directory-indexer 1.0.0 → 1.1.0

package/README.md

@@ -274,6 +274,9 @@ export DIRECTORY_INDEXER_DATA_DIR="/opt/ai-knowledge-base"
 export QDRANT_ENDPOINT="http://localhost:6333"
 export OLLAMA_ENDPOINT="http://localhost:11434"
 
+# OpenAI provider: custom OpenAI-compatible endpoint (default: https://api.openai.com/v1)
+export OPENAI_ENDPOINT="https://api.openai.com/v1"
+
 # Optional API keys
 export OPENAI_API_KEY="your-key-here"
 export QDRANT_API_KEY="your-key-here"

package/dist/cli-handlers.js

@@ -9,13 +9,16 @@ async function handleIndex(paths, options) {
   const config = await loadConfig({ verbose: options.verbose });
   await validateIndexPrerequisites(config);
   console.log(`Indexing ${paths.length} ${paths.length === 1 ? "directory" : "directories"}: ${paths.join(", ")}`);
-  if (!options.verbose) {
+  if (!config.verbose) {
     console.log("Run with --verbose for detailed per-file indexing reports");
     console.log("Indexing can be safely stopped and resumed - progress is automatically saved");
     console.log("You can start using the MCP server while indexing continues");
     console.log("Indexing may take time due to embedding generation - see project README for performance tips");
   }
-  const result = await indexDirectories(paths, config);
+  const result = await indexDirectories(paths, config, {
+    progress: (m) => console.log(m),
+    error: (m) => console.error(m)
+  });
   console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, cleaned up ${result.deleted} deleted files, ${result.failed} failed`);
   if (result.errors.length > 0) {
     console.log(`Errors: [`);

