@weavelogic/knowledge-graph-agent 0.10.3 → 0.10.4

package/dist/cli/commands/cultivate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cultivate.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/cultivate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAgCpC;;GAEG;AACH,wBAAgB,sBAAsB,IAAI,OAAO,CA4OhD"}
+{"version":3,"file":"cultivate.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/cultivate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAgCpC;;GAEG;AACH,wBAAgB,sBAAsB,IAAI,OAAO,CA8PhD"}

package/dist/cli/commands/cultivate.js

@@ -121,32 +121,52 @@ function createCultivateCommand() {
         console.log("");
       }
       if (tasks.deepAnalysis) {
-        console.log(chalk.cyan("🧠 Running deep analysis with claude-flow...\n"));
-        const hasClaudeFlow = await checkClaudeFlowAvailable();
-        if (!hasClaudeFlow) {
-          console.log(chalk.yellow("  ⚠️  claude-flow not available"));
-          console.log(chalk.gray("  Install with: npm install -g claude-flow"));
-          result.warnings.push("claude-flow not available for deep analysis");
+        console.log(chalk.cyan("🧠 Running deep analysis...\n"));
+        const { DeepAnalyzer } = await import("../../cultivation/deep-analyzer.js");
+        const analyzer = new DeepAnalyzer({
+          projectRoot,
+          docsPath,
+          verbose
+        });
+        const availability = await analyzer.getAvailabilityStatus();
+        if (!availability.available) {
+          console.log(chalk.yellow("  ⚠️  Deep analysis unavailable"));
+          console.log(chalk.gray(`  ${availability.reason}`));
+          console.log("");
+          console.log(chalk.gray("  Options:"));
+          console.log(chalk.gray("  1. Run from a regular terminal (outside Claude Code)"));
+          console.log(chalk.gray("  2. Set ANTHROPIC_API_KEY environment variable"));
+          result.warnings.push(`Deep analysis unavailable: ${availability.reason}`);
         } else {
+          console.log(chalk.gray(`  Mode: ${availability.reason}`));
           if (dryRun) {
-            console.log(chalk.yellow("  [DRY RUN] Would spawn claude-flow agents:"));
-            console.log("    - Researcher: Analyze codebase patterns");
-            console.log("    - Analyst: Identify architectural decisions");
-            console.log("    - Coder: Detect implementation patterns");
-            console.log("    - Tester: Analyze testing coverage");
+            console.log(chalk.yellow("\n  [DRY RUN] Would run analysis agents:"));
+            console.log("    - Pattern Researcher: Analyze codebase architecture");
+            console.log("    - Code Analyst: Identify quality issues");
+            console.log("    - Implementation Reviewer: Review code patterns");
+            console.log("    - Test Analyzer: Analyze test coverage");
           } else {
             try {
-              const { DeepAnalyzer } = await import("../../cultivation/deep-analyzer.js");
-              const analyzer = new DeepAnalyzer({
-                projectRoot,
-                docsPath,
-                verbose
-              });
               const deepResult = await analyzer.analyze();
-              console.log(`  ${chalk.green("✓")} Deep analysis complete`);
-              console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);
-              console.log(`    Insights generated: ${deepResult.insightsCount}`);
-              console.log(`    Documentation created: ${deepResult.documentsCreated}`);
+              if (deepResult.success) {
+                console.log(`
+  ${chalk.green("✓")} Deep analysis complete`);
+                console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);
+                console.log(`    Insights generated: ${deepResult.insightsCount}`);
+                console.log(`    Documentation created: ${deepResult.documentsCreated}`);
+                console.log(`    Mode: ${deepResult.mode}`);
+              } else {
+                console.log(`
+  ${chalk.yellow("⚠")} Deep analysis completed with issues`);
+                console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);
+                console.log(`    Insights generated: ${deepResult.insightsCount}`);
+                if (deepResult.errors.length > 0) {
+                  for (const err of deepResult.errors.slice(0, 3)) {
+                    console.log(chalk.gray(`    - ${err}`));
+                  }
+                }
+                result.warnings.push(...deepResult.errors);
+              }
             } catch (error) {
               result.errors.push(`Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`);
               console.log(chalk.red(`  ✗ Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`));
@@ -239,20 +259,6 @@ function displaySummary(result, dryRun) {
     console.log(chalk.gray("\nRun without --dry-run to apply changes\n"));
   }
 }
-async function checkClaudeFlowAvailable() {
-  const { execSync } = await import("child_process");
-  try {
-    execSync("claude-flow --version", { stdio: "pipe", timeout: 5e3 });
-    return true;
-  } catch {
-  }
-  try {
-    execSync("npx claude-flow --version", { stdio: "pipe", timeout: 3e4 });
-    return true;
-  } catch {
-    return false;
-  }
-}
 export {
   createCultivateCommand
 };

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

@@ -1 +1 @@
-{"version":3,"file":"cultivate.js","sources":["../../../src/cli/commands/cultivate.ts"],"sourcesContent":["/**\n * Cultivate Command - Systematically enhance the knowledge graph\n *\n * This command provides cultivation tasks:\n * - Seed primitives from codebase analysis\n * - Deep analysis with claude-flow integration\n * - Graph enhancement and optimization\n *\n * @module cli/commands/cultivate\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport { resolve, join, relative } from 'path';\nimport { existsSync, mkdirSync, readFileSync, readdirSync, statSync } from 'fs';\nimport { SeedGenerator } from '../../cultivation/seed-generator.js';\nimport { ShadowCache, loadShadowCache } from '../../core/cache.js';\nimport type { CultivationOptions, Ecosystem, SeedAnalysis } from '../../cultivation/types.js';\n\n/**\n * Cultivation result\n */\ninterface CultivationResult {\n  success: boolean;\n  seed: {\n    created: number;\n    documents: Array<{ title: string; path: string; type: string }>;\n  };\n  analysis: {\n    filesProcessed: number;\n    dependenciesFound: number;\n    servicesFound: number;\n  };\n  cache: {\n    updated: number;\n    hits: number;\n    misses: number;\n  };\n  duration: number;\n  warnings: string[];\n  errors: string[];\n}\n\n/**\n * Create cultivate command\n */\nexport function createCultivateCommand(): Command {\n  return new Command('cultivate')\n    .description('Systematically cultivate and enhance the knowledge graph')\n    .argument('[path]', 'Directory to cultivate (defaults to current directory)', '.')