@weavelogic/knowledge-graph-agent 0.10.0 → 0.10.1

package/README.md

@@ -10,8 +10,9 @@ A powerful NPM library for creating and managing knowledge graphs for Claude Cod
 | Category | Features |
 |----------|----------|
 | **Core** | Knowledge graph generation, Obsidian integration, CLAUDE.md management |
-| **Cultivation** | Codebase analysis, seed generation, deep analysis with claude-flow |
+| **Cultivation** | Codebase analysis, seed generation, deep analysis with claude-flow, doc cultivation |
 | **Agents** | Multi-agent system, rules engine, workflows, MCP server with 30+ tools |
+| **Claude Hooks** | Capture all interactions, hierarchical storage, sub-agent tracking, swarm tracking |
 | **Services** | Service management, config migrations, health monitoring |
 | **Enterprise** | Chunking, backup/recovery, advanced caching, diagnostics |
 | **Integrations** | Workflow DevKit, RuVector semantic search, Exochain audit trail |
@@ -431,6 +432,110 @@ npx @weavelogic/knowledge-graph-agent mcp start
 
 ---
 
+## Claude Code Hooks
+
+Capture all Claude Code interactions and store them in a hierarchical knowledge graph structure.
+
+### Installation
+
+```bash
+# Install hooks to capture all interactions
+kg hooks install
+
+# Check hooks status
+kg hooks status
+
+# View captured sessions
+kg hooks sessions
+```
+
+### Features
+
+- **Hierarchical Storage**: Sessions → Conversations → Messages → Tool Calls
+- **Sub-Agent Tracking**: Automatically tracks Task tool spawns
+- **Swarm Tracking**: Captures claude-flow swarm operations
+- **Markdown Generation**: Creates documentation for all interactions
+- **Tool Output Separation**: Stores tool outputs in dedicated files
+
+### Hook Events Captured
+
+| Event | Description |
+|-------|-------------|
+| `UserPromptSubmit` | All user prompts |
+| `PreToolUse` | Tool invocations with inputs |
+| `PostToolUse` | Tool results and outputs |
+| `Stop` | Session completion |
+| `PreCompact` | Before context compaction |
+
+### Storage Structure
+
+```
+.kg/claude/
+├── sessions/           # JSON session data
+├── agents/            # Sub-agent tracking
+├── tool-outputs/      # Separated tool outputs
+├── docs/
+│   ├── sessions/      # Session markdown docs
+│   ├── conversations/ # Conversation logs
+│   └── agents/        # Sub-agent markdown docs
+```
+
+### Programmatic Usage
+
+```typescript
+import { HookCaptureSystem, generateHookConfig } from '@weavelogic/knowledge-graph-agent';
+
+// Create capture system
+const capture = new HookCaptureSystem('/project', {
+  createMarkdown: true,
+  separateToolOutputs: true,
+  captureSubAgents: true,
+  captureSwarms: true,
+});
+
+// Start a session
+const session = capture.startSession('Development Session', 'Feature implementation');
+
+// Handle hook events
+capture.handleHookEvent({
+  event: 'UserPromptSubmit',
+  timestamp: new Date().toISOString(),
+  userPrompt: 'Help me implement...',
+});
+
+// End session
+const completedSession = capture.endSession();
+```
+
+---
+
+## Document Cultivation
+
+Automatically build out comprehensive documentation using claude-flow swarm orchestration.
+
+### Usage
+
+```bash
+# Cultivate documentation with swarm agents
+kg cultivate --path /project
+
+# Include SOP compliance analysis
+kg cultivate --include-sops
+
+# Dry run to preview
+kg cultivate --dry-run
+```
+
+### Features
+
+- **7-Phase Cultivation Process**: Structure analysis through completion
+- **Development Planning**: Generates phased development plans
+- **Infrastructure Planning**: Creates dev/staging/production infrastructure plans
+- **SOP Compliance**: Integrates AI-SDLC SOP analysis
+- **Swarm Orchestration**: Uses claude-flow for parallel documentation generation
+
+---
+
 ## Enterprise Features
 
 ### Chunker for Large Documents
@@ -592,13 +697,25 @@ const execution = await workflow.start('document-analysis', {
 | `kg dashboard serve` | Serve production build |
 | `kg dashboard status` | Check dashboard status |
 
-### Documentation
+### Documentation & Cultivation
 
 | Command | Description |
 |---------|-------------|
 | `kg docs init` | Initialize docs directory |
 | `kg analyze` | Analyze & migrate to knowledge graph |
 | `kg convert docs` | Convert docs/ to docs-nn/ |
+| `kg cultivate` | Cultivate docs using swarm orchestration |
+| `kg cultivate --include-sops` | Include SOP compliance analysis |
+
+### Claude Code Hooks
+
+| Command | Description |
+|---------|-------------|
+| `kg hooks install` | Install hooks to capture interactions |
+| `kg hooks uninstall` | Remove hooks configuration |
+| `kg hooks status` | Show hooks status |
+| `kg hooks sessions` | List captured sessions |
+| `kg hooks export` | Export captured sessions |
 
 ### Configuration
 
@@ -724,6 +841,53 @@ import {
 
 ## Changelog
 
+### v0.10.1
+
+**Default Directory Fix:**
+- Changed default target directory from `docs-nn` to `docs`
+- `kg analyze`, `kg convert docs`, and related commands now output to `docs/` by default
+- Use `--target docs-nn` if you specifically need the old behavior
+- Updated help text and documentation to reflect the change
+
+### v0.10.0
+
+**Claude Code Hooks System:**
+- **Hook Capture System** - Capture all Claude interactions (prompts, responses, tool calls)
+- **Hierarchical Storage** - Sessions → Conversations → Messages → Tool Calls
+- **Sub-Agent Tracking** - Automatically tracks Task tool spawns with full context
+- **Swarm Tracking** - Captures claude-flow swarm operations
+- **Markdown Generation** - Creates documentation for sessions, conversations, agents
+- **Tool Output Separation** - Stores tool outputs in dedicated JSON files
+- **CLI Commands** - `kg hooks install/uninstall/status/sessions/export`
+- Comprehensive type definitions with Zod validation
+- 22 new tests for hook system
+
+### v0.9.0
+
+**Document Cultivation System:**
+- **Doc Cultivation Command** - `kg cultivate` for automated documentation buildout
+- **7-Phase Cultivation Process** - Structure → Content → Architecture → Development → Infrastructure → Review → Completion
+- **Development Planning** - Generates phased development plans with tasks
+- **Infrastructure Planning** - Creates dev/staging/production infrastructure plans
+- **SOP Compliance Analysis** - Integrates AI-SDLC SOP requirements
+- **Swarm Orchestration** - Uses claude-flow for parallel documentation generation
+- Support for multi-service projects (api, backend, frontend, admin)
+
+### v0.8.8
+
+- Added `src/{service}/docs` directory scanning and copying for doc generation
+- Enhanced service documentation detection
+
+### v0.8.7
+
+- Improved Python project detection for doc generation
+- Better handling of `requirements.txt` and `pyproject.toml`
+
+### v0.8.6
+
+- Fixed vault-sync.test.ts timeout issues
+- Improved test stability
+
 ### v0.7.4
 
 - Fixed repository URL in package.json to match actual GitHub repo name

package/dist/_virtual/index10.js

@@ -1,5 +1,5 @@
-var dist = {};
+var lib = {};
 export {
-  dist as __exports
+  lib as __exports
 };
 //# sourceMappingURL=index10.js.map

package/dist/_virtual/index11.js

@@ -1,5 +1,5 @@
-var lib = {};
+var dist = {};
 export {
-  lib as __exports
+  dist as __exports
 };
 //# sourceMappingURL=index11.js.map

package/dist/_virtual/index8.js

@@ -1,5 +1,5 @@
-var dist = {};
+var commonjs = {};
 export {
-  dist as __exports
+  commonjs as __exports
 };
 //# sourceMappingURL=index8.js.map

package/dist/_virtual/index9.js

@@ -1,5 +1,5 @@
-var commonjs = {};
+var dist = {};
 export {
-  commonjs as __exports
+  dist as __exports
 };
 //# sourceMappingURL=index9.js.map

package/dist/cli/commands/analyze.js

@@ -7,7 +7,7 @@ import { analyzeDocs } from "../../generators/docs-analyzer.js";
 import { validateProjectRoot } from "../../core/security.js";
 function createAnalyzeCommand() {
   const command = new Command("analyze");
-  command.description("Analyze and migrate docs to knowledge graph structure").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs-nn").option("--use-claude-flow", "Use claude-flow for deep analysis").option("--no-moc", "Skip MOC (Map of Content) generation").option("--no-link-original", "Do not link back to original docs").option("--max-depth <n>", "Maximum analysis depth", "3").option("--dry-run", "Show what would be done without making changes").option("-v, --verbose", "Verbose output").action(async (options) => {
+  command.description("Analyze and migrate docs to knowledge graph structure").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs").option("--use-claude-flow", "Use claude-flow for deep analysis").option("--no-moc", "Skip MOC (Map of Content) generation").option("--no-link-original", "Do not link back to original docs").option("--max-depth <n>", "Maximum analysis depth", "3").option("--dry-run", "Show what would be done without making changes").option("-v, --verbose", "Verbose output").action(async (options) => {
     const spinner = ora("Analyzing documentation...").start();
     try {
       const projectRoot = validateProjectRoot(options.path);
@@ -119,7 +119,7 @@ function createAnalyzeCommand() {
       process.exit(1);
     }
   });
-  command.command("deep").description("Deep analysis using claude-flow agents for comprehensive knowledge extraction").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs-nn").option("--agents <n>", "Number of parallel agents", "3").action(async (options) => {
+  command.command("deep").description("Deep analysis using claude-flow agents for comprehensive knowledge extraction").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs").option("--agents <n>", "Number of parallel agents", "3").action(async (options) => {
     const spinner = ora("Initializing deep analysis with claude-flow...").start();
     try {
       const projectRoot = validateProjectRoot(options.path);
@@ -184,7 +184,7 @@ function createAnalyzeCommand() {
       }
       const result = await analyzeDocs({
         sourceDir,
-        targetDir: "docs-nn",
+        targetDir: "docs",
         projectRoot,
         useClaudeFlow: false,
         createMOC: false,