package/dist/cli-handlers.js.map

@@ -1 +1 @@
-{"version":3,"file":"cli-handlers.js","sources":["../src/cli-handlers.ts"],"sourcesContent":["import { indexDirectories } from './indexing.js';\nimport { searchContent, findSimilarFiles, getFileContent } from './search.js';\nimport { loadConfig } from './config.js';\nimport { getIndexStatus } from './storage.js';\nimport { startMcpServer } from './mcp.js';\nimport { validateIndexPrerequisites, validateSearchPrerequisites, getServiceStatus } from './prerequisites.js';\nimport { resetEnvironment } from './reset.js';\n\nexport interface IndexOptions {\n  verbose?: boolean;\n}\n\nexport interface SearchOptions {\n  limit?: number;\n  showChunks?: boolean;\n  verbose?: boolean;\n}\n\nexport interface SimilarOptions {\n  limit?: number;\n  verbose?: boolean;\n}\n\nexport interface GetOptions {\n  chunks?: string;\n  verbose?: boolean;\n}\n\nexport interface ServeOptions {\n  verbose?: boolean;\n}\n\nexport interface ResetOptions {\n  force?: boolean;\n  verbose?: boolean;\n}\n\nexport interface StatusOptions {\n  verbose?: boolean;\n}\n\nexport async function handleIndex(paths: string[], options: IndexOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateIndexPrerequisites(config);\n  \n  console.log(`Indexing ${paths.length} ${paths.length === 1 ? 'directory' : 'directories'}: ${paths.join(', ')}`);\n  if (!options.verbose) {\n    console.log('Run with --verbose for detailed per-file indexing reports');\n    console.log('Indexing can be safely stopped and resumed - progress is automatically saved');\n    console.log('You can start using the MCP server while indexing continues');\n    console.log('Indexing may take time due to embedding generation - see project README for performance tips');\n  }\n  \n  const result = await indexDirectories(paths, config);\n  console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, cleaned up ${result.deleted} deleted files, ${result.failed} failed`);\n  \n  if (result.errors.length > 0) {\n    console.log(`Errors: [`);\n    result.errors.forEach(error => {\n      console.log(`  '${error}'`);\n    });\n    console.log(`]`);\n  }\n}\n\nexport async function handleSearch(query: string, options: SearchOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateSearchPrerequisites(config);\n  \n  const results = await searchContent(query, { limit: options.limit || 10 });\n  \n  if (results.length === 0) {\n    console.log('No results found');\n    return;\n  }\n\n  console.log(`Found ${results.length} results:\\n`);\n  results.forEach((result, index) => {\n    console.log(`${index + 1}. ${result.filePath}`);\n    console.log(`   Score: ${result.score.toFixed(3)} (${result.matchingChunks} chunks)`);\n    \n    if (options.showChunks && result.chunks.length > 0) {\n      console.log(`   Chunks:`);\n      result.chunks.forEach(chunk => {\n        console.log(`     - Chunk ${chunk.chunkId}: ${chunk.score.toFixed(3)}`);\n      });\n    }\n    \n    console.log();\n  });\n}\n\nexport async function handleSimilar(filePath: string, options: SimilarOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateSearchPrerequisites(config);\n  \n  const results = await findSimilarFiles(filePath, options.limit || 10);\n  \n  if (results.length === 0) {\n    console.log('No similar files found');\n    return;\n  }\n\n  console.log(`Found ${results.length} similar files:\\n`);\n  results.forEach((result, index) => {\n    console.log(`${index + 1}. ${result.filePath}`);\n    console.log(`   Similarity: ${result.score.toFixed(3)}`);\n    console.log();\n  });\n}\n\nexport async function handleGet(filePath: string, options: GetOptions): Promise<void> {\n  await loadConfig({ verbose: options.verbose });\n  const content = await getFileContent(filePath, options.chunks);\n  console.log(content);\n}\n\nexport async function handleServe(options: ServeOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await startMcpServer(config);\n}\n\nexport async function handleReset(options: ResetOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await resetEnvironment(config, { \n    force: options.force, \n    verbose: options.verbose \n  });\n}\n\nexport async function handleStatus(options: StatusOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  const [status, serviceStatus] = await Promise.all([\n    getIndexStatus(),\n    getServiceStatus(config)\n  ]);\n  \n  console.log('Directory Indexer Status Report');\n  console.log('=====================================');\n  console.log('');\n  console.log('SERVICE STATUS:');\n  console.log(`  • Qdrant database: ${serviceStatus.qdrant ? 'Connected' : 'Disconnected'}`);\n  console.log(`  • Embedding service (${serviceStatus.embeddingProvider}): ${serviceStatus.embedding ? 'Connected' : 'Disconnected'}`);\n  console.log('');\n  console.log('OVERVIEW:');\n  console.log(`  • ${status.directoriesIndexed} directories have been indexed`);\n  console.log(`  • ${status.filesIndexed} files processed for semantic search`);\n  console.log(`  • ${status.chunksIndexed} text chunks available for AI search`);\n  console.log(`  • Database storage: ${status.databaseSize}`);\n  console.log(`  • Most recent indexing: ${status.lastIndexed || 'No indexing performed yet'}`);\n  \n  if (status.errors.length > 0) {\n    console.log(`  • Processing errors encountered: ${status.errors.length}`);\n    if (options.verbose) {\n      console.log('');\n      console.log('RECENT ERRORS:');\n      status.errors.slice(0, 5).forEach(error => {\n        console.log(`  - ${error}`);\n      });\n    }\n  }\n  \n  console.log('');\n  console.log('INDEXED DIRECTORIES:');\n  if (status.directories.length === 0) {\n    console.log('  No directories have been indexed yet.');\n    console.log('  Run \"directory-indexer index <path>\" to start indexing.');\n  } else {\n    status.directories.forEach(dir => {\n      console.log('');\n      console.log(`  Directory: ${dir.path}`);\n      console.log(`    • Indexing status: ${dir.status}`);\n      console.log(`    • Files processed: ${dir.filesCount}`);\n      console.log(`    • Searchable chunks: ${dir.chunksCount}`);\n      console.log(`    • Last indexed: ${dir.lastIndexed || 'Never completed'}`);\n      if (dir.errors.length > 0) {\n        console.log(`    • Files with errors: ${dir.errors.length}`);\n        if (options.verbose) {\n          console.log('    • Recent errors:');\n          dir.errors.slice(0, 3).forEach(error => {\n            console.log(`      - ${error}`);\n          });\n        }\n      }\n    });\n  }\n  \n  if (status.workspaces.length > 0) {\n    console.log('');\n    console.log('WORKSPACES:');\n    console.log(`  • ${status.workspaceHealth.healthy} healthy, ${status.workspaceHealth.warnings} warnings, ${status.workspaceHealth.errors} errors`);\n    \n    if (status.workspaceHealth.errors > 0) {\n      console.log('');\n      console.log('WORKSPACE ERRORS:');\n      status.workspaceHealth.criticalIssues.forEach(issue => {\n        console.log(`  ❌ ${issue}`);\n      });\n    }\n    \n    if (status.workspaceHealth.recommendations.length > 0) {\n      console.log('');\n      console.log('WORKSPACE RECOMMENDATIONS:');\n      status.workspaceHealth.recommendations.forEach(rec => {\n        console.log(`  💡 ${rec}`);\n      });\n    }\n    \n    if (options.verbose) {\n      console.log('');\n      console.log('WORKSPACE DETAILS:');\n      status.workspaces.forEach(workspace => {\n        console.log('');\n        console.log(`  Workspace: ${workspace.name}`);\n        console.log(`    • Status: ${workspace.health.status}`);\n        console.log(`    • Paths: ${workspace.paths.join(', ')}`);\n        console.log(`    • Files: ${workspace.filesCount}, Chunks: ${workspace.chunksCount}`);\n        if (workspace.health.issues.length > 0) {\n          console.log(`    • Issues: ${workspace.health.issues.join('; ')}`);\n        }\n      });\n    }\n  }\n\n  if (!status.qdrantConsistency.isConsistent) {\n    console.log('');\n    console.log('SYSTEM STATUS:');\n    status.qdrantConsistency.issues.forEach(issue => {\n      console.log(`  • ${issue}`);\n    });\n    console.log('');\n    console.log('Note: Status messages above may be normal during setup or active indexing.');\n  } else {\n    console.log('');\n    console.log('SYSTEM STATUS:');\n    console.log('  • All systems operational - 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+{"version":3,"file":"cli-handlers.js","sources":["../src/cli-handlers.ts"],"sourcesContent":["import { indexDirectories } from './indexing.js';\nimport { searchContent, findSimilarFiles, getFileContent } from './search.js';\nimport { loadConfig } from './config.js';\nimport { getIndexStatus } from './storage.js';\nimport { startMcpServer } from './mcp.js';\nimport { validateIndexPrerequisites, validateSearchPrerequisites, getServiceStatus } from './prerequisites.js';\nimport { resetEnvironment } from './reset.js';\n\nexport interface IndexOptions {\n  verbose?: boolean;\n}\n\nexport interface SearchOptions {\n  limit?: number;\n  showChunks?: boolean;\n  verbose?: boolean;\n}\n\nexport interface SimilarOptions {\n  limit?: number;\n  verbose?: boolean;\n}\n\nexport interface GetOptions {\n  chunks?: string;\n  verbose?: boolean;\n}\n\nexport interface ServeOptions {\n  verbose?: boolean;\n}\n\nexport interface ResetOptions {\n  force?: boolean;\n  verbose?: boolean;\n}\n\nexport interface StatusOptions {\n  verbose?: boolean;\n}\n\nexport async function handleIndex(paths: string[], options: IndexOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateIndexPrerequisites(config);\n  \n  console.log(`Indexing ${paths.length} ${paths.length === 1 ? 