@weavelogic/knowledge-graph-agent 0.8.1 → 0.8.3

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

@@ -1 +1 @@
-{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/graph.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC;;GAEG;AACH,wBAAgB,kBAAkB,IAAI,OAAO,CA6J5C"}
+{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/graph.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC;;GAEG;AACH,wBAAgB,kBAAkB,IAAI,OAAO,CAkM5C"}

package/dist/cli/commands/graph.js

@@ -7,15 +7,36 @@ import { updateGraph, generateAndSave } from "../../generators/graph-generator.j
 import { validateProjectRoot, validateDocsPath } from "../../core/security.js";
 function createGraphCommand() {
   const command = new Command("graph");
-  command.description("Generate or update knowledge graph from documentation").option("-p, --path <path>", "Project root path", ".").option("-d, --docs <path>", "Docs directory path", "docs").option("-u, --update", "Incremental update instead of full regeneration").option("-v, --verbose", "Show detailed output").action(async (options) => {
+  command.description("Generate or update knowledge graph from documentation").option("-p, --path <path>", "Project root path", ".").option("-d, --docs <path>", "Docs directory path", "docs").option("-i, --include <paths>", "Additional paths to include (comma-separated)").option("-a, --all", "Scan entire project for markdown files").option("-u, --update", "Incremental update instead of full regeneration").option("-v, --verbose", "Show detailed output").action(async (options) => {
     const spinner = ora("Generating knowledge graph...").start();
     try {
       const projectRoot = validateProjectRoot(options.path);
-      const docsPath = validateDocsPath(projectRoot, options.docs);
       const dbPath = join(projectRoot, ".kg", "knowledge.db");
-      if (!existsSync(docsPath)) {
-        spinner.fail(`Docs directory not found: ${docsPath}`);
-        console.log(chalk.gray("  Run ") + chalk.cyan("kg docs init") + chalk.gray(" to create it"));
+      const sourcePaths = [];
+      if (options.all) {
+        sourcePaths.push(projectRoot);
+      } else {
+        const docsPath = validateDocsPath(projectRoot, options.docs);
+        if (existsSync(docsPath)) {
+          sourcePaths.push(docsPath);
+        }
+        if (options.include) {
+          const additionalPaths = options.include.split(",").map((p) => p.trim());
+          for (const relPath of additionalPaths) {
+            const fullPath = join(projectRoot, relPath);
+            if (existsSync(fullPath)) {
+              sourcePaths.push(fullPath);
+            } else if (options.verbose) {
+              console.log(chalk.yellow(`  Skipping non-existent path: ${relPath}`));
+            }
+          }
+        }
+      }
+      if (sourcePaths.length === 0) {
+        spinner.fail("No documentation directories found");
+        console.log(chalk.gray("  Run ") + chalk.cyan("kg docs init") + chalk.gray(" to create docs/"));
+        console.log(chalk.gray("  Or use ") + chalk.cyan("--include <paths>") + chalk.gray(" to specify paths"));
+        console.log(chalk.gray("  Or use ") + chalk.cyan("--all") + chalk.gray(" to scan entire project"));
         process.exit(1);
       }
       if (!existsSync(join(projectRoot, ".kg"))) {
@@ -23,10 +44,13 @@ function createGraphCommand() {
         console.log(chalk.gray("  Run ") + chalk.cyan("kg init") + chalk.gray(" first"));
         process.exit(1);
       }
+      if (options.verbose) {
+        console.log(chalk.gray(`  Scanning paths: ${sourcePaths.join(", ")}`));
+      }
       let result;
       if (options.update && existsSync(dbPath)) {
         spinner.text = "Updating knowledge graph...";
-        result = await updateGraph(dbPath, docsPath);
+        result = await updateGraph(dbPath, sourcePaths[0], sourcePaths);
         spinner.succeed("Knowledge graph updated!");
         console.log();
         console.log(chalk.white("  Changes:"));
@@ -34,11 +58,13 @@ function createGraphCommand() {
         console.log(chalk.blue(`    Updated: ${result.updated}`));
         console.log(chalk.yellow(`    Removed: ${result.removed}`));
       } else {
-        spinner.text = "Scanning documentation...";
+        spinner.text = options.all ? "Scanning entire project..." : "Scanning documentation...";
         result = await generateAndSave(
           {
             projectRoot,
-            outputPath: docsPath
+            outputPath: sourcePaths[0],
+            additionalPaths: sourcePaths.slice(1),
+            scanAll: options.all
           },
           dbPath
         );
@@ -49,6 +75,7 @@ function createGraphCommand() {
         }
         console.log();
         console.log(chalk.white("  Statistics:"));
+        console.log(chalk.gray(`    Paths scanned: ${sourcePaths.length}`));
         console.log(chalk.gray(`    Files scanned: ${result.stats.filesScanned}`));
         console.log(chalk.green(`    Nodes created: ${result.stats.nodesCreated}`));
         console.log(chalk.blue(`    Edges created: ${result.stats.edgesCreated}`));