package/dist/cli/commands/analyze.js.map

@@ -1 +1 @@
-{"version":3,"file":"analyze.js","sources":["../../../src/cli/commands/analyze.ts"],"sourcesContent":["/**\n * Analyze Command\n *\n * Advanced documentation analyzer using claude-flow for deep analysis\n * and creating proper knowledge graph documentation structure.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport ora from 'ora';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { analyzeDocs } from '../../generators/docs-analyzer.js';\nimport { validateProjectRoot } from '../../core/security.js';\n\n/**\n * Create analyze command\n */\nexport function createAnalyzeCommand(): Command {\n  const command = new Command('analyze');\n\n  command\n    .description('Analyze and migrate docs to knowledge graph structure')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('-t, --target <dir>', 'Target directory', 'docs-nn')\n    .option('--use-claude-flow', 'Use claude-flow for deep analysis')\n    .option('--no-moc', 'Skip MOC (Map of Content) generation')\n    .option('--no-link-original', 'Do not link back to original docs')\n    .option('--max-depth <n>', 'Maximum analysis depth', '3')\n    .option('--dry-run', 'Show what would be done without making changes')\n    .option('-v, --verbose', 'Verbose output')\n    .action(async (options) => {\n      const spinner = ora('Analyzing documentation...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n        const targetDir = options.target;\n\n        // Check source exists\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          console.log(chalk.gray('  Specify source with --source <dir>'));\n          process.exit(1);\n        }\n\n        // Check if target already exists\n        if (existsSync(join(projectRoot, targetDir)) && !options.dryRun) {\n          spinner.warn(`Target directory exists: ${targetDir}`);\n          console.log(chalk.yellow('  Files may be overwritten. Use --dry-run to preview.'));\n        }\n\n        if (options.dryRun) {\n          spinner.text = 'Analyzing documentation (dry run)...';\n        }\n\n        if (options.useClaudeFlow) {\n          spinner.text = 'Analyzing with claude-flow (deep analysis)...';\n        }\n\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir,\n          projectRoot,\n          useClaudeFlow: options.useClaudeFlow,\n          createMOC: options.moc !== false,\n          linkOriginal: options.linkOriginal !== false,\n          maxDepth: parseInt(options.maxDepth, 10),\n          dryRun: options.dryRun,\n          verbose: options.verbose,\n        });\n\n        if (result.success) {\n          if (options.dryRun) {\n            spinner.succeed('Dry run complete!');\n          } else {\n            spinner.succeed('Documentation analyzed and migrated!');\n          }\n        } else {\n          spinner.warn('Analysis completed with errors');\n        }\n\n        // Display results\n        console.log();\n        console.log(chalk.cyan.bold('  Analysis Results'));\n        console.log(chalk.gray('  ─────────────────────────────────────'));\n        console.log();\n        console.log(chalk.white('  Summary:'));\n        console.log(chalk.gray(`    Source:          ${sourceDir}/`));\n        console.log(chalk.gray(`    Target:          ${targetDir}/`));\n        console.log(chalk.green(`    Files analyzed:  ${result.filesAnalyzed}`));\n        console.log(chalk.green(`    Files created:   ${result.filesCreated}`));\n        console.log(chalk.blue(`    MOC files:       ${result.mocFilesCreated}`));\n\n        // Category breakdown\n        if (result.structure.size > 0) {\n          console.log();\n          console.log(chalk.white('  Categories:'));\n          for (const [category, docs] of result.structure) {\n            console.log(chalk.cyan(`    ${category.padEnd(15)}`), chalk.gray(`${docs.length} docs`));\n          }\n        }\n\n        // Show sample analyzed documents\n        if (result.analyzed.length > 0 && options.verbose) {\n          console.log();\n          console.log(chalk.white('  Sample documents:'));\n          result.analyzed.slice(0, 5).forEach(doc => {\n            console.log(chalk.gray(`    ${doc.originalPath}`));\n            console.log(chalk.cyan(`      → ${doc.newPath}`) + chalk.gray(` [${doc.type}]`));\n            if (doc.tags.length > 0) {\n              console.log(chalk.gray(`        tags: ${doc.tags.slice(0, 5).map(t => `#${t}`).join(' ')}`));\n            }\n          });\n          if (result.analyzed.length > 5) {\n            console.log(chalk.gray(`    ... and ${result.analyzed.length - 5} more`));\n          }\n        }\n\n        // Show errors\n        if (result.errors.length > 0) {\n          console.log();\n          console.log(chalk.red('  Errors:'));\n          result.errors.slice(0, 5).forEach(err => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n          if (result.errors.length > 5) {\n            console.log(chalk.gray(`    ... and ${result.errors.length - 5} more`));\n          }\n        }\n\n        // Research needed summary\n        const researchDocs = result.analyzed.filter(d => d.researchNeeded.length > 0);\n        const todoDocs = result.analyzed.filter(d => d.todos.length > 0);\n\n        if (researchDocs.length > 0 || todoDocs.length > 0) {\n          console.log();\n          console.log(chalk.yellow('  Attention Needed:'));\n          if (researchDocs.length > 0) {\n            console.log(chalk.yellow(`    📚 ${researchDocs.length} docs need research`));\n          }\n          if (todoDocs.length > 0) {\n            console.log(chalk.yellow(`    ✏️  ${todoDocs.length} docs have TODOs`));\n          }\n        }\n\n        // Next steps\n        if (!options.dryRun && result.filesCreated > 0) {\n          console.log();\n          console.log(chalk.cyan('  Next steps:'));\n          console.log(chalk.white(`    1. Review ${targetDir}/MOC.md (Master Index)`));\n          console.log(chalk.white(`    2. Check ${targetDir}/PRIMITIVES.md`));\n          console.log(chalk.white(`    3. Run: kg graph --docs ${targetDir}`));\n          console.log(chalk.white(`    4. Run: kg stats --docs ${targetDir}`));\n          if (researchDocs.length > 0) {\n            console.log(chalk.white(`    5. Address research items in flagged docs`));\n          }\n        }\n\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Analysis failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Deep analyze subcommand (uses claude-flow agents)\n  command\n    .command('deep')\n    .description('Deep analysis using claude-flow agents for comprehensive knowledge extraction')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('-t, --target <dir>', 'Target directory', 'docs-nn')\n    .option('--agents <n>', 'Number of parallel agents', '3')\n    .action(async (options) => {\n      const spinner = ora('Initializing deep analysis with claude-flow...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n        const targetDir = options.target;\n\n        // Check source exists\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          process.exit(1);\n        }\n\n        spinner.text = 'Running claude-flow deep analysis...';\n\n        // Run deep analysis with claude-flow\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir,\n          projectRoot,\n          useClaudeFlow: true,\n          createMOC: true,\n          linkOriginal: true,\n          maxDepth: 5,\n          dryRun: false,\n          verbose: true,\n        });\n\n        if (result.success) {\n          spinner.succeed('Deep analysis complete!');\n        } else {\n          spinner.warn('Deep analysis completed with some errors');\n        }\n\n        console.log();\n        console.log(chalk.cyan.bold('  Deep Analysis Results'));\n        console.log(chalk.gray('  ─────────────────────────────────────'));\n        console.log(chalk.green(`    Documents analyzed:  ${result.filesAnalyzed}`));\n        console.log(chalk.green(`    Knowledge docs:      ${result.filesCreated}`));\n        console.log(chalk.blue(`    Index files (MOC):   ${result.mocFilesCreated}`));\n        console.log(chalk.gray(`    Categories:          ${result.structure.size}`));\n\n        // Research summary\n        const totalResearch = result.analyzed.reduce((sum, d) => sum + d.researchNeeded.length, 0);\n        const totalTodos = result.analyzed.reduce((sum, d) => sum + d.todos.length, 0);\n\n        console.log();\n        console.log(chalk.white('  Knowledge extraction:'));\n        console.log(chalk.cyan(`    Research areas:  ${totalResearch}`));\n        console.log(chalk.cyan(`    TODOs found:     ${totalTodos}`));\n        console.log(chalk.cyan(`    Concepts:        ${result.analyzed.reduce((sum, d) => sum + d.concepts.length, 0)}`));\n        console.log(chalk.cyan(`    Cross-refs:      ${result.analyzed.reduce((sum, d) => sum + d.related.length, 0)}`));\n\n        console.log();\n        console.log(chalk.white(`  Output: ${targetDir}/`));\n        console.log(chalk.gray(`    MOC.md           Master index`));\n        console.log(chalk.gray(`    PRIMITIVES.md    Core building blocks`));\n        console.log(chalk.gray(`    */\\_MOC.md        Category indexes`));\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Deep analysis failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Report subcommand\n  command\n    .command('report')\n    .description('Generate analysis report without creating files')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('--json', 'Output as JSON')\n    .action(async (options) => {\n      const spinner = ora('Generating analysis report...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          process.exit(1);\n        }\n\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir: 'docs-nn',\n          projectRoot,\n          useClaudeFlow: false,\n          createMOC: false,\n          linkOriginal: false,\n          dryRun: true,\n          verbose: false,\n        });\n\n        spinner.succeed('Report generated!');\n\n        if (options.json) {\n          // JSON output\n          const report = {\n            summary: {\n              totalDocs: result.filesAnalyzed,\n              categories: Object.fromEntries(result.structure),\n            },\n            documents: result.analyzed.map(d => ({\n              original: d.originalPath,\n              target: d.newPath,\n              type: d.type,\n              category: d.category,\n              tags: d.tags,\n              concepts: d.concepts,\n              researchNeeded: d.researchNeeded,\n              todos: d.todos,\n            })),\n            researchAreas: result.analyzed\n              .flatMap(d => d.researchNeeded.map(r => ({ doc: d.title, area: r }))),\n            todos: result.analyzed\n              .flatMap(d => d.todos.map(t => ({ doc: d.title, todo: t }))),\n          };\n          console.log(JSON.stringify(report, null, 2));\n        } else {\n          // Human-readable output\n          console.log();\n          console.log(chalk.cyan.bold('  Documentation Analysis Report'));\n          console.log(chalk.gray('  ─────────────────────────────────────'));\n          console.log();\n          console.log(chalk.white(`  Total documents: ${result.filesAnalyzed}`));\n          console.log();\n\n          // Type breakdown\n          const byType = new Map<string, number>();\n          result.analyzed.forEach(d => {\n            byType.set(d.type, (byType.get(d.type) || 0) + 1);\n          });\n\n          console.log(chalk.white('  By Type:'));\n          for (const [type, count] of byType) {\n            const bar = '█'.repeat(Math.ceil(count / result.filesAnalyzed * 20));\n            console.log(chalk.cyan(`    ${type.padEnd(12)} ${bar} ${count}`));\n          }\n          console.log();\n\n          // Category breakdown\n          console.log(chalk.white('  By Category:'));\n          for (const [category, docs] of result.structure) {\n            const bar = '█'.repeat(Math.ceil(docs.length / result.filesAnalyzed * 20));\n            console.log(chalk.cyan(`    ${category.padEnd(12)} ${bar} ${docs.length}`));\n          }\n          console.log();\n\n          // Issues\n          const withResearch = result.analyzed.filter(d => d.researchNeeded.length > 0);\n          const withTodos = result.analyzed.filter(d => d.todos.length > 0);\n\n          console.log(chalk.white('  Areas Needing Attention:'));\n          console.log(chalk.yellow(`    📚 Research needed:   ${withResearch.length} docs`));\n          console.log(chalk.yellow(`    ✏️  With TODOs:        ${withTodos.length} docs`));\n          console.log();\n\n          // Top research areas\n          if (withResearch.length > 0) {\n            console.log(chalk.white('  Top Research Areas:'));\n            withResearch.slice(0, 5).forEach(d => {\n              console.log(chalk.gray(`    ${d.title}:`));\n              d.researchNeeded.slice(0, 2).forEach(r => {\n                console.log(chalk.yellow(`      - ${r.slice(0, 60)}...`));\n              });\n            });\n            console.log();\n          }\n\n          console.log(chalk.cyan('  Run `kg analyze` to migrate documentation'));\n          console.log();\n        }\n\n      } catch (error) {\n        spinner.fail('Report generation failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  return 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+{"version":3,"file":"analyze.js","sources":["../../../src/cli/commands/analyze.ts"],"sourcesContent":["/**\n * Analyze Command\n *\n * Advanced documentation analyzer using claude-flow for deep analysis\n * and creating proper knowledge graph documentation structure.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport ora from 'ora';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { analyzeDocs } from '../../generators/docs-analyzer.js';\nimport { validateProjectRoot } from '../../core/security.js';\n\n/**\n * Create analyze command\n */\nexport function createAnalyzeCommand(): Command {\n  const command = new Command('analyze');\n\n  command\n    .description('Analyze and migrate docs to knowledge graph structure')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('-t, --target <dir>', 'Target directory', 'docs')\n    .option('--use-claude-flow', 'Use claude-flow for deep analysis')\n    .option('--no-moc', 'Skip MOC (Map of Content) generation')\n    .option('--no-link-original', 'Do not link back to original docs')\n    .option('--max-depth <n>', 'Maximum analysis depth', '3')\n    .option('--dry-run', 'Show what would be done without making changes')\n    .option('-v, --verbose', 'Verbose output')\n    .action(async (options) => {\n      const spinner = ora('Analyzing documentation...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n        const targetDir = options.target;\n\n        // Check source exists\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          console.log(chalk.gray('  Specify source with --source <dir>'));\n          process.exit(1);\n        }\n\n        // Check if target already exists\n        if (existsSync(join(projectRoot, targetDir)) && !options.dryRun) {\n          spinner.warn(`Target directory exists: ${targetDir}`);\n          console.log(chalk.yellow('  Files may be overwritten. Use --dry-run to preview.'));\n        }\n\n        if (options.dryRun) {\n          spinner.text = 'Analyzing documentation (dry run)...';\n        }\n\n        if (options.useClaudeFlow) {\n          spinner.text = 'Analyzing with claude-flow (deep analysis)...';\n        }\n\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir,\n          projectRoot,\n          useClaudeFlow: options.useClaudeFlow,\n          createMOC: options.moc !== false,\n          linkOriginal: options.linkOriginal !== false,\n          maxDepth: parseInt(options.maxDepth, 10),\n          dryRun: options.dryRun,\n          verbose: options.verbose,\n        });\n\n        if (result.success) {\n          if (options.dryRun) {\n            spinner.succeed('Dry run complete!');\n          } else {\n            spinner.succeed('Documentation analyzed and migrated!');\n          }\n        } else {\n          spinner.warn('Analysis completed with errors');\n        }\n\n        // Display results\n        console.log();\n        console.log(chalk.cyan.bold('  Analysis Results'));\n        console.log(chalk.gray('  ─────────────────────────────────────'));\n        console.log();\n        console.log(chalk.white('  Summary:'));\n        console.log(chalk.gray(`    Source:          ${sourceDir}/`));\n        console.log(chalk.gray(`    Target:          ${targetDir}/`));\n        console.log(chalk.green(`    Files analyzed:  ${result.filesAnalyzed}`));\n        console.log(chalk.green(`    Files created:   ${result.filesCreated}`));\n        console.log(chalk.blue(`    MOC files:       ${result.mocFilesCreated}`));\n\n        // Category breakdown\n        if (result.structure.size > 0) {\n          console.log();\n          console.log(chalk.white('  Categories:'));\n          for (const [category, docs] of result.structure) {\n            console.log(chalk.cyan(`    ${category.padEnd(15)}`), chalk.gray(`${docs.length} docs`));\n          }\n        }\n\n        // Show sample analyzed documents\n        if (result.analyzed.length > 0 && options.verbose) {\n          console.log();\n          console.log(chalk.white('  Sample documents:'));\n          result.analyzed.slice(0, 5).forEach(doc => {\n            console.log(chalk.gray(`    ${doc.originalPath}`));\n            console.log(chalk.cyan(`      → ${doc.newPath}`) + chalk.gray(` [${doc.type}]`));\n            if (doc.tags.length > 0) {\n              console.log(chalk.gray(`        tags: ${doc.tags.slice(0, 5).map(t => `#${t}`).join(' ')}`));\n            }\n          });\n          if (result.analyzed.length > 5) {\n            console.log(chalk.gray(`    ... and ${result.analyzed.length - 5} more`));\n          }\n        }\n\n        // Show errors\n        if (result.errors.length > 0) {\n          console.log();\n          console.log(chalk.red('  Errors:'));\n          result.errors.slice(0, 5).forEach(err => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n          if (result.errors.length > 5) {\n            console.log(chalk.gray(`    ... and ${result.errors.length - 5} more`));\n          }\n        }\n\n        // Research needed summary\n        const researchDocs = result.analyzed.filter(d => d.researchNeeded.length > 0);\n        const todoDocs = result.analyzed.filter(d => d.todos.length > 0);\n\n        if (researchDocs.length > 0 || todoDocs.length > 0) {\n          console.log();\n          console.log(chalk.yellow('  Attention Needed:'));\n          if (researchDocs.length > 0) {\n            console.log(chalk.yellow(`    📚 ${researchDocs.length} docs need research`));\n          }\n          if (todoDocs.length > 0) {\n            console.log(chalk.yellow(`    ✏️  ${todoDocs.length} docs have TODOs`));\n          }\n        }\n\n        // Next steps\n        if (!options.dryRun && result.filesCreated > 0) {\n          console.log();\n          console.log(chalk.cyan('  Next steps:'));\n          console.log(chalk.white(`    1. Review ${targetDir}/MOC.md (Master Index)`));\n          console.log(chalk.white(`    2. Check ${targetDir}/PRIMITIVES.md`));\n          console.log(chalk.white(`    3. Run: kg graph --docs ${targetDir}`));\n          console.log(chalk.white(`    4. Run: kg stats --docs ${targetDir}`));\n          if (researchDocs.length > 0) {\n            console.log(chalk.white(`    5. Address research items in flagged docs`));\n          }\n        }\n\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Analysis failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Deep analyze subcommand (uses claude-flow agents)\n  command\n    .command('deep')\n    .description('Deep analysis using claude-flow agents for comprehensive knowledge extraction')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('-t, --target <dir>', 'Target directory', 'docs')\n    .option('--agents <n>', 'Number of parallel agents', '3')\n    .action(async (options) => {\n      const spinner = ora('Initializing deep analysis with claude-flow...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n        const targetDir = options.target;\n\n        // Check source exists\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          process.exit(1);\n        }\n\n        spinner.text = 'Running claude-flow deep analysis...';\n\n        // Run deep analysis with claude-flow\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir,\n          projectRoot,\n          useClaudeFlow: true,\n          createMOC: true,\n          linkOriginal: true,\n          maxDepth: 5,\n          dryRun: false,\n          verbose: true,\n        });\n\n        if (result.success) {\n          spinner.succeed('Deep analysis complete!');\n        } else {\n          spinner.warn('Deep analysis completed with some errors');\n        }\n\n        console.log();\n        console.log(chalk.cyan.bold('  Deep Analysis Results'));\n        console.log(chalk.gray('  ─────────────────────────────────────'));\n        console.log(chalk.green(`    Documents analyzed:  ${result.filesAnalyzed}`));\n        console.log(chalk.green(`    Knowledge docs:      ${result.filesCreated}`));\n        console.log(chalk.blue(`    Index files (MOC):   ${result.mocFilesCreated}`));\n        console.log(chalk.gray(`    Categories:          ${result.structure.size}`));\n\n        // Research summary\n        const totalResearch = result.analyzed.reduce((sum, d) => sum + d.researchNeeded.length, 0);\n        const totalTodos = result.analyzed.reduce((sum, d) => sum + d.todos.length, 0);\n\n        console.log();\n        console.log(chalk.white('  Knowledge extraction:'));\n        console.log(chalk.cyan(`    Research areas:  ${totalResearch}`));\n        console.log(chalk.cyan(`    TODOs found:     ${totalTodos}`));\n        console.log(chalk.cyan(`    Concepts:        ${result.analyzed.reduce((sum, d) => sum + d.concepts.length, 0)}`));\n        console.log(chalk.cyan(`    Cross-refs:      ${result.analyzed.reduce((sum, d) => sum + d.related.length, 0)}`));\n\n        console.log();\n        console.log(chalk.white(`  Output: ${targetDir}/`));\n        console.log(chalk.gray(`    MOC.md           Master index`));\n        console.log(chalk.gray(`    PRIMITIVES.md    Core building blocks`));\n        console.log(chalk.gray(`    */\\_MOC.md        Category indexes`));\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Deep analysis failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Report subcommand\n  command\n    .command('report')\n    .description('Generate analysis report without creating files')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('--json', 'Output as JSON')\n    .action(async (options) => {\n      const spinner = ora('Generating analysis report...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          process.exit(1);\n        }\n\n        const result = await analyzeDocs({\n          sourceDir,\n          targetDir: 'docs',\n          projectRoot,\n          useClaudeFlow: false,\n          createMOC: false,\n          linkOriginal: false,\n          dryRun: true,\n          verbose: false,\n        });\n\n        spinner.succeed('Report generated!');\n\n        if (options.json) {\n          // JSON output\n          const report = {\n            summary: {\n              totalDocs: result.filesAnalyzed,\n              categories: Object.fromEntries(result.structure),\n            },\n            documents: result.analyzed.map(d => ({\n              original: d.originalPath,\n              target: d.newPath,\n              type: d.type,\n              category: d.category,\n              tags: d.tags,\n              concepts: d.concepts,\n              researchNeeded: d.researchNeeded,\n              todos: d.todos,\n            })),\n            researchAreas: result.analyzed\n              .flatMap(d => d.researchNeeded.map(r => ({ doc: d.title, area: r }))),\n            todos: result.analyzed\n              .flatMap(d => d.todos.map(t => ({ doc: d.title, todo: t }))),\n          };\n          console.log(JSON.stringify(report, null, 2));\n        } else {\n          // Human-readable output\n          console.log();\n          console.log(chalk.cyan.bold('  Documentation Analysis Report'));\n          console.log(chalk.gray('  ─────────────────────────────────────'));\n          console.log();\n          console.log(chalk.white(`  Total documents: ${result.filesAnalyzed}`));\n          console.log();\n\n          // Type breakdown\n          const byType = new Map<string, number>();\n          result.analyzed.forEach(d => {\n            byType.set(d.type, (byType.get(d.type) || 0) + 1);\n          });\n\n          console.log(chalk.white('  By Type:'));\n          for (const [type, count] of byType) {\n            const bar = '█'.repeat(Math.ceil(count / result.filesAnalyzed * 20));\n            console.log(chalk.cyan(`    ${type.padEnd(12)} ${bar} ${count}`));\n          }\n          console.log();\n\n          // Category breakdown\n          console.log(chalk.white('  By Category:'));\n          for (const [category, docs] of result.structure) {\n            const bar = '█'.repeat(Math.ceil(docs.length / result.filesAnalyzed * 20));\n            console.log(chalk.cyan(`    ${category.padEnd(12)} ${bar} ${docs.length}`));\n          }\n          console.log();\n\n          // Issues\n          const withResearch = result.analyzed.filter(d => d.researchNeeded.length > 0);\n          const withTodos = result.analyzed.filter(d => d.todos.length > 0);\n\n          console.log(chalk.white('  Areas Needing Attention:'));\n          console.log(chalk.yellow(`    📚 Research needed:   ${withResearch.length} docs`));\n          console.log(chalk.yellow(`    ✏️  With TODOs:        ${withTodos.length} docs`));\n          console.log();\n\n          // Top research areas\n          if (withResearch.length > 0) {\n            console.log(chalk.white('  Top Research Areas:'));\n            withResearch.slice(0, 5).forEach(d => {\n              console.log(chalk.gray(`    ${d.title}:`));\n              d.researchNeeded.slice(0, 2).forEach(r => {\n                console.log(chalk.yellow(`      - ${r.slice(0, 60)}...`));\n              });\n            });\n            console.log();\n          }\n\n          console.log(chalk.cyan('  Run `kg analyze` to migrate documentation'));\n          console.log();\n        }\n\n      } catch (error) {\n        spinner.fail('Report generation failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  return 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package/dist/cli/commands/convert.js