'directory' : 'directories'}: ${paths.join(', ')}`);\n  if (!config.verbose) {\n    console.log('Run with --verbose for detailed per-file indexing reports');\n    console.log('Indexing can be safely stopped and resumed - progress is automatically saved');\n    console.log('You can start using the MCP server while indexing continues');\n    console.log('Indexing may take time due to embedding generation - see project README for performance tips');\n  }\n  \n  const result = await indexDirectories(paths, config, {\n    progress: m => console.log(m),\n    error: m => console.error(m)\n  });\n  console.log(`Indexed ${result.indexed} files, skipped ${result.skipped} files, cleaned up ${result.deleted} deleted files, ${result.failed} failed`);\n  \n  if (result.errors.length > 0) {\n    console.log(`Errors: [`);\n    result.errors.forEach(error => {\n      console.log(`  '${error}'`);\n    });\n    console.log(`]`);\n  }\n}\n\nexport async function handleSearch(query: string, options: SearchOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateSearchPrerequisites(config);\n  \n  const results = await searchContent(query, { limit: options.limit || 10 });\n  \n  if (results.length === 0) {\n    console.log('No results found');\n    return;\n  }\n\n  console.log(`Found ${results.length} results:\\n`);\n  results.forEach((result, index) => {\n    console.log(`${index + 1}. ${result.filePath}`);\n    console.log(`   Score: ${result.score.toFixed(3)} (${result.matchingChunks} chunks)`);\n    \n    if (options.showChunks && result.chunks.length > 0) {\n      console.log(`   Chunks:`);\n      result.chunks.forEach(chunk => {\n        console.log(`     - Chunk ${chunk.chunkId}: ${chunk.score.toFixed(3)}`);\n      });\n    }\n    \n    console.log();\n  });\n}\n\nexport async function handleSimilar(filePath: string, options: SimilarOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await validateSearchPrerequisites(config);\n  \n  const results = await findSimilarFiles(filePath, options.limit || 10);\n  \n  if (results.length === 0) {\n    console.log('No similar files found');\n    return;\n  }\n\n  console.log(`Found ${results.length} similar files:\\n`);\n  results.forEach((result, index) => {\n    console.log(`${index + 1}. ${result.filePath}`);\n    console.log(`   Similarity: ${result.score.toFixed(3)}`);\n    console.log();\n  });\n}\n\nexport async function handleGet(filePath: string, options: GetOptions): Promise<void> {\n  await loadConfig({ verbose: options.verbose });\n  const content = await getFileContent(filePath, options.chunks);\n  console.log(content);\n}\n\nexport async function handleServe(options: ServeOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await startMcpServer(config);\n}\n\nexport async function handleReset(options: ResetOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  await resetEnvironment(config, { \n    force: options.force, \n    verbose: options.verbose \n  });\n}\n\nexport async function handleStatus(options: StatusOptions): Promise<void> {\n  const config = await loadConfig({ verbose: options.verbose });\n  const [status, serviceStatus] = await Promise.all([\n    getIndexStatus(),\n    getServiceStatus(config)\n  ]);\n  \n  console.log('Directory Indexer Status Report');\n  console.log('=====================================');\n  console.log('');\n  console.log('SERVICE STATUS:');\n  console.log(`  • Qdrant database: ${serviceStatus.qdrant ? 'Connected' : 'Disconnected'}`);\n  console.log(`  • Embedding service (${serviceStatus.embeddingProvider}): ${serviceStatus.embedding ? 'Connected' : 'Disconnected'}`);\n  console.log('');\n  console.log('OVERVIEW:');\n  console.log(`  • ${status.directoriesIndexed} directories have been indexed`);\n  console.log(`  • ${status.filesIndexed} files processed for semantic search`);\n  console.log(`  • ${status.chunksIndexed} text chunks available for AI search`);\n  console.log(`  • Database storage: ${status.databaseSize}`);\n  console.log(`  • Most recent indexing: ${status.lastIndexed || 'No indexing performed yet'}`);\n  \n  if (status.errors.length > 0) {\n    console.log(`  • Processing errors encountered: ${status.errors.length}`);\n    if (options.verbose) {\n      console.log('');\n      console.log('RECENT ERRORS:');\n      status.errors.slice(0, 5).forEach(error => {\n        console.log(`  - ${error}`);\n      });\n    }\n  }\n  \n  console.log('');\n  console.log('INDEXED DIRECTORIES:');\n  if (status.directories.length === 0) {\n    console.log('  No directories have been indexed yet.');\n    console.log('  Run \"directory-indexer index <path>\" to start indexing.');\n  } else {\n    status.directories.forEach(dir => {\n      console.log('');\n      console.log(`  Directory: ${dir.path}`);\n      console.log(`    • Indexing status: ${dir.status}`);\n      console.log(`    • Files processed: ${dir.filesCount}`);\n      console.log(`    • Searchable chunks: ${dir.chunksCount}`);\n      console.log(`    • Last indexed: ${dir.lastIndexed || 'Never completed'}`);\n      if (dir.errors.length > 0) {\n        console.log(`    • Files with errors: ${dir.errors.length}`);\n        if (options.verbose) {\n          console.log('    • Recent errors:');\n          dir.errors.slice(0, 3).forEach(error => {\n            console.log(`      - ${error}`);\n          });\n        }\n      }\n    });\n  }\n  \n  if (status.workspaces.length > 0) {\n    console.log('');\n    console.log('WORKSPACES:');\n    console.log(`  • ${status.workspaceHealth.healthy} healthy, ${status.workspaceHealth.warnings} warnings, ${status.workspaceHealth.errors} errors`);\n    \n    if (status.workspaceHealth.errors > 0) {\n      console.log('');\n      console.log('WORKSPACE ERRORS:');\n      status.workspaceHealth.criticalIssues.forEach(issue => {\n        console.log(`  ❌ ${issue}`);\n      });\n    }\n    \n    if (status.workspaceHealth.recommendations.length > 0) {\n      console.log('');\n      console.log('WORKSPACE RECOMMENDATIONS:');\n      status.workspaceHealth.recommendations.forEach(rec => {\n        console.log(`  💡 ${rec}`);\n      });\n    }\n    \n    if (options.verbose) {\n      console.log('');\n      console.log('WORKSPACE DETAILS:');\n      status.workspaces.forEach(workspace => {\n        console.log('');\n        console.log(`  Workspace: ${workspace.name}`);\n        console.log(`    • Status: ${workspace.health.status}`);\n        console.log(`    • Paths: ${workspace.paths.join(', ')}`);\n        console.log(`    • Files: ${workspace.filesCount}, Chunks: ${workspace.chunksCount}`);\n        if (workspace.health.issues.length > 0) {\n          console.log(`    • Issues: ${workspace.health.issues.join('; ')}`);\n        }\n      });\n    }\n  }\n\n  if (!status.qdrantConsistency.isConsistent) {\n    console.log('');\n    console.log('SYSTEM STATUS:');\n    status.qdrantConsistency.issues.forEach(issue => {\n      console.log(`  • ${issue}`);\n    });\n    console.log('');\n    console.log('Note: Status messages above may be normal during setup or active indexing.');\n  } else {\n    console.log('');\n    console.log('SYSTEM STATUS:');\n    console.log('  • All systems operational - 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package/dist/cli.js