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

@@ -1 +1 @@
-{"version":3,"file":"graph.js","sources":["../../../src/cli/commands/graph.ts"],"sourcesContent":["/**\n * Graph Command\n *\n * Generate and update knowledge graph from documentation.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport ora from 'ora';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { generateAndSave, updateGraph } from '../../generators/graph-generator.js';\nimport { validateProjectRoot, validateDocsPath } from '../../core/security.js';\n\n/**\n * Create graph command\n */\nexport function createGraphCommand(): Command {\n  const command = new Command('graph');\n\n  command\n    .description('Generate or update knowledge graph from documentation')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-d, --docs <path>', 'Docs directory path', 'docs')\n    .option('-u, --update', 'Incremental update instead of full regeneration')\n    .option('-v, --verbose', 'Show detailed output')\n    .action(async (options) => {\n      const spinner = ora('Generating knowledge graph...').start();\n\n      try {\n        // Validate paths to prevent traversal attacks\n        const projectRoot = validateProjectRoot(options.path);\n        const docsPath = validateDocsPath(projectRoot, options.docs);\n        const dbPath = join(projectRoot, '.kg', 'knowledge.db');\n\n        // Check if docs exist\n        if (!existsSync(docsPath)) {\n          spinner.fail(`Docs directory not found: ${docsPath}`);\n          console.log(chalk.gray('  Run ') + chalk.cyan('kg docs init') + chalk.gray(' to create it'));\n          process.exit(1);\n        }\n\n        // Check if KG is initialized\n        if (!existsSync(join(projectRoot, '.kg'))) {\n          spinner.fail('Knowledge graph not initialized');\n          console.log(chalk.gray('  Run ') + chalk.cyan('kg init') + chalk.gray(' first'));\n          process.exit(1);\n        }\n\n        let result;\n\n        if (options.update && existsSync(dbPath)) {\n          // Incremental update\n          spinner.text = 'Updating knowledge graph...';\n          result = await updateGraph(dbPath, docsPath);\n\n          spinner.succeed('Knowledge graph updated!');\n\n          console.log();\n          console.log(chalk.white('  Changes:'));\n          console.log(chalk.green(`    Added:   ${result.added}`));\n          console.log(chalk.blue(`    Updated: ${result.updated}`));\n          console.log(chalk.yellow(`    Removed: ${result.removed}`));\n\n        } else {\n          // Full generation\n          spinner.text = 'Scanning documentation...';\n\n          result = await generateAndSave(\n            {\n              projectRoot,\n              outputPath: docsPath,\n            },\n            dbPath\n          );\n\n          if (result.success) {\n            spinner.succeed('Knowledge graph generated!');\n          } else {\n            spinner.warn('Knowledge graph generated with errors');\n          }\n\n          console.log();\n          console.log(chalk.white('  Statistics:'));\n          console.log(chalk.gray(`    Files scanned: ${result.stats.filesScanned}`));\n          console.log(chalk.green(`    Nodes created: ${result.stats.nodesCreated}`));\n          console.log(chalk.blue(`    Edges created: ${result.stats.edgesCreated}`));\n        }\n\n        // Show errors if any\n        const errors = 'errors' in result ? result.errors : result.stats?.errors;\n        if (errors && errors.length > 0) {\n          console.log();\n          console.log(chalk.yellow('  Warnings:'));\n          errors.slice(0, 5).forEach((err: string) => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n          if (errors.length > 5) {\n            console.log(chalk.gray(`    ... and ${errors.length - 5} more`));\n          }\n        }\n\n        console.log();\n        console.log(chalk.cyan('Next: ') + chalk.white('kg stats') + chalk.gray(' to view graph statistics'));\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Failed to generate knowledge graph');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Add subcommands\n  command\n    .command('analyze')\n    .description('Analyze graph structure and suggest improvements')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .action(async (options) => {\n      const spinner = ora('Analyzing graph...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const dbPath = join(projectRoot, '.kg', 'knowledge.db');\n\n        if (!existsSync(dbPath)) {\n          spinner.fail('Knowledge graph not found. Run \"kg graph\" first.');\n          process.exit(1);\n        }\n\n        const { createDatabase } = await import('../../core/database.js');\n        const db = createDatabase(dbPath);\n\n        const stats = db.getStats();\n        spinner.succeed('Graph analysis complete!');\n\n        console.log();\n        console.log(chalk.white('  Graph Health:'));\n\n        // Orphan analysis\n        if (stats.orphanNodes > 0) {\n          console.log(chalk.yellow(`    ⚠ ${stats.orphanNodes} orphan nodes (no links)`));\n        } else {\n          console.log(chalk.green('    ✓ No orphan nodes'));\n        }\n\n        // Connection density\n        const density = stats.avgLinksPerNode;\n        if (density < 1) {\n          console.log(chalk.yellow(`    ⚠ Low link density (${density} avg links/node)`));\n        } else {\n          console.log(chalk.green(`    ✓ Good link density (${density} avg links/node)`));\n        }\n\n        // Most connected nodes\n        if (stats.mostConnected.length > 0) {\n          console.log();\n          console.log(chalk.white('  Most Connected:'));\n          stats.mostConnected.forEach(({ id, connections }) => {\n            console.log(chalk.gray(`    ${id}: ${connections} connections`));\n          });\n        }\n\n        db.close();\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  return command;\n}\n"],"names":[],"mappings":";;;;;;;AAiBO,SAAS,qBAA8B;AAC5C,QAAM,UAAU,IAAI,QAAQ,OAAO;AAEnC,UACG,YAAY,uDAAuD,EACnE,OAAO,qBAAqB,qBAAqB,GAAG,EACpD,OAAO,qBAAqB,uBAAuB,MAAM,EACzD,OAAO,gBAAgB,iDAAiD,EACxE,OAAO,iBAAiB,sBAAsB,EAC9C,OAAO,OAAO,YAAY;AACzB,UAAM,UAAU,IAAI,+BAA+B,EAAE,MAAA;AAErD,QAAI;AAEF,YAAM,cAAc,oBAAoB,QAAQ,IAAI;AACpD,YAAM,WAAW,iBAAiB,aAAa,QAAQ,IAAI;AAC3D,YAAM,SAAS,KAAK,aAAa,OAAO,cAAc;AAGtD,UAAI,CAAC,WAAW,QAAQ,GAAG;AACzB,gBAAQ,KAAK,6BAA6B,QAAQ,EAAE;AACpD,gBAAQ,IAAI,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,cAAc,IAAI,MAAM,KAAK,eAAe,CAAC;AAC3F,gBAAQ,KAAK,CAAC;AAAA,MAChB;AAGA,UAAI,CAAC,WAAW,KAAK,aAAa,KAAK,CAAC,GAAG;AACzC,gBAAQ,KAAK,iCAAiC;AAC9C,gBAAQ,IAAI,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,SAAS,IAAI,MAAM,KAAK,QAAQ,CAAC;AAC/E,gBAAQ,KAAK,CAAC;AAAA,MAChB;AAEA,UAAI;AAEJ,UAAI,QAAQ,UAAU,WAAW,MAAM,GAAG;AAExC,gBAAQ,OAAO;AACf,iBAAS,MAAM,YAAY,QAAQ,QAAQ;AAE3C,gBAAQ,QAAQ,0BAA0B;AAE1C,gBAAQ,IAAA;AACR,gBAAQ,IAAI,MAAM,MAAM,YAAY,CAAC;AACrC,gBAAQ,IAAI,MAAM,MAAM,gBAAgB,OAAO,KAAK,EAAE,CAAC;AACvD,gBAAQ,IAAI,MAAM,KAAK,gBAAgB,OAAO,OAAO,EAAE,CAAC;AACxD,gBAAQ,IAAI,MAAM,OAAO,gBAAgB,OAAO,OAAO,EAAE,CAAC;AAAA,MAE5D,OAAO;AAEL,gBAAQ,OAAO;AAEf,iBAAS,MAAM;AAAA,UACb;AAAA,YACE;AAAA,YACA,YAAY;AAAA,UAAA;AAAA,UAEd;AAAA,QAAA;AAGF,YAAI,OAAO,SAAS;AAClB,kBAAQ,QAAQ,4BAA4B;AAAA,QAC9C,OAAO;AACL,kBAAQ,KAAK,uCAAuC;AAAA,QACtD;AAEA,gBAAQ,IAAA;AACR,gBAAQ,IAAI,MAAM,MAAM,eAAe,CAAC;AACxC,gBAAQ,IAAI,MAAM,KAAK,sBAAsB,OAAO,MAAM,YAAY,EAAE,CAAC;AACzE,gBAAQ,IAAI,MAAM,MAAM,sBAAsB,OAAO,MAAM,YAAY,EAAE,CAAC;AAC1E,gBAAQ,IAAI,MAAM,KAAK,sBAAsB,OAAO,MAAM,YAAY,EAAE,CAAC;AAAA,MAC3E;AAGA,YAAM,SAAS,YAAY,SAAS,OAAO,SAAS,OAAO,OAAO;AAClE,UAAI,UAAU,OAAO,SAAS,GAAG;AAC/B,gBAAQ,IAAA;AACR,gBAAQ,IAAI,MAAM,OAAO,aAAa,CAAC;AACvC,eAAO,MAAM,GAAG,CAAC,EAAE,QAAQ,CAAC,QAAgB;AAC1C,kBAAQ,IAAI,MAAM,KAAK,SAAS,GAAG,EAAE,CAAC;AAAA,QACxC,CAAC;AACD,YAAI,OAAO,SAAS,GAAG;AACrB,kBAAQ,IAAI,MAAM,KAAK,eAAe,OAAO,SAAS,CAAC,OAAO,CAAC;AAAA,QACjE;AAAA,MACF;AAEA,cAAQ,IAAA;AACR,cAAQ,IAAI,MAAM,KAAK,QAAQ,IAAI,MAAM,MAAM,UAAU,IAAI,MAAM,KAAK,2BAA2B,CAAC;AACpG,cAAQ,IAAA;AAAA,IAEV,SAAS,OAAO;AACd,cAAQ,KAAK,oCAAoC;AACjD,cAAQ,MAAM,MAAM,IAAI,OAAO,KAAK,CAAC,CAAC;AACtC,cAAQ,KAAK,CAAC;AAAA,IAChB;AAAA,EACF,CAAC;AAGH,UACG,QAAQ,SAAS,EACjB,YAAY,kDAAkD,EAC9D,OAAO,qBAAqB,qBAAqB,GAAG,EACpD,OAAO,OAAO,YAAY;AACzB,UAAM,UAAU,IAAI,oBAAoB,EAAE,MAAA;AAE1C,QAAI;AACF,YAAM,cAAc,oBAAoB,QAAQ,IAAI;AACpD,YAAM,SAAS,KAAK,aAAa,OAAO,cAAc;AAEtD,UAAI,CAAC,WAAW,MAAM,GAAG;AACvB,gBAAQ,KAAK,kDAAkD;AAC/D,gBAAQ,KAAK,CAAC;AAAA,MAChB;AAEA,YAAM,EAAE,eAAA,IAAmB,MAAM,OAAO,wBAAwB;AAChE,YAAM,KAAK,eAAe,MAAM;AAEhC,YAAM,QAAQ,GAAG,SAAA;AACjB,cAAQ,QAAQ,0BAA0B;AAE1C,cAAQ,IAAA;AACR,cAAQ,IAAI,MAAM,MAAM,iBAAiB,CAAC;AAG1C,UAAI,MAAM,cAAc,GAAG;AACzB,gBAAQ,IAAI,MAAM,OAAO,SAAS,MAAM,WAAW,0BAA0B,CAAC;AAAA,MAChF,OAAO;AACL,gBAAQ,IAAI,MAAM,MAAM,uBAAuB,CAAC;AAAA,MAClD;AAGA,YAAM,UAAU,MAAM;AACtB,UAAI,UAAU,GAAG;AACf,gBAAQ,IAAI,MAAM,OAAO,2BAA2B,OAAO,kBAAkB,CAAC;AAAA,MAChF,OAAO;AACL,gBAAQ,IAAI,MAAM,MAAM,4BAA4B,OAAO,kBAAkB,CAAC;AAAA,MAChF;AAGA,UAAI,MAAM,cAAc,SAAS,GAAG;AAClC,gBAAQ,IAAA;AACR,gBAAQ,IAAI,MAAM,MAAM,mBAAmB,CAAC;AAC5C,cAAM,cAAc,QAAQ,CAAC,EAAE,IAAI,kBAAkB;AACnD,kBAAQ,IAAI,MAAM,KAAK,OAAO,EAAE,KAAK,WAAW,cAAc,CAAC;AAAA,QACjE,CAAC;AAAA,MACH;AAEA,SAAG,MAAA;AACH,cAAQ,IAAA;AAAA,IAEV,SAAS,OAAO;AACd,cAAQ,KAAK,iBAAiB;AAC9B,cAAQ,MAAM,MAAM,IAAI,OAAO,KAAK,CAAC,CAAC;AACtC,cAAQ,KAAK,CAAC;AAAA,IAChB;AAAA,EACF,CAAC;AAEH,SAAO;AACT;"}