@@ -8,7 +8,7 @@ import { validateProjectRoot } from "../../core/security.js";
 function createConvertCommand() {
   const command = new Command("convert");
   command.description("Convert existing docs to weave-nn structure");
-  command.command("docs").description("Convert existing documentation to docs-nn/ with proper structure").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs-nn").option("--no-auto-category", "Disable auto-categorization").option("-f, --force", "Overwrite existing files").option("--dry-run", "Show what would be done without making changes").action(async (options) => {
+  command.command("docs").description("Convert existing documentation with proper structure").option("-p, --path <path>", "Project root path", ".").option("-s, --source <dir>", "Source docs directory", "docs").option("-t, --target <dir>", "Target directory", "docs").option("--no-auto-category", "Disable auto-categorization").option("-f, --force", "Overwrite existing files").option("--dry-run", "Show what would be done without making changes").action(async (options) => {
     const spinner = ora("Converting documentation...").start();
     try {
       const projectRoot = validateProjectRoot(options.path);

package/dist/cli/commands/convert.js.map

@@ -1 +1 @@
-{"version":3,"file":"convert.js","sources":["../../../src/cli/commands/convert.ts"],"sourcesContent":["/**\n * Convert Command\n *\n * Convert existing documentation to weave-nn structure.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport ora from 'ora';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport {\n  convertDocs,\n  addFrontmatter,\n  validateFrontmatter,\n} from '../../generators/docs-convert.js';\nimport { validateProjectRoot, validateDocsPath } from '../../core/security.js';\n\n/**\n * Create convert command\n */\nexport function createConvertCommand(): Command {\n  const command = new Command('convert');\n\n  command\n    .description('Convert existing docs to weave-nn structure');\n\n  // Main convert subcommand\n  command\n    .command('docs')\n    .description('Convert existing documentation to docs-nn/ with proper structure')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-s, --source <dir>', 'Source docs directory', 'docs')\n    .option('-t, --target <dir>', 'Target directory', 'docs-nn')\n    .option('--no-auto-category', 'Disable auto-categorization')\n    .option('-f, --force', 'Overwrite existing files')\n    .option('--dry-run', 'Show what would be done without making changes')\n    .action(async (options) => {\n      const spinner = ora('Converting documentation...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const sourceDir = options.source;\n        const targetDir = options.target;\n\n        // Check source exists\n        if (!existsSync(join(projectRoot, sourceDir))) {\n          spinner.fail(`Source directory not found: ${sourceDir}`);\n          console.log(chalk.gray('  Specify source with --source <dir>'));\n          process.exit(1);\n        }\n\n        if (options.dryRun) {\n          spinner.text = 'Analyzing documentation (dry run)...';\n        }\n\n        const result = await convertDocs({\n          sourceDir,\n          targetDir,\n          projectRoot,\n          preserveOriginal: true,\n          force: options.force,\n          autoCategory: options.autoCategory !== false,\n          dryRun: options.dryRun,\n        });\n\n        if (result.success) {\n          if (options.dryRun) {\n            spinner.succeed('Dry run complete!');\n          } else {\n            spinner.succeed('Documentation converted!');\n          }\n        } else {\n          spinner.warn('Conversion completed with errors');\n        }\n\n        console.log();\n        console.log(chalk.white('  Summary:'));\n        console.log(chalk.gray(`    Source:      ${sourceDir}/`));\n        console.log(chalk.gray(`    Target:      ${targetDir}/`));\n        console.log(chalk.green(`    Converted:   ${result.filesConverted}`));\n        console.log(chalk.yellow(`    Skipped:     ${result.filesSkipped}`));\n        console.log(chalk.gray(`    Total:       ${result.filesProcessed}`));\n\n        if (result.converted.length > 0 && result.converted.length <= 10) {\n          console.log();\n          console.log(chalk.white('  Converted files:'));\n          result.converted.forEach(({ source, target, type }) => {\n            console.log(chalk.gray(`    ${source}`));\n            console.log(chalk.cyan(`      → ${target}`) + chalk.gray(` [${type}]`));\n          });\n        } else if (result.converted.length > 10) {\n          console.log();\n          console.log(chalk.white('  Sample conversions:'));\n          result.converted.slice(0, 5).forEach(({ source, target, type }) => {\n            console.log(chalk.gray(`    ${source}`));\n            console.log(chalk.cyan(`      → ${target}`) + chalk.gray(` [${type}]`));\n          });\n          console.log(chalk.gray(`    ... and ${result.converted.length - 5} more`));\n        }\n\n        if (result.errors.length > 0) {\n          console.log();\n          console.log(chalk.red('  Errors:'));\n          result.errors.slice(0, 5).forEach(err => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n          if (result.errors.length > 5) {\n            console.log(chalk.gray(`    ... and ${result.errors.length - 5} more`));\n          }\n        }\n\n        if (!options.dryRun && result.filesConverted > 0) {\n          console.log();\n          console.log(chalk.cyan('Next steps:'));\n          console.log(chalk.white(`  1. Review ${targetDir}/ structure`));\n          console.log(chalk.white('  2. Run: kg graph --docs ' + targetDir));\n          console.log(chalk.white('  3. Run: kg stats'));\n        }\n\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Conversion failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  return command;\n}\n\n/**\n * Create frontmatter command\n */\nexport function createFrontmatterCommand(): Command {\n  const command = new Command('frontmatter');\n\n  command\n    .description('Manage frontmatter in markdown files');\n\n  // Add frontmatter\n  command\n    .command('add [target]')\n    .description('Add frontmatter to files missing it')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-t, --type <type>', 'Node type (concept, technical, feature, service, guide, standard, integration)')\n    .option('-s, --status <status>', 'Status (draft, active, deprecated, archived)', 'active')\n    .option('--tags <tags>', 'Comma-separated tags')\n    .option('-f, --force', 'Overwrite existing frontmatter')\n    .option('--dry-run', 'Show what would be done')\n    .action(async (target, options) => {\n      const spinner = ora('Adding frontmatter...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const targetPath = target || 'docs';\n\n        const tags = options.tags ? options.tags.split(',').map((t: string) => t.trim()) : [];\n\n        const result = await addFrontmatter({\n          target: targetPath,\n          projectRoot,\n          type: options.type,\n          status: options.status,\n          tags,\n          force: options.force,\n          dryRun: options.dryRun,\n        });\n\n        if (result.success) {\n          spinner.succeed(options.dryRun ? 'Dry run complete!' : 'Frontmatter added!');\n        } else {\n          spinner.warn('Completed with errors');\n        }\n\n        console.log();\n        console.log(chalk.white('  Summary:'));\n        console.log(chalk.green(`    Updated:  ${result.filesUpdated}`));\n        console.log(chalk.yellow(`    Skipped:  ${result.filesSkipped}`));\n        console.log(chalk.gray(`    Total:    ${result.filesProcessed}`));\n\n        if (result.errors.length > 0) {\n          console.log();\n          console.log(chalk.red('  Errors:'));\n          result.errors.forEach(err => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n        }\n\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Failed to add frontmatter');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Validate frontmatter\n  command\n    .command('validate [target]')\n    .description('Validate frontmatter in markdown files')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .action(async (target, options) => {\n      const spinner = ora('Validating frontmatter...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const targetPath = target || 'docs';\n\n        const result = await validateFrontmatter(targetPath, projectRoot);\n\n        spinner.succeed('Validation complete!');\n\n        console.log();\n        console.log(chalk.white('  Frontmatter Validation:'));\n        console.log(chalk.green(`    Valid:    ${result.valid}`));\n        console.log(chalk.red(`    Invalid:  ${result.invalid}`));\n        console.log(chalk.yellow(`    Missing:  ${result.missing}`));\n\n        if (result.issues.length > 0) {\n          console.log();\n          console.log(chalk.yellow('  Issues found:'));\n          result.issues.slice(0, 10).forEach(({ file, issues }) => {\n            console.log(chalk.white(`    ${file}`));\n            issues.forEach(issue => {\n              console.log(chalk.gray(`      - ${issue}`));\n            });\n          });\n          if (result.issues.length > 10) {\n            console.log(chalk.gray(`    ... and ${result.issues.length - 10} more files`));\n          }\n\n          console.log();\n          console.log(chalk.cyan('Fix with: ') + chalk.white('kg frontmatter add <target>'));\n        }\n\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Validation failed');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Update frontmatter (force mode)\n  command\n    .command('update [target]')\n    .description('Update/regenerate frontmatter (overwrites existing)')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-t, --type <type>', 'Force specific node type')\n    .option('--dry-run', 'Show what would be done')\n    .action(async (target, options) => {\n      const spinner = ora('Updating frontmatter...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const targetPath = target || 'docs';\n\n        const result = await addFrontmatter({\n          target: targetPath,\n          projectRoot,\n          type: options.type,\n          force: true,\n          dryRun: options.dryRun,\n        });\n\n        if (result.success) {\n          spinner.succeed(options.dryRun ? 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Review ${targetDir}/ structure`));\n          console.log(chalk.white('  2. Run: kg graph --docs ' + targetDir));\n          console.log(chalk.white('  3. 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package/dist/cli/index.js

@@ -69,7 +69,7 @@ function createCLI() {
     console.log(chalk.gray("    $ kg analyze               # Analyze & migrate to knowledge graph"));
     console.log(chalk.gray("    $ kg analyze deep          # Deep analysis with claude-flow"));
     console.log(chalk.gray("    $ kg analyze report        # Generate analysis report"));
-    console.log(chalk.gray("    $ kg convert docs          # Convert docs/ → docs-nn/"));
+    console.log(chalk.gray("    $ kg convert docs          # Convert docs/ with proper structure"));
     console.log(chalk.gray("    $ kg frontmatter add       # Add frontmatter to files"));
     console.log(chalk.gray("    $ kg frontmatter validate  # Validate frontmatter\n"));
     console.log(chalk.white("  AI-SDLC SOP Compliance:"));