@@ -8,6 +8,13 @@ const __dirname$1 = dirname(fileURLToPath(import.meta.url));
 const packageJsonPath = join(__dirname$1, "../package.json");
 const packageJson = JSON.parse(readFileSync(packageJsonPath, "utf-8"));
 const VERSION = packageJson.version;
+function parseLimit(value) {
+  const limit = Number.parseInt(value);
+  if (Number.isNaN(limit) || limit < 1) {
+    throw new Error("Invalid --limit: must be a positive integer");
+  }
+  return limit;
+}
 async function main() {
   const program = new Command();
   program.name("directory-indexer").description("AI-powered directory indexing with semantic search").version(VERSION);
@@ -22,7 +29,7 @@ async function main() {
   program.command("search").description("Search indexed content semantically").argument("<query>", "Search query").option("-l, --limit <number>", "Maximum number of results", "10").option("-c, --show-chunks", "Show individual chunk scores and IDs").option("-v, --verbose", "Enable verbose logging").action(async (query, options) => {
     try {
       await handleSearch(query, {
-        limit: parseInt(options.limit),
+        limit: parseLimit(options.limit),
         showChunks: options.showChunks,
         verbose: options.verbose
       });
@@ -34,7 +41,7 @@ async function main() {
   program.command("similar").description("Find files similar to a given file").argument("<file>", "File path to find similar files for").option("-l, --limit <number>", "Maximum number of results", "10").option("-v, --verbose", "Enable verbose logging").action(async (filePath, options) => {
     try {
       await handleSimilar(filePath, {
-        limit: parseInt(options.limit),
+        limit: parseLimit(options.limit),
         verbose: options.verbose
       });
     } catch (error) {