\n    .option('--dry-run', 'Preview changes without executing', false)\n    .option('-d, --docs <path>', 'Documentation path', 'docs')\n    .option('-v, --verbose', 'Verbose output', false)\n    .option('--seed', 'Bootstrap vault with primitives from codebase analysis', false)\n    .option('--deep-analysis', 'Use claude-flow agents for deep analysis', false)\n    .option('--cache', 'Use shadow cache for incremental updates', true)\n    .option('--ecosystem <ecosystems>', 'Filter to specific ecosystems (comma-separated)', undefined)\n    .option('--include-dev', 'Include dev dependencies', false)\n    .option('--major-only', 'Only process major dependencies', false)\n    .option('--refresh-cache', 'Force refresh the shadow cache', false)\n    .action(async (targetPath: string, options: {\n      dryRun?: boolean;\n      docs?: string;\n      verbose?: boolean;\n      seed?: boolean;\n      deepAnalysis?: boolean;\n      cache?: boolean;\n      ecosystem?: string;\n      includeDev?: boolean;\n      majorOnly?: boolean;\n      refreshCache?: boolean;\n    }) => {\n      const projectRoot = resolve(targetPath);\n      const docsPath = options.docs || 'docs';\n      const verbose = options.verbose || false;\n      const dryRun = options.dryRun || false;\n\n      console.log(chalk.bold.green('\\n🌱 Knowledge Graph Cultivator\\n'));\n      console.log(`  Project: ${projectRoot}`);\n      console.log(`  Docs: ${docsPath}`);\n      if (dryRun) {\n        console.log(`  Mode: ${chalk.yellow('Dry Run')}`);\n      }\n      console.log('');\n\n      // Determine tasks\n      const tasks = {\n        seed: options.seed || false,\n        deepAnalysis: options.deepAnalysis || false,\n      };\n\n      // If no tasks selected, show help\n      if (!tasks.seed && !tasks.deepAnalysis) {\n        console.log(chalk.yellow('💡 No tasks selected. Use one or more of:'));\n        console.log('  --seed           Bootstrap vault with primitives from codebase');\n        console.log('  --deep-analysis  Use claude-flow for deep codebase analysis');\n        console.log('');\n        console.log(chalk.gray('Options:'));\n        console.log('  --dry-run        Preview without writing files');\n        console.log('  --cache          Use shadow cache for incremental updates (default: true)');\n        console.log('  --refresh-cache  Force refresh the shadow cache');\n        console.log('  --ecosystem      Filter to ecosystems (nodejs,python,rust,go,php,java)');\n        console.log('  --include-dev    Include dev dependencies');\n        console.log('  --major-only     Only process major dependencies');\n        console.log('');\n        console.log('Run \"kg cultivate --help\" for more options');\n        return;\n      }\n\n      const startTime = Date.now();\n      const result: CultivationResult = {\n        success: true,\n        seed: { created: 0, documents: [] },\n        analysis: { filesProcessed: 0, dependenciesFound: 0, servicesFound: 0 },\n        cache: { updated: 0, hits: 0, misses: 0 },\n        duration: 0,\n        warnings: [],\n        errors: [],\n      };\n\n      try {\n        // Initialize shadow cache\n        let cache: ShadowCache | undefined;\n        if (options.cache !== false) {\n          console.log(chalk.cyan('📦 Initializing shadow cache...'));\n          cache = await loadShadowCache(projectRoot);\n\n          if (options.refreshCache) {\n            cache.clear();\n            console.log(chalk.gray('  Cache cleared (refresh mode)'));\n          }\n\n          const stats = cache.getStats();\n          console.log(chalk.gray(`  Entries: ${stats.totalEntries}, Hit rate: ${(stats.hitRate * 100).toFixed(1)}%`));\n          console.log('');\n        }\n\n        // Task 1: Seed primitives\n        if (tasks.seed) {\n          console.log(chalk.cyan('🌱 Seeding primitives from codebase...\\n'));\n\n          // Parse ecosystem filter\n          let ecosystems: Ecosystem[] | undefined;\n          if (options.ecosystem) {\n            ecosystems = options.ecosystem.split(',').map(e => e.trim() as Ecosystem);\n            console.log(chalk.gray(`  Ecosystems: ${ecosystems.join(', ')}`));\n          }\n\n          // Create generator\n          const generator = await SeedGenerator.create(projectRoot, docsPath);\n\n          // Analyze\n          console.log(chalk.gray('  Analyzing codebase...'));\n          const analysis = await generator.analyze();\n\n          result.analysis = {\n            filesProcessed: analysis.metadata.filesScanned,\n            dependenciesFound: analysis.dependencies.length,\n            servicesFound: analysis.services.length,\n          };\n\n          // Display analysis\n          console.log(`\\n  ${chalk.bold('Analysis Results:')}`);\n          console.log(`    Languages: ${analysis.languages.join(', ') || 'none'}`);\n          console.log(`    Dependencies: ${analysis.dependencies.length}`);\n          console.log(`    Frameworks: ${analysis.frameworks.length}`);\n          console.log(`    Services: ${analysis.services.length}`);\n          console.log(`    Deployments: ${analysis.deployments.length}`);\n\n          if (verbose) {\n            displayDetailedAnalysis(analysis);\n          }\n\n          console.log('');\n\n          // Generate primitives\n          console.log(chalk.gray('  Generating primitive nodes...'));\n          const documents = await generator.generatePrimitives(analysis);\n\n          if (dryRun) {\n            console.log(`\\n  ${chalk.yellow('[DRY RUN]')} Would create ${documents.length} primitives:`);\n            for (const doc of documents.slice(0, 10)) {\n              console.log(`    - ${doc.frontmatter.type}: ${doc.title}`);\n            }\n            if (documents.length > 10) {\n              console.log(`    ... and ${documents.length - 10} more`);\n            }\n            result.seed.documents = documents.map(d => ({\n              title: d.title,\n              path: d.path,\n              type: d.frontmatter.type || 'unknown',\n            }));\n          } else {\n            const writeResult = await generator.writePrimitives(documents);\n            result.seed.created = writeResult.documentsGenerated.length;\n            result.seed.documents = writeResult.documentsGenerated;\n\n            console.log(`\\n  ${chalk.green('✓')} Created ${writeResult.documentsGenerated.length} primitives`);\n\n            if (writeResult.warnings.length > 0) {\n              result.warnings.push(...writeResult.warnings);\n              if (verbose) {\n                console.log(chalk.yellow(`  Warnings: ${writeResult.warnings.length}`));\n              }\n            }\n\n            if (writeResult.errors.length > 0) {\n              result.errors.push(...writeResult.errors);\n              console.log(chalk.red(`  Errors: ${writeResult.errors.length}`));\n            }\n          }\n\n          console.log('');\n        }\n\n        // Task 2: Deep Analysis with claude-flow\n        if (tasks.deepAnalysis) {\n          console.log(chalk.cyan('🧠 Running deep analysis with claude-flow...\\n'));\n\n          // Check if claude-flow is available\n          const hasClaudeFlow = await checkClaudeFlowAvailable();\n\n          if (!hasClaudeFlow) {\n            console.log(chalk.yellow('  ⚠️  claude-flow not available'));\n            console.log(chalk.gray('  Install with: npm install -g claude-flow'));\n            result.warnings.push('claude-flow not available for deep analysis');\n          } else {\n            if (dryRun) {\n              console.log(chalk.yellow('  [DRY RUN] Would spawn claude-flow agents:'));\n              console.log('    - Researcher: Analyze codebase patterns');\n              console.log('    - Analyst: Identify architectural decisions');\n              console.log('    - Coder: Detect implementation patterns');\n              console.log('    - Tester: Analyze testing coverage');\n            } else {\n              // Import and run DeepAnalyzer\n              try {\n                const { DeepAnalyzer } = await import('../../cultivation/deep-analyzer.js');\n                const analyzer = new DeepAnalyzer({\n                  projectRoot,\n                  docsPath,\n                  verbose,\n                });\n\n                const deepResult = await analyzer.analyze();\n\n                console.log(`  ${chalk.green('✓')} Deep analysis complete`);\n                console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);\n                console.log(`    Insights generated: ${deepResult.insightsCount}`);\n                