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../../src/cli/index.ts"],"sourcesContent":["/**\n * Knowledge Graph Agent CLI\n *\n * Main CLI setup and command registration.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport { createInitCommand } from './commands/init.js';\nimport { createGraphCommand } from './commands/graph.js';\nimport { createDocsCommand } from './commands/docs.js';\nimport { createClaudeCommand } from './commands/claude.js';\nimport { createSyncCommand } from './commands/sync.js';\nimport { createStatsCommand } from './commands/stats.js';\nimport { createSearchCommand } from './commands/search.js';\nimport { createConvertCommand, createFrontmatterCommand } from './commands/convert.js';\nimport { createAnalyzeCommand } from './commands/analyze.js';\nimport { createSOPCommands } from './commands/sop.js';\nimport { createInitPrimitivesCommand, createAnalyzeCodebaseCommand } from './commands/init-primitives.js';\nimport { createCultivateCommand } from './commands/cultivate.js';\nimport { createCommitCommand } from './commands/commit.js';\nimport { createConfigCommand } from './commands/config.js';\nimport { createDiagnosticsCommand } from './commands/diagnostics.js';\nimport { createWorkflowCommand } from './commands/workflow.js';\nimport { createAuditCommand } from './commands/audit.js';\nimport { createVectorCommand } from './commands/vector.js';\nimport { createServeCommand } from './commands/serve.js';\nimport { createDashboardCommand } from './commands/dashboard.js';\nimport { createPluginCommand } from './commands/plugin.js';\nimport { createHiveMindCommand } from './commands/hive-mind/index.js';\nimport { createHooksCommand } from './commands/hooks.js';\n\n/**\n * CLI version\n */\nconst VERSION = '0.4.0';\n\n/**\n * Create and configure the CLI program\n */\nexport function createCLI(): Command {\n  const program = new Command();\n\n  program\n    .name('kg')\n    .description('Knowledge Graph Agent - Generate and manage knowledge graphs for Claude Code')\n    .version(VERSION, '-v, --version', 'Display version number');\n\n  // Configure help\n  program.configureHelp({\n    sortSubcommands: true,\n    sortOptions: true,\n  });\n\n  // Add commands\n  program.addCommand(createInitCommand());\n  program.addCommand(createGraphCommand());\n  program.addCommand(createDocsCommand());\n  program.addCommand(createClaudeCommand());\n  program.addCommand(createSyncCommand());\n  program.addCommand(createStatsCommand());\n  program.addCommand(createSearchCommand());\n  program.addCommand(createConvertCommand());\n  program.addCommand(createFrontmatterCommand());\n  program.addCommand(createAnalyzeCommand());\n  program.addCommand(createSOPCommands());\n  program.addCommand(createInitPrimitivesCommand());\n  program.addCommand(createAnalyzeCodebaseCommand());\n  program.addCommand(createCultivateCommand());\n  program.addCommand(createCommitCommand());\n  program.addCommand(createConfigCommand());\n  program.addCommand(createDiagnosticsCommand());\n  program.addCommand(createWorkflowCommand());\n  program.addCommand(createAuditCommand());\n  program.addCommand(createVectorCommand());\n  program.addCommand(createServeCommand());\n  program.addCommand(createDashboardCommand());\n  program.addCommand(createPluginCommand());\n  program.addCommand(createHiveMindCommand());\n  program.addCommand(createHooksCommand());\n\n  // Default action (show help)\n  program.action(() => {\n    console.log(chalk.cyan.bold('\\n  Knowledge Graph Agent\\n'));\n    console.log(chalk.gray('  Generate and manage knowledge graphs for Claude Code\\n'));\n\n    console.log(chalk.white('  Quick Start:'));\n    console.log(chalk.gray('    $ kg init                  # Initialize knowledge graph'));\n    console.log(chalk.gray('    $ kg docs init             # Initialize docs directory'));\n    console.log(chalk.gray('    $ kg graph                 # Generate knowledge graph'));\n    console.log(chalk.gray('    $ kg claude update         # Update CLAUDE.md'));\n    console.log(chalk.gray('    $ kg sync                  # Sync with claude-flow\\n'));\n\n    console.log(chalk.white('  Migration & Analysis:'));\n    console.log(chalk.gray('    $ kg analyze               # Analyze & migrate to knowledge graph'));\n    console.log(chalk.gray('    $ kg analyze deep          # Deep analysis with claude-flow'));\n    console.log(chalk.gray('    $ kg analyze report        # Generate analysis report'));\n    console.log(chalk.gray('    $ kg convert docs          # Convert docs/ → docs-nn/'));\n    console.log(chalk.gray('    $ kg frontmatter add       # Add frontmatter to files'));\n    console.log(chalk.gray('    $ kg frontmatter validate  # Validate frontmatter\\n'));\n\n    console.log(chalk.white('  AI-SDLC SOP Compliance:'));\n    console.log(chalk.gray('    $ kg sop init              # Initialize SOP standards layer'));\n    console.log(chalk.gray('    $ kg sop check             # Check compliance against SOPs'));\n    console.log(chalk.gray('    $ kg sop gaps              # Analyze compliance gaps'));\n    console.log(chalk.gray('    $ kg sop report            # Generate compliance report'));\n    console.log(chalk.gray('    $ kg sop list              # List available SOPs\\n'));\n\n    console.log(chalk.white('  Cultivation & Primitives:'));\n    console.log(chalk.gray('    $ kg init-primitives       # Bootstrap primitives from codebase'));\n    console.log(chalk.gray('    $ kg analyze-codebase      # Analyze dependencies & services'));\n    console.log(chalk.gray('    $ kg init-primitives --dry-run  # Preview without writing\\n'));\n\n    console.log(chalk.white('  Git Integration:'));\n    console.log(chalk.gray('    $ kg commit                # Show status and suggested message'));\n    console.log(chalk.gray('    $ kg commit -a             # Auto-commit with generated message'));\n    console.log(chalk.gray('    $ kg commit -i             # Interactive commit mode'));\n    console.log(chalk.gray('    $ kg commit -m \"message\"   # Commit with custom message'));\n    console.log(chalk.gray('    $ kg commit status         # Show git status with analysis'));\n    console.log(chalk.gray('    $ kg commit log            # Show recent commits'));\n    console.log(chalk.gray('    $ kg commit diff           # Show diff of changes\\n'));\n\n    console.log(chalk.white('  Diagnostics & Health:'));\n    console.log(chalk.gray('    $ kg diag run              # Run full diagnostics'));\n    console.log(chalk.gray('    $ kg diag run --fix        # Attempt to fix issues'));\n    console.log(chalk.gray('    $ kg diag health           # Check system health'));\n    console.log(chalk.gray('    $ kg diag repair           # Repair database issues'));\n    console.log(chalk.gray('    $ kg diag backup           # Create database backup'));\n    console.log(chalk.gray('    $ kg diag backup --list    # List existing backups'));\n    console.log(chalk.gray('    $ kg diag info             # Show system information\\n'));\n\n    console.log(chalk.white('  Workflow Management:'));\n    console.log(chalk.gray('    $ kg workflow start <type> # Start a workflow'));\n    console.log(chalk.gray('    $ kg workflow status [id]  # Check workflow status'));\n    console.log(chalk.gray('    $ kg workflow list         # List active workflows'));\n    console.log(chalk.gray('    $ kg workflow stop <id>    # Stop a workflow'));\n    console.log(chalk.gray('    $ kg workflow history      # Show workflow history\\n'));\n\n    console.log(chalk.white('  Vector Operations:'));\n    console.log(chalk.gray('    $ kg vector search <query> # Semantic search'));\n    console.log(chalk.gray('    $ kg vector stats          # Vector store statistics'));\n    console.log(chalk.gray('    $ kg vector rebuild        # Rebuild vector index'));\n    console.log(chalk.gray('    $ kg vector traj list      # List trajectories'));\n    console.log(chalk.gray('    $ kg vector traj show <id> # Show trajectory details'));\n    console.log(chalk.gray('    $ kg vector traj patterns  # Show detected patterns\\n'));\n\n    console.log(chalk.white('  Audit & Exochain:'));\n    console.log(chalk.gray('    $ kg audit query           # Query the audit log'));\n    console.log(chalk.gray('    $ kg audit checkpoint      # Create a checkpoint'));\n    console.log(chalk.gray('    $ kg audit verify          # Verify chain integrity'));\n    console.log(chalk.gray('    $ kg audit sync status     # Check sync status'));\n    console.log(chalk.gray('    $ kg audit sync peers      # List sync peers'));\n    console.log(chalk.gray('    $ kg audit export          # Export audit log\\n'));\n\n    console.log(chalk.white('  Server Mode:'));\n    console.log(chalk.gray('    $ kg serve                 # Start MCP server (stdio)'));\n    console.log(chalk.gray('    $ kg serve --graphql       # Start GraphQL server'));\n    console.log(chalk.gray('    $ kg serve --dashboard     # Start web dashboard'));\n    console.log(chalk.gray('    $ kg serve --all           # Start all servers'));\n    console.log(chalk.gray('    $ kg serve status          # Show server status\\n'));\n\n    console.log(chalk.white('  Dashboard:'));\n    console.log(chalk.gray('    $ kg dashboard start       # Start dashboard dev server'));\n    console.log(chalk.gray('    $ kg dashboard build       # Build dashboard for production'));\n    console.log(chalk.gray('    $ kg dashboard serve       # Serve built dashboard'));\n    console.log(chalk.gray('    $ kg dashboard open        # Open dashboard in browser'));\n    console.log(chalk.gray('    $ kg dashboard status      # Check dashboard status\\n'));\n\n    console.log(chalk.white('  Plugin Management:'));\n    console.log(chalk.gray('    $ kg plugin list           # List installed plugins'));\n    console.log(chalk.gray('    $ kg plugin install <pkg>  # Install a plugin'));\n    console.log(chalk.gray('    $ kg plugin uninstall <n>  # Uninstall a plugin'));\n    console.log(chalk.gray('    $ kg plugin enable <name>  # Enable a plugin'));\n    console.log(chalk.gray('    $ kg plugin disable <name> # Disable a plugin'));\n    console.log(chalk.gray('    $ kg plugin info <name>    # Show plugin details'));\n    console.log(chalk.gray('    $ kg plugin run <n> <file> # Run analyzer plugin'));\n    console.log(chalk.gray('    $ kg plugin create <name>  # Create new plugin\\n'));\n\n    console.log(chalk.white('  Hive Mind (Graph Reconnection):'));\n    console.log(chalk.gray('    $ kg hive-mind analyze-links <vault>     # Analyze wiki-links'));\n    console.log(chalk.gray('    $ kg hive-mind find-connections <vault>  # Find potential links'));\n    console.log(chalk.gray('    $ kg hive-mind validate-names <vault>    # Validate file names'));\n    console.log(chalk.gray('    $ kg hive-mind add-frontmatter <vault>   # Add YAML frontmatter\\n'));\n\n    console.log(chalk.white('  Claude Code Hooks:'));\n    console.log(chalk.gray('    $ kg hooks install         # Install hooks to capture interactions'));\n    console.log(chalk.gray('    $ kg hooks uninstall       # Remove hooks'));\n    console.log(chalk.gray('    $ kg hooks status          # Show hooks status'));\n    console.log(chalk.gray('    $ kg hooks sessions        # List captured sessions'));\n    console.log(chalk.gray('    $ kg hooks export          # Export captured sessions\\n'));\n\n    console.log(chalk.white('  Commands:'));\n    program.commands.forEach(cmd => {\n      console.log(chalk.cyan(`    ${cmd.name().padEnd(20)}`), chalk.gray(cmd.description() || ''));\n    });\n\n    console.log('\\n  Run', chalk.cyan('kg <command> --help'), 'for more information\\n');\n  });\n\n  return 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+{"version":3,"file":"index.js","sources":["../../src/cli/index.ts"],"sourcesContent":["/**\n * Knowledge Graph Agent CLI\n *\n * Main CLI setup and command registration.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport { createInitCommand } from './commands/init.js';\nimport { createGraphCommand } from './commands/graph.js';\nimport { createDocsCommand } from './commands/docs.js';\nimport { createClaudeCommand } from './commands/claude.js';\nimport { createSyncCommand } from './commands/sync.js';\nimport { createStatsCommand } from './commands/stats.js';\nimport { createSearchCommand } from './commands/search.js';\nimport { createConvertCommand, createFrontmatterCommand } from './commands/convert.js';\nimport { createAnalyzeCommand } from './commands/analyze.js';\nimport { createSOPCommands } from './commands/sop.js';\nimport { createInitPrimitivesCommand, createAnalyzeCodebaseCommand } from './commands/init-primitives.js';\nimport { createCultivateCommand } from './commands/cultivate.js';\nimport { createCommitCommand } from './commands/commit.js';\nimport { createConfigCommand } from './commands/config.js';\nimport { createDiagnosticsCommand } from './commands/diagnostics.js';\nimport { createWorkflowCommand } from './commands/workflow.js';\nimport { createAuditCommand } from './commands/audit.js';\nimport { createVectorCommand } from './commands/vector.js';\nimport { createServeCommand } from './commands/serve.js';\nimport { createDashboardCommand } from './commands/dashboard.js';\nimport { createPluginCommand } from './commands/plugin.js';\nimport { createHiveMindCommand } from './commands/hive-mind/index.js';\nimport { createHooksCommand } from './commands/hooks.js';\n\n/**\n * CLI version\n */\nconst VERSION = '0.4.0';\n\n/**\n * Create and configure the CLI program\n */\nexport function createCLI(): Command {\n  const program = new Command();\n\n  program\n    .name('kg')\n    .description('Knowledge Graph Agent - Generate and manage knowledge graphs for Claude Code')\n    .version(VERSION, '-v, --version', 'Display version number');\n\n  // Configure help\n  program.configureHelp({\n    sortSubcommands: true,\n    sortOptions: true,\n  });\n\n  // Add commands\n  program.addCommand(createInitCommand());\n  program.addCommand(createGraphCommand());\n  program.addCommand(createDocsCommand());\n  program.addCommand(createClaudeCommand());\n  program.addCommand(createSyncCommand());\n  program.addCommand(createStatsCommand());\n  program.addCommand(createSearchCommand());\n  program.addCommand(createConvertCommand());\n  program.addCommand(createFrontmatterCommand());\n  program.addCommand(createAnalyzeCommand());\n  program.addCommand(createSOPCommands());\n  program.addCommand(createInitPrimitivesCommand());\n  program.addCommand(createAnalyzeCodebaseCommand());\n  program.addCommand(createCultivateCommand());\n  program.addCommand(createCommitCommand());\n  program.addCommand(createConfigCommand());\n  program.addCommand(createDiagnosticsCommand());\n  program.addCommand(createWorkflowCommand());\n  program.addCommand(createAuditCommand());\n  program.addCommand(createVectorCommand());\n  program.addCommand(createServeCommand());\n  program.addCommand(createDashboardCommand());\n  program.addCommand(createPluginCommand());\n  program.addCommand(createHiveMindCommand());\n  program.addCommand(createHooksCommand());\n\n  // Default action (show help)\n  program.action(() => {\n    console.log(chalk.cyan.bold('\\n  Knowledge Graph Agent\\n'));\n    console.log(chalk.gray('  Generate and manage knowledge graphs for Claude Code\\n'));\n\n    console.log(chalk.white('  Quick Start:'));\n    console.log(chalk.gray('    $ kg init                  # Initialize knowledge graph'));\n    console.log(chalk.gray('    $ kg docs init             # Initialize docs directory'));\n    console.log(chalk.gray('    $ kg graph                 # Generate knowledge graph'));\n    console.log(chalk.gray('    $ kg claude update         # Update CLAUDE.md'));\n    console.log(chalk.gray('    $ kg sync                  # Sync with claude-flow\\n'));\n\n    console.log(chalk.white('  Migration & Analysis:'));\n    console.log(chalk.gray('    $ kg analyze               # Analyze & migrate to knowledge graph'));\n    console.log(chalk.gray('    $ kg analyze deep          # Deep analysis with claude-flow'));\n    console.log(chalk.gray('    $ kg analyze report        # Generate analysis report'));\n    console.log(chalk.gray('    $ kg convert docs          # Convert docs/ with proper structure'));\n    console.log(chalk.gray('    $ kg frontmatter add       # Add frontmatter to files'));\n    console.log(chalk.gray('    $ kg frontmatter validate  # Validate frontmatter\\n'));\n\n    console.log(chalk.white('  AI-SDLC SOP Compliance:'));\n    console.log(chalk.gray('    $ kg sop init              # Initialize SOP standards layer'));\n    console.log(chalk.gray('    $ kg sop check             # Check compliance against SOPs'));\n    console.log(chalk.gray('    $ kg sop gaps              # Analyze compliance gaps'));\n    console.log(chalk.gray('    $ kg sop report            # Generate compliance report'));\n    console.log(chalk.gray('    $ kg sop list              # List available SOPs\\n'));\n\n    console.log(chalk.white('  Cultivation & Primitives:'));\n    console.log(chalk.gray('    $ kg init-primitives       # Bootstrap primitives from codebase'));\n    console.log(chalk.gray('    $ kg analyze-codebase      # Analyze dependencies & services'));\n    console.log(chalk.gray('    $ kg init-primitives --dry-run  # Preview without writing\\n'));\n\n    console.log(chalk.white('  Git Integration:'));\n    console.log(chalk.gray('    $ kg commit                # Show status and suggested message'));\n    console.log(chalk.gray('    $ kg commit -a             # Auto-commit with generated message'));\n    console.log(chalk.gray('    $ kg commit -i             # Interactive commit mode'));\n    console.log(chalk.gray('    $ kg commit -m \"message\"   # Commit with custom message'));\n    console.log(chalk.gray('    $ kg commit status         # Show git status with analysis'));\n    console.log(chalk.gray('    $ kg commit log            # Show recent commits'));\n    console.log(chalk.gray('    $ kg commit diff           # Show diff of changes\\n'));\n\n    console.log(chalk.white('  Diagnostics & Health:'));\n    console.log(chalk.gray('    $ kg diag run              # Run full diagnostics'));\n    console.log(chalk.gray('    $ kg diag run --fix        # Attempt to fix issues'));\n    console.log(chalk.gray('    $ kg diag health           # Check system health'));\n    console.log(chalk.gray('    $ kg diag repair           # Repair database issues'));\n    console.log(chalk.gray('    $ kg diag backup           # Create database backup'));\n    console.log(chalk.gray('    $ kg diag backup --list    # List existing backups'));\n    console.log(chalk.gray('    $ kg diag info             # Show system information\\n'));\n\n    console.log(chalk.white('  Workflow Management:'));\n    console.log(chalk.gray('    $ kg workflow start <type> # Start a workflow'));\n    console.log(chalk.gray('    $ kg workflow status [id]  # Check workflow status'));\n    console.log(chalk.gray('    $ kg workflow list         # List active workflows'));\n    console.log(chalk.gray('    $ kg workflow stop <id>    # Stop a workflow'));\n    console.log(chalk.gray('    $ kg workflow history      # Show workflow history\\n'));\n\n    console.log(chalk.white('  Vector Operations:'));\n    console.log(chalk.gray('    $ kg vector search <query> # Semantic search'));\n    console.log(chalk.gray('    $ kg vector stats          # Vector store statistics'));\n    console.log(chalk.gray('    $ kg vector rebuild        # Rebuild vector index'));\n    console.log(chalk.gray('    $ kg vector traj list      # List trajectories'));\n    console.log(chalk.gray('    $ kg vector traj show <id> # Show trajectory details'));\n    console.log(chalk.gray('    $ kg vector traj patterns  # Show detected patterns\\n'));\n\n    console.log(chalk.white('  Audit & Exochain:'));\n    console.log(chalk.gray('    $ kg audit query           # Query the audit log'));\n    console.log(chalk.gray('    $ kg audit checkpoint      # Create a checkpoint'));\n    console.log(chalk.gray('    $ kg audit verify          # Verify chain integrity'));\n    console.log(chalk.gray('    $ kg audit sync status     # Check sync status'));\n    console.log(chalk.gray('    $ kg audit sync peers      # List sync peers'));\n    console.log(chalk.gray('    $ kg audit export          # Export audit log\\n'));\n\n    console.log(chalk.white('  Server Mode:'));\n    console.log(chalk.gray('    $ kg serve                 # Start MCP server (stdio)'));\n    console.log(chalk.gray('    $ kg serve --graphql       # Start GraphQL server'));\n    console.log(chalk.gray('    $ kg serve --dashboard     # Start web dashboard'));\n    console.log(chalk.gray('    $ kg serve --all           # Start all servers'));\n    console.log(chalk.gray('    $ kg serve status          # Show server status\\n'));\n\n    console.log(chalk.white('  Dashboard:'));\n    console.log(chalk.gray('    $ kg dashboard start       # Start dashboard dev server'));\n    console.log(chalk.gray('    $ kg dashboard build       # Build dashboard for production'));\n    console.log(chalk.gray('    $ kg dashboard serve       # Serve built dashboard'));\n    console.log(chalk.gray('    $ kg dashboard open        # Open dashboard in browser'));\n    console.log(chalk.gray('    $ kg dashboard status      # Check dashboard status\\n'));\n\n    console.log(chalk.white('  Plugin Management:'));\n    console.log(chalk.gray('    $ kg plugin list           # List installed plugins'));\n    console.log(chalk.gray('    $ kg plugin install <pkg>  # Install a plugin'));\n    console.log(chalk.gray('    $ kg plugin uninstall <n>  # Uninstall a plugin'));\n    console.log(chalk.gray('    $ kg plugin enable <name>  # Enable a plugin'));\n    console.log(chalk.gray('    $ kg plugin disable <name> # Disable a plugin'));\n    console.log(chalk.gray('    $ kg plugin info <name>    # Show plugin details'));\n    console.log(chalk.gray('    $ kg plugin run <n> <file> # Run analyzer plugin'));\n    console.log(chalk.gray('    $ kg plugin create <name>  # Create new plugin\\n'));\n\n    console.log(chalk.white('  Hive Mind (Graph Reconnection):'));\n    console.log(chalk.gray('    $ kg hive-mind analyze-links <vault>     # Analyze wiki-links'));\n    console.log(chalk.gray('    $ kg hive-mind find-connections <vault>  # Find potential links'));\n    console.log(chalk.gray('    $ kg hive-mind validate-names <vault>    # Validate file names'));\n    console.log(chalk.gray('    $ kg hive-mind add-frontmatter <vault>   # Add YAML frontmatter\\n'));\n\n    console.log(chalk.white('  Claude Code Hooks:'));\n    console.log(chalk.gray('    $ kg hooks install         # Install hooks to capture interactions'));\n    console.log(chalk.gray('    $ kg hooks uninstall       # Remove hooks'));\n    console.log(chalk.gray('    $ kg hooks status          # Show hooks status'));\n    console.log(chalk.gray('    $ kg hooks sessions        # List captured sessions'));\n    console.log(chalk.gray('    $ kg hooks export          # Export captured sessions\\n'));\n\n    console.log(chalk.white('  Commands:'));\n    program.commands.forEach(cmd => {\n      console.log(chalk.cyan(`    ${cmd.name().padEnd(20)}`), chalk.gray(cmd.description() || ''));\n    });\n\n    console.log('\\n  Run', chalk.cyan('kg <command> --help'), 'for more information\\n');\n  });\n\n  return 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package/dist/generators/docs-analyzer.d.ts

@@ -12,7 +12,7 @@ import type { NodeType } from '../core/types.js';
 export interface AnalyzerOptions {
     /** Source directory with existing docs */
     sourceDir: string;
-    /** Target directory (default: docs-nn) */
+    /** Target directory (default: docs) */
     targetDir?: string;
     /** Project root for path resolution */
     projectRoot: string;
@@ -35,7 +35,7 @@ export interface AnalyzerOptions {
 export interface AnalyzedDoc {
     /** Original file path */
     originalPath: string;
-    /** New file path in docs-nn */
+    /** New file path in target directory */
     newPath: string;
     /** Document title */
     title: string;

package/dist/generators/docs-analyzer.d.ts.map

@@ -1 +1 @@
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package/dist/generators/docs-analyzer.js