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"file":"cli.js","sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { fileURLToPath } from 'url';\nimport { readFileSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { \n  handleIndex, \n  handleSearch, \n  handleSimilar, \n  handleGet, \n  handleServe, \n  handleReset, \n  handleStatus \n} from './cli-handlers.js';\n\n// Read version from package.json\nconst __dirname = dirname(fileURLToPath(import.meta.url));\nconst packageJsonPath = join(__dirname, '../package.json');\nconst packageJson = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));\nconst VERSION = packageJson.version;\n\nexport async function main() {\n  const program = new Command();\n  \n  program\n    .name('directory-indexer')\n    .description('AI-powered directory indexing with semantic search')\n    .version(VERSION);\n\n  program\n    .command('index')\n    .description('Index directories for semantic search')\n    .argument('<paths...>', 'Directory paths to index')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (paths: string[], options) => {\n      try {\n        await handleIndex(paths, options);\n      } catch (error) {\n        console.error('Error indexing directories:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('search')\n    .description('Search indexed content semantically')\n    .argument('<query>', 'Search query')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await handleSearch(query, {\n          limit: parseInt(options.limit),\n          showChunks: options.showChunks,\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error searching content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('similar')\n    .description('Find files similar to a given file')\n    .argument('<file>', 'File path to find similar files for')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleSimilar(filePath, {\n          limit: parseInt(options.limit),\n          verbose: options.verbose\n        });\n      } catch (error) {\n        console.error('Error finding similar files:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('get')\n    .description('Get file content')\n    .argument('<file>', 'File path to retrieve')\n    .option('-c, --chunks <range>', 'Chunk range (e.g., \"2-5\")')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleGet(filePath, options);\n      } catch (error) {\n        console.error('Error getting file content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('serve')\n    .description('Start MCP server')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleServe(options);\n      } catch (error) {\n        console.error('Error starting MCP server:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('reset')\n    .description('Reset directory-indexer data (database and vector collection)')\n    .option('--force', 'Skip confirmation prompt')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleReset(options);\n      } catch (error) {\n        if (error instanceof Error && error.message === 'Reset cancelled by user') {\n          console.log('\\nReset cancelled.');\n          process.exit(0);\n        }\n        console.error('Error during reset:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('status')\n    .description('Show indexing status')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleStatus(options);\n      } catch (error) {\n        console.error('Error getting status:', error);\n        process.exit(1);\n      }\n    });\n\n  await program.parseAsync();\n}\n\n// Main function is already exported 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+{"version":3,"file":"cli.js","sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { fileURLToPath } from 'url';\nimport { readFileSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { \n  handleIndex, \n  handleSearch, \n  handleSimilar, \n  handleGet, \n  handleServe, \n  handleReset, \n  handleStatus \n} from './cli-handlers.js';\n\n// Read version from package.json\nconst __dirname = dirname(fileURLToPath(import.meta.url));\nconst packageJsonPath = join(__dirname, '../package.json');\nconst packageJson = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));\nconst VERSION = packageJson.version;\n\nfunction parseLimit(value: string): number {\n  const limit = Number.parseInt(value);\n  if (Number.isNaN(limit) || limit < 1) {\n    throw new Error('Invalid --limit: must be a positive integer');\n  }\n  return limit;\n}\n\nexport async function main() {\n  const program = new Command();\n\n  program\n    .name('directory-indexer')\n    .description('AI-powered directory indexing with semantic search')\n    .version(VERSION);\n\n  program\n    .command('index')\n    .description('Index directories for semantic search')\n    .argument('<paths...>', 'Directory paths to index')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (paths: string[], options) => {\n      try {\n        await handleIndex(paths, options);\n      } catch (error) {\n        console.error('Error indexing directories:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('search')\n    .description('Search indexed content semantically')\n    .argument('<query>', 'Search query')\n    .option('-l, --limit <number>', 'Maximum number of results', '10')\n    .option('-c, --show-chunks', 'Show individual chunk scores and IDs')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (query: string, options) => {\n      try {\n        await 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.argument('<file>', 'File path to retrieve')\n    .option('-c, --chunks <range>', 'Chunk range (e.g., \"2-5\")')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (filePath: string, options) => {\n      try {\n        await handleGet(filePath, options);\n      } catch (error) {\n        console.error('Error getting file content:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('serve')\n    .description('Start MCP server')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async (options) => {\n      try {\n        await handleServe(options);\n      } catch (error) {\n        console.error('Error starting MCP server:', error);\n        process.exit(1);\n      }\n    });\n\n  program\n    .command('reset')\n    .description('Reset directory-indexer data (database and vector collection)')\n    .option('--force', 'Skip confirmation prompt')\n    .option('-v, --verbose', 'Enable verbose logging')\n    .action(async 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package/dist/config.js