+{"version":3,"file":"graph.js","sources":["../../../src/cli/commands/graph.ts"],"sourcesContent":["/**\n * Graph Command\n *\n * Generate and update knowledge graph from documentation.\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport ora from 'ora';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { generateAndSave, updateGraph } from '../../generators/graph-generator.js';\nimport { validateProjectRoot, validateDocsPath } from '../../core/security.js';\n\n/**\n * Create graph command\n */\nexport function createGraphCommand(): Command {\n  const command = new Command('graph');\n\n  command\n    .description('Generate or update knowledge graph from documentation')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .option('-d, --docs <path>', 'Docs directory path', 'docs')\n    .option('-i, --include <paths>', 'Additional paths to include (comma-separated)')\n    .option('-a, --all', 'Scan entire project for markdown files')\n    .option('-u, --update', 'Incremental update instead of full regeneration')\n    .option('-v, --verbose', 'Show detailed output')\n    .action(async (options) => {\n      const spinner = ora('Generating knowledge graph...').start();\n\n      try {\n        // Validate paths to prevent traversal attacks\n        const projectRoot = validateProjectRoot(options.path);\n        const dbPath = join(projectRoot, '.kg', 'knowledge.db');\n\n        // Build list of source paths\n        const sourcePaths: string[] = [];\n\n        if (options.all) {\n          // Scan entire project\n          sourcePaths.push(projectRoot);\n        } else {\n          // Add main docs path\n          const docsPath = validateDocsPath(projectRoot, options.docs);\n          if (existsSync(docsPath)) {\n            sourcePaths.push(docsPath);\n          }\n\n          // Add additional include paths\n          if (options.include) {\n            const additionalPaths = options.include.split(',').map((p: string) => p.trim());\n            for (const relPath of additionalPaths) {\n              const fullPath = join(projectRoot, relPath);\n              if (existsSync(fullPath)) {\n                sourcePaths.push(fullPath);\n              } else if (options.verbose) {\n                console.log(chalk.yellow(`  Skipping non-existent path: ${relPath}`));\n              }\n            }\n          }\n        }\n\n        // Check if any source paths exist\n        if (sourcePaths.length === 0) {\n          spinner.fail('No documentation directories found');\n          console.log(chalk.gray('  Run ') + chalk.cyan('kg docs init') + chalk.gray(' to create docs/'));\n          console.log(chalk.gray('  Or use ') + chalk.cyan('--include <paths>') + chalk.gray(' to specify paths'));\n          console.log(chalk.gray('  Or use ') + chalk.cyan('--all') + chalk.gray(' to scan entire project'));\n          process.exit(1);\n        }\n\n        // Check if KG is initialized\n        if (!existsSync(join(projectRoot, '.kg'))) {\n          spinner.fail('Knowledge graph not initialized');\n          console.log(chalk.gray('  Run ') + chalk.cyan('kg init') + chalk.gray(' first'));\n          process.exit(1);\n        }\n\n        if (options.verbose) {\n          console.log(chalk.gray(`  Scanning paths: ${sourcePaths.join(', ')}`));\n        }\n\n        let result;\n\n        if (options.update && existsSync(dbPath)) {\n          // Incremental update\n          spinner.text = 'Updating knowledge graph...';\n          result = await updateGraph(dbPath, sourcePaths[0], sourcePaths);\n\n          spinner.succeed('Knowledge graph updated!');\n\n          console.log();\n          console.log(chalk.white('  Changes:'));\n          console.log(chalk.green(`    Added:   ${result.added}`));\n          console.log(chalk.blue(`    Updated: ${result.updated}`));\n          console.log(chalk.yellow(`    Removed: ${result.removed}`));\n\n        } else {\n          // Full generation\n          spinner.text = options.all ? 'Scanning entire project...' : 'Scanning documentation...';\n\n          result = await generateAndSave(\n            {\n              projectRoot,\n              outputPath: sourcePaths[0],\n              additionalPaths: sourcePaths.slice(1),\n              scanAll: options.all,\n            },\n            dbPath\n          );\n\n          if (result.success) {\n            spinner.succeed('Knowledge graph generated!');\n          } else {\n            spinner.warn('Knowledge graph generated with errors');\n          }\n\n          console.log();\n          console.log(chalk.white('  Statistics:'));\n          console.log(chalk.gray(`    Paths scanned: ${sourcePaths.length}`));\n          console.log(chalk.gray(`    Files scanned: ${result.stats.filesScanned}`));\n          console.log(chalk.green(`    Nodes created: ${result.stats.nodesCreated}`));\n          console.log(chalk.blue(`    Edges created: ${result.stats.edgesCreated}`));\n        }\n\n        // Show errors if any\n        const errors = 'errors' in result ? result.errors : result.stats?.errors;\n        if (errors && errors.length > 0) {\n          console.log();\n          console.log(chalk.yellow('  Warnings:'));\n          errors.slice(0, 5).forEach((err: string) => {\n            console.log(chalk.gray(`    - ${err}`));\n          });\n          if (errors.length > 5) {\n            console.log(chalk.gray(`    ... and ${errors.length - 5} more`));\n          }\n        }\n\n        console.log();\n        console.log(chalk.cyan('Next: ') + chalk.white('kg stats') + chalk.gray(' to view graph statistics'));\n        console.log();\n\n      } catch (error) {\n        spinner.fail('Failed to generate knowledge graph');\n        console.error(chalk.red(String(error)));\n        process.exit(1);\n      }\n    });\n\n  // Add subcommands\n  command\n    .command('analyze')\n    .description('Analyze graph structure and suggest improvements')\n    .option('-p, --path <path>', 'Project root path', '.')\n    .action(async (options) => {\n      const spinner = ora('Analyzing graph...').start();\n\n      try {\n        const projectRoot = validateProjectRoot(options.path);\n        const dbPath = join(projectRoot, '.kg', 'knowledge.db');\n\n        if (!existsSync(dbPath)) {\n          spinner.fail('Knowledge graph not found. Run \"kg graph\" first.');\n          process.exit(1);\n        }\n\n        const { createDatabase } = await import('../../core/database.js');\n        const db = createDatabase(dbPath);\n\n        const stats = db.getStats();\n        spinner.succeed('Graph analysis complete!');\n\n        console.log();\n        console.log(chalk.white('  Graph Health:'));\n\n        // Orphan analysis\n        if (stats.orphanNodes > 0) {\n          console.log(chalk.yellow(`    ⚠ ${stats.orphanNodes} orphan nodes (no links)`));\n        } else {\n          console.log(chalk.green('    ✓ No orphan nodes'));\n        }\n\n        // Connection density\n        const density = stats.avgLinksPerNode;\n        if (density < 1) {\n          console.log(chalk.yellow(`    ⚠ Low link density (${density} avg links/node)`));\n        } else {\n          console.log(chalk.green(`    ✓ Good link density (${density} avg links/node)`));\n        }\n\n        // Most connected nodes\n        if (stats.mostConnected.length > 0) {\n          console.log();\n          console.log(chalk.white('  Most Connected:'));\n          stats.mostConnected.forEach(({ id, connections }) => {\n            console.log(chalk.gray(`    ${id}: ${connections} connections`));\n          });\n        }\n\n        db.close();\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  return 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package/dist/core/database.d.ts