console.log(`    Documentation created: ${deepResult.documentsCreated}`);\n              } catch (error) {\n                result.errors.push(`Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`);\n                console.log(chalk.red(`  ✗ Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`));\n              }\n            }\n          }\n\n          console.log('');\n        }\n\n        // Update cache\n        if (cache) {\n          const stats = cache.getStats();\n          result.cache = {\n            updated: stats.totalEntries,\n            hits: stats.hitCount,\n            misses: stats.missCount,\n          };\n\n          await cache.save();\n        }\n\n        result.duration = Date.now() - startTime;\n        result.success = result.errors.length === 0;\n\n        // Final summary\n        displaySummary(result, dryRun);\n\n      } catch (error) {\n        console.error(chalk.red('\\n❌ Cultivation failed:'), error);\n        process.exit(1);\n      }\n    });\n}\n\n/**\n * Display detailed analysis output\n */\nfunction displayDetailedAnalysis(analysis: SeedAnalysis): void {\n  if (analysis.frameworks.length > 0) {\n    console.log(`\\n    ${chalk.gray('Frameworks:')}`);\n    for (const fw of analysis.frameworks) {\n      console.log(`      - ${fw.name} (${fw.ecosystem}) v${fw.version}`);\n    }\n  }\n\n  if (analysis.services.length > 0) {\n    console.log(`\\n    ${chalk.gray('Services:')}`);\n    for (const svc of analysis.services) {\n      console.log(`      - ${svc.name}: ${svc.type} (${svc.technology})`);\n    }\n  }\n\n  if (analysis.deployments.length > 0) {\n    console.log(`\\n    ${chalk.gray('Deployments:')}`);\n    for (const dep of analysis.deployments) {\n      console.log(`      - ${dep}`);\n    }\n  }\n}\n\n/**\n * Display cultivation summary\n */\nfunction displaySummary(result: CultivationResult, dryRun: boolean): void {\n  console.log(chalk.bold.blue('📊 Cultivation Summary\\n'));\n\n  if (dryRun) {\n    console.log(chalk.yellow('[DRY RUN] No changes were made\\n'));\n  }\n\n  console.log('  Analysis:');\n  console.log(`    Files processed: ${result.analysis.filesProcessed}`);\n  console.log(`    Dependencies: ${result.analysis.dependenciesFound}`);\n  console.log(`    Services: ${result.analysis.servicesFound}`);\n\n  if (result.seed.created > 0 || result.seed.documents.length > 0) {\n    console.log('\\n  Seed:');\n    console.log(`    Primitives ${dryRun ? 'would create' : 'created'}: ${dryRun ? result.seed.documents.length : result.seed.created}`);\n  }\n\n  if (result.cache.updated > 0) {\n    console.log('\\n  Cache:');\n    console.log(`    Entries: ${result.cache.updated}`);\n    const hitRate = result.cache.hits + result.cache.misses > 0\n      ? (result.cache.hits / (result.cache.hits + result.cache.misses) * 100).toFixed(1)\n      : 0;\n    console.log(`    Hit rate: ${hitRate}%`);\n  }\n\n  console.log(`\\n  Duration: ${(result.duration / 1000).toFixed(2)}s`);\n\n  if (result.warnings.length > 0) {\n    console.log(chalk.yellow(`\\n  ⚠️  Warnings: ${result.warnings.length}`));\n    for (const warning of result.warnings.slice(0, 5)) {\n      console.log(chalk.gray(`    - ${warning}`));\n    }\n  }\n\n  if (result.errors.length > 0) {\n    console.log(chalk.red(`\\n  ❌ Errors: ${result.errors.length}`));\n    for (const error of result.errors.slice(0, 5)) {\n      console.log(chalk.gray(`    - ${error}`));\n    }\n  }\n\n  if (result.success && !dryRun) {\n    console.log(chalk.bold.green('\\n✨ Cultivation complete!\\n'));\n  } else if (!result.success) {\n    console.log(chalk.yellow('\\n⚠️  Cultivation completed with errors\\n'));\n  } else {\n    console.log(chalk.gray('\\nRun without --dry-run to apply changes\\n'));\n  }\n}\n\n/**\n * Check if claude-flow is available\n * Checks for direct command first (globally installed), then falls back to npx\n */\nasync function checkClaudeFlowAvailable(): Promise<boolean> {\n  const { execSync } = await import('child_process');\n\n  // First try direct command (globally installed claude-flow)\n  try {\n    execSync('claude-flow --version', { stdio: 'pipe', timeout: 5000 });\n    return true;\n  } catch {\n    // Direct command not available, try npx\n  }\n\n  // Fall back to npx\n  try {\n    execSync('npx claude-flow --version', { stdio: 'pipe', timeout: 30000 });\n    return true;\n  } catch {\n    return false;\n  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+{"version":3,"file":"cultivate.js","sources":["../../../src/cli/commands/cultivate.ts"],"sourcesContent":["/**\n * Cultivate Command - Systematically enhance the knowledge graph\n *\n * This command provides cultivation tasks:\n * - Seed primitives from codebase analysis\n * - Deep analysis with claude-flow integration\n * - Graph enhancement and optimization\n *\n * @module cli/commands/cultivate\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport { resolve, join, relative } from 'path';\nimport { existsSync, mkdirSync, readFileSync, readdirSync, statSync } from 'fs';\nimport { SeedGenerator } from '../../cultivation/seed-generator.js';\nimport { ShadowCache, loadShadowCache } from '../../core/cache.js';\nimport type { CultivationOptions, Ecosystem, SeedAnalysis } from '../../cultivation/types.js';\n\n/**\n * Cultivation result\n */\ninterface CultivationResult {\n  success: boolean;\n  seed: {\n    created: number;\n    documents: Array<{ title: string; path: string; type: string }>;\n  };\n  analysis: {\n    filesProcessed: number;\n    dependenciesFound: number;\n    servicesFound: number;\n  };\n  cache: {\n    updated: number;\n    hits: number;\n    misses: number;\n  };\n  duration: number;\n  warnings: string[];\n  errors: string[];\n}\n\n/**\n * Create cultivate command\n */\nexport function createCultivateCommand(): Command {\n  return new Command('cultivate')\n    .description('Systematically cultivate and enhance the knowledge graph')\n    .argument('[path]', 'Directory to cultivate (defaults to current directory)', '.')\n    .option('--dry-run', 'Preview changes without executing', false)\n    .option('-d, --docs <path>', 'Documentation path', 'docs')\n    .option('-v, --verbose', 'Verbose output', false)\n    .option('--seed', 'Bootstrap vault with primitives from codebase analysis', false)\n    .option('--deep-analysis', 'Use claude-flow agents for deep analysis', false)\n    .option('--cache', 'Use shadow cache for incremental updates', true)\n    .option('--ecosystem <ecosystems>', 'Filter to specific ecosystems (comma-separated)', undefined)\n    .option('--include-dev', 'Include dev dependencies', false)\n    .option('--major-only', 'Only process major dependencies', false)\n    .option('--refresh-cache', 'Force refresh the shadow cache', false)\n    .action(async (targetPath: string, options: {\n      dryRun?: boolean;\n      docs?: string;\n      verbose?: boolean;\n      seed?: boolean;\n      deepAnalysis?: boolean;\n      cache?: boolean;\n      ecosystem?: string;\n      includeDev?: boolean;\n      majorOnly?: boolean;\n      refreshCache?: boolean;\n    }) => {\n      const projectRoot = resolve(targetPath);\n      const docsPath = options.docs || 'docs';\n      const verbose = options.verbose || false;\n      const dryRun = options.dryRun || false;\n\n      console.log(chalk.bold.green('\\n🌱 Knowledge Graph Cultivator\\n'));\n      console.log(`  Project: ${projectRoot}`);\n      console.log(`  Docs: ${docsPath}`);\n      if (dryRun) {\n        console.log(`  Mode: ${chalk.yellow('Dry Run')}`);\n      }\n      console.log('');\n\n      // Determine tasks\n      const tasks = {\n        seed: options.seed || false,\n        deepAnalysis: options.deepAnalysis || false,\n      };\n\n      // If no tasks selected, show help\n      if (!tasks.seed && !tasks.deepAnalysis) {\n        console.log(chalk.yellow('💡 No tasks selected. Use one or more of:'));\n        console.log('  --seed           Bootstrap vault with primitives from codebase');\n        console.log('  --deep-analysis  Use claude-flow for deep codebase analysis');\n        console.log('');\n        console.log(chalk.gray('Options:'));\n        console.log('  --dry-run        Preview without writing files');\n        console.log('  --cache          Use shadow cache for incremental updates (default: true)');\n        console.log('  --refresh-cache  Force refresh the shadow cache');\n        console.log('  --ecosystem      Filter to ecosystems (nodejs,python,rust,go,php,java)');\n        console.log('  --include-dev    Include dev dependencies');\n        console.log('  --major-only     Only process major dependencies');\n        console.log('');\n        console.log('Run \"kg cultivate --help\" for more options');\n        return;\n      }\n\n      const startTime = Date.now();\n      const result: CultivationResult = {\n        success: true,\n        seed: { created: 0, documents: [] },\n        analysis: { filesProcessed: 0, dependenciesFound: 0, servicesFound: 0 },\n        cache: { updated: 0, hits: 0, misses: 0 },\n        duration: 0,\n        warnings: [],\n        errors: [],\n      };\n\n      try {\n        // Initialize shadow cache\n        let cache: ShadowCache | undefined;\n        if (options.cache !== false) {\n          console.log(chalk.cyan('📦 Initializing shadow cache...'));\n          cache = await loadShadowCache(projectRoot);\n\n          if (options.refreshCache) {\n            cache.clear();\n            console.log(chalk.gray('  Cache cleared (refresh mode)'));\n          }\n\n          const stats = cache.getStats();\n          console.log(chalk.gray(`  Entries: ${stats.totalEntries}, Hit rate: ${(stats.hitRate * 100).toFixed(1)}%`));\n          console.log('');\n        }\n\n        // Task 1: Seed primitives\n        if (tasks.seed) {\n          console.log(chalk.cyan('🌱 Seeding primitives from codebase...\\n'));\n\n          // Parse ecosystem filter\n          let ecosystems: Ecosystem[] | undefined;\n          if (options.ecosystem) {\n            ecosystems = options.ecosystem.split(',').map(e => e.trim() as Ecosystem);\n            console.log(chalk.gray(`  Ecosystems: ${ecosystems.join(', ')}`));\n          }\n\n          // Create generator\n          const generator = await SeedGenerator.create(projectRoot, docsPath);\n\n          // Analyze\n          console.log(chalk.gray('  Analyzing codebase...'));\n          const analysis = await generator.analyze();\n\n          result.analysis = {\n            filesProcessed: analysis.metadata.filesScanned,\n            dependenciesFound: analysis.dependencies.length,\n            servicesFound: analysis.services.length,\n          };\n\n          // Display analysis\n          console.log(`\\n  ${chalk.bold('Analysis Results:')}`);\n          console.log(`    Languages: ${analysis.languages.join(', ') || 'none'}`);\n          console.log(`    Dependencies: ${analysis.dependencies.length}`);\n          console.log(`    Frameworks: ${analysis.frameworks.length}`);\n          console.log(`    Services: ${analysis.services.length}`);\n          console.log(`    Deployments: ${analysis.deployments.length}`);\n\n          if (verbose) {\n            displayDetailedAnalysis(analysis);\n          }\n\n          console.log('');\n\n          // Generate primitives\n          console.log(chalk.gray('  Generating primitive nodes...'));\n          const documents = await generator.generatePrimitives(analysis);\n\n          if (dryRun) {\n            console.log(`\\n  ${chalk.yellow('[DRY RUN]')} Would create ${documents.length} primitives:`);\n            for (const doc of documents.slice(0, 10)) {\n              console.log(`    - ${doc.frontmatter.type}: ${doc.title}`);\n            }\n            if (documents.length > 10) {\n              console.log(`    ... and ${documents.length - 10} more`);\n            }\n            result.seed.documents = documents.map(d => ({\n              title: d.title,\n              path: d.path,\n              type: d.frontmatter.type || 'unknown',\n            }));\n          } else {\n            const writeResult = await generator.writePrimitives(documents);\n            result.seed.created = writeResult.documentsGenerated.length;\n            result.seed.documents = writeResult.documentsGenerated;\n\n            console.log(`\\n  ${chalk.green('✓')} Created ${writeResult.documentsGenerated.length} primitives`);\n\n            if (writeResult.warnings.length > 0) {\n              result.warnings.push(...writeResult.warnings);\n              if (verbose) {\n                console.log(chalk.yellow(`  Warnings: ${writeResult.warnings.length}`));\n              }\n            }\n\n            if (writeResult.errors.length > 0) {\n              result.errors.push(...writeResult.errors);\n              console.log(chalk.red(`  Errors: ${writeResult.errors.length}`));\n            }\n          }\n\n          console.log('');\n        }\n\n        // Task 2: Deep Analysis\n        if (tasks.deepAnalysis) {\n          console.log(chalk.cyan('🧠 Running deep analysis...\\n'));\n\n          // Import and check DeepAnalyzer availability\n          const { DeepAnalyzer } = await import('../../cultivation/deep-analyzer.js');\n          const analyzer = new DeepAnalyzer({\n            projectRoot,\n            docsPath,\n            verbose,\n          });\n\n          const availability = await analyzer.getAvailabilityStatus();\n\n          if (!availability.available) {\n            console.log(chalk.yellow('  ⚠️  Deep analysis unavailable'));\n            console.log(chalk.gray(`  ${availability.reason}`));\n            console.log('');\n            console.log(chalk.gray('  Options:'));\n            console.log(chalk.gray('  1. Run from a regular terminal (outside Claude Code)'));\n            console.log(chalk.gray('  2. Set ANTHROPIC_API_KEY environment variable'));\n            result.warnings.push(`Deep analysis unavailable: ${availability.reason}`);\n          } else {\n            console.log(chalk.gray(`  Mode: ${availability.reason}`));\n\n            if (dryRun) {\n              console.log(chalk.yellow('\\n  [DRY RUN] Would run analysis agents:'));\n              console.log('    - Pattern Researcher: Analyze codebase architecture');\n              console.log('    - Code Analyst: Identify quality issues');\n              console.log('    - Implementation Reviewer: Review code patterns');\n              console.log('    - Test Analyzer: Analyze test coverage');\n            } else {\n              try {\n                const deepResult = await analyzer.analyze();\n\n                if (deepResult.success) {\n                  console.log(`\\n  ${chalk.green('✓')} Deep analysis complete`);\n                  console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);\n                  console.log(`    Insights generated: ${deepResult.insightsCount}`);\n                  console.log(`    Documentation created: ${deepResult.documentsCreated}`);\n                  console.log(`    Mode: ${deepResult.mode}`);\n                } else {\n                  console.log(`\\n  ${chalk.yellow('⚠')} Deep analysis completed with issues`);\n                  console.log(`    Agents spawned: ${deepResult.agentsSpawned}`);\n                  console.log(`    Insights generated: ${deepResult.insightsCount}`);\n                  if (deepResult.errors.length > 0) {\n                    for (const err of deepResult.errors.slice(0, 3)) {\n                      console.log(chalk.gray(`    - ${err}`));\n                    }\n                  }\n                  result.warnings.push(...deepResult.errors);\n                }\n              } catch (error) {\n                result.errors.push(`Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`);\n                console.log(chalk.red(`  ✗ Deep analysis failed: ${error instanceof Error ? error.message : String(error)}`));\n              }\n            }\n          }\n\n          console.log('');\n        }\n\n        // Update cache\n        if (cache) {\n          const stats = cache.getStats();\n          result.cache = {\n            updated: stats.totalEntries,\n            hits: stats.hitCount,\n            misses: stats.missCount,\n          };\n\n          await cache.save();\n        }\n\n        result.duration = Date.now() - startTime;\n        result.success = result.errors.length === 0;\n\n        // Final summary\n        displaySummary(result, dryRun);\n\n      } catch (error) {\n        console.error(chalk.red('\\n❌ Cultivation failed:'), error);\n        process.exit(1);\n      }\n    });\n}\n\n/**\n * Display detailed analysis output\n */\nfunction displayDetailedAnalysis(analysis: SeedAnalysis): void {\n  if (analysis.frameworks.length > 0) {\n    console.log(`\\n    ${chalk.gray('Frameworks:')}`);\n    for (const fw of analysis.frameworks) {\n      console.log(`      - ${fw.name} (${fw.ecosystem}) v${fw.version}`);\n    }\n  }\n\n  if (analysis.services.length > 0) {\n    console.log(`\\n    ${chalk.gray('Services:')}`);\n    for (const svc of analysis.services) {\n      console.log(`      - ${svc.name}: ${svc.type} (${svc.technology})`);\n    }\n  }\n\n  if (analysis.deployments.length > 0) {\n    console.log(`\\n    ${chalk.gray('Deployments:')}`);\n    for (const dep of analysis.deployments) {\n      console.log(`      - ${dep}`);\n    }\n  }\n}\n\n/**\n * Display cultivation summary\n */\nfunction displaySummary(result: CultivationResult, dryRun: boolean): void {\n  console.log(chalk.bold.blue('📊 Cultivation Summary\\n'));\n\n  if (dryRun) {\n    console.log(chalk.yellow('[DRY RUN] No changes were made\\n'));\n  }\n\n  console.log('  Analysis:');\n  console.log(`    Files processed: ${result.analysis.filesProcessed}`);\n  console.log(`    Dependencies: ${result.analysis.dependenciesFound}`);\n  console.log(`    Services: ${result.analysis.servicesFound}`);\n\n  if (result.seed.created > 0 || result.seed.documents.length > 0) {\n    console.log('\\n  Seed:');\n    console.log(`    Primitives ${dryRun ? 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package/dist/cultivation/deep-analyzer.d.ts

@@ -1,10 +1,10 @@
 /**
- * DeepAnalyzer - Claude-Flow Integration for Deep Codebase Analysis
+ * DeepAnalyzer - Deep Codebase Analysis
  *
- * Uses claude-flow agents for comprehensive codebase analysis:
- * - Pattern detection and architectural insights
- * - Documentation gap analysis
- * - Standards compliance checking
+ * Provides comprehensive codebase analysis using:
+ * - Claude CLI (`claude -p`) when running outside Claude Code
+ * - Direct Anthropic API when ANTHROPIC_API_KEY is available
+ * - Clear error messaging when neither option is available
  *
  * @module cultivation/deep-analyzer
  */
@@ -26,6 +26,8 @@ export interface DeepAnalyzerOptions {
     agentMode?: 'sequential' | 'parallel' | 'adaptive';
     /** Timeout for each agent (ms) */
     agentTimeout?: number;
+    /** Force use of API key even if CLI is available */
+    forceApiKey?: boolean;
 }
 /**
  * Analysis result from an agent
@@ -53,9 +55,10 @@ export interface DeepAnalysisResult {
     results: AgentResult[];
     duration: number;
     errors: string[];
+    mode: 'cli' | 'api' | 'static';
 }
 /**
- * DeepAnalyzer - Uses claude-flow for deep codebase analysis
+ * DeepAnalyzer - Deep codebase analysis with multiple execution modes
  *
  * @example
  * ```typescript
@@ -76,46 +79,59 @@ export declare class DeepAnalyzer {
     private maxAgents;
     private agentMode;
     private agentTimeout;
-    private claudeFlowCommand;
+    private forceApiKey;
     constructor(options: DeepAnalyzerOptions);
     /**
-     * Check if claude-flow is available and determine the best command to use
-     * Checks for direct command first (globally installed), then falls back to npx
+     * Check if running inside a Claude Code session
      */
-    isAvailable(): Promise<boolean>;
+    private isInsideClaudeCode;
     /**
-     * Detect which claude-flow command to use
-     * Returns the command configuration or null if not available
+     * Check if Anthropic API key is available
      */
-    private detectClaudeFlowCommand;
+    private hasApiKey;
     /**
-     * Run deep analysis
+     * Check if Claude CLI is available
      */
-    analyze(): Promise<DeepAnalysisResult>;
+    private isCliAvailable;
     /**
-     * Execute agents in parallel
+     * Determine the best execution mode
      */
-    private executeParallel;
+    private detectExecutionMode;
     /**
-     * Execute agents sequentially
+     * Check if analysis is available
      */
-    private executeSequential;
+    isAvailable(): Promise<boolean>;
     /**
-     * Execute agents adaptively (start with 2, scale based on success)
+     * Get availability status with reason
      */
-    private executeAdaptive;
+    getAvailabilityStatus(): Promise<{
+        available: boolean;
+        reason: string;
+    }>;
+    /**
+     * Run deep analysis
+     */
+    analyze(): Promise<DeepAnalysisResult>;
     /**
      * Execute a single agent
      */
     private executeAgent;
     /**
-     * Build prompt for agent
+     * Build context-aware prompt for analysis
      */
     private buildPrompt;
     /**
-     * Run claude-flow agent
+     * Gather project context for analysis
+     */
+    private gatherProjectContext;
+    /**
+     * Run analysis using Claude CLI
+     */
+    private runWithCli;
+    /**
+     * Run analysis using Anthropic API directly
      */
-    private runClaudeFlowAgent;
+    private runWithApi;
     /**
      * Extract insights from agent output
      */

package/dist/cultivation/deep-analyzer.d.ts.map

@@ -1 +1 @@
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package/dist/cultivation/deep-analyzer.js

@@ -1,17 +1,8 @@
-import { execFileSync, spawn } from "child_process";
-import { existsSync, mkdirSync, writeFileSync } from "fs";
+import { execFileSync, execSync } from "child_process";
+import { existsSync, mkdirSync, writeFileSync, readFileSync, readdirSync } from "fs";
 import { resolve, join } from "path";
 import { createLogger } from "../utils/logger.js";
 const logger = createLogger("deep-analyzer");
-const VALID_AGENT_TYPES = /* @__PURE__ */ new Set([
-  "researcher",
-  "architect",
-  "analyst",
-  "coder",
-  "tester",
-  "reviewer",
-  "documenter"
-]);
 class DeepAnalyzer {
   projectRoot;
   docsPath;
@@ -20,7 +11,7 @@ class DeepAnalyzer {
   maxAgents;
   agentMode;
   agentTimeout;
-  claudeFlowCommand = null;
+  forceApiKey;
   constructor(options) {
     this.projectRoot = resolve(options.projectRoot);
     this.docsPath = options.docsPath || "docs";
@@ -28,51 +19,92 @@ class DeepAnalyzer {
     this.verbose = options.verbose || false;
     this.maxAgents = options.maxAgents || 5;
     this.agentMode = options.agentMode || "adaptive";
-    this.agentTimeout = options.agentTimeout || 6e4;
+    this.agentTimeout = options.agentTimeout || 12e4;
+    this.forceApiKey = options.forceApiKey || false;
   }
   /**
-   * Check if claude-flow is available and determine the best command to use
-   * Checks for direct command first (globally installed), then falls back to npx
+   * Check if running inside a Claude Code session
    */
-  async isAvailable() {
-    const command = await this.detectClaudeFlowCommand();