@@ -27,6 +27,14 @@ const ConfigSchema = z.object({
     maxFileSize: z.number().positive(),
     ignorePatterns: z.array(z.string()),
     respectGitignore: z.boolean()
+  }).superRefine((indexing, ctx) => {
+    if (indexing.chunkOverlap >= indexing.chunkSize) {
+      ctx.addIssue({
+        code: "custom",
+        path: ["chunkOverlap"],
+        message: "chunkOverlap must be smaller than chunkSize"
+      });
+    }
   }),
   dataDir: z.string(),
   verbose: z.boolean(),
@@ -92,7 +100,7 @@ function loadConfig(options = {}) {
     embedding: {
       provider: process.env.EMBEDDING_PROVIDER || "ollama",
       model: process.env.EMBEDDING_MODEL || "nomic-embed-text",
-      endpoint: process.env.OLLAMA_ENDPOINT || "http://127.0.0.1:11434"
+      endpoint: process.env.EMBEDDING_PROVIDER === "openai" ? process.env.OPENAI_ENDPOINT || "https://api.openai.com/v1" : process.env.OLLAMA_ENDPOINT || "http://127.0.0.1:11434"
     },
     indexing: {
       chunkSize: parseInt(process.env.CHUNK_SIZE || "512"),

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/embedding.js

@@ -86,7 +86,7 @@ class OpenAIEmbeddingProvider {
   dimensions = 1536;
   async generateEmbedding(text) {
     try {
-      const response = await fetch("https://api.openai.com/v1/embeddings", {
+      const response = await fetch(`${this.config.endpoint}/embeddings`, {
         method: "POST",
         headers: {
           "Content-Type": "application/json",
@@ -108,7 +108,7 @@ class OpenAIEmbeddingProvider {
   }
   async generateEmbeddings(texts) {
     try {
-      const response = await fetch("https://api.openai.com/v1/embeddings", {
+      const response = await fetch(`${this.config.endpoint}/embeddings`, {
         method: "POST",
         headers: {
           "Content-Type": "application/json",

package/dist/embedding.js.map

@@ -1 +1 @@
-{"version":3,"file":"embedding.js","sources":["../src/embedding.ts"],"sourcesContent":["import { Config } from './config.js';\n\nexport interface EmbeddingProvider {\n  name: string;\n  dimensions: number;\n  generateEmbedding(text: string): Promise<number[]>;\n  generateEmbeddings(texts: string[]): Promise<number[][]>;\n}\n\nexport interface EmbeddingConfig {\n  model: string;\n  endpoint: string;\n  dimensions: number;\n}\n\nexport class EmbeddingError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'EmbeddingError';\n  }\n}\n\nclass MockEmbeddingProvider implements EmbeddingProvider {\n  name = 'mock';\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  get dimensions(): number {\n    return this.config.dimensions;\n  }\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    const hash = this.hashString(text);\n    return Array.from({ length: this.dimensions }, (_, i) => \n      Math.sin(hash + i) * 0.1\n    );\n  }\n  \n  async generateEmbeddings(texts: string[]): Promise<number[][]> {\n    return Promise.all(texts.map(text => this.generateEmbedding(text)));\n  }\n  \n  private hashString(str: string): number {\n    let hash = 0;\n    for (let i = 0; i < str.length; i++) {\n      const char = str.charCodeAt(i);\n      hash = ((hash << 5) - hash) + char;\n      hash = hash & hash;\n    }\n    return Math.abs(hash);\n  }\n}\n\nclass OllamaEmbeddingProvider implements EmbeddingProvider {\n  name = 'ollama';\n  dimensions = 768;\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    try {\n      const response = await fetch(`${this.config.endpoint}/api/embed`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          model: this.config.model,\n          input: text\n        })\n      });\n      \n      if (!response.ok) {\n  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+{"version":3,"file":"embedding.js","sources":["../src/embedding.ts"],"sourcesContent":["import { Config } from './config.js';\n\nexport interface EmbeddingProvider {\n  name: string;\n  dimensions: number;\n  generateEmbedding(text: string): Promise<number[]>;\n  generateEmbeddings(texts: string[]): Promise<number[][]>;\n}\n\nexport interface EmbeddingConfig {\n  model: string;\n  endpoint: string;\n  dimensions: number;\n}\n\nexport class EmbeddingError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'EmbeddingError';\n  }\n}\n\nclass MockEmbeddingProvider implements EmbeddingProvider {\n  name = 'mock';\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  get dimensions(): number {\n    return this.config.dimensions;\n  }\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    const hash = this.hashString(text);\n    return Array.from({ length: this.dimensions }, (_, i) => \n      Math.sin(hash + i) * 0.1\n    );\n  }\n  \n  async generateEmbeddings(texts: string[]): Promise<number[][]> {\n    return Promise.all(texts.map(text => this.generateEmbedding(text)));\n  }\n  \n  private hashString(str: string): number {\n    let hash = 0;\n    for (let i = 0; i < str.length; i++) {\n      const char = str.charCodeAt(i);\n      hash = ((hash << 5) - hash) + char;\n      hash = hash & hash;\n    }\n    return Math.abs(hash);\n  }\n}\n\nclass OllamaEmbeddingProvider implements EmbeddingProvider {\n  name = 'ollama';\n  dimensions = 768;\n  \n  constructor(private config: EmbeddingConfig) {}\n  \n  async generateEmbedding(text: string): Promise<number[]> {\n    try {\n      const response = await fetch(`${this.config.endpoint}/api/embed`, {\n        method: 'POST',\n        headers: { 'Content-Type': 'application/json' },\n        body: JSON.stringify({\n          model: this.config.model,\n          input: text\n        })\n      });\n      \n      if (!response.ok) {\n  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package/dist/indexing.js