@@ -54,6 +54,10 @@ export declare class KnowledgeGraphDatabase {
      * Delete node
      */
     deleteNode(id: string): boolean;
+    /**
+     * Clear all nodes and edges (for full regeneration)
+     */
+    clearAll(): void;
     /**
      * Update tags for a node
      */

package/dist/core/database.d.ts.map

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package/dist/core/database.js

@@ -237,6 +237,14 @@ class KnowledgeGraphDatabase {
     const result = stmt.run(id);
     return result.changes > 0;
   }
+  /**
+   * Clear all nodes and edges (for full regeneration)
+   */
+  clearAll() {
+    this.db.exec("DELETE FROM edges");
+    this.db.exec("DELETE FROM node_tags");
+    this.db.exec("DELETE FROM nodes");
+  }
   // ========================================================================
   // Tag Operations
   // ========================================================================

package/dist/core/database.js.map

@@ -1 +1 @@
-{"version":3,"file":"database.js","sources":["../../src/core/database.ts"],"sourcesContent":["/**\n * Knowledge Graph Database\n *\n * SQLite database for persistent storage of knowledge graph data.\n * Compatible with claude-flow database patterns.\n */\n\nimport Database from 'better-sqlite3';\nimport { existsSync, mkdirSync } from 'fs';\nimport { dirname } from 'path';\nimport type {\n  KnowledgeNode,\n  GraphEdge,\n  GraphStats,\n  NodeType,\n  NodeStatus,\n} from './types.js';\n\n/**\n * Safely parse JSON with fallback\n * Prevents error leakage from malformed JSON\n */\nfunction safeJsonParse<T>(str: string | null | undefined, fallback: T): T {\n  if (!str) return fallback;\n  try {\n    return JSON.parse(str) as T;\n  } catch {\n    return fallback;\n  }\n}\n\nconst SCHEMA_SQL = `\n-- Knowledge Graph Schema v1.0\n\n-- Nodes table\nCREATE TABLE IF NOT EXISTS nodes (\n  id TEXT PRIMARY KEY,\n  path TEXT NOT NULL UNIQUE,\n  filename TEXT NOT NULL,\n  title TEXT NOT NULL,\n  type 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content_rowid='rowid'\n);\n\n-- Triggers for FTS sync\nCREATE TRIGGER IF NOT EXISTS nodes_ai AFTER INSERT ON nodes BEGIN\n  INSERT INTO nodes_fts(rowid, title, content) VALUES (NEW.rowid, NEW.title, NEW.content);\nEND;\n\nCREATE TRIGGER IF NOT EXISTS nodes_ad AFTER DELETE ON nodes BEGIN\n  INSERT INTO nodes_fts(nodes_fts, rowid, title, content) VALUES('delete', OLD.rowid, OLD.title, OLD.content);\nEND;\n\nCREATE TRIGGER IF NOT EXISTS nodes_au AFTER UPDATE ON nodes BEGIN\n  INSERT INTO nodes_fts(nodes_fts, rowid, title, content) VALUES('delete', OLD.rowid, OLD.title, OLD.content);\n  INSERT INTO nodes_fts(rowid, title, content) VALUES (NEW.rowid, NEW.title, NEW.content);\nEND;\n\n-- Initialize metadata\nINSERT OR IGNORE INTO metadata (key, value) VALUES ('version', '1.0.0');\nINSERT OR IGNORE INTO metadata (key, value) VALUES ('created', datetime('now'));\n`;\n\n/**\n * Knowledge Graph Database\n */\nexport class KnowledgeGraphDatabase {\n  private db: Database.Database;\n  private dbPath: string;\n\n  constructor(dbPath: string) {\n    this.dbPath = dbPath;\n\n    // Ensure directory exists\n    const dir = dirname(dbPath);\n    if (!existsSync(dir)) {\n      mkdirSync(dir, { recursive: true });\n    }\n\n    // Open database\n    this.db = new Database(dbPath);\n    this.db.pragma('journal_mode = WAL');\n    this.db.pragma('foreign_keys = ON');\n    this.db.pragma('busy_timeout = 5000');\n\n    // Initialize schema\n    this.db.exec(SCHEMA_SQL);\n  }\n\n  // ========================================================================\n  // Node Operations\n  // ========================================================================\n\n  /**\n   * Insert or update a node\n   */\n  upsertNode(node: KnowledgeNode): void {\n    const stmt = this.db.prepare(`\n      INSERT INTO nodes (id, path, filename, title, type, status, content, frontmatter, word_count, updated_at)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, datetime('now'))\n      ON CONFLICT(id) DO UPDATE SET\n    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{\n    const stmt = this.db.prepare('SELECT * FROM nodes WHERE path = ?');\n    const row = stmt.get(path) as NodeRow | undefined;\n    if (!row) return null;\n    return this.rowToNode(row);\n  }\n\n  /**\n   * Get all nodes\n   */\n  getAllNodes(): KnowledgeNode[] {\n    const stmt = this.db.prepare('SELECT * FROM nodes ORDER BY title');\n    const rows = stmt.all() as NodeRow[];\n    return rows.map(row => this.rowToNode(row));\n  }\n\n  /**\n   * Get nodes by type\n   */\n  getNodesByType(type: NodeType): KnowledgeNode[] {\n    const stmt = this.db.prepare('SELECT * FROM nodes WHERE type = ? ORDER BY title');\n    const rows = stmt.all(type) as NodeRow[];\n    return rows.map(row => this.rowToNode(row));\n  }\n\n  /**\n   * Get nodes by status\n   */\n  getNodesByStatus(status: NodeStatus): KnowledgeNode[] {\n    const stmt = this.db.prepare('SELECT * FROM nodes WHERE status = ? ORDER BY title');\n    const rows = stmt.all(status) as NodeRow[];\n    return rows.map(row => this.rowToNode(row));\n  }\n\n  /**\n   * Get nodes by tag\n   */\n  getNodesByTag(tag: string): KnowledgeNode[] {\n    const stmt = this.db.prepare(`\n      SELECT n.* FROM nodes n\n      JOIN node_tags nt ON n.id = nt.node_id\n      JOIN tags t ON nt.tag_id = t.id\n      WHERE t.name = ?\n      ORDER BY n.title\n    `);\n    const rows = stmt.all(tag) as NodeRow[];\n    return rows.map(row => this.rowToNode(row));\n  }\n\n  /**\n   * Sanitize FTS5 query to prevent query injection\n   * Escapes special FTS5 operators and quotes terms\n   */\n  private sanitizeFtsQuery(query: string): string {\n    if (!query || typeof query !== 'string') return '';\n\n    // Remove FTS5 special operators: * \" ( ) : ^ - AND OR NOT NEAR\n    const sanitized = query\n      .replace(/[*\"():^\\-]/g, ' ')  // Remove special chars\n      .replace(/\\b(AND|OR|NOT|NEAR)\\b/gi, '') // Remove boolean operators\n      .trim()\n      .split(/\\s+/)\n      .filter(term => term.length > 0 && term.length < 100) // Limit term length\n      .slice(0, 20)  // Limit number of terms\n      .map(term => `\"${term.replace(/\"/g, '')}\"`)  // Quote each term safely\n      .join(' ');\n\n    return sanitized;\n  }\n\n  /**\n   * Search nodes by title or content\n   */\n  searchNodes(query: string, limit = 50): KnowledgeNode[] {\n    const sanitizedQuery = this.sanitizeFtsQuery(query);\n\n    // Return empty if no valid search terms\n    if (!sanitizedQuery) {\n      return [];\n    }\n\n    // Enforce reasonable limit\n    const safeLimit = Math.min(Math.max(1, limit), 100);\n\n    const stmt = this.db.prepare(`\n      SELECT n.* FROM nodes n\n      JOIN nodes_fts fts ON n.rowid = fts.rowid\n      WHERE nodes_fts MATCH ?\n      ORDER BY rank\n      LIMIT ?\n    `);\n    const rows = stmt.all(sanitizedQuery, safeLimit) as NodeRow[];\n    return rows.map(row => this.rowToNode(row));\n  }\n\n  /**\n   * Delete node\n   */\n  deleteNode(id: string): boolean {\n    const stmt = this.db.prepare('DELETE FROM nodes WHERE id = ?');\n    const result = stmt.run(id);\n    return result.changes > 0;\n  }\n\n  // ========================================================================\n  // Tag Operations\n  // ========================================================================\n\n  /**\n   * Update tags for a node\n   */\n  private updateNodeTags(nodeId: string, tags: string[]): void {\n    // Remove existing tags\n    this.db.prepare('DELETE FROM node_tags WHERE node_id = ?').run(nodeId);\n\n    // Insert new tags\n    const getOrCreateTag = this.db.prepare(`\n      INSERT INTO tags (name) VALUES (?)