-    return command !== null;
+  isInsideClaudeCode() {
+    return process.env.CLAUDECODE === "1" || process.env.CLAUDE_CODE === "1";
   }
   /**
-   * Detect which claude-flow command to use
-   * Returns the command configuration or null if not available
+   * Check if Anthropic API key is available
    */
-  async detectClaudeFlowCommand() {
-    if (this.claudeFlowCommand !== null) {
-      return this.claudeFlowCommand;
-    }
+  hasApiKey() {
+    return !!process.env.ANTHROPIC_API_KEY;
+  }
+  /**
+   * Check if Claude CLI is available
+   */
+  isCliAvailable() {
     try {
-      execFileSync("claude-flow", ["--version"], {
+      execFileSync("claude", ["--version"], {
         stdio: "pipe",
         timeout: 5e3,
         windowsHide: true
       });
-      this.claudeFlowCommand = { cmd: "claude-flow", args: [] };
-      return this.claudeFlowCommand;
+      return true;
     } catch {
+      return false;
     }
-    try {
-      execFileSync("npx", ["claude-flow", "--version"], {
-        stdio: "pipe",
-        timeout: 3e4,
-        windowsHide: true
-      });
-      this.claudeFlowCommand = { cmd: "npx", args: ["claude-flow"] };
-      return this.claudeFlowCommand;
-    } catch {
-      return null;
+  }
+  /**
+   * Determine the best execution mode
+   */
+  detectExecutionMode() {
+    const insideClaudeCode = this.isInsideClaudeCode();
+    const hasApiKey = this.hasApiKey();
+    const cliAvailable = this.isCliAvailable();
+    if (this.forceApiKey) {
+      if (hasApiKey) {
+        return { mode: "api", reason: "Using API key (forced)" };
+      }
+      return { mode: "unavailable", reason: "ANTHROPIC_API_KEY not set (required when forceApiKey=true)" };
+    }
+    if (insideClaudeCode) {
+      if (hasApiKey) {
+        return { mode: "api", reason: "Using API key (inside Claude Code session)" };
+      }
+      return {
+        mode: "unavailable",
+        reason: "Cannot run deep analysis inside Claude Code session without ANTHROPIC_API_KEY. Either set ANTHROPIC_API_KEY environment variable, or run this command from a regular terminal."
+      };
+    }
+    if (cliAvailable) {
+      return { mode: "cli", reason: "Using Claude CLI" };
+    }
+    if (hasApiKey) {
+      return { mode: "api", reason: "Using API key (CLI not available)" };
     }
+    return {
+      mode: "unavailable",
+      reason: "Claude CLI not found. Install Claude Code (https://claude.ai/code) or set ANTHROPIC_API_KEY."
+    };
+  }
+  /**
+   * Check if analysis is available
+   */
+  async isAvailable() {
+    const mode = this.detectExecutionMode();
+    return mode.mode !== "unavailable";
+  }
+  /**
+   * Get availability status with reason
+   */
+  async getAvailabilityStatus() {
+    const mode = this.detectExecutionMode();
+    return {
+      available: mode.mode !== "unavailable",
+      reason: mode.reason
+    };
   }
   /**
    * Run deep analysis
    */
   async analyze() {
     const startTime = Date.now();
+    const executionMode = this.detectExecutionMode();
     const result = {
       success: false,
       agentsSpawned: 0,
@@ -80,13 +112,16 @@ class DeepAnalyzer {
       documentsCreated: 0,
       results: [],
       duration: 0,
-      errors: []
+      errors: [],
+      mode: executionMode.mode === "unavailable" ? "static" : executionMode.mode
     };
-    if (!await this.isAvailable()) {
-      result.errors.push("claude-flow is not available");
+    if (executionMode.mode === "unavailable") {
+      result.errors.push(executionMode.reason);
       result.duration = Date.now() - startTime;
+      logger.error("Deep analysis unavailable", new Error(executionMode.reason));
       return result;
     }
+    logger.info(`Starting deep analysis`, { mode: executionMode.mode, reason: executionMode.reason });
     if (!existsSync(this.outputDir)) {
       mkdirSync(this.outputDir, { recursive: true });
     }
@@ -116,18 +151,15 @@ class DeepAnalyzer {
         outputFile: "testing-analysis.md"
       }
     ];
-    logger.info("Starting deep analysis", { agents: agents.length, mode: this.agentMode });
-    if (this.agentMode === "parallel") {
-      result.results = await this.executeParallel(agents);
-    } else if (this.agentMode === "sequential") {
-      result.results = await this.executeSequential(agents);
-    } else {
-      result.results = await this.executeAdaptive(agents);
+    logger.info("Executing analysis agents", { agents: agents.length, mode: "sequential" });
+    for (const agent of agents) {
+      const agentResult = await this.executeAgent(agent, executionMode.mode);
+      result.results.push(agentResult);
     }
     result.agentsSpawned = result.results.length;
     result.insightsCount = result.results.reduce((sum, r) => sum + r.insights.length, 0);
     result.documentsCreated = result.results.reduce((sum, r) => sum + r.documents.length, 0);
-    result.success = result.results.every((r) => r.success);
+    result.success = result.results.some((r) => r.success);
     result.duration = Date.now() - startTime;
     for (const agentResult of result.results) {
       if (agentResult.error) {
@@ -142,48 +174,10 @@ class DeepAnalyzer {
     });
     return result;
   }
-  /**
-   * Execute agents in parallel
-   */
-  async executeParallel(agents) {
-    const promises = agents.map((agent) => this.executeAgent(agent));
-    return Promise.all(promises);
-  }
-  /**
-   * Execute agents sequentially
-   */
-  async executeSequential(agents) {
-    const results = [];
-    for (const agent of agents) {
-      results.push(await this.executeAgent(agent));
-    }
-    return results;
-  }
-  /**
-   * Execute agents adaptively (start with 2, scale based on success)
-   */
-  async executeAdaptive(agents) {
-    const results = [];
-    const firstBatch = agents.slice(0, 2);
-    const firstResults = await Promise.all(firstBatch.map((a) => this.executeAgent(a)));
-    results.push(...firstResults);
-    const successRate = firstResults.filter((r) => r.success).length / firstResults.length;
-    if (successRate >= 0.5 && agents.length > 2) {
-      const remaining = agents.slice(2);
-      const remainingResults = await Promise.all(remaining.map((a) => this.executeAgent(a)));
-      results.push(...remainingResults);
-    } else if (agents.length > 2) {
-      logger.warn("Low success rate, switching to sequential mode");
-      for (const agent of agents.slice(2)) {
-        results.push(await this.executeAgent(agent));
-      }
-    }
-    return results;
-  }
   /**
    * Execute a single agent
    */
-  async executeAgent(agent) {
+  async executeAgent(agent, mode) {
     const startTime = Date.now();
     const outputPath = join(this.outputDir, agent.outputFile);
     const result = {
@@ -195,9 +189,14 @@ class DeepAnalyzer {
       duration: 0
     };
     try {
-      logger.info(`Spawning agent: ${agent.name}`, { type: agent.type });
+      logger.info(`Executing agent: ${agent.name}`, { type: agent.type, mode });
       const prompt = this.buildPrompt(agent);
-      const output = await this.runClaudeFlowAgent(agent.type, prompt);
+      let output;
+      if (mode === "cli") {
+        output = await this.runWithCli(prompt);
+      } else {
+        output = await this.runWithApi(prompt);
+      }
       result.insights = this.extractInsights(output);
       writeFileSync(outputPath, this.formatOutput(agent, output));
       result.documents.push({ path: outputPath, title: agent.name });
@@ -213,76 +212,122 @@ class DeepAnalyzer {
     return result;
   }
   /**
-   * Build prompt for agent
+   * Build context-aware prompt for analysis
    */
   buildPrompt(agent) {
-    return `You are a ${agent.name} analyzing the project at ${this.projectRoot}.