@@ -1,9 +1,10 @@
 import { promises } from "fs";
+import { createHash } from "node:crypto";
 import { join } from "path";
 import { getFileInfo, normalizePath, shouldIgnoreFile, isDirectory, isFile, isSupportedFileType } from "./utils.js";
 import { loadGitignoreRules } from "./gitignore.js";
 import { generateEmbedding } from "./embedding.js";
-import { initializeStorage } from "./storage.js";
+import { initializeStorage, ensureCollectionDimensions } from "./storage.js";
 import { log } from "./logger.js";
 class IndexingError extends Error {
   constructor(message, cause) {
@@ -12,6 +13,10 @@ class IndexingError extends Error {
     this.name = "IndexingError";
   }
 }
+function pointIdFor(filePath, chunkId) {
+  const hex = createHash("sha256").update(`${filePath}:${chunkId}`).digest("hex").slice(0, 32);
+  return `${hex.slice(0, 8)}-${hex.slice(8, 12)}-${hex.slice(12, 16)}-${hex.slice(16, 20)}-${hex.slice(20, 32)}`;
+}
 function chunkText(content, chunkSize, overlap) {
   if (content.length <= chunkSize) {
     return [{
@@ -51,10 +56,16 @@ async function scanDirectory(dirPath, options) {
   const gitignoreFilter = options.respectGitignore ? await loadGitignoreRules(dirPath) : null;
   async function walkDirectory(currentPath) {
     const normalizedPath = normalizePath(currentPath);
-    if (visited.has(normalizedPath)) {
+    let realPath = normalizedPath;
+    try {
+      realPath = normalizePath(await promises.realpath(normalizedPath));
+    } catch {
+      realPath = normalizedPath;
+    }
+    if (visited.has(realPath)) {
       return;
     }
-    visited.add(normalizedPath);
+    visited.add(realPath);
     try {
       const relativePath = normalizedPath.startsWith(basePath) ? normalizedPath.slice(basePath.length + 1) : normalizedPath;
       if (shouldIgnoreFile(normalizedPath, relativePath, options.ignorePatterns, gitignoreFilter)) {
@@ -96,31 +107,38 @@ async function shouldReprocessFile(filePath, existingRecord, config) {
     const fs2 = await import("fs/promises");
     const currentStats = await fs2.stat(filePath);
     const existingModTime = new Date(existingRecord.modifiedTime);
-    if (currentStats.mtime <= existingModTime) {
+    if (currentStats.mtime.getTime() === existingModTime.getTime()) {
       return false;
     }
     const currentFileInfo = await getFileInfo(filePath);
     return currentFileInfo.hash !== existingRecord.hash;
   } catch (modtimeError) {
     if (config.verbose) {
-      console.log(`Warning: Could not check modification time for ${filePath}:`, modtimeError);
+      log("warning", `Could not check modification time for ${filePath}`, {
+        error: modtimeError instanceof Error ? modtimeError.message : String(modtimeError)
+      });
     }
     try {
       const currentFileInfo = await getFileInfo(filePath);
       return currentFileInfo.hash !== existingRecord.hash;
     } catch (hashError) {
       if (config.verbose) {
-        console.log(`Warning: Could not compute hash for ${filePath}:`, hashError);
+        log("warning", `Could not compute hash for ${filePath}`, {
+          error: hashError instanceof Error ? hashError.message : String(hashError)
+        });
       }
       return true;
     }
   }
 }
-async function indexDirectories(paths, config) {
+async function indexDirectories(paths, config, reporters = {}) {
+  const progress = reporters.progress ?? ((message) => log("info", message));
+  const reportError = reporters.error ?? ((message) => log("error", message));
   let indexed = 0;
   let skipped = 0;
   let failed = 0;
   let deleted = 0;
+  let collectionEnsured = false;
   const errors = [];
   const scanOptions = {
     ignorePatterns: config.indexing.ignorePatterns,
@@ -132,19 +150,19 @@ async function indexDirectories(paths, config) {
   for (const path of paths) {
     try {
       if (config.verbose) {
-        console.log(`Scanning directory: ${path}`);
+        progress(`Scanning directory: ${path}`);
       }
       const files = await scanDirectory(path, scanOptions);
       totalFiles += files.length;
       if (config.verbose) {
-        console.log(`Found ${files.length} files to process in ${path}`);
+        progress(`Found ${files.length} files to process in ${path}`);
       }
     } catch {
     }
   }
   if (!config.verbose && totalFiles > 0) {
-    console.log("");
-    console.log(`Found ${totalFiles} files to process (checking for changes...)`);
+    progress("");
+    progress(`Found ${totalFiles} files to process (checking for changes...)`);
   }
   for (const path of paths) {
     try {
@@ -153,19 +171,22 @@ async function indexDirectories(paths, config) {
       const files = await scanDirectory(path, scanOptions);
       const dirStartIndexed = indexed;
       const dirStartSkipped = skipped;
+      let dirHadFailure = false;
       const progressInterval = totalFiles > 1e3 ? 50 : 10;
       for (const file of files) {
+        let chunks = [];
         try {
           const existingFile = await sqlite.getFile(file.path);
           if (existingFile) {
-            const needsReprocessing = await shouldReprocessFile(file.path, existingFile, config);
+            const hasStoredFailure = existingFile.errors?.some((error) => error.startsWith("Failed to process")) ?? false;
+            const needsReprocessing = hasStoredFailure || await shouldReprocessFile(file.path, existingFile, config);
             if (!needsReprocessing) {
               skipped++;
               if (config.verbose) {
-                console.log(`  Skipped: ${file.path} (unchanged)`);
+                progress(`  Skipped: ${file.path} (unchanged)`);
               }
               if (!config.verbose && (indexed + skipped) % progressInterval === 0) {
-                console.log(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);
+                progress(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);
               }
               continue;
             }
@@ -179,15 +200,17 @@ async function indexDirectories(paths, config) {
             continue;
           }
           const content = rawContent.replace(/\r\n/g, "\n");
-          const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);
+          chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);
           await sqlite.upsertFile(file, chunks);
           for (let i = 0; i < chunks.length; i++) {
             const chunk = chunks[i];
             const embedding = await generateEmbedding(chunk.content, config);
-            const hashNum = parseInt(file.hash.slice(0, 8), 16);
-            const pointId = hashNum % 1e6 * 1e3 + parseInt(chunk.id);
+            if (!collectionEnsured) {
+              await ensureCollectionDimensions(sqlite, qdrant, config, embedding.length);
+              collectionEnsured = true;
+            }
             const point = {
-              id: pointId,
+              id: pointIdFor(file.path, chunk.id),
               vector: embedding,
               payload: {
                 filePath: file.path,
@@ -201,10 +224,10 @@ async function indexDirectories(paths, config) {
           }
           indexed++;
           if (config.verbose) {
-            console.log(`  Indexed: ${file.path} (${chunks.length} chunks)`);
+            progress(`  Indexed: ${file.path} (${chunks.length} chunks)`);
           }
           if (!config.verbose && (indexed + skipped) % progressInterval === 0) {
-            console.log(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);
+            progress(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);
           }
         } catch (error) {
           const errorMessage = error instanceof Error ? error.message : String(error);
@@ -212,7 +235,9 @@ async function indexDirectories(paths, config) {
           const fullError = `Failed to process ${file.path}: ${errorMessage}${causeMessage}`;
           errors.push(fullError);
           failed++;
-          console.error(`❌ ${fullError}`);
+          dirHadFailure = true;
+          reportError(`❌ ${fullError}`);
+          await sqlite.upsertFile(file, chunks, [fullError]);
         }
       }
       const indexedFiles = await sqlite.getFilesByDirectory(normalizedPath);
@@ -224,26 +249,26 @@ async function indexDirectories(paths, config) {
           await sqlite.deleteFile(deletedFile.path);
           deleted++;
           if (config.verbose) {
-            console.log(`  Cleaned up deleted file: ${deletedFile.path}`);
+            progress(`  Cleaned up deleted file: ${deletedFile.path}`);
           }
         } catch (error) {
           const errorMessage = error instanceof Error ? error.message : String(error);
           const fullError = `Failed to clean up deleted file ${deletedFile.path}: ${errorMessage}`;
           errors.push(fullError);
           failed++;
-          console.error(`❌ ${fullError}`);
+          dirHadFailure = true;
+          reportError(`❌ ${fullError}`);
         }
       }
-      const directoryErrors = errors.filter((err) => err.includes(path));
-      const directoryStatus = directoryErrors.length > 0 ? "failed" : "completed";
+      const directoryStatus = dirHadFailure ? "failed" : "completed";
       await sqlite.upsertDirectory(normalizedPath, directoryStatus);
       const dirFiles = files.length;
       const dirIndexed = indexed - dirStartIndexed;
       const dirSkipped = skipped - dirStartSkipped;
       if (config.verbose) {
-        console.log(`Directory ${path} completed: ${dirIndexed} indexed, ${dirSkipped} skipped`);
+        progress(`Directory ${path} completed: ${dirIndexed} indexed, ${dirSkipped} skipped`);
       } else {
-        console.log(`Directory ${path} completed: ${dirFiles} files processed`);
+        progress(`Directory ${path} completed: ${dirFiles} files processed`);
       }
     } catch (error) {
       const normalizedPath = normalizePath(path);
@@ -258,6 +283,7 @@ export {
   chunkText,
   getFileMetadata,
   indexDirectories,
+  pointIdFor,
   scanDirectory
 };
 //# sourceMappingURL=indexing.js.map

package/dist/indexing.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexing.js","sources":["../src/indexing.ts"],"sourcesContent":["import { promises as fs } from 'fs';\nimport { join } from 'path';\nimport { Config } from './config.js';\nimport {\n  FileInfo,\n  ChunkInfo,\n  normalizePath,\n  getFileInfo,\n  shouldIgnoreFile,\n  isSupportedFileType,\n  isDirectory,\n  isFile\n} from './utils.js';\nimport { loadGitignoreRules } from './gitignore.js';\nimport { generateEmbedding } from './embedding.js';\nimport { initializeStorage, FileRecord } from './storage.js';\nimport { log } from './logger.js';\n\nexport interface ScanOptions {\n  ignorePatterns: string[];\n  maxFileSize: number;\n  respectGitignore: boolean;\n}\n\nexport interface IndexResult {\n  indexed: number;\n  skipped: number;\n  failed: number;\n  deleted: number;\n  errors: string[];\n}\n\nexport class IndexingError extends Error {\n  constructor(message: string, public override cause?: Error) {\n    super(message);\n    this.name = 'IndexingError';\n  }\n}\n\nexport function chunkText(content: string, chunkSize: number, overlap: number): ChunkInfo[] {\n  if (content.length <= chunkSize) {\n    return [{\n      id: '0',\n      content,\n      startIndex: 0,\n      endIndex: content.length\n    }];\n  }\n\n  const chunks: ChunkInfo[] = [];\n  let startIndex = 0;\n  let chunkId = 0;\n\n  while (startIndex < content.length) {\n    const endIndex = Math.min(startIndex + chunkSize, content.length);\n    const chunkContent = content.slice(startIndex, endIndex);\n\n    chunks.push({\n      id: chunkId.toString(),\n      content: chunkContent,\n      startIndex,\n      endIndex\n    });\n\n    chunkId++;\n    const nextStart = endIndex - overlap;\n\n    if (nextStart <= startIndex) {\n      startIndex = startIndex + Math.max(1, chunkSize - overlap);\n    } else {\n      startIndex = nextStart;\n    }\n\n    if (startIndex >= content.length) break;\n  }\n\n  return chunks;\n}\n\nexport async function scanDirectory(dirPath: string, options: ScanOptