img.shields.io/badge/commands-22-green)](.claude/commands/)
 [![License](https://img.shields.io/badge/license-MIT-purple)](LICENSE)
 [![Token Efficiency](https://img.shields.io/badge/token%20savings-87%25-orange)](docs/TOKEN_EFFICIENCY.md)
 
@@ -469,17 +469,17 @@ MIT License - see [LICENSE](LICENSE) file for details.
 - [🔴 test: add failing tests for learn.js functions (TDD RED)](../../commit/8b90d58)
 - [🔴 test: add failing tests for formatBytes and estimateTokens (TDD RED)](../../commit/1fdac58)
 - [🔴 test: add failing tests for findBrokenLinks (TDD RED phase)](../../commit/8ec6319)
-- [feat: add specification keyword recognition to tone agent](../../commit/ee8b0a1)
-- [feat: add tone agent invocation to /docs command](../../commit/914540a)
-- [feat: add documentation-tone agent for friendly docs](../../commit/5ee6ca4)
-- [feat: add TDD templates and README section](../../commit/5bd9acb)
-- [feat: add automatic commit example updates to docs (TDD)](../../commit/aa00002)
-- [fix: remove broken links from README to fix CI](../../commit/dec5953)
-- [fix: add package-lock.json to fix GitHub Actions npm cache error](../../commit/63283a3)
-- [🟢 fix: use process.cwd() instead of __dirname for paths (TDD GREEN)](../../commit/e2e81e6)
-- [docs: capture learnings from test watch simplification](../../commit/4668363)
-- [docs: improve documentation tone and specification keyword consistency](../../commit/9a0d86b)
-- [docs: add persuasive TDD guides for skeptics](../../commit/5dfc663)
+- [feat: remove 3 more complex maintenance commands](../../commit/993dd82)
+- [feat: remove all detailed command variants for token efficiency](../../commit/0e46070)
+- [feat: remove all recovery commands per quality audit](../../commit/50be84f)
+- [feat: add repo-quality-auditor agent for comprehensive quality analysis](../../commit/e498add)
+- [feat: implement test coverage using Node's built-in test runner](../../commit/fca9905)
+- [fix: remove duplicate /planning/reflect command](../../commit/d00bd7c)
+- [fix: add missing frontmatter to 5 commands](../../commit/73f0e62)
+- [fix: update COMMAND_CATALOG with all 37 commands and improve auditor](../../commit/6c3351a)
+- [docs: update COMMAND_CATALOG to reflect consolidation complete](../../commit/15815ad)
+- [docs: update COMMAND_CATALOG after recovery removal](../../commit/838bdcd)
+- [docs: tone down TDD cheerleading to be more realistic](../../commit/4466c42)
+- [refactor: remove edit-not-create command](../../commit/087df25)
 - [refactor: switch test watching from Vite to Node.js --watch](../../commit/09c904e)
 - [refactor: simplify tests to smoke tests only](../../commit/f84cac6)
-- [refactor: optimize docs command for token efficiency](../../commit/3ad4b0d)

docs/COMMAND_CATALOG.md

@@ -2,76 +2,46 @@
 
 Complete list of all available Claude Code commands organized by category.
 
-Last updated: 2025-08-16  
-Total Commands: 26
+Last updated: 2025-08-17  
+Total Commands: 22
 
-## Core Workflow Commands (6)
+## Core Workflow Commands (13)
+
+### /atomic-commit
+Enforce atomic commit discipline for 1-3 file changes  
+Location: `.claude/commands/atomic-commit.md`
 
 ### /commit
 Quality-checked commit workflow with automatic pre-commit validation  
 Location: `.claude/commands/commit.md`
 
-### /push
-Push commits to remote repository  
-Location: `.claude/commands/push.md`
-
-### /hygiene
-Project health check - code quality, tests, dependencies, and git status  
-Location: `.claude/commands/hygiene.md`
-
-### /todo
-Task management and tracking system with ACTIVE_WORK.md integration  
-Location: `.claude/commands/todo.md`
-
-### /monitor
-Monitor GitHub repository for test failures and pull requests  
-Location: `.claude/commands/monitor.md`
-
-### /tdd
-Your new best friend - TDD workflow that makes Claude amazing  
-Location: `.claude/commands/tdd.md`
-
-## Documentation Commands (3)
+### /context-manage
+Optimize Claude Code context window usage  
+Location: `.claude/commands/context-manage.md`
 
 ### /docs
 Documentation maintenance and validation  
 Location: `.claude/commands/docs.md`
 
+### /hygiene
+Project health check - code quality, tests, dependencies, and git status  
+Location: `.claude/commands/hygiene.md`
+
 ### /learn
 Capture insights and learnings from development work  
 Location: `.claude/commands/learn.md`
 
-### /update-docs
-Update README with current command count and descriptions  
-Location: `.claude/commands/maintenance/update-docs.md`
-
-## Planning Commands (6)
-
-### /design
-Feature planning and design documentation system  
-Location: `.claude/commands/planning/design.md`
-
-### /estimate
-Get intelligent Claude usage estimates for development tasks  
-Location: `.claude/commands/planning/estimate.md`
-
-### /idea
-Quick capture of ideas for future consideration  
-Location: `.claude/commands/planning/idea.md`
-
-### /ideation
-AI-powered development ideation and brainstorming  
-Location: `.claude/commands/planning/ideation.md`
-
-### /defer
-Task deferral and backlog management system  
-Location: `.claude/commands/planning/defer.md`
+### /monitor
+Monitor GitHub repository for test failures and pull requests  
+Location: `.claude/commands/monitor.md`
 
 ### /next
 Get AI-recommended next steps and development priorities  
 Location: `.claude/commands/next.md`
 
-## Reflection Commands (2)
+### /push
+Push commits to remote repository  
+Location: `.claude/commands/push.md`
 
 ### /reflect
 Pause and reflect on current work  
@@ -81,64 +51,60 @@ Location: `.claude/commands/reflect.md`
 Capture current session with metadata for future analysis  
 Location: `.claude/commands/retrospective.md`
 
-## Maintenance Commands (7)
+### /tdd
+Your new best friend - TDD workflow that makes Claude amazing  
+Location: `.claude/commands/tdd.md`
+
+### /todo
+Task management and tracking system with ACTIVE_WORK.md integration  
+Location: `.claude/commands/todo.md`
+
+## Maintenance Commands (4)
 
 ### /archive
-Archive old files and directories  
+Archive completed work and capture lessons learned  
 Location: `.claude/commands/maintenance/archive.md`
 
-### /issue
-Create and manage GitHub issues  
-Location: `.claude/commands/maintenance/issue.md`
-
 ### /maintainability
 Code maintainability analysis and improvement recommendations  
 Location: `.claude/commands/maintenance/maintainability.md`
 
 ### /session-history
-Manage and analyze session history  
+Save and manage Claude Code conversation transcripts for analysis  
 Location: `.claude/commands/maintenance/session-history.md`
 
-### /sync-issues
-Sync open GitHub issues into ACTIVE_WORK.md for unified task tracking  
-Location: `.claude/commands/maintenance/sync-issues.md`
+### /update-docs
+Update README with current command count and descriptions  
+Location: `.claude/commands/maintenance/update-docs.md`
+
+## Planning Commands (5)
 
-### /version-tag
-Version tagging and release management workflow  
-Location: `.claude/commands/maintenance/version-tag.md`
+### /defer
+Task deferral and backlog management system  
+Location: `.claude/commands/planning/defer.md`
 
-### /context-manage
-Optimize Claude Code context window usage  
-Location: `.claude/commands/context-manage.md`
+### /design
+Feature planning and design documentation system  
+Location: `.claude/commands/planning/design.md`
 
-## Special Purpose Commands (2)
+### /estimate
+Get intelligent Claude usage estimates for development tasks  
+Location: `.claude/commands/planning/estimate.md`
 
-### /atomic-commit
-Enforce atomic commit discipline for 1-3 file changes  
-Location: `.claude/commands/atomic-commit.md`
+### /idea
+Quick capture of ideas for future consideration  
+Location: `.claude/commands/planning/idea.md`
 
-### /edit-not-create
-Smart file decision process - prefer editing existing files over creating new ones  
-Location: `.claude/commands/edit-not-create.md`
+### /ideation
+AI-powered development ideation and brainstorming based on code analysis  
+Location: `.claude/commands/planning/ideation.md`
 
 ---
 
 ## Command Categories Summary
 
 | Category | Count | Purpose |
 |----------|-------|---------|
-| Core Workflow | 6 | Daily development tasks |
-| Documentation | 3 | Docs and learning capture |
-| Planning | 6 | Planning and ideation |
-| Reflection | 2 | Session analysis |
-| Maintenance | 7 | Repository maintenance |
-| Special Purpose | 2 | Specific workflows |
-
-## Notes
-
-- **Completed Consolidation**: Reduced from 37 to 26 commands
-- Removed: 4 recovery commands (overly complex)
-- Removed: 6 detailed variants (saved 1919 lines!)
-- Removed: 1 duplicate reflect command
-- **Token Efficiency**: Commands now delegate to npm scripts
-- Some large commands remain (issue, version-tag, design) for future simplification
+| Core Workflow | 13 | Daily development tasks |
+| Maintenance | 4 | Repository maintenance |
+| Planning | 5 | Planning and ideation |