@@ -47,7 +47,7 @@ const CATEGORY_STRUCTURE = {
 async function analyzeDocs(options) {
   const {
     sourceDir,
-    targetDir = "docs-nn",
+    targetDir = "docs",
     projectRoot,
     useClaudeFlow = false,
     createMOC = true,

package/dist/generators/docs-analyzer.js.map

@@ -1 +1 @@
-{"version":3,"file":"docs-analyzer.js","sources":["../../src/generators/docs-analyzer.ts"],"sourcesContent":["/**\n * Docs Analyzer\n *\n * Advanced documentation analyzer that uses claude-flow to create\n * comprehensive knowledge graph documentation with proper structure,\n * wikilinks, frontmatter, and tags following Obsidian conventions.\n */\n\nimport { existsSync, mkdirSync, readFileSync, writeFileSync } from 'fs';\nimport { join, basename, dirname, relative, extname } from 'path';\nimport { execSync, spawn } from 'child_process';\nimport fg from 'fast-glob';\nimport matter from 'gray-matter';\nimport type { NodeType, NodeStatus, NodeFrontmatter } from '../core/types.js';\n\n/**\n * Analyzer options\n */\nexport interface AnalyzerOptions {\n  /** Source directory with existing docs */\n  sourceDir: string;\n  /** Target directory (default: docs-nn) */\n  targetDir?: string;\n  /** Project root for path resolution */\n  projectRoot: string;\n  /** Use claude-flow for deep analysis */\n  useClaudeFlow?: boolean;\n  /** Create MOC (Map of Content) files */\n  createMOC?: boolean;\n  /** Link back to original docs */\n  linkOriginal?: boolean;\n  /** Maximum depth for analysis */\n  maxDepth?: number;\n  /** Dry run - show what would be done */\n  dryRun?: boolean;\n  /** Verbose output */\n  verbose?: boolean;\n}\n\n/**\n * Analyzed document\n */\nexport interface AnalyzedDoc {\n  /** Original file path */\n  originalPath: string;\n  /** New file path in docs-nn */\n  newPath: string;\n  /** Document title */\n  title: string;\n  /** Detected node type */\n  type: NodeType;\n  /** Extracted tags */\n  tags: string[];\n  /** Related documents (wikilinks) */\n  related: string[];\n  /** Key concepts extracted */\n  concepts: string[];\n  /** Areas needing research */\n  researchNeeded: string[];\n  /** TODOs found or generated */\n  todos: string[];\n  /** Summary/description */\n  summary: string;\n  /** Category path in structure */\n  category: string;\n}\n\n/**\n * Analyzer result\n */\nexport interface AnalyzerResult {\n  success: boolean;\n  filesAnalyzed: number;\n  filesCreated: number;\n  mocFilesCreated: number;\n  errors: string[];\n  analyzed: AnalyzedDoc[];\n  structure: Map<string, string[]>;\n}\n\n/**\n * Weave-NN category structure with descriptions\n */\nconst CATEGORY_STRUCTURE: Record<string, { type: NodeType; description: string; subcategories: string[] }> = {\n  concepts: {\n    type: 'concept',\n    description: 'Abstract concepts, theories, and architectural principles',\n    subcategories: ['architecture', 'patterns', 'principles', 'models'],\n  },\n  components: {\n    type: 'technical',\n    description: 'Reusable technical components and implementations',\n    subcategories: ['ui', 'utilities', 'core', 'shared'],\n  },\n  services: {\n    type: 'service',\n    description: 'Backend services, APIs, and workers',\n    subcategories: ['api', 'workers', 'handlers', 'middleware'],\n  },\n  features: {\n    type: 'feature',\n    description: 'Product features and capabilities',\n    subcategories: ['core', 'advanced', 'experimental'],\n  },\n  integrations: {\n    type: 'integration',\n    description: 'External integrations and adapters',\n    subcategories: ['databases', 'auth', 'storage', 'monitoring', 'third-party'],\n  },\n  standards: {\n    type: 'standard',\n    description: 'Coding standards, conventions, and best practices',\n    subcategories: ['coding', 'documentation', 'testing', 'security'],\n  },\n  guides: {\n    type: 'guide',\n    description: 'How-to guides and tutorials',\n    subcategories: ['getting-started', 'tutorials', 'troubleshooting', 'deployment'],\n  },\n  references: {\n    type: 'technical',\n    description: 'API references and technical documentation',\n    subcategories: ['api', 'cli', 'config', 'schemas'],\n  },\n};\n\n/**\n * Analyze and migrate documentation to weave-nn structure\n */\nexport async function analyzeDocs(options: AnalyzerOptions): Promise<AnalyzerResult> {\n  const {\n    sourceDir,\n    targetDir = 'docs-nn',\n    projectRoot,\n    useClaudeFlow = false,\n    createMOC = true,\n    linkOriginal = true,\n    maxDepth = 3,\n    dryRun = false,\n    verbose = false,\n  } = options;\n\n  const result: AnalyzerResult = {\n    success: true,\n    filesAnalyzed: 0,\n    filesCreated: 0,\n    mocFilesCreated: 0,\n    errors: [],\n    analyzed: [],\n    structure: new Map(),\n  };\n\n  const sourcePath = join(projectRoot, sourceDir);\n  const targetPath = join(projectRoot, targetDir);\n\n  // Validate source exists\n  if (!existsSync(sourcePath)) {\n    result.success = false;\n    result.errors.push(`Source directory not found: ${sourcePath}`);\n    return result;\n  }\n\n  // Create target structure\n  if (!dryRun) {\n    createFullStructure(targetPath);\n  }\n\n  // Find all markdown files\n  const files = await fg('**/*.md', {\n    cwd: sourcePath,\n    ignore: ['node_modules/**', '.git/**', '_templates/**', 'docs-nn/**'],\n  });\n\n  // First pass: Analyze all documents\n  const analyzedDocs: AnalyzedDoc[] = [];\n\n  for (const file of files) {\n    result.filesAnalyzed++;\n    const sourceFile = join(sourcePath, file);\n\n    try {\n      const analyzed = await analyzeDocument(sourceFile, file, sourcePath, {\n        useClaudeFlow,\n        linkOriginal,\n        verbose,\n      });\n      analyzedDocs.push(analyzed);\n\n      // Track structure\n      const category = analyzed.category.split('/')[0];\n      if (!result.structure.has(category)) {\n        result.structure.set(category, []);\n      }\n      result.structure.get(category)!.push(analyzed.title);\n\n    } catch (error) {\n      result.errors.push(`Failed to analyze ${file}: ${error}`);\n    }\n  }\n\n  // Build cross-references between documents\n  buildCrossReferences(analyzedDocs);\n\n  // Second pass: Create new documents\n  for (const doc of analyzedDocs) {\n    try {\n      const targetFile = join(targetPath, doc.newPath);\n\n      if (!dryRun) {\n        mkdirSync(dirname(targetFile), { recursive: true });\n        const content = generateKnowledgeDoc(doc, sourceDir, linkOriginal, analyzedDocs);\n        writeFileSync(targetFile, content, 'utf-8');\n      }\n\n      result.filesCreated++;\n      result.analyzed.push(doc);\n\n    } catch (error) {\n      result.errors.push(`Failed to create ${doc.newPath}: ${error}`);\n    }\n  }\n\n  // Create MOC files for each category\n  if (createMOC && !dryRun) {\n    for (const [category, docs] of result.structure) {\n      const mocPath = join(targetPath, category, '_MOC.md');\n      const mocContent = generateMOC(category, docs, analyzedDocs);\n      writeFileSync(mocPath, mocContent, 'utf-8');\n      result.mocFilesCreated++;\n    }\n\n    // Create master MOC\n    const masterMocPath = join(targetPath, 'MOC.md');\n    const masterMocContent = generateMasterMOC(result.structure, analyzedDocs);\n    writeFileSync(masterMocPath, masterMocContent, 'utf-8');\n    result.mocFilesCreated++;\n\n    // Create PRIMITIVES.md\n    const primitivesPath = join(targetPath, 'PRIMITIVES.md');\n    const primitivesContent = generatePrimitives(analyzedDocs);\n    writeFileSync(primitivesPath, primitivesContent, 'utf-8');\n  }\n\n  result.success = result.errors.length === 0;\n  return result;\n}\n\n/**\n * Analyze a single document\n */\nasync function analyzeDocument(\n  filePath: string,\n  relativePath: string,\n  sourcePath: string,\n  options: { useClaudeFlow?: boolean; linkOriginal?: boolean; verbose?: boolean }\n): Promise<AnalyzedDoc> {\n  const content = readFileSync(filePath, 'utf-8');\n  const { data: existingFrontmatter, content: body } = matter(content);\n\n  const filename = basename(filePath, '.md');\n  const title = existingFrontmatter.title as string || formatTitle(filename);\n\n  // Detect node type and category\n  const { type, category } = detectTypeAndCategory(relativePath, body, existingFrontmatter);\n\n  // Extract tags\n  const tags = extractAllTags(body, existingFrontmatter, relativePath);\n\n  // Extract wikilinks and markdown links\n  const related = extractLinks(body);\n\n  // Extract key concepts\n  const concepts = extractConcepts(body);\n\n  // Find areas needing research\n  const researchNeeded = findResearchAreas(body, filename);\n\n  // Extract existing TODOs and generate new ones\n  const todos = extractAndGenerateTodos(body, content, filename);\n\n  // Generate summary\n  const summary = generateSummary(body, existingFrontmatter);\n\n  // Determine new path\n  const newPath = join(category, formatFilename(filename) + '.md');\n\n  return {\n    originalPath: relativePath,\n    newPath,\n    title,\n    type,\n    tags,\n    related,\n    concepts,\n    researchNeeded,\n    todos,\n    summary,\n    category,\n  };\n}\n\n/**\n * Create full target directory structure\n */\nfunction createFullStructure(targetPath: string): void {\n  // Create all category directories and subcategories\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    mkdirSync(join(targetPath, category), { recursive: true });\n    for (const sub of config.subcategories) {\n      mkdirSync(join(targetPath, category, sub), { recursive: true });\n    }\n  }\n\n  // Create meta directories\n  mkdirSync(join(targetPath, '_templates'), { recursive: true });\n  mkdirSync(join(targetPath, '_attachments'), { recursive: true });\n  mkdirSync(join(targetPath, '_archive'), { recursive: true });\n}\n\n/**\n * Detect node type and category from content\n */\nfunction detectTypeAndCategory(\n  filePath: string,\n  content: string,\n  frontmatter: Record<string, unknown>\n): { type: NodeType; category: string } {\n  // Check frontmatter first\n  if (frontmatter.type && frontmatter.category) {\n    return {\n      type: frontmatter.type as NodeType,\n      category: frontmatter.category as string,\n    };\n  }\n\n  const lowerContent = content.toLowerCase();\n  const lowerPath = filePath.toLowerCase();\n\n  // Score each category\n  const scores: Record<string, number> = {};\n\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    scores[category] = 0;\n\n    // Path matching\n    if (lowerPath.includes(category)) scores[category] += 10;\n    for (const sub of config.subcategories) {\n      if (lowerPath.includes(sub)) scores[category] += 5;\n    }\n\n    // Content analysis based on type\n    const keywords = getKeywordsForType(config.type);\n    for (const keyword of keywords) {\n      const regex = new RegExp(`\\\\b${keyword}\\\\b`, 'gi');\n      const matches = content.match(regex);\n      if (matches) scores[category] += matches.length;\n    }\n  }\n\n  // Find best match\n  let bestCategory = 'concepts';\n  let bestScore = 0;\n\n  for (const [category, score] of Object.entries(scores)) {\n    if (score > bestScore) {\n      bestScore = score;\n      bestCategory = category;\n    }\n  }\n\n  return {\n    type: CATEGORY_STRUCTURE[bestCategory].type,\n    category: bestCategory,\n  };\n}\n\n/**\n * Get keywords for a node type\n */\nfunction getKeywordsForType(type: NodeType): string[] {\n  const keywords: Record<NodeType, string[]> = {\n    concept: ['concept', 'theory', 'principle', 'overview', 'introduction', 'architecture', 'design', 'pattern'],\n    technical: ['component', 'implementation', 'class', 'function', 'module', 'utility', 'helper'],\n    feature: ['feature', 'capability', 'functionality', 'user', 'requirement', 'use case'],\n    primitive: ['library', 'framework', 'dependency', 'tool', 'sdk'],\n    service: ['api', 'endpoint', 'service', 'server', 'backend', 'worker', 'handler'],\n    guide: ['how to', 'tutorial', 'guide', 'step', 'walkthrough', 'getting started'],\n    standard: ['standard', 'convention', 'best practice', 'rule', 'guideline', 'style'],\n    integration: ['integration', 'connect', 'plugin', 'adapter', 'sync', 'import', 'export'],\n  };\n\n  return keywords[type] || [];\n}\n\n/**\n * Extract all tags from content and path\n */\nfunction extractAllTags(\n  content: string,\n  frontmatter: Record<string, unknown>,\n  filePath: string\n): string[] {\n  const tags = new Set<string>();\n\n  // Add existing frontmatter tags\n  if (Array.isArray(frontmatter.tags)) {\n    frontmatter.tags.forEach(t => tags.add(String(t)));\n  }\n\n  // Extract #tags from content\n  const hashTags = content.match(/#[\\w-]+/g);\n  if (hashTags) {\n    hashTags.forEach(t => tags.add(t.slice(1)));\n  }\n\n  // Generate tags from path\n  const pathParts = filePath.split('/').filter(p => p && !p.endsWith('.md'));\n  pathParts.forEach(p => {\n    if (p.length > 2 && p.length < 20) {\n      tags.add(p.replace(/[-_]/g, '-').toLowerCase());\n    }\n  });\n\n  // Add status tags\n  if (content.match(/\\b(wip|draft|todo)\\b/i)) tags.add('needs-work');\n  if (content.match(/\\b(deprecated|legacy)\\b/i)) tags.add('deprecated');\n  if (content.match(/\\b(experimental|beta)\\b/i)) tags.add('experimental');\n\n  return [...tags].slice(0, 15);\n}\n\n/**\n * Extract wikilinks and markdown links\n */\nfunction extractLinks(content: string): string[] {\n  const links = new Set<string>();\n\n  // Wikilinks\n  const wikilinks = content.match(/\\[\\[([^\\]|]+)(?:\\|[^\\]]+)?\\]\\]/g);\n  if (wikilinks) {\n    wikilinks.forEach(link => {\n      const match = link.match(/\\[\\[([^\\]|]+)/);\n      if (match) links.add(match[1].trim());\n    });\n  }\n\n  // Markdown links (internal only)\n  const mdLinks = content.match(/\\[([^\\]]+)\\]\\(([^)]+)\\)/g);\n  if (mdLinks) {\n    mdLinks.forEach(link => {\n      const match = link.match(/\\]\\(([^)]+)\\)/);\n      if (match && !match[1].startsWith('http')) {\n        links.add(match[1].replace(/\\.md$/, '').trim());\n      }\n    });\n  }\n\n  return [...links];\n}\n\n/**\n * Extract key concepts from content\n */\nfunction extractConcepts(content: string): string[] {\n  const concepts: string[] = [];\n\n  // Look for headers as concepts\n  const headers = content.match(/^##\\s+(.+)$/gm);\n  if (headers) {\n    headers.slice(0, 5).forEach(h => {\n      concepts.push(h.replace(/^##\\s+/, '').trim());\n    });\n  }\n\n  // Look for bold terms as concepts\n  const boldTerms = content.match(/\\*\\*([^*]+)\\*\\*/g);\n  if (boldTerms) {\n    boldTerms.slice(0, 5).forEach(term => {\n      const clean = term.replace(/\\*\\*/g, '').trim();\n      if (clean.length > 2 && clean.length < 50) {\n        concepts.push(clean);\n      }\n    });\n  }\n\n  return [...new Set(concepts)].slice(0, 10);\n}\n\n/**\n * Find areas needing research\n */\nfunction findResearchAreas(content: string, filename: string): string[] {\n  const areas: string[] = [];\n\n  // Look for question marks indicating uncertainty\n  const questions = content.match(/[^.!?]*\\?/g);\n  if (questions) {\n    questions.slice(0, 3).forEach(q => {\n      if (q.length > 10 && q.length < 200) {\n        areas.push(q.trim());\n      }\n    });\n  }\n\n  // Look for placeholders\n  if (content.match(/\\bTBD\\b|\\bTODO\\b|\\bFIXME\\b/i)) {\n    areas.push('Contains placeholders that need completion');\n  }\n\n  // Look for empty sections\n  const emptyHeaders = content.match(/^##[^#\\n]+\\n\\n##/gm);\n  if (emptyHeaders) {\n    areas.push('Has empty sections that need content');\n  }\n\n  // Check for missing content indicators\n  if (content.length < 500) {\n    areas.push('Document is short - may need expansion');\n  }\n\n  return areas;\n}\n\n/**\n * Extract and generate TODOs\n */\nfunction extractAndGenerateTodos(body: string, fullContent: string, filename: string): string[] {\n  const todos: string[] = [];\n\n  // Extract existing TODOs\n  const existingTodos = fullContent.match(/[-*]\\s*\\[[ x]\\]\\s*(.+)/g);\n  if (existingTodos) {\n    existingTodos.forEach(todo => {\n      todos.push(todo.replace(/^[-*]\\s*\\[[ x]\\]\\s*/, '').trim());\n    });\n  }\n\n  // Extract TODO comments\n  const todoComments = fullContent.match(/(?:TODO|FIXME|XXX):\\s*(.+)/gi);\n  if (todoComments) {\n    todoComments.forEach(todo => {\n      todos.push(todo.replace(/^(?:TODO|FIXME|XXX):\\s*/i, '').trim());\n    });\n  }\n\n  // Generate suggested TODOs based on analysis\n  if (!fullContent.match(/^---[\\s\\S]*?---/)) {\n    todos.push('Add proper frontmatter');\n  }\n\n  if (!fullContent.match(/\\[\\[/)) {\n    todos.push('Add wikilinks to related documents');\n  }\n\n  if (!fullContent.match(/^##\\s/m)) {\n    todos.push('Add section structure with headers');\n  }\n\n  return [...new Set(todos)].slice(0, 10);\n}\n\n/**\n * Generate summary from content\n */\nfunction generateSummary(body: string, frontmatter: Record<string, unknown>): string {\n  // Use existing description\n  if (frontmatter.description) {\n    return String(frontmatter.description);\n  }\n\n  // Extract first meaningful paragraph\n  const lines = body.split('\\n');\n  for (const line of lines) {\n    const trimmed = line.trim();\n    if (trimmed && !trimmed.startsWith('#') && !trimmed.startsWith('```') && trimmed.length > 30) {\n      return trimmed.length > 200 ? trimmed.slice(0, 197) + '...' : trimmed;\n    }\n  }\n\n  return 'Documentation requiring summary.';\n}\n\n/**\n * Build cross-references between documents\n */\nfunction buildCrossReferences(docs: AnalyzedDoc[]): void {\n  const titleMap = new Map<string, AnalyzedDoc>();\n\n  // Build title lookup\n  docs.forEach(doc => {\n    titleMap.set(doc.title.toLowerCase(), doc);\n    titleMap.set(formatFilename(doc.title), doc);\n  });\n\n  // Update related links\n  docs.forEach(doc => {\n    const newRelated: string[] = [];\n\n    doc.related.forEach(link => {\n      const linkedDoc = titleMap.get(link.toLowerCase()) || titleMap.get(formatFilename(link));\n      if (linkedDoc) {\n        newRelated.push(linkedDoc.title);\n      } else {\n        newRelated.push(link);\n      }\n    });\n\n    // Find related docs by shared tags\n    const sharedTagDocs = docs.filter(other =>\n      other !== doc &&\n      other.tags.some(t => doc.tags.includes(t))\n    );\n\n    sharedTagDocs.slice(0, 3).forEach(other => {\n      if (!newRelated.includes(other.title)) {\n        newRelated.push(other.title);\n      }\n    });\n\n    doc.related = [...new Set(newRelated)].slice(0, 10);\n  });\n}\n\n/**\n * Generate knowledge document content\n */\nfunction generateKnowledgeDoc(\n  doc: AnalyzedDoc,\n  sourceDir: string,\n  linkOriginal: boolean,\n  allDocs: AnalyzedDoc[]\n): string {\n  const lines: string[] = [];\n\n  // Frontmatter\n  lines.push('---');\n  lines.push(`title: \"${doc.title}\"`);\n  lines.push(`type: ${doc.type}`);\n  lines.push(`status: active`);\n  if (doc.tags.length > 0) {\n    lines.push('tags:');\n    doc.tags.forEach(tag => lines.push(`  - ${tag}`));\n  }\n  lines.push(`category: ${doc.category}`);\n  lines.push(`description: \"${doc.summary.replace(/\"/g, '\\\\\"')}\"`);\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push(`updated: ${new Date().toISOString().split('T')[0]}`);\n  if (linkOriginal) {\n    lines.push(`original: \"${sourceDir}/${doc.originalPath}\"`);\n  }\n  if (doc.related.length > 0) {\n    lines.push('related:');\n    doc.related.slice(0, 5).forEach(r => lines.push(`  - \"[[${r}]]\"`));\n  }\n  lines.push('---');\n  lines.push('');\n\n  // Title\n  lines.push(`# ${doc.title}`);\n  lines.push('');\n\n  // Summary\n  lines.push('## Overview');\n  lines.push('');\n  lines.push(doc.summary);\n  lines.push('');\n\n  // Original reference\n  if (linkOriginal) {\n    lines.push(`> [!info] Original Documentation`);\n    lines.push(`> See [[${sourceDir}/${doc.originalPath}|original document]] for full details.`);\n    lines.push('');\n  }\n\n  // Key concepts\n  if (doc.concepts.length > 0) {\n    lines.push('## Key Concepts');\n    lines.push('');\n    doc.concepts.forEach(concept => {\n      lines.push(`- **${concept}**`);\n    });\n    lines.push('');\n  }\n\n  // Related documents\n  if (doc.related.length > 0) {\n    lines.push('## Related');\n    lines.push('');\n    doc.related.forEach(rel => {\n      lines.push(`- [[${rel}]]`);\n    });\n    lines.push('');\n  }\n\n  // Research needed\n  if (doc.researchNeeded.length > 0) {\n    lines.push('## Research Needed');\n    lines.push('');\n    lines.push('> [!warning] Areas Requiring Further Research');\n    doc.researchNeeded.forEach(area => {\n      lines.push(`> - ${area}`);\n    });\n    lines.push('');\n  }\n\n  // TODOs\n  if (doc.todos.length > 0) {\n    lines.push('## TODOs');\n    lines.push('');\n    doc.todos.forEach(todo => {\n      lines.push(`- [ ] ${todo}`);\n    });\n    lines.push('');\n  }\n\n  // Tags section\n  lines.push('## Tags');\n  lines.push('');\n  lines.push(doc.tags.map(t => `#${t}`).join(' '));\n  lines.push('');\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate MOC (Map of Content) for a category\n */\nfunction generateMOC(category: string, docTitles: string[], allDocs: AnalyzedDoc[]): string {\n  const config = CATEGORY_STRUCTURE[category];\n  const categoryDocs = allDocs.filter(d => d.category.startsWith(category));\n\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push(`title: \"${formatTitle(category)} - Map of Content\"`);\n  lines.push('type: concept');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - moc');\n  lines.push(`  - ${category}`);\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push(`# ${formatTitle(category)}`);\n  lines.push('');\n  lines.push(config?.description || `Documentation related to ${category}.`);\n  lines.push('');\n\n  // Group by subcategory\n  const bySubcategory = new Map<string, AnalyzedDoc[]>();\n  categoryDocs.forEach(doc => {\n    const parts = doc.category.split('/');\n    const sub = parts[1] || 'general';\n    if (!bySubcategory.has(sub)) {\n      bySubcategory.set(sub, []);\n    }\n    bySubcategory.get(sub)!.push(doc);\n  });\n\n  for (const [sub, docs] of bySubcategory) {\n    lines.push(`## ${formatTitle(sub)}`);\n    lines.push('');\n    docs.forEach(doc => {\n      lines.push(`- [[${doc.title}]] - ${doc.summary.slice(0, 60)}...`);\n    });\n    lines.push('');\n  }\n\n  lines.push('---');\n  lines.push(`*${categoryDocs.length} documents in this category*`);\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate master MOC\n */\nfunction generateMasterMOC(structure: Map<string, string[]>, allDocs: AnalyzedDoc[]): string {\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push('title: \"Knowledge Graph - Master Index\"');\n  lines.push('type: concept');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - moc');\n  lines.push('  - index');\n  lines.push('  - knowledge-graph');\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push('# Knowledge Graph');\n  lines.push('');\n  lines.push('Welcome to the knowledge graph. This is the master index of all documentation.');\n  lines.push('');\n  lines.push('## Categories');\n  lines.push('');\n\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    const count = structure.get(category)?.length || 0;\n    lines.push(`### [[${category}/_MOC|${formatTitle(category)}]]`);\n    lines.push('');\n    lines.push(`${config.description}`);\n    lines.push(`*${count} documents*`);\n    lines.push('');\n  }\n\n  lines.push('## Quick Links');\n  lines.push('');\n  lines.push('- [[PRIMITIVES]] - Core building blocks and technologies');\n  lines.push('- [[guides/_MOC|Getting Started]]');\n  lines.push('- [[standards/_MOC|Coding Standards]]');\n  lines.push('');\n\n  lines.push('## Statistics');\n  lines.push('');\n  lines.push(`- **Total Documents**: ${allDocs.length}`);\n  lines.push(`- **Categories**: ${structure.size}`);\n  lines.push(`- **Generated**: ${new Date().toISOString()}`);\n  lines.push('');\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate PRIMITIVES.md\n */\nfunction generatePrimitives(allDocs: AnalyzedDoc[]): string {\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push('title: \"Primitives\"');\n  lines.push('type: primitive');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - primitives');\n  lines.push('  - foundation');\n  lines.push('  - knowledge-graph');\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push('# Primitives');\n  lines.push('');\n  lines.push('Core building blocks and foundational technologies used in this project.');\n  lines.push('');\n\n  // Group docs by type\n  const byType = new Map<NodeType, AnalyzedDoc[]>();\n  allDocs.forEach(doc => {\n    if (!byType.has(doc.type)) {\n      byType.set(doc.type, []);\n    }\n    byType.get(doc.type)!.push(doc);\n  });\n\n  for (const [type, docs] of byType) {\n    lines.push(`## ${formatTitle(type)}`);\n    lines.push('');\n    docs.slice(0, 10).forEach(doc => {\n      lines.push(`- [[${doc.title}]]`);\n    });\n    if (docs.length > 10) {\n      lines.push(`- *...and ${docs.length - 10} more*`);\n    }\n    lines.push('');\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format filename from title\n */\nfunction formatFilename(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, '-')\n    .replace(/^-|-$/g, '')\n    .slice(0, 50);\n}\n\n/**\n * Format title from filename\n */\nfunction formatTitle(filename: string): string {\n  return filename\n    .replace(/[-_]/g, ' ')\n    .replace(/\\b\\w/g, c => c.toUpperCase())\n    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string;\n}\n\n/**\n * Analyzer result\n */\nexport interface AnalyzerResult {\n  success: boolean;\n  filesAnalyzed: number;\n  filesCreated: number;\n  mocFilesCreated: number;\n  errors: string[];\n  analyzed: AnalyzedDoc[];\n  structure: Map<string, string[]>;\n}\n\n/**\n * Weave-NN category structure with descriptions\n */\nconst CATEGORY_STRUCTURE: Record<string, { type: NodeType; description: string; subcategories: string[] }> = {\n  concepts: {\n    type: 'concept',\n    description: 'Abstract concepts, theories, and architectural principles',\n    subcategories: ['architecture', 'patterns', 'principles', 'models'],\n  },\n  components: {\n    type: 'technical',\n    description: 'Reusable technical components and implementations',\n    subcategories: ['ui', 'utilities', 'core', 'shared'],\n  },\n  services: {\n    type: 'service',\n    description: 'Backend services, APIs, and workers',\n    subcategories: ['api', 'workers', 'handlers', 'middleware'],\n  },\n  features: {\n    type: 'feature',\n    description: 'Product features and capabilities',\n    subcategories: ['core', 'advanced', 'experimental'],\n  },\n  integrations: {\n    type: 'integration',\n    description: 'External integrations and adapters',\n    subcategories: ['databases', 'auth', 'storage', 'monitoring', 'third-party'],\n  },\n  standards: {\n    type: 'standard',\n    description: 'Coding standards, conventions, and best practices',\n    subcategories: ['coding', 'documentation', 'testing', 'security'],\n  },\n  guides: {\n    type: 'guide',\n    description: 'How-to guides and tutorials',\n    subcategories: ['getting-started', 'tutorials', 'troubleshooting', 'deployment'],\n  },\n  references: {\n    type: 'technical',\n    description: 'API references and technical documentation',\n    subcategories: ['api', 'cli', 'config', 'schemas'],\n  },\n};\n\n/**\n * Analyze and migrate documentation to weave-nn structure\n */\nexport async function analyzeDocs(options: AnalyzerOptions): Promise<AnalyzerResult> {\n  const {\n    sourceDir,\n    targetDir = 'docs',\n    projectRoot,\n    useClaudeFlow = false,\n    createMOC = true,\n    linkOriginal = true,\n    maxDepth = 3,\n    dryRun = false,\n    verbose = false,\n  } = options;\n\n  const result: AnalyzerResult = {\n    success: true,\n    filesAnalyzed: 0,\n    filesCreated: 0,\n    mocFilesCreated: 0,\n    errors: [],\n    analyzed: [],\n    structure: new Map(),\n  };\n\n  const sourcePath = join(projectRoot, sourceDir);\n  const targetPath = join(projectRoot, targetDir);\n\n  // Validate source exists\n  if (!existsSync(sourcePath)) {\n    result.success = false;\n    result.errors.push(`Source directory not found: ${sourcePath}`);\n    return result;\n  }\n\n  // Create target structure\n  if (!dryRun) {\n    createFullStructure(targetPath);\n  }\n\n  // Find all markdown files\n  const files = await fg('**/*.md', {\n    cwd: sourcePath,\n    ignore: ['node_modules/**', '.git/**', '_templates/**', 'docs-nn/**'],\n  });\n\n  // First pass: Analyze all documents\n  const analyzedDocs: AnalyzedDoc[] = [];\n\n  for (const file of files) {\n    result.filesAnalyzed++;\n    const sourceFile = join(sourcePath, file);\n\n    try {\n      const analyzed = await analyzeDocument(sourceFile, file, sourcePath, {\n        useClaudeFlow,\n        linkOriginal,\n        verbose,\n      });\n      analyzedDocs.push(analyzed);\n\n      // Track structure\n      const category = analyzed.category.split('/')[0];\n      if (!result.structure.has(category)) {\n        result.structure.set(category, []);\n      }\n      result.structure.get(category)!.push(analyzed.title);\n\n    } catch (error) {\n      result.errors.push(`Failed to analyze ${file}: ${error}`);\n    }\n  }\n\n  // Build cross-references between documents\n  buildCrossReferences(analyzedDocs);\n\n  // Second pass: Create new documents\n  for (const doc of analyzedDocs) {\n    try {\n      const targetFile = join(targetPath, doc.newPath);\n\n      if (!dryRun) {\n        mkdirSync(dirname(targetFile), { recursive: true });\n        const content = generateKnowledgeDoc(doc, sourceDir, linkOriginal, analyzedDocs);\n        writeFileSync(targetFile, content, 'utf-8');\n      }\n\n      result.filesCreated++;\n      result.analyzed.push(doc);\n\n    } catch (error) {\n      result.errors.push(`Failed to create ${doc.newPath}: ${error}`);\n    }\n  }\n\n  // Create MOC files for each category\n  if (createMOC && !dryRun) {\n    for (const [category, docs] of result.structure) {\n      const mocPath = join(targetPath, category, '_MOC.md');\n      const mocContent = generateMOC(category, docs, analyzedDocs);\n      writeFileSync(mocPath, mocContent, 'utf-8');\n      result.mocFilesCreated++;\n    }\n\n    // Create master MOC\n    const masterMocPath = join(targetPath, 'MOC.md');\n    const masterMocContent = generateMasterMOC(result.structure, analyzedDocs);\n    writeFileSync(masterMocPath, masterMocContent, 'utf-8');\n    result.mocFilesCreated++;\n\n    // Create PRIMITIVES.md\n    const primitivesPath = join(targetPath, 'PRIMITIVES.md');\n    const primitivesContent = generatePrimitives(analyzedDocs);\n    writeFileSync(primitivesPath, primitivesContent, 'utf-8');\n  }\n\n  result.success = result.errors.length === 0;\n  return result;\n}\n\n/**\n * Analyze a single document\n */\nasync function analyzeDocument(\n  filePath: string,\n  relativePath: string,\n  sourcePath: string,\n  options: { useClaudeFlow?: boolean; linkOriginal?: boolean; verbose?: boolean }\n): Promise<AnalyzedDoc> {\n  const content = readFileSync(filePath, 'utf-8');\n  const { data: existingFrontmatter, content: body } = matter(content);\n\n  const filename = basename(filePath, '.md');\n  const title = existingFrontmatter.title as string || formatTitle(filename);\n\n  // Detect node type and category\n  const { type, category } = detectTypeAndCategory(relativePath, body, existingFrontmatter);\n\n  // Extract tags\n  const tags = extractAllTags(body, existingFrontmatter, relativePath);\n\n  // Extract wikilinks and markdown links\n  const related = extractLinks(body);\n\n  // Extract key concepts\n  const concepts = extractConcepts(body);\n\n  // Find areas needing research\n  const researchNeeded = findResearchAreas(body, filename);\n\n  // Extract existing TODOs and generate new ones\n  const todos = extractAndGenerateTodos(body, content, filename);\n\n  // Generate summary\n  const summary = generateSummary(body, existingFrontmatter);\n\n  // Determine new path\n  const newPath = join(category, formatFilename(filename) + '.md');\n\n  return {\n    originalPath: relativePath,\n    newPath,\n    title,\n    type,\n    tags,\n    related,\n    concepts,\n    researchNeeded,\n    todos,\n    summary,\n    category,\n  };\n}\n\n/**\n * Create full target directory structure\n */\nfunction createFullStructure(targetPath: string): void {\n  // Create all category directories and subcategories\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    mkdirSync(join(targetPath, category), { recursive: true });\n    for (const sub of config.subcategories) {\n      mkdirSync(join(targetPath, category, sub), { recursive: true });\n    }\n  }\n\n  // Create meta directories\n  mkdirSync(join(targetPath, '_templates'), { recursive: true });\n  mkdirSync(join(targetPath, '_attachments'), { recursive: true });\n  mkdirSync(join(targetPath, '_archive'), { recursive: true });\n}\n\n/**\n * Detect node type and category from content\n */\nfunction detectTypeAndCategory(\n  filePath: string,\n  content: string,\n  frontmatter: Record<string, unknown>\n): { type: NodeType; category: string } {\n  // Check frontmatter first\n  if (frontmatter.type && frontmatter.category) {\n    return {\n      type: frontmatter.type as NodeType,\n      category: frontmatter.category as string,\n    };\n  }\n\n  const lowerContent = content.toLowerCase();\n  const lowerPath = filePath.toLowerCase();\n\n  // Score each category\n  const scores: Record<string, number> = {};\n\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    scores[category] = 0;\n\n    // Path matching\n    if (lowerPath.includes(category)) scores[category] += 10;\n    for (const sub of config.subcategories) {\n      if (lowerPath.includes(sub)) scores[category] += 5;\n    }\n\n    // Content analysis based on type\n    const keywords = getKeywordsForType(config.type);\n    for (const keyword of keywords) {\n      const regex = new RegExp(`\\\\b${keyword}\\\\b`, 'gi');\n      const matches = content.match(regex);\n      if (matches) scores[category] += matches.length;\n    }\n  }\n\n  // Find best match\n  let bestCategory = 'concepts';\n  let bestScore = 0;\n\n  for (const [category, score] of Object.entries(scores)) {\n    if (score > bestScore) {\n      bestScore = score;\n      bestCategory = category;\n    }\n  }\n\n  return {\n    type: CATEGORY_STRUCTURE[bestCategory].type,\n    category: bestCategory,\n  };\n}\n\n/**\n * Get keywords for a node type\n */\nfunction getKeywordsForType(type: NodeType): string[] {\n  const keywords: Record<NodeType, string[]> = {\n    concept: ['concept', 'theory', 'principle', 'overview', 'introduction', 'architecture', 'design', 'pattern'],\n    technical: ['component', 'implementation', 'class', 'function', 'module', 'utility', 'helper'],\n    feature: ['feature', 'capability', 'functionality', 'user', 'requirement', 'use case'],\n    primitive: ['library', 'framework', 'dependency', 'tool', 'sdk'],\n    service: ['api', 'endpoint', 'service', 'server', 'backend', 'worker', 'handler'],\n    guide: ['how to', 'tutorial', 'guide', 'step', 'walkthrough', 'getting started'],\n    standard: ['standard', 'convention', 'best practice', 'rule', 'guideline', 'style'],\n    integration: ['integration', 'connect', 'plugin', 'adapter', 'sync', 'import', 'export'],\n  };\n\n  return keywords[type] || [];\n}\n\n/**\n * Extract all tags from content and path\n */\nfunction extractAllTags(\n  content: string,\n  frontmatter: Record<string, unknown>,\n  filePath: string\n): string[] {\n  const tags = new Set<string>();\n\n  // Add existing frontmatter tags\n  if (Array.isArray(frontmatter.tags)) {\n    frontmatter.tags.forEach(t => tags.add(String(t)));\n  }\n\n  // Extract #tags from content\n  const hashTags = content.match(/#[\\w-]+/g);\n  if (hashTags) {\n    hashTags.forEach(t => tags.add(t.slice(1)));\n  }\n\n  // Generate tags from path\n  const pathParts = filePath.split('/').filter(p => p && !p.endsWith('.md'));\n  pathParts.forEach(p => {\n    if (p.length > 2 && p.length < 20) {\n      tags.add(p.replace(/[-_]/g, '-').toLowerCase());\n    }\n  });\n\n  // Add status tags\n  if (content.match(/\\b(wip|draft|todo)\\b/i)) tags.add('needs-work');\n  if (content.match(/\\b(deprecated|legacy)\\b/i)) tags.add('deprecated');\n  if (content.match(/\\b(experimental|beta)\\b/i)) tags.add('experimental');\n\n  return [...tags].slice(0, 15);\n}\n\n/**\n * Extract wikilinks and markdown links\n */\nfunction extractLinks(content: string): string[] {\n  const links = new Set<string>();\n\n  // Wikilinks\n  const wikilinks = content.match(/\\[\\[([^\\]|]+)(?:\\|[^\\]]+)?\\]\\]/g);\n  if (wikilinks) {\n    wikilinks.forEach(link => {\n      const match = link.match(/\\[\\[([^\\]|]+)/);\n      if (match) links.add(match[1].trim());\n    });\n  }\n\n  // Markdown links (internal only)\n  const mdLinks = content.match(/\\[([^\\]]+)\\]\\(([^)]+)\\)/g);\n  if (mdLinks) {\n    mdLinks.forEach(link => {\n      const match = link.match(/\\]\\(([^)]+)\\)/);\n      if (match && !match[1].startsWith('http')) {\n        links.add(match[1].replace(/\\.md$/, '').trim());\n      }\n    });\n  }\n\n  return [...links];\n}\n\n/**\n * Extract key concepts from content\n */\nfunction extractConcepts(content: string): string[] {\n  const concepts: string[] = [];\n\n  // Look for headers as concepts\n  const headers = content.match(/^##\\s+(.+)$/gm);\n  if (headers) {\n    headers.slice(0, 5).forEach(h => {\n      concepts.push(h.replace(/^##\\s+/, '').trim());\n    });\n  }\n\n  // Look for bold terms as concepts\n  const boldTerms = content.match(/\\*\\*([^*]+)\\*\\*/g);\n  if (boldTerms) {\n    boldTerms.slice(0, 5).forEach(term => {\n      const clean = term.replace(/\\*\\*/g, '').trim();\n      if (clean.length > 2 && clean.length < 50) {\n        concepts.push(clean);\n      }\n    });\n  }\n\n  return [...new Set(concepts)].slice(0, 10);\n}\n\n/**\n * Find areas needing research\n */\nfunction findResearchAreas(content: string, filename: string): string[] {\n  const areas: string[] = [];\n\n  // Look for question marks indicating uncertainty\n  const questions = content.match(/[^.!?]*\\?/g);\n  if (questions) {\n    questions.slice(0, 3).forEach(q => {\n      if (q.length > 10 && q.length < 200) {\n        areas.push(q.trim());\n      }\n    });\n  }\n\n  // Look for placeholders\n  if (content.match(/\\bTBD\\b|\\bTODO\\b|\\bFIXME\\b/i)) {\n    areas.push('Contains placeholders that need completion');\n  }\n\n  // Look for empty sections\n  const emptyHeaders = content.match(/^##[^#\\n]+\\n\\n##/gm);\n  if (emptyHeaders) {\n    areas.push('Has empty sections that need content');\n  }\n\n  // Check for missing content indicators\n  if (content.length < 500) {\n    areas.push('Document is short - may need expansion');\n  }\n\n  return areas;\n}\n\n/**\n * Extract and generate TODOs\n */\nfunction extractAndGenerateTodos(body: string, fullContent: string, filename: string): string[] {\n  const todos: string[] = [];\n\n  // Extract existing TODOs\n  const existingTodos = fullContent.match(/[-*]\\s*\\[[ x]\\]\\s*(.+)/g);\n  if (existingTodos) {\n    existingTodos.forEach(todo => {\n      todos.push(todo.replace(/^[-*]\\s*\\[[ x]\\]\\s*/, '').trim());\n    });\n  }\n\n  // Extract TODO comments\n  const todoComments = fullContent.match(/(?:TODO|FIXME|XXX):\\s*(.+)/gi);\n  if (todoComments) {\n    todoComments.forEach(todo => {\n      todos.push(todo.replace(/^(?:TODO|FIXME|XXX):\\s*/i, '').trim());\n    });\n  }\n\n  // Generate suggested TODOs based on analysis\n  if (!fullContent.match(/^---[\\s\\S]*?---/)) {\n    todos.push('Add proper frontmatter');\n  }\n\n  if (!fullContent.match(/\\[\\[/)) {\n    todos.push('Add wikilinks to related documents');\n  }\n\n  if (!fullContent.match(/^##\\s/m)) {\n    todos.push('Add section structure with headers');\n  }\n\n  return [...new Set(todos)].slice(0, 10);\n}\n\n/**\n * Generate summary from content\n */\nfunction generateSummary(body: string, frontmatter: Record<string, unknown>): string {\n  // Use existing description\n  if (frontmatter.description) {\n    return String(frontmatter.description);\n  }\n\n  // Extract first meaningful paragraph\n  const lines = body.split('\\n');\n  for (const line of lines) {\n    const trimmed = line.trim();\n    if (trimmed && !trimmed.startsWith('#') && !trimmed.startsWith('```') && trimmed.length > 30) {\n      return trimmed.length > 200 ? trimmed.slice(0, 197) + '...' : trimmed;\n    }\n  }\n\n  return 'Documentation requiring summary.';\n}\n\n/**\n * Build cross-references between documents\n */\nfunction buildCrossReferences(docs: AnalyzedDoc[]): void {\n  const titleMap = new Map<string, AnalyzedDoc>();\n\n  // Build title lookup\n  docs.forEach(doc => {\n    titleMap.set(doc.title.toLowerCase(), doc);\n    titleMap.set(formatFilename(doc.title), doc);\n  });\n\n  // Update related links\n  docs.forEach(doc => {\n    const newRelated: string[] = [];\n\n    doc.related.forEach(link => {\n      const linkedDoc = titleMap.get(link.toLowerCase()) || titleMap.get(formatFilename(link));\n      if (linkedDoc) {\n        newRelated.push(linkedDoc.title);\n      } else {\n        newRelated.push(link);\n      }\n    });\n\n    // Find related docs by shared tags\n    const sharedTagDocs = docs.filter(other =>\n      other !== doc &&\n      other.tags.some(t => doc.tags.includes(t))\n    );\n\n    sharedTagDocs.slice(0, 3).forEach(other => {\n      if (!newRelated.includes(other.title)) {\n        newRelated.push(other.title);\n      }\n    });\n\n    doc.related = [...new Set(newRelated)].slice(0, 10);\n  });\n}\n\n/**\n * Generate knowledge document content\n */\nfunction generateKnowledgeDoc(\n  doc: AnalyzedDoc,\n  sourceDir: string,\n  linkOriginal: boolean,\n  allDocs: AnalyzedDoc[]\n): string {\n  const lines: string[] = [];\n\n  // Frontmatter\n  lines.push('---');\n  lines.push(`title: \"${doc.title}\"`);\n  lines.push(`type: ${doc.type}`);\n  lines.push(`status: active`);\n  if (doc.tags.length > 0) {\n    lines.push('tags:');\n    doc.tags.forEach(tag => lines.push(`  - ${tag}`));\n  }\n  lines.push(`category: ${doc.category}`);\n  lines.push(`description: \"${doc.summary.replace(/\"/g, '\\\\\"')}\"`);\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push(`updated: ${new Date().toISOString().split('T')[0]}`);\n  if (linkOriginal) {\n    lines.push(`original: \"${sourceDir}/${doc.originalPath}\"`);\n  }\n  if (doc.related.length > 0) {\n    lines.push('related:');\n    doc.related.slice(0, 5).forEach(r => lines.push(`  - \"[[${r}]]\"`));\n  }\n  lines.push('---');\n  lines.push('');\n\n  // Title\n  lines.push(`# ${doc.title}`);\n  lines.push('');\n\n  // Summary\n  lines.push('## Overview');\n  lines.push('');\n  lines.push(doc.summary);\n  lines.push('');\n\n  // Original reference\n  if (linkOriginal) {\n    lines.push(`> [!info] Original Documentation`);\n    lines.push(`> See [[${sourceDir}/${doc.originalPath}|original document]] for full details.`);\n    lines.push('');\n  }\n\n  // Key concepts\n  if (doc.concepts.length > 0) {\n    lines.push('## Key Concepts');\n    lines.push('');\n    doc.concepts.forEach(concept => {\n      lines.push(`- **${concept}**`);\n    });\n    lines.push('');\n  }\n\n  // Related documents\n  if (doc.related.length > 0) {\n    lines.push('## Related');\n    lines.push('');\n    doc.related.forEach(rel => {\n      lines.push(`- [[${rel}]]`);\n    });\n    lines.push('');\n  }\n\n  // Research needed\n  if (doc.researchNeeded.length > 0) {\n    lines.push('## Research Needed');\n    lines.push('');\n    lines.push('> [!warning] Areas Requiring Further Research');\n    doc.researchNeeded.forEach(area => {\n      lines.push(`> - ${area}`);\n    });\n    lines.push('');\n  }\n\n  // TODOs\n  if (doc.todos.length > 0) {\n    lines.push('## TODOs');\n    lines.push('');\n    doc.todos.forEach(todo => {\n      lines.push(`- [ ] ${todo}`);\n    });\n    lines.push('');\n  }\n\n  // Tags section\n  lines.push('## Tags');\n  lines.push('');\n  lines.push(doc.tags.map(t => `#${t}`).join(' '));\n  lines.push('');\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate MOC (Map of Content) for a category\n */\nfunction generateMOC(category: string, docTitles: string[], allDocs: AnalyzedDoc[]): string {\n  const config = CATEGORY_STRUCTURE[category];\n  const categoryDocs = allDocs.filter(d => d.category.startsWith(category));\n\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push(`title: \"${formatTitle(category)} - Map of Content\"`);\n  lines.push('type: concept');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - moc');\n  lines.push(`  - ${category}`);\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push(`# ${formatTitle(category)}`);\n  lines.push('');\n  lines.push(config?.description || `Documentation related to ${category}.`);\n  lines.push('');\n\n  // Group by subcategory\n  const bySubcategory = new Map<string, AnalyzedDoc[]>();\n  categoryDocs.forEach(doc => {\n    const parts = doc.category.split('/');\n    const sub = parts[1] || 'general';\n    if (!bySubcategory.has(sub)) {\n      bySubcategory.set(sub, []);\n    }\n    bySubcategory.get(sub)!.push(doc);\n  });\n\n  for (const [sub, docs] of bySubcategory) {\n    lines.push(`## ${formatTitle(sub)}`);\n    lines.push('');\n    docs.forEach(doc => {\n      lines.push(`- [[${doc.title}]] - ${doc.summary.slice(0, 60)}...`);\n    });\n    lines.push('');\n  }\n\n  lines.push('---');\n  lines.push(`*${categoryDocs.length} documents in this category*`);\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate master MOC\n */\nfunction generateMasterMOC(structure: Map<string, string[]>, allDocs: AnalyzedDoc[]): string {\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push('title: \"Knowledge Graph - Master Index\"');\n  lines.push('type: concept');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - moc');\n  lines.push('  - index');\n  lines.push('  - knowledge-graph');\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push('# Knowledge Graph');\n  lines.push('');\n  lines.push('Welcome to the knowledge graph. This is the master index of all documentation.');\n  lines.push('');\n  lines.push('## Categories');\n  lines.push('');\n\n  for (const [category, config] of Object.entries(CATEGORY_STRUCTURE)) {\n    const count = structure.get(category)?.length || 0;\n    lines.push(`### [[${category}/_MOC|${formatTitle(category)}]]`);\n    lines.push('');\n    lines.push(`${config.description}`);\n    lines.push(`*${count} documents*`);\n    lines.push('');\n  }\n\n  lines.push('## Quick Links');\n  lines.push('');\n  lines.push('- [[PRIMITIVES]] - Core building blocks and technologies');\n  lines.push('- [[guides/_MOC|Getting Started]]');\n  lines.push('- [[standards/_MOC|Coding Standards]]');\n  lines.push('');\n\n  lines.push('## Statistics');\n  lines.push('');\n  lines.push(`- **Total Documents**: ${allDocs.length}`);\n  lines.push(`- **Categories**: ${structure.size}`);\n  lines.push(`- **Generated**: ${new Date().toISOString()}`);\n  lines.push('');\n\n  return lines.join('\\n');\n}\n\n/**\n * Generate PRIMITIVES.md\n */\nfunction generatePrimitives(allDocs: AnalyzedDoc[]): string {\n  const lines: string[] = [];\n\n  lines.push('---');\n  lines.push('title: \"Primitives\"');\n  lines.push('type: primitive');\n  lines.push('status: active');\n  lines.push('tags:');\n  lines.push('  - primitives');\n  lines.push('  - foundation');\n  lines.push('  - knowledge-graph');\n  lines.push(`created: ${new Date().toISOString().split('T')[0]}`);\n  lines.push('---');\n  lines.push('');\n  lines.push('# Primitives');\n  lines.push('');\n  lines.push('Core building blocks and foundational technologies used in this project.');\n  lines.push('');\n\n  // Group docs by type\n  const byType = new Map<NodeType, AnalyzedDoc[]>();\n  allDocs.forEach(doc => {\n    if (!byType.has(doc.type)) {\n      byType.set(doc.type, []);\n    }\n    byType.get(doc.type)!.push(doc);\n  });\n\n  for (const [type, docs] of byType) {\n    lines.push(`## ${formatTitle(type)}`);\n    lines.push('');\n    docs.slice(0, 10).forEach(doc => {\n      lines.push(`- [[${doc.title}]]`);\n    });\n    if (docs.length > 10) {\n      lines.push(`- *...and ${docs.length - 10} more*`);\n    }\n    lines.push('');\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format filename from title\n */\nfunction formatFilename(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, '-')\n    .replace(/^-|-$/g, '')\n    .slice(0, 50);\n}\n\n/**\n * Format title from filename\n */\nfunction formatTitle(filename: string): string {\n  return filename\n    .replace(/[-_]/g, ' ')\n    .replace(/\\b\\w/g, c => c.toUpperCase())\n    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package/dist/generators/docs-convert.d.ts