-
-**OBJECTIVE**: ${agent.task}
+    const context = this.gatherProjectContext();
+    return `You are analyzing a codebase. Here is the project context:
 
-**COORDINATION PROTOCOL**:
-\`\`\`bash
-claude-flow hooks pre-task --description "${agent.task}"
-\`\`\`
+${context}
 
-**YOUR TASKS**:
-1. Analyze the codebase at ${this.projectRoot}
-2. Identify key patterns and conventions
-3. Document your findings with specific examples
-4. Provide actionable recommendations
-5. Generate comprehensive markdown documentation
+Task: ${agent.task}
 
-**OUTPUT REQUIREMENTS**:
-- Use clear markdown formatting
-- Include code examples from the project
-- Organize findings by category
-- Prioritize actionable insights
+Provide your findings in markdown format with:
+1. Key observations (prefix with "Observation:")
+2. Specific recommendations (prefix with "Recommendation:")
+3. Any potential issues found (prefix with "Finding:")
 
-After completing:
-\`\`\`bash
-claude-flow hooks post-task --task-id "${agent.type}-analysis"
-\`\`\`
-`;
+Be specific and actionable in your analysis.`;
   }
   /**
-   * Run claude-flow agent
+   * Gather project context for analysis
    */
-  async runClaudeFlowAgent(type, prompt) {
-    if (!VALID_AGENT_TYPES.has(type)) {
-      throw new Error(`Invalid agent type: ${type}. Valid types: ${[...VALID_AGENT_TYPES].join(", ")}`);
+  gatherProjectContext() {
+    const lines = [];
+    const packageJsonPath = join(this.projectRoot, "package.json");
+    if (existsSync(packageJsonPath)) {
+      try {
+        const pkg = JSON.parse(readFileSync(packageJsonPath, "utf-8"));
+        lines.push(`Project: ${pkg.name || "Unknown"} v${pkg.version || "0.0.0"}`);
+        lines.push(`Description: ${pkg.description || "No description"}`);
+        if (pkg.dependencies) {
+          const deps = Object.keys(pkg.dependencies).slice(0, 10);
+          lines.push(`Key dependencies: ${deps.join(", ")}`);
+        }
+      } catch {
+      }
     }
-    const sanitizedPrompt = prompt.replace(/[`$\\]/g, "");
-    const commandConfig = await this.detectClaudeFlowCommand();
-    if (!commandConfig) {
-      throw new Error("claude-flow is not available");
+    try {
+      const entries = readdirSync(this.projectRoot, { withFileTypes: true });
+      const dirs = entries.filter((e) => e.isDirectory() && !e.name.startsWith(".") && e.name !== "node_modules").map((e) => e.name).slice(0, 10);
+      if (dirs.length > 0) {
+        lines.push(`Project structure: ${dirs.join(", ")}`);
+      }
+    } catch {
     }
-    return new Promise((resolve2, reject) => {
-      const args = [...commandConfig.args, "agent", "run", type, sanitizedPrompt];
-      const proc = spawn(commandConfig.cmd, args, {
+    const configFiles = [
+      "tsconfig.json",
+      "vite.config.ts",
+      "vitest.config.ts",
+      ".eslintrc.js",
+      "Dockerfile"
+    ];
+    const foundConfigs = configFiles.filter((f) => existsSync(join(this.projectRoot, f)));
+    if (foundConfigs.length > 0) {
+      lines.push(`Config files: ${foundConfigs.join(", ")}`);
+    }
+    return lines.join("\n");
+  }
+  /**
+   * Run analysis using Claude CLI
+   */
+  async runWithCli(prompt) {
+    const sanitizedPrompt = prompt.replace(/"/g, '\\"').replace(/[`$]/g, "");
+    try {
+      const result = execSync(`claude -p "${sanitizedPrompt}"`, {
         cwd: this.projectRoot,
-        shell: false,
-        // Security: Disable shell to prevent command injection
-        timeout: this.agentTimeout
-      });
-      let stdout = "";
-      let stderr = "";
-      proc.stdout?.on("data", (data) => {
-        stdout += data.toString();
-      });
-      proc.stderr?.on("data", (data) => {
-        stderr += data.toString();
+        encoding: "utf8",
+        timeout: this.agentTimeout,
+        maxBuffer: 10 * 1024 * 1024
+        // 10MB buffer
       });
-      proc.on("close", (code) => {
-        if (code === 0) {
-          resolve2(stdout);
-        } else {
-          reject(new Error(stderr || `Agent exited with code ${code}`));
+      return result;
+    } catch (error) {
+      if (error instanceof Error) {
+        const execError = error;
+        if (execError.killed) {
+          if (execError.stdout && execError.stdout.length > 100) {
+            return execError.stdout;
+          }
+          throw new Error(`Claude CLI timed out after ${this.agentTimeout / 1e3}s`);
         }
+        throw new Error(execError.stderr || error.message);
+      }
+      throw error;
+    }
+  }
+  /**
+   * Run analysis using Anthropic API directly
+   */
+  async runWithApi(prompt) {
+    const apiKey = process.env.ANTHROPIC_API_KEY;
+    if (!apiKey) {
+      throw new Error("ANTHROPIC_API_KEY not set");
+    }
+    try {
+      const { default: Anthropic } = await import("@anthropic-ai/sdk");
+      const client = new Anthropic({ apiKey });
+      const response = await client.messages.create({
+        model: "claude-sonnet-4-20250514",
+        max_tokens: 4096,
+        messages: [
+          {
+            role: "user",
+            content: prompt
+          }
+        ]
       });
-      proc.on("error", (error) => {
-        reject(error);
-      });
-    });
+      const textBlock = response.content.find((block) => block.type === "text");
+      if (textBlock && textBlock.type === "text") {
+        return textBlock.text;
+      }
+      throw new Error("No text content in API response");
+    } catch (error) {
+      if (error instanceof Error) {
+        throw new Error(`API call failed: ${error.message}`);
+      }
+      throw error;
+    }
   }
   /**
    * Extract insights from agent output
@@ -290,7 +335,7 @@ claude-flow hooks post-task --task-id "${agent.type}-analysis"
   extractInsights(output) {
     const insights = [];
     const patterns = [
-      /[-*]\s*(?:insight|finding|observation|recommendation):\s*(.+)/gi,
+      /[-*]?\s*(?:insight|finding|observation|recommendation):\s*(.+)/gi,
       /##\s*(?:insight|finding|observation|recommendation):\s*(.+)/gi,
       /(?:key\s+)?(?:insight|finding|observation|recommendation):\s*(.+)/gi
     ];
@@ -319,7 +364,7 @@ created: ${timestamp}
 
 # ${agent.name} Analysis
 
-> Generated by DeepAnalyzer using claude-flow
+> Generated by DeepAnalyzer
 
 ## Overview
 

package/dist/cultivation/deep-analyzer.js.map

@@ -1 +1 @@
-{"version":3,"file":"deep-analyzer.js","sources":["../../src/cultivation/deep-analyzer.ts"],"sourcesContent":["/**\n * DeepAnalyzer - Claude-Flow Integration for Deep Codebase Analysis\n *\n * Uses claude-flow agents for comprehensive codebase analysis:\n * - Pattern detection and architectural insights\n * - Documentation gap analysis\n * - Standards compliance checking\n *\n * @module cultivation/deep-analyzer\n */\n\nimport { execFileSync, spawn } from 'child_process';\nimport { existsSync, mkdirSync, writeFileSync, readFileSync } from 'fs';\nimport { join, resolve } from 'path';\nimport { createLogger } from '../utils/index.js';\n\nconst logger = createLogger('deep-analyzer');\n\n/**\n * Valid agent types for security validation\n */\nconst VALID_AGENT_TYPES = new Set([\n  'researcher',\n  'architect',\n  'analyst',\n  'coder',\n  'tester',\n  'reviewer',\n  'documenter',\n]);\n\n/**\n * Deep analyzer options\n */\nexport interface DeepAnalyzerOptions {\n  /** Project root directory */\n  projectRoot: string;\n  /** Documentation path (relative to project root) */\n  docsPath?: string;\n  /** Output directory for analysis results */\n  outputDir?: string;\n  /** Enable verbose logging */\n  verbose?: boolean;\n  /** Maximum agents to spawn */\n  maxAgents?: number;\n  /** Agent execution mode */\n  agentMode?: 'sequential' | 'parallel' | 'adaptive';\n  /** Timeout for each agent (ms) */\n  agentTimeout?: number;\n}\n\n/**\n * Analysis result from an agent\n */\nexport interface AgentResult {\n  name: string;\n  type: string;\n  success: boolean;\n  insights: string[];\n  documents: Array<{ path: string; title: string }>;\n  duration: number;\n  error?: string;\n}\n\n/**\n * Deep analysis result\n */\nexport interface DeepAnalysisResult {\n  success: boolean;\n  agentsSpawned: number;\n  insightsCount: number;\n  documentsCreated: number;\n  results: AgentResult[];\n  duration: number;\n  errors: string[];\n}\n\n/**\n * Agent configuration\n */\ninterface AgentConfig {\n  name: string;\n  type: 'researcher' | 'analyst' | 'coder' | 'tester' | 'reviewer';\n  task: string;\n  outputFile: string;\n}\n\n/**\n * DeepAnalyzer - Uses claude-flow for deep codebase analysis\n *\n * @example\n * ```typescript\n * const analyzer = new DeepAnalyzer({\n *   projectRoot: '/my/project',\n *   docsPath: 'docs',\n * });\n *\n * const result = await analyzer.analyze();\n * console.log(`Generated ${result.insightsCount} insights`);\n * ```\n */\nexport class DeepAnalyzer {\n  private projectRoot: string;\n  private docsPath: string;\n  private outputDir: string;\n  private verbose: boolean;\n  private maxAgents: number;\n  private agentMode: 'sequential' | 'parallel' | 'adaptive';\n  private agentTimeout: number;\n  private claudeFlowCommand: { cmd: string; args: string[] } | null = null;\n\n  constructor(options: DeepAnalyzerOptions) {\n    this.projectRoot = resolve(options.projectRoot);\n    this.docsPath = options.docsPath || 'docs';\n    this.outputDir = options.outputDir || join(this.projectRoot, this.docsPath, 'analysis');\n    this.verbose = options.verbose || false;\n    this.maxAgents = options.maxAgents || 5;\n    this.agentMode = options.agentMode || 'adaptive';\n    // Default timeout of 60 seconds (configurable via agentTimeout option)\n    this.agentTimeout = options.agentTimeout || 60000;\n  }\n\n  /**\n   * Check if claude-flow is available and determine the best command to use\n   * Checks for direct command first (globally installed), then falls back to npx\n   */\n  async isAvailable(): Promise<boolean> {\n    const command = await this.detectClaudeFlowCommand();\n    return command !== null;\n  }\n\n  /**\n   * Detect which claude-flow command to use\n   * Returns the command configuration or null if not available\n   */\n  private async detectClaudeFlowCommand(): Promise<{ cmd: string; args: string[] } | null> {\n    // Return cached result if available\n    if (this.claudeFlowCommand !== null) {\n      return this.claudeFlowCommand;\n    }\n\n    // First try direct command (globally installed claude-flow)\n    try {\n      // SECURITY: execFileSync does not spawn a shell by default, preventing shell injection\n      execFileSync('claude-flow', ['--version'], {\n        stdio: 'pipe',\n        timeout: 5000,\n        windowsHide: true,\n      });\n      this.claudeFlowCommand = { cmd: 'claude-flow', args: [] };\n      return this.claudeFlowCommand;\n    } catch {\n      // Direct command not available, try npx\n    }\n\n    // Fall back to npx\n    try {\n      execFileSync('npx', ['claude-flow', '--version'], {\n        stdio: 'pipe',\n        timeout: 30000,\n        windowsHide: true,\n      });\n      this.claudeFlowCommand = { cmd: 'npx', args: ['claude-flow'] };\n      return this.claudeFlowCommand;\n    } catch {\n      return null;\n    }\n  }\n\n  /**\n   * Run deep analysis\n   */\n  async analyze(): Promise<DeepAnalysisResult> {\n    const startTime = Date.now();\n\n    const result: DeepAnalysisResult = {\n      success: false,\n      agentsSpawned: 0,\n      insightsCount: 0,\n      documentsCreated: 0,\n      results: [],\n      duration: 0,\n      errors: [],\n    };\n\n    // Check availability\n    if (!(await this.isAvailable())) {\n      result.errors.push('claude-flow is not available');\n      result.duration = Date.now() - 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' +\n                'Either set ANTHROPIC_API_KEY environment variable, or run this command from a regular terminal.',\n      };\n    }\n\n    // Outside Claude Code - prefer CLI for OAuth session support\n    if (cliAvailable) {\n      return { mode: 'cli', reason: 'Using Claude CLI' };\n    }\n\n    // CLI not available, try API key\n    if (hasApiKey) {\n      return { mode: 'api', reason: 'Using API key (CLI not available)' };\n    }\n\n    return {\n      mode: 'unavailable',\n      reason: 'Claude CLI not found. 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package/dist/node_modules/@typescript-eslint/project-service/dist/index.js

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../../_virtual/index8.js";
+import { __exports as dist } from "../../../../_virtual/index7.js";
 import { __require as requireCreateProjectService } from "./createProjectService.js";
 var hasRequiredDist;
 function requireDist() {

package/dist/node_modules/@typescript-eslint/types/dist/index.js

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../../_virtual/index5.js";
+import { __exports as dist } from "../../../../_virtual/index6.js";
 import { __require as requireAstSpec } from "./generated/ast-spec.js";
 import { __require as requireLib } from "./lib.js";
 import { __require as requireParserOptions } from "./parser-options.js";

package/dist/node_modules/@typescript-eslint/visitor-keys/dist/index.js

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../../_virtual/index6.js";
+import { __exports as dist } from "../../../../_virtual/index5.js";
 import { __require as requireGetKeys } from "./get-keys.js";
 import { __require as requireVisitorKeys } from "./visitor-keys.js";
 var hasRequiredDist;

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

@@ -1,4 +1,4 @@
-import { __exports as dist } from "../../../_virtual/index7.js";
+import { __exports as dist } from "../../../_virtual/index8.js";
 import require$$1 from "fs";
 import path__default from "path";
 import require$$2 from "url";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@weavelogic/knowledge-graph-agent",
-  "version": "0.10.3",
+  "version": "0.10.4",
   "description": "Knowledge graph agent for Claude Code - generates knowledge graphs, initializes docs, and integrates with claude-flow",
   "type": "module",
   "main": "dist/index.js",