scripts/docs.js

@@ -14,8 +14,23 @@ const command = process.argv[2] || 'all';
 function countCommands() {
   try {
     const commandsDir = path.join(process.cwd(), '.claude', 'commands');
-    const files = fs.readdirSync(commandsDir).filter(f => f.endsWith('.md'));
-    return files.length;
+    let count = 0;
+    
+    function countInDir(dir) {
+      const items = fs.readdirSync(dir);
+      for (const item of items) {
+        const fullPath = path.join(dir, item);
+        const stat = fs.statSync(fullPath);
+        if (stat.isDirectory()) {
+          countInDir(fullPath);
+        } else if (item.endsWith('.md') && item !== 'README.md') {
+          count++;
+        }
+      }
+    }
+    
+    countInDir(commandsDir);
+    return count;
   } catch {
     return 0;
   }
@@ -152,37 +167,80 @@ function updateCommandCatalog() {
 
   const catalogPath = path.join(process.cwd(), 'docs', 'COMMAND_CATALOG.md');
   const commandsDir = path.join(process.cwd(), '.claude', 'commands');
-  const files = fs.readdirSync(commandsDir).filter(f => f.endsWith('.md'));
+  
+  // Recursively find all command files
+  const commands = [];
+  
+  function scanDir(dir, prefix = '') {
+    const items = fs.readdirSync(dir);
+    for (const item of items) {
+      const fullPath = path.join(dir, item);
+      const stat = fs.statSync(fullPath);
+      if (stat.isDirectory()) {
+        scanDir(fullPath, prefix ? `${prefix}/${item}` : item);
+      } else if (item.endsWith('.md') && item !== 'README.md') {
+        const content = fs.readFileSync(fullPath, 'utf8');
+        const descMatch = content.match(/^description:\s*(.+)$/m);
+        const name = item.replace('.md', '');
+        const desc = descMatch ? descMatch[1] : 'No description';
+        const location = prefix ? `${prefix}/${name}` : name;
+        commands.push({ 
+          name, 
+          desc, 
+          location,
+          category: prefix || 'Core'
+        });
+      }
+    }
+  }
+  
+  scanDir(commandsDir);
+  
+  // Group by category
+  const categories = {};
+  commands.forEach(cmd => {
+    if (!categories[cmd.category]) {
+      categories[cmd.category] = [];
+    }
+    categories[cmd.category].push(cmd);
+  });
+  
+  // Sort categories and commands
+  const categoryOrder = ['Core', 'maintenance', 'planning'];
+  const sortedCategories = categoryOrder.filter(cat => categories[cat]);
+  
+  // Format categories nicely
+  const categoryNames = {
+    'Core': 'Core Workflow Commands',
+    'maintenance': 'Maintenance Commands',
+    'planning': 'Planning Commands'
+  };
 
   let catalogContent = `# Command Catalog
 
-Complete list of available Claude Code commands.
+Complete list of all available Claude Code commands organized by category.
 
-Last updated: ${new Date().toISOString().split('T')[0]}
-
-## Available Commands
+Last updated: ${new Date().toISOString().split('T')[0]}  
+Total Commands: ${commands.length}
 
 `;
 
-  // Group commands by category (could be enhanced)
-  const commands = [];
-  for (const file of files) {
-    const content = fs.readFileSync(path.join(commandsDir, file), 'utf8');
-    const descMatch = content.match(/^description:\s*(.+)$/m);
-    const name = file.replace('.md', '');
-    const desc = descMatch ? descMatch[1] : 'No description';
-    commands.push({ name, desc });
+  for (const cat of sortedCategories) {
+    const cmds = categories[cat];
+    catalogContent += `## ${categoryNames[cat] || cat} (${cmds.length})\n\n`;
+    cmds.sort((a, b) => a.name.localeCompare(b.name));
+    cmds.forEach(cmd => {
+      catalogContent += `### /${cmd.name}\n${cmd.desc}  \nLocation: \`.claude/commands/${cmd.location}.md\`\n\n`;
+    });
   }
 
-  // Sort alphabetically
-  commands.sort((a, b) => a.name.localeCompare(b.name));
-  
-  // Add to catalog
-  commands.forEach(cmd => {
-    catalogContent += `### /${cmd.name}\n\n${cmd.desc}\n\nLocation: \`.claude/commands/${cmd.name}.md\`\n\n---\n\n`;
-  });
-  
-  catalogContent += `\n## Total Commands: ${commands.length}\n`;
+  // Add summary table
+  catalogContent += `---\n\n## Command Categories Summary\n\n`;
+  catalogContent += `| Category | Count | Purpose |\n`;
+  catalogContent += `|----------|-------|---------|\n`;
+  catalogContent += `| Core Workflow | ${categories['Core']?.length || 0} | Daily development tasks |\n`;
+  catalogContent += `| Maintenance | ${categories['maintenance']?.length || 0} | Repository maintenance |\n`;
+  catalogContent += `| Planning | ${categories['planning']?.length || 0} | Planning and ideation |\n`;
 
   // Write catalog file
   fs.writeFileSync(catalogPath, catalogContent);