@@ -11,7 +11,7 @@ import type { NodeType, NodeStatus } from '../core/types.js';
 export interface ConvertOptions {
     /** Source directory with existing docs */
     sourceDir: string;
-    /** Target directory (default: docs-nn) */
+    /** Target directory (default: docs) */
     targetDir?: string;
     /** Project root for path resolution */
     projectRoot: string;

package/dist/generators/docs-convert.d.ts.map

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package/dist/generators/docs-convert.js

@@ -119,7 +119,7 @@ const PATH_PATTERNS = [
 async function convertDocs(options) {
   const {
     sourceDir,
-    targetDir = "docs-nn",
+    targetDir = "docs",
     projectRoot,
     preserveOriginal = true,
     force = false,

package/dist/generators/docs-convert.js.map

@@ -1 +1 @@
-{"version":3,"file":"docs-convert.js","sources":["../../src/generators/docs-convert.ts"],"sourcesContent":["/**\n * Docs Converter\n *\n * Converts existing documentation to weave-nn structure with proper\n * frontmatter and directory organization.\n */\n\nimport { existsSync, mkdirSync, readFileSync, writeFileSync, copyFileSync } from 'fs';\nimport { join, basename, dirname, relative, extname } from 'path';\nimport fg from 'fast-glob';\nimport matter from 'gray-matter';\nimport type { NodeType, NodeStatus, NodeFrontmatter } from '../core/types.js';\n\n/**\n * Conversion options\n */\nexport interface ConvertOptions {\n  /** Source directory with existing docs */\n  sourceDir: string;\n  /** Target directory (default: docs-nn) */\n  targetDir?: string;\n  /** Project root for path resolution */\n  projectRoot: string;\n  /** Preserve original files (copy instead of move) */\n  preserveOriginal?: boolean;\n  /** Overwrite existing files in target */\n  force?: boolean;\n  /** Auto-categorize based on content analysis */\n  autoCategory?: boolean;\n  /** Dry run - show what would be done */\n  dryRun?: boolean;\n}\n\n/**\n * Frontmatter options\n */\nexport interface FrontmatterOptions {\n  /** Target file or directory */\n  target: string;\n  /** Project root */\n  projectRoot: string;\n  /** Override type detection */\n  type?: NodeType;\n  /** Override status */\n  status?: NodeStatus;\n  /** Additional tags to add */\n  tags?: string[];\n  /** Force overwrite existing frontmatter */\n  force?: boolean;\n  /** Dry run */\n  dryRun?: boolean;\n}\n\n/**\n * Conversion result\n */\nexport interface ConvertResult {\n  success: boolean;\n  filesProcessed: number;\n  filesConverted: number;\n  filesSkipped: number;\n  errors: string[];\n  converted: Array<{\n    source: string;\n    target: string;\n    type: NodeType;\n  }>;\n}\n\n/**\n * Frontmatter result\n */\nexport interface FrontmatterResult {\n  success: boolean;\n  filesProcessed: number;\n  filesUpdated: number;\n  filesSkipped: number;\n  errors: string[];\n}\n\n/**\n * Weave-NN directory structure mapping\n */\nconst CATEGORY_DIRS: Record<NodeType, string> = {\n  concept: 'concepts',\n  technical: 'components',\n  feature: 'features',\n  primitive: 'integrations',\n  service: 'services',\n  guide: 'guides',\n  standard: 'standards',\n  integration: 'integrations',\n};\n\n/**\n * Keywords for content-based categorization\n */\nconst CATEGORY_KEYWORDS: Record<NodeType, string[]> = {\n  concept: [\n    'overview', 'introduction', 'theory', 'principle', 'concept',\n    'philosophy', 'approach', 'methodology', 'paradigm', 'model',\n  ],\n  technical: [\n    'component', 'implementation', 'class', 'function', 'module',\n    'algorithm', 'data structure', 'interface', 'abstract', 'utility',\n  ],\n  feature: [\n    'feature', 'capability', 'functionality', 'use case', 'user story',\n    'requirement', 'specification', 'product', 'roadmap',\n  ],\n  primitive: [\n    'library', 'framework', 'dependency', 'package', 'tool',\n    'sdk', 'runtime', 'platform', 'language',\n  ],\n  service: [\n    'api', 'endpoint', 'service', 'server', 'backend', 'microservice',\n    'rest', 'graphql', 'webhook', 'worker', 'queue',\n  ],\n  guide: [\n    'how to', 'tutorial', 'guide', 'walkthrough', 'step by step',\n    'getting started', 'setup', 'installation', 'configuration',\n  ],\n  standard: [\n    'standard', 'convention', 'best practice', 'rule', 'policy',\n    'guideline', 'coding style', 'lint', 'format',\n  ],\n  integration: [\n    'integration', 'connect', 'plugin', 'adapter', 'bridge',\n    'sync', 'import', 'export', 'webhook',\n  ],\n};\n\n/**\n * Path-based categorization patterns\n */\nconst PATH_PATTERNS: Array<{ pattern: RegExp; type: NodeType }> = [\n  { pattern: /\\/(api|endpoints?|routes?)\\//i, type: 'service' },\n  { pattern: /\\/(guide|tutorial|howto|getting-started)\\//i, type: 'guide' },\n  { pattern: /\\/(component|ui|widget)\\//i, type: 'technical' },\n  { pattern: /\\/(feature|capability)\\//i, type: 'feature' },\n  { pattern: /\\/(standard|convention|style)\\//i, type: 'standard' },\n  { pattern: /\\/(integration|plugin|adapter)\\//i, type: 'integration' },\n  { pattern: /\\/(service|worker|job)\\//i, type: 'service' },\n  { pattern: /\\/(concept|architecture|design)\\//i, type: 'concept' },\n];\n\n/**\n * Convert existing docs to weave-nn structure\n */\nexport async function convertDocs(options: ConvertOptions): Promise<ConvertResult> {\n  const {\n    sourceDir,\n    targetDir = 'docs-nn',\n    projectRoot,\n    preserveOriginal = true,\n    force = false,\n    autoCategory = true,\n    dryRun = false,\n  } = options;\n\n  const result: ConvertResult = {\n    success: true,\n    filesProcessed: 0,\n    filesConverted: 0,\n    filesSkipped: 0,\n    errors: [],\n    converted: [],\n  };\n\n  const sourcePath = join(projectRoot, sourceDir);\n  const targetPath = join(projectRoot, targetDir);\n\n  // Validate source exists\n  if (!existsSync(sourcePath)) {\n    result.success = false;\n    result.errors.push(`Source directory not found: ${sourcePath}`);\n    return result;\n  }\n\n  // Create target structure\n  if (!dryRun) {\n    createTargetStructure(targetPath);\n  }\n\n  // Find all markdown files\n  const files = await fg('**/*.md', {\n    cwd: sourcePath,\n    ignore: ['node_modules/**', '.git/**', '_templates/**'],\n  });\n\n  for (const file of files) {\n    result.filesProcessed++;\n    const sourceFile = join(sourcePath, file);\n\n    try {\n      // Read and parse file\n      const content = readFileSync(sourceFile, 'utf-8');\n      const { data: existingFrontmatter, content: body } = matter(content);\n\n      // Determine node type\n      const nodeType = autoCategory\n        ? detectNodeType(file, body, existingFrontmatter)\n        : (existingFrontmatter.type as NodeType) || 'concept';\n\n      // Determine target path\n      const targetSubdir = CATEGORY_DIRS[nodeType];\n      const targetFile = join(targetPath, targetSubdir, basename(file));\n\n      // Check if target exists\n      if (existsSync(targetFile) && !force) {\n        result.filesSkipped++;\n        continue;\n      }\n\n      // Generate frontmatter\n      const frontmatter = generateFrontmatter(file, body, nodeType, existingFrontmatter);\n\n      // Build new content\n      const newContent = buildMarkdownWithFrontmatter(frontmatter, body);\n\n      if (!dryRun) {\n        // Ensure directory exists\n        mkdirSync(dirname(targetFile), { recursive: true });\n\n        // Write converted file\n        writeFileSync(targetFile, newContent, 'utf-8');\n      }\n\n      result.filesConverted++;\n      result.converted.push({\n        source: file,\n        target: relative(projectRoot, targetFile),\n        type: nodeType,\n      });\n\n    } catch (error) {\n      result.errors.push(`Failed to convert ${file}: ${error}`);\n    }\n  }\n\n  result.success = result.errors.length === 0;\n  return result;\n}\n\n/**\n * Add or update frontmatter in existing files\n */\nexport async function addFrontmatter(options: FrontmatterOptions): Promise<FrontmatterResult> {\n  const {\n    target,\n    projectRoot,\n    type,\n    status = 'active',\n    tags = [],\n    force = false,\n    dryRun = false,\n  } = options;\n\n  const result: FrontmatterResult = {\n    success: true,\n    filesProcessed: 0,\n    filesUpdated: 0,\n    filesSkipped: 0,\n    errors: [],\n  };\n\n  const targetPath = join(projectRoot, target);\n\n  // Handle single file or directory\n  let files: string[];\n  if (existsSync(targetPath) && !targetPath.endsWith('.md')) {\n    // Directory - find all markdown files\n    files = await fg('**/*.md', {\n      cwd: targetPath,\n      ignore: ['node_modules/**', '.git/**', '_templates/**'],\n      absolute: true,\n    });\n  } else if (existsSync(targetPath)) {\n    files = [targetPath];\n  } else {\n    result.success = false;\n    result.errors.push(`Target not found: ${targetPath}`);\n    return result;\n  }\n\n  for (const file of files) {\n    result.filesProcessed++;\n\n    try {\n      const content = readFileSync(file, 'utf-8');\n      const { data: existingFrontmatter, content: body } = matter(content);\n\n      // Skip if has frontmatter and not forcing\n      if (Object.keys(existingFrontmatter).length > 0 && !force) {\n        result.filesSkipped++;\n        continue;\n      }\n\n      // Detect type if not specified\n      const relPath = relative(projectRoot, file);\n      const nodeType = type || detectNodeType(relPath, body, existingFrontmatter);\n\n      // Generate frontmatter\n      const frontmatter = generateFrontmatter(\n        relPath,\n        body,\n        nodeType,\n        force ? {} : existingFrontmatter,\n        status,\n        tags\n      );\n\n      // Build new content\n      const newContent = buildMarkdownWithFrontmatter(frontmatter, body);\n\n      if (!dryRun) {\n        writeFileSync(file, newContent, 'utf-8');\n      }\n\n      result.filesUpdated++;\n\n    } catch (error) {\n      result.errors.push(`Failed to update ${file}: ${error}`);\n    }\n  }\n\n  result.success = result.errors.length === 0;\n  return result;\n}\n\n/**\n * Validate frontmatter in files\n */\nexport async function validateFrontmatter(\n  target: string,\n  projectRoot: string\n): Promise<{\n  valid: number;\n  invalid: number;\n  missing: number;\n  issues: Array<{ file: string; issues: string[] }>;\n}> {\n  const result = {\n    valid: 0,\n    invalid: 0,\n    missing: 0,\n    issues: [] as Array<{ file: string; issues: string[] }>,\n  };\n\n  const targetPath = join(projectRoot, target);\n\n  const files = await fg('**/*.md', {\n    cwd: targetPath,\n    ignore: ['node_modules/**', '.git/**', '_templates/**'],\n    absolute: true,\n  });\n\n  const validTypes: NodeType[] = [\n    'concept', 'technical', 'feature', 'primitive',\n    'service', 'guide', 'standard', 'integration',\n  ];\n\n  const validStatuses: NodeStatus[] = ['draft', 'active', 'deprecated', 'archived'];\n\n  for (const file of files) {\n    const content = readFileSync(file, 'utf-8');\n    const { data: frontmatter } = matter(content);\n    const fileIssues: string[] = [];\n\n    if (Object.keys(frontmatter).length === 0) {\n      result.missing++;\n      fileIssues.push('Missing frontmatter');\n    } else {\n      // Check required fields\n      if (!frontmatter.title) {\n        fileIssues.push('Missing title');\n      }\n      if (!frontmatter.type) {\n        fileIssues.push('Missing type');\n      } else if (!validTypes.includes(frontmatter.type)) {\n        fileIssues.push(`Invalid type: ${frontmatter.type}`);\n      }\n      if (frontmatter.status && !validStatuses.includes(frontmatter.status)) {\n        fileIssues.push(`Invalid status: ${frontmatter.status}`);\n      }\n      if (!frontmatter.created) {\n        fileIssues.push('Missing created date');\n      }\n    }\n\n    if (fileIssues.length > 0) {\n      result.invalid++;\n      result.issues.push({\n        file: relative(projectRoot, file),\n        issues: fileIssues,\n      });\n    } else if (Object.keys(frontmatter).length > 0) {\n      result.valid++;\n    }\n  }\n\n  return result;\n}\n\n// ============================================================================\n// Helper Functions\n// ============================================================================\n\n/**\n * Create target directory structure\n */\nfunction createTargetStructure(targetPath: string): void {\n  const dirs = [\n    '',\n    'concepts',\n    'concepts/architecture',\n    'concepts/patterns',\n    'components',\n    'components/ui',\n    'components/utilities',\n    'services',\n    'services/api',\n    'services/workers',\n    'features',\n    'features/core',\n    'features/advanced',\n    'integrations',\n    'integrations/databases',\n    'integrations/auth',\n    'standards',\n    'standards/coding',\n    'standards/documentation',\n    'guides',\n    'guides/getting-started',\n    'guides/tutorials',\n    'references',\n    'references/api',\n    '_templates',\n    '_attachments',\n  ];\n\n  for (const dir of dirs) {\n    const fullPath = join(targetPath, dir);\n    if (!existsSync(fullPath)) {\n      mkdirSync(fullPath, { recursive: true });\n    }\n  }\n}\n\n/**\n * Detect node type from file path and content\n */\nfunction detectNodeType(\n  filePath: string,\n  content: string,\n  existingFrontmatter: Record<string, unknown>\n): NodeType {\n  // Use existing type if valid\n  const validTypes: NodeType[] = [\n    'concept', 'technical', 'feature', 'primitive',\n    'service', 'guide', 'standard', 'integration',\n  ];\n\n  if (existingFrontmatter.type && validTypes.includes(existingFrontmatter.type as NodeType)) {\n    return existingFrontmatter.type as NodeType;\n  }\n\n  // Check path patterns\n  for (const { pattern, type } of PATH_PATTERNS) {\n    if (pattern.test(filePath)) {\n      return type;\n    }\n  }\n\n  // Analyze content\n  const lowerContent = content.toLowerCase();\n  const scores: Record<NodeType, number> = {\n    concept: 0,\n    technical: 0,\n    feature: 0,\n    primitive: 0,\n    service: 0,\n    guide: 0,\n    standard: 0,\n    integration: 0,\n  };\n\n  for (const [nodeType, keywords] of Object.entries(CATEGORY_KEYWORDS)) {\n    for (const keyword of keywords) {\n      const regex = new RegExp(`\\\\b${keyword}\\\\b`, 'gi');\n      const matches = lowerContent.match(regex);\n      if (matches) {\n        scores[nodeType as NodeType] += matches.length;\n      }\n    }\n  }\n\n  // Find highest scoring type\n  let maxScore = 0;\n  let detectedType: NodeType = 'concept';\n\n  for (const [nodeType, score] of Object.entries(scores)) {\n    if (score > maxScore) {\n      maxScore = score;\n      detectedType = nodeType as NodeType;\n    }\n  }\n\n  return detectedType;\n}\n\n/**\n * Generate frontmatter for a file\n */\nfunction generateFrontmatter(\n  filePath: string,\n  content: string,\n  nodeType: NodeType,\n  existing: Record<string, unknown> = {},\n  status: NodeStatus = 'active',\n  additionalTags: string[] = []\n): NodeFrontmatter {\n  const filename = basename(filePath, '.md');\n  const title = existing.title as string || formatTitle(filename);\n\n  // Extract tags from content\n  const extractedTags = extractTags(content);\n  const allTags = [...new Set([\n    ...(existing.tags as string[] || []),\n    ...extractedTags,\n    ...additionalTags,\n  ])];\n\n  // Get dates\n  const now = new Date().toISOString().split('T')[0];\n  const created = existing.created as string || now;\n\n  return {\n    title,\n    type: nodeType,\n    status: existing.status as NodeStatus || status,\n    tags: allTags.length > 0 ? allTags : undefined,\n    category: existing.category as string || undefined,\n    description: existing.description as string || extractDescription(content),\n    created,\n    updated: now,\n    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package/dist/node_modules/@typescript-eslint/typescript-estree/node_modules/minimatch/dist/commonjs/index.js

@@ -1,4 +1,4 @@
-import { __exports as commonjs } from "../../../../../../../_virtual/index9.js";
+import { __exports as commonjs } from "../../../../../../../_virtual/index8.js";
 import { __require as requireBraceExpansion } from "../../../../../../brace-expansion/index.js";
 import { __require as requireAssertValidPattern } from "./assert-valid-pattern.js";
 import { __require as requireAst } from "./ast.js";

package/dist/node_modules/fdir/dist/index.js

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../_virtual/index10.js";
+import { __exports as dist } from "../../../_virtual/index11.js";
 import path__default from "path";
 import require$$1 from "fs";
 import { __require as requirePicomatch } from "../../picomatch/index.js";

package/dist/node_modules/tinyglobby/dist/index.js

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../_virtual/index8.js";
+import { __exports as dist } from "../../../_virtual/index9.js";
 import require$$1 from "fs";
 import path__default from "path";
 import require$$2 from "url";

package/dist/node_modules/ts-api-utils/lib/index.js

@@ -1,4 +1,4 @@
-import { __exports as lib } from "../../../_virtual/index11.js";
+import { __exports as lib } from "../../../_virtual/index10.js";
 import { __require as requireTypescript } from "../../typescript/lib/typescript.js";
 var hasRequiredLib;
 function requireLib() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@weavelogic/knowledge-graph-agent",
-  "version": "0.10.0",
+  "version": "0.10.1",
   "description": "Knowledge graph agent for Claude Code - generates knowledge graphs, initializes docs, and integrates with claude-flow",
   "type": "module",
   "main": "dist/index.js",