\n      ON CONFLICT(name) DO UPDATE SET name = excluded.name\n      RETURNING id\n    `);\n\n    const insertNodeTag = this.db.prepare(\n      'INSERT OR IGNORE INTO node_tags (node_id, tag_id) VALUES (?, ?)'\n    );\n\n    for (const tag of tags) {\n      const result = getOrCreateTag.get(tag) as { id: number };\n      insertNodeTag.run(nodeId, result.id);\n    }\n  }\n\n  /**\n   * Get tags for a node\n   */\n  getNodeTags(nodeId: string): string[] {\n    const stmt = this.db.prepare(`\n      SELECT t.name FROM tags t\n      JOIN node_tags nt ON t.id = nt.tag_id\n      WHERE nt.node_id = ?\n      ORDER BY t.name\n    `);\n    const rows = stmt.all(nodeId) as Array<{ name: string }>;\n    return rows.map(r => r.name);\n  }\n\n  /**\n   * Get all tags with counts\n   */\n  getAllTags(): Array<{ name: string; count: number }> {\n    const stmt = this.db.prepare(`\n      SELECT t.name, COUNT(nt.node_id) as count\n      FROM tags t\n      LEFT JOIN node_tags nt ON t.id = nt.tag_id\n      GROUP BY t.id\n      ORDER BY count DESC, t.name\n    `);\n    return stmt.all() as Array<{ name: string; count: number }>;\n  }\n\n  // ========================================================================\n  // Edge Operations\n  // ========================================================================\n\n  /**\n   * Add edge\n   */\n  addEdge(edge: GraphEdge): void {\n    const stmt = this.db.prepare(`\n      INSERT INTO edges (source_id, target_id, type, weight, context)\n      VALUES (?, ?, ?, ?, ?)\n    `);\n    stmt.run(edge.source, edge.target, edge.type, edge.weight, edge.context);\n  }\n\n  /**\n   * Get outgoing edges for a node\n   */\n  getOutgoingEdges(nodeId: string): GraphEdge[] {\n    const stmt = this.db.prepare('SELECT * FROM edges WHERE source_id = ?');\n    const rows = stmt.all(nodeId) as EdgeRow[];\n    return rows.map(row => this.rowToEdge(row));\n  }\n\n  /**\n   * Get incoming edges for a node\n   */\n  getIncomingEdges(nodeId: string): GraphEdge[] {\n    const stmt = this.db.prepare('SELECT * FROM edges WHERE target_id = ?');\n    const rows = stmt.all(nodeId) as EdgeRow[];\n    return rows.map(row => this.rowToEdge(row));\n  }\n\n  /**\n   * Delete edges for a node\n   */\n  deleteNodeEdges(nodeId: string): void {\n    this.db.prepare('DELETE FROM edges WHERE source_id = ?').run(nodeId);\n  }\n\n  // ========================================================================\n  // Statistics\n  // ========================================================================\n\n  /**\n   * Get graph statistics\n   */\n  getStats(): GraphStats {\n    const totalNodes = (this.db.prepare('SELECT COUNT(*) as count FROM nodes').get() as { count: number }).count;\n    const totalEdges = (this.db.prepare('SELECT COUNT(*) as count FROM edges').get() as { count: number }).count;\n\n    const typeStats = this.db.prepare(`\n      SELECT type, COUNT(*) as count FROM nodes GROUP BY type\n    `).all() as Array<{ type: NodeType; count: number }>;\n\n    const statusStats = this.db.prepare(`\n      SELECT status, COUNT(*) as count FROM nodes GROUP BY status\n    `).all() as Array<{ status: NodeStatus; count: number }>;\n\n    const nodesByType: Record<NodeType, number> = {\n      concept: 0, technical: 0, feature: 0, primitive: 0,\n      service: 0, guide: 0, standard: 0, integration: 0,\n    };\n    for (const { type, count } of typeStats) {\n      nodesByType[type] = count;\n    }\n\n    const nodesByStatus: Record<NodeStatus, number> = {\n      draft: 0, active: 0, deprecated: 0, archived: 0,\n    };\n    for (const { status, count } of statusStats) {\n      nodesByStatus[status] = count;\n    }\n\n    const orphanNodes = (this.db.prepare(`\n      SELECT COUNT(*) as count FROM nodes n\n      WHERE NOT EXISTS (SELECT 1 FROM edges e WHERE e.source_id = n.id OR e.target_id = n.id)\n    `).get() as { count: number }).count;\n\n    const avgLinksPerNode = totalNodes > 0 ? totalEdges / totalNodes : 0;\n\n    const mostConnected = this.db.prepare(`\n      SELECT n.id, (\n        (SELECT COUNT(*) FROM edges WHERE source_id = n.id) +\n        (SELECT COUNT(*) FROM edges WHERE target_id = n.id)\n      ) as connections\n      FROM nodes n\n      ORDER BY connections DESC\n      LIMIT 5\n    `).all() as Array<{ id: string; connections: number }>;\n\n    return {\n      totalNodes,\n      totalEdges,\n      nodesByType,\n      nodesByStatus,\n      orphanNodes,\n      avgLinksPerNode: Math.round(avgLinksPerNode * 100) / 100,\n      mostConnected,\n    };\n  }\n\n  // ========================================================================\n  // Metadata Operations\n  // ========================================================================\n\n  /**\n   * Get metadata value\n   */\n  getMetadata(key: string): string | null {\n    const stmt = this.db.prepare('SELECT value FROM metadata WHERE key = ?');\n    const row = stmt.get(key) as { value: string } | undefined;\n    return row?.value ?? null;\n  }\n\n  /**\n   * Set metadata value\n   */\n  setMetadata(key: string, value: string): void {\n    const stmt = this.db.prepare(`\n      INSERT INTO metadata (key, value, updated_at) VALUES (?, ?, datetime('now'))\n      ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = datetime('now')\n    `);\n    stmt.run(key, value);\n  }\n\n  // ========================================================================\n  // Utilities\n  // ========================================================================\n\n  /**\n   * Convert database row to KnowledgeNode\n   */\n  private rowToNode(row: NodeRow): KnowledgeNode {\n    const tags = this.getNodeTags(row.id);\n    const outgoingEdges = this.getOutgoingEdges(row.id);\n    const incomingEdges = this.getIncomingEdges(row.id);\n\n    return {\n      id: row.id,\n      path: row.path,\n      filename: row.filename,\n      title: row.title,\n      type: row.type as NodeType,\n      status: row.status as NodeStatus,\n      content: row.content || '',\n      frontmatter: safeJsonParse(row.frontmatter, {}),\n      tags,\n      outgoingLinks: outgoingEdges.map(e => ({\n        target: e.target,\n        type: 'wikilink' as const,\n        context: e.context,\n      })),\n      incomingLinks: incomingEdges.map(e => ({\n        target: e.source,\n        type: 'backlink' as const,\n        context: e.context,\n      })),\n      wordCount: row.word_count,\n      lastModified: new Date(row.updated_at),\n    };\n  }\n\n  /**\n   * Convert database row to GraphEdge\n   */\n  private rowToEdge(row: EdgeRow): GraphEdge {\n    return {\n      source: row.source_id,\n      target: row.target_id,\n      type: row.type as GraphEdge['type'],\n      weight: row.weight,\n      context: row.context ?? undefined,\n    };\n  }\n\n  /**\n   * Close database connection\n   */\n  close(): void {\n    this.db.close();\n  }\n\n  /**\n   * Get raw database instance\n   */\n  getDatabase(): Database.Database {\n    return this.db;\n  }\n}\n\n// Row types for database queries\ninterface NodeRow {\n  id: string;\n  path: string;\n  filename: string;\n  title: string;\n  type: string;\n  status: string;\n  content: string | null;\n  frontmatter: string | null;\n  word_count: number;\n  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package/dist/core/types.d.ts

@@ -174,6 +174,8 @@ export interface GeneratorOptions {
     outputPath: string;
     includeExamples?: boolean;
     force?: boolean;
+    additionalPaths?: string[];
+    scanAll?: boolean;
 }
 export interface GeneratedDocument {
     path: string;

package/dist/core/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sources":["../../src/core/types.ts"],"sourcesContent":["/**\n * Knowledge Graph Agent - Core Types\n *\n * Type definitions for the knowledge graph system.\n */\n\nimport { z } from 'zod';\n\n// ============================================================================\n// Node Types\n// ============================================================================\n\nexport type NodeType =\n  | 'concept'      // Abstract concepts and ideas\n  | 'technical'    // Technical components and implementations\n  | 'feature'      // Product features and capabilities\n  | 'primitive'    // Base technology primitives (frameworks, libraries)\n  | 'service'      // Backend services and APIs\n  | 'guide'        // How-to guides and tutorials\n  | 'standard'     // Coding standards and conventions\n  | 'integration'; // External integrations\n\nexport type NodeStatus = 'draft' | 'active' | 'deprecated' | 'archived';\n\nexport interface NodeLink {\n  target: string; 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 // Source node ID\n  target: string;  // Target node ID\n  type: 'link' | 'reference' | 'parent' | 'related';\n  weight: number;  // Relationship strength 0-1\n  context?: string;\n}\n\nexport interface KnowledgeGraph {\n  nodes: Map<string, KnowledgeNode>;\n  edges: GraphEdge[];\n  metadata: GraphMetadata;\n}\n\nexport interface GraphMetadata {\n  name: string;\n  version: string;\n  created: string;\n  updated: string;\n  nodeCount: number;\n  edgeCount: number;\n  rootPath: string;\n}\n\nexport interface GraphStats {\n  totalNodes: number;\n  totalEdges: number;\n  nodesByType: Record<NodeType, number>;\n  nodesByStatus: Record<NodeStatus, number>;\n  orphanNodes: number;\n  avgLinksPerNode: number;\n  mostConnected: Array<{ id: string; connections: number }>;\n}\n\n// ============================================================================\n// Configuration Types\n// ============================================================================\n\nexport const ConfigSchema = z.object({\n  // Project settings\n  projectRoot: z.string().default('.'),\n  docsRoot: z.string().default('./docs'),\n  vaultName: z.string().optional(),\n\n  // Graph settings\n  graph: z.object({\n    includePatterns: z.array(z.string()).default(['**/*.md']),\n    excludePatterns: z.array(z.string()).default([\n      'node_modules/**',\n      'dist/**',\n      '.git/**',\n    ]),\n    maxDepth: z.number().default(10),\n  }).default({}),\n\n  // Database settings\n  database: z.object({\n    path: z.string().default('./.kg/knowledge.db'),\n    enableWAL: z.boolean().default(true),\n  }).default({}),\n\n  // Claude-Flow integration\n  claudeFlow: z.object({\n    enabled: z.boolean().default(true),\n    namespace: z.string().default('knowledge-graph'),\n    syncOnChange: z.boolean().default(true),\n  }).default({}),\n\n  // Templates\n  templates: z.object({\n    customPath: z.string().optional(),\n    defaultType: z.enum(['concept', 'technical', 'feature', 'primitive', 'service', 'guide', 'standard', 'integration']).default('concept'),\n  }).default({}),\n});\n\nexport type KGConfig = z.infer<typeof ConfigSchema>;\n\n// ============================================================================\n// Generator Types\n// ============================================================================\n\nexport interface GeneratorOptions {\n  projectRoot: string;\n  outputPath: string;\n  includeExamples?: boolean;\n  force?: boolean;\n  additionalPaths?: string[];\n  scanAll?: boolean;\n}\n\nexport interface GeneratedDocument {\n  path: string;\n  title: string;\n  type: NodeType;\n  content: string;\n  frontmatter: NodeFrontmatter;\n}\n\nexport interface DocsInitOptions {\n  projectRoot: string;\n  docsPath?: string;\n  template?: string;\n  includeExamples?: boolean;\n  detectFramework?: boolean;\n}\n\nexport interface DocsInitResult {\n  success: boolean;\n  docsPath: string;\n  filesCreated: string[];\n  errors: string[];\n}\n\n// ============================================================================\n// Claude-Flow Integration Types\n// ============================================================================\n\nexport interface MemoryEntry {\n  key: string;\n  value: unknown;\n  namespace?: string;\n  ttl?: number;\n  metadata?: Record<string, unknown>;\n}\n\nexport interface SyncResult {\n  synced: number;\n  failed: number;\n  errors: Array<{ key: string; error: string }>;\n}\n\n// ============================================================================\n// CLAUDE.md Template Types\n// ============================================================================\n\nexport interface ClaudeMdSection {\n  title: string;\n  content: string;\n  order: number;\n}\n\nexport interface ClaudeMdTemplate {\n  name: string;\n  description: string;\n  sections: ClaudeMdSection[];\n  variables: Record<string, string>;\n}\n\nexport interface ClaudeMdGeneratorOptions {\n  projectRoot: string;\n  outputPath?: string;\n  template?: string;\n  includeKnowledgeGraph?: boolean;\n  includeClaudeFlow?: boolean;\n  customSections?: ClaudeMdSection[];\n}\n"],"names":[],"mappings":";AAuGO,MAAM,eAAe,EAAE,OAAO;AAAA;AAAA,EAEnC,aAAa,EAAE,SAAS,QAAQ,GAAG;AAAA,EACnC,UAAU,EAAE,SAAS,QAAQ,QAAQ;AAAA,EACrC,WAAW,EAAE,OAAA,EAAS,SAAA;AAAA;AAAA,EAGtB,OAAO,EAAE,OAAO;AAAA,IACd,iBAAiB,EAAE,MAAM,EAAE,OAAA,CAAQ,EAAE,QAAQ,CAAC,SAAS,CAAC;AAAA,IACxD,iBAAiB,EAAE,MAAM,EAAE,OAAA,CAAQ,EAAE,QAAQ;AAAA,MAC3C;AAAA,MACA;AAAA,MACA;AAAA,IAAA,CACD;AAAA,IACD,UAAU,EAAE,OAAA,EAAS,QAAQ,EAAE;AAAA,EAAA,CAChC,EAAE,QAAQ,EAAE;AAAA;AAAA,EAGb,UAAU,EAAE,OAAO;AAAA,IACjB,MAAM,EAAE,SAAS,QAAQ,oBAAoB;AAAA,IAC7C,WAAW,EAAE,QAAA,EAAU,QAAQ,IAAI;AAAA,EAAA,CACpC,EAAE,QAAQ,EAAE;AAAA;AAAA,EAGb,YAAY,EAAE,OAAO;AAAA,IACnB,SAAS,EAAE,UAAU,QAAQ,IAAI;AAAA,IACjC,WAAW,EAAE,SAAS,QAAQ,iBAAiB;AAAA,IAC/C,cAAc,EAAE,QAAA,EAAU,QAAQ,IAAI;AAAA,EAAA,CACvC,EAAE,QAAQ,EAAE;AAAA;AAAA,EAGb,WAAW,EAAE,OAAO;AAAA,IAClB,YAAY,EAAE,OAAA,EAAS,SAAA;AAAA,IACvB,aAAa,EAAE,KAAK,CAAC,WAAW,aAAa,WAAW,aAAa,WAAW,SAAS,YAAY,aAAa,CAAC,EAAE,QAAQ,SAAS;AAAA,EAAA,CACvI,EAAE,QAAQ,CAAA,CAAE;AACf,CAAC;"}

package/dist/generators/graph-generator.d.ts

@@ -6,7 +6,7 @@
 import type { GeneratorOptions } from '../core/types.js';
 import { KnowledgeGraphManager } from '../core/graph.js';
 /**
- * Generate knowledge graph from docs directory
+ * Generate knowledge graph from docs directory (or multiple directories)
  */
 export declare function generateGraph(options: GeneratorOptions): Promise<{
     graph: KnowledgeGraphManager;
@@ -32,7 +32,7 @@ export declare function generateAndSave(options: GeneratorOptions, dbPath: strin
 /**
  * Generate graph from existing database (incremental update)
  */
-export declare function updateGraph(dbPath: string, docsRoot: string): Promise<{
+export declare function updateGraph(dbPath: string, docsRoot: string, allPaths?: string[]): Promise<{
     added: number;
     updated: number;
     removed: number;

package/dist/generators/graph-generator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"graph-generator.d.ts","sourceRoot":"","sources":["../../src/generators/graph-generator.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAMH,OAAO,KAAK,EAMV,gBAAgB,EAEjB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AASzD;;GAEG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC;IACtE,KAAK,EAAE,qBAAqB,CAAC;IAC7B,KAAK,EAAE;QACL,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACH,CAAC,CAwED;AAED;;GAEG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,gBAAgB,EACzB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC;IACT,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE;QACL,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACH,CAAC,CA6BD;AAgND;;GAEG;AACH,wBAAsB,WAAW,CAC/B,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC;IACT,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAAC,CA4DD"}
+{"version":3,"file":"graph-generator.d.ts","sourceRoot":"","sources":["../../src/generators/graph-generator.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAMH,OAAO,KAAK,EAMV,gBAAgB,EAEjB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AASzD;;GAEG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC;IACtE,KAAK,EAAE,qBAAqB,CAAC;IAC7B,KAAK,EAAE;QACL,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACH,CAAC,CAgGD;AAED;;GAEG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,gBAAgB,EACzB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC;IACT,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE;QACL,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACH,CAAC,CAgCD;AAgND;;GAEG;AACH,wBAAsB,WAAW,CAC/B,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,MAAM,EAAE,GAClB,OAAO,CAAC;IACT,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAAC,CAgFD"}

package/dist/generators/graph-generator.js

@@ -7,7 +7,7 @@ import { KnowledgeGraphDatabase } from "../core/database.js";
 const WIKILINK_PATTERN = /\[\[([^\]|]+)(?:\|([^\]]+))?\]\]/g;
 const MARKDOWN_LINK_PATTERN = /\[([^\]]+)\]\(([^)]+)\)/g;
 async function generateGraph(options) {
-  const { projectRoot, outputPath } = options;
+  const { projectRoot, outputPath, additionalPaths = [], scanAll } = options;
   const stats = {
     filesScanned: 0,
     nodesCreated: 0,
@@ -18,18 +18,39 @@ async function generateGraph(options) {
     basename(projectRoot),
     projectRoot
   );
-  const files = await fg("**/*.md", {
-    cwd: outputPath,
-    ignore: ["node_modules/**", ".git/**", "_templates/**"],
-    absolute: true
-  });
-  stats.filesScanned = files.length;
+  const pathsToScan = scanAll ? [projectRoot] : [outputPath, ...additionalPaths];
+  const allFiles = [];
+  for (const scanPath of pathsToScan) {
+    const files = await fg("**/*.md", {
+      cwd: scanPath,
+      ignore: [
+        "node_modules/**",
+        ".git/**",
+        "**/_templates/**",
+        // Templates anywhere in tree
+        "**/dist/**",
+        "**/build/**",
+        "**/.hive-mind/**"
+        // Hive mind internal files
+      ],
+      absolute: true,
+      dot: true
+      // Include hidden directories like .claude/
+    });
+    for (const filePath of files) {
+      allFiles.push({ filePath, baseDir: projectRoot });
+    }
+  }
+  stats.filesScanned = allFiles.length;
   const nodeMap = /* @__PURE__ */ new Map();
-  for (const filePath of files) {
+  for (const { filePath, baseDir } of allFiles) {
     try {
-      const node = await parseMarkdownFile(filePath, outputPath);
-      nodeMap.set(node.id, node);
-      stats.nodesCreated++;
+      const node = await parseMarkdownFile(filePath, baseDir);
+      const uniqueId = scanAll ? node.id : node.id;
+      if (!nodeMap.has(uniqueId)) {
+        nodeMap.set(uniqueId, node);
+        stats.nodesCreated++;
+      }
     } catch (error) {
       stats.errors.push(`Failed to parse ${filePath}: ${error}`);
     }
@@ -63,6 +84,7 @@ async function generateAndSave(options, dbPath) {
   const { graph, stats } = await generateGraph(options);
   const db = new KnowledgeGraphDatabase(dbPath);
   try {
+    db.clearAll();
     const nodes = graph.getAllNodes();
     const edges = graph.getAllEdges();
     for (const node of nodes) {
@@ -211,7 +233,7 @@ function inferNodeType(declaredType, path) {
 function formatTitle(filename) {
   return filename.replace(/-/g, " ").replace(/_/g, " ").replace(/\b\w/g, (c) => c.toUpperCase());
 }
-async function updateGraph(dbPath, docsRoot) {
+async function updateGraph(dbPath, docsRoot, allPaths) {
   const result = {
     added: 0,
     updated: 0,
@@ -222,23 +244,41 @@ async function updateGraph(dbPath, docsRoot) {
   try {
     const existingNodes = db.getAllNodes();
     const existingPaths = new Set(existingNodes.map((n) => n.path));
-    const currentFiles = await fg("**/*.md", {
-      cwd: docsRoot,
-      ignore: ["node_modules/**", ".git/**", "_templates/**"]
-    });
-    const currentPaths = new Set(currentFiles);
+    const pathsToScan = allPaths || [docsRoot];
+    const allCurrentFiles = [];
+    for (const scanPath of pathsToScan) {
+      const files = await fg("**/*.md", {
+        cwd: scanPath,
+        ignore: [
+          "node_modules/**",
+          ".git/**",
+          "**/_templates/**",
+          // Templates anywhere in tree
+          "**/dist/**",
+          "**/build/**",
+          "**/.hive-mind/**"
+          // Hive mind internal files
+        ],
+        dot: true
+        // Include hidden directories like .claude/
+      });
+      for (const file of files) {
+        allCurrentFiles.push({ filePath: file, baseDir: scanPath });
+      }
+    }
+    const currentPaths = new Set(allCurrentFiles.map((f) => f.filePath));
     for (const node of existingNodes) {
       if (!currentPaths.has(node.path)) {
         db.deleteNode(node.id);
         result.removed++;
       }
     }
-    for (const filePath of currentFiles) {
-      const fullPath = join(docsRoot, filePath);
+    for (const { filePath, baseDir } of allCurrentFiles) {
+      const fullPath = join(baseDir, filePath);
       try {
-        const node = await parseMarkdownFile(fullPath, docsRoot);
-        if (existingPaths.has(filePath)) {
-          const existing = existingNodes.find((n) => n.path === filePath);
+        const node = await parseMarkdownFile(fullPath, baseDir);
+        if (existingPaths.has(node.path)) {
+          const existing = existingNodes.find((n) => n.path === node.path);
           if (existing && node.lastModified > existing.lastModified) {
             db.deleteNodeEdges(node.id);
             db.upsertNode(node);

package/dist/generators/graph-generator.js.map

@@ -1 +1 @@
-{"version":3,"file":"graph-generator.js","sources":["../../src/generators/graph-generator.ts"],"sourcesContent":["/**\n * Knowledge Graph Generator\n *\n * Scans documentation and generates a knowledge graph from markdown files.\n */\n\nimport { readFileSync, statSync } from 'fs';\nimport { join, basename, relative, extname } from 'path';\nimport fg from 'fast-glob';\nimport matter from 'gray-matter';\nimport type {\n  KnowledgeNode,\n  NodeType,\n  NodeStatus,\n  NodeLink,\n  NodeFrontmatter,\n  GeneratorOptions,\n  GeneratedDocument,\n} from '../core/types.js';\nimport { KnowledgeGraphManager } from '../core/graph.js';\nimport { KnowledgeGraphDatabase } from '../core/database.js';\n\n/**\n * Link extraction patterns\n */\nconst WIKILINK_PATTERN = /\\[\\[([^\\]|]+)(?:\\|([^\\]]+))?\\]\\]/g;\nconst MARKDOWN_LINK_PATTERN = /\\[([^\\]]+)\\]\\(([^)]+)\\)/g;\n\n/**\n * Generate knowledge graph from docs directory\n */\nexport async function generateGraph(options: GeneratorOptions): Promise<{\n  graph: KnowledgeGraphManager;\n  stats: {\n    filesScanned: number;\n    nodesCreated: number;\n    edgesCreated: number;\n    errors: string[];\n  };\n}> {\n  const { projectRoot, outputPath } = options;\n\n  const stats = {\n    filesScanned: 0,\n    nodesCreated: 0,\n    edgesCreated: 0,\n    errors: [] as string[],\n  };\n\n  // Create graph manager\n  const graph = new KnowledgeGraphManager(\n    basename(projectRoot),\n    projectRoot\n  );\n\n  // Find all markdown files\n  const files = await fg('**/*.md', {\n    cwd: outputPath,\n    ignore: ['node_modules/**', '.git/**', '_templates/**'],\n    absolute: true,\n  });\n\n  stats.filesScanned = files.length;\n\n  // First pass: Create all nodes\n  const nodeMap = new Map<string, KnowledgeNode>();\n\n  for (const filePath of files) {\n    try {\n      const node = await parseMarkdownFile(filePath, outputPath);\n      nodeMap.set(node.id, node);\n      stats.nodesCreated++;\n    } catch (error) {\n      stats.errors.push(`Failed to parse ${filePath}: ${error}`);\n    }\n  }\n\n  // Second pass: Resolve links and add to graph\n  for (const node of nodeMap.values()) {\n    // Resolve outgoing links\n    const resolvedLinks: NodeLink[] = [];\n\n    for (const link of node.outgoingLinks) {\n      // Try to resolve the link target\n      const targetId = resolveLink(link.target, node.path, nodeMap);\n\n      if (targetId) {\n        resolvedLinks.push({\n          ...link,\n          target: targetId,\n        });\n\n        // Create backlink in target node\n        const targetNode = nodeMap.get(targetId);\n        if (targetNode) {\n          targetNode.incomingLinks.push({\n            target: node.id,\n            type: 'backlink',\n            text: node.title,\n          });\n        }\n\n        stats.edgesCreated++;\n      }\n    }\n\n    node.outgoingLinks = resolvedLinks;\n    graph.addNode(node);\n  }\n\n  return { graph, stats };\n}\n\n/**\n * Generate graph and save to database\n */\nexport async function generateAndSave(\n  options: GeneratorOptions,\n  dbPath: string\n): Promise<{\n  success: boolean;\n  stats: {\n    filesScanned: number;\n    nodesCreated: number;\n    edgesCreated: number;\n    errors: string[];\n  };\n}> {\n  const { graph, stats } = await generateGraph(options);\n\n  // Save to database\n  const db = new KnowledgeGraphDatabase(dbPath);\n\n  try {\n    const nodes = graph.getAllNodes();\n    const edges = graph.getAllEdges();\n\n    for (const node of nodes) {\n      db.upsertNode(node);\n    }\n\n    for (const edge of edges) {\n      db.addEdge(edge);\n    }\n\n    db.setMetadata('lastGenerated', new Date().toISOString());\n    db.setMetadata('nodeCount', String(stats.nodesCreated));\n    db.setMetadata('edgeCount', String(stats.edgesCreated));\n\n    return { success: true, stats };\n  } catch (error) {\n    stats.errors.push(`Database error: ${error}`);\n    return { success: false, stats };\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * Parse a markdown file into a knowledge node\n */\nasync function parseMarkdownFile(\n  filePath: string,\n  docsRoot: string\n): Promise<KnowledgeNode> {\n  const content = readFileSync(filePath, 'utf-8');\n  const stat = statSync(filePath);\n  const { data, content: body } = matter(content);\n\n  // Extract filename and path\n  const filename = basename(filePath, '.md');\n  const relativePath = relative(docsRoot, filePath);\n\n  // Generate ID from relative path\n  const id = relativePath\n    .replace(/\\.md$/, '')\n    .replace(/\\\\/g, '/')\n    .replace(/[^a-z0-9/]+/gi, '-')\n    .toLowerCase();\n\n  // Extract links from content\n  const outgoingLinks = extractLinks(body);\n\n  // Determine node type from frontmatter or path\n  const type = inferNodeType(data.type, relativePath);\n  const status = (data.status as NodeStatus) || 'active';\n\n  // Build frontmatter\n  const frontmatter: NodeFrontmatter = {\n    title: data.title || formatTitle(filename),\n    type,\n    status,\n    tags: Array.isArray(data.tags) ? data.tags : [],\n    category: data.category,\n    description: data.description,\n    created: data.created || stat.birthtime.toISOString().split('T')[0],\n    updated: data.updated || stat.mtime.toISOString().split('T')[0],\n    aliases: data.aliases,\n    related: data.related,\n    ...data,\n  };\n\n  // Calculate word count\n  const wordCount = body\n    .replace(/[#*`\\[\\]()]/g, '')\n    .split(/\\s+/)\n    .filter(Boolean).length;\n\n  return {\n    id,\n    path: relativePath,\n    filename,\n    title: frontmatter.title || formatTitle(filename),\n    type,\n    status,\n    content: body,\n    frontmatter,\n    tags: frontmatter.tags || [],\n    outgoingLinks,\n    incomingLinks: [], // Will be filled in second pass\n    wordCount,\n    lastModified: stat.mtime,\n  };\n}\n\n/**\n * Extract links from markdown content\n */\nfunction extractLinks(content: string): NodeLink[] {\n  const links: NodeLink[] = [];\n  const seen = new Set<string>();\n\n  // Extract wikilinks\n  let match: RegExpExecArray | null;\n  while ((match = WIKILINK_PATTERN.exec(content)) !== null) {\n    const target = match[1].trim();\n    const text = match[2]?.trim();\n\n    if (!seen.has(target)) {\n      seen.add(target);\n      links.push({\n        target,\n        type: 'wikilink',\n        text,\n      });\n    }\n  }\n\n  // Extract markdown links (only internal ones)\n  while ((match = MARKDOWN_LINK_PATTERN.exec(content)) !== null) {\n    const text = match[1].trim();\n    const target = match[2].trim();\n\n    // Skip external URLs\n    if (target.startsWith('http://') || target.startsWith('https://')) {\n      continue;\n    }\n\n    if (!seen.has(target)) {\n      seen.add(target);\n      links.push({\n        target,\n        type: 'markdown',\n        text,\n      });\n    }\n  }\n\n  return links;\n}\n\n/**\n * Resolve a link target to a node ID\n */\nfunction resolveLink(\n  target: string,\n  currentPath: string,\n  nodeMap: Map<string, KnowledgeNode>\n): string | null {\n  // Clean target\n  const cleanTarget = target\n    .replace(/\\.md$/, '')\n    .replace(/^\\.\\//, '')\n    .toLowerCase();\n\n  // Try direct match\n  for (const [id, node] of nodeMap) {\n    // Match by ID\n    if (id === cleanTarget) {\n      return id;\n    }\n\n    // Match by filename\n    if (node.filename.toLowerCase() === cleanTarget) {\n      return id;\n    }\n\n    // Match by title\n    if (node.title.toLowerCase() === cleanTarget) {\n      return id;\n    }\n\n    // Match by alias\n    if (node.frontmatter.aliases?.some(\n      a => a.toLowerCase() === cleanTarget\n    )) {\n      return id;\n    }\n  }\n\n  // Try relative path resolution\n  const currentDir = currentPath.replace(/[^/]+$/, '');\n  const relativePath = join(currentDir, cleanTarget)\n    .replace(/\\\\/g, '/')\n    .replace(/^\\//, '');\n\n  for (const [id, node] of nodeMap) {\n    if (id === relativePath || 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package/dist/node_modules/@typescript-eslint/types/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 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/index5.js";
+import { __exports as dist } from "../../../../_virtual/index6.js";
 import { __require as requireGetKeys } from "./get-keys.js";
 import { __require as requireVisitorKeys } from "./visitor-keys.js";
 var hasRequiredDist;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@weavelogic/knowledge-graph-agent",
-  "version": "0.8.1",
+  "version": "0.8.3",
   "description": "Knowledge graph agent for Claude Code - generates knowledge graphs, initializes docs, and integrates with claude-flow",
   "type": "module",
   "main": "dist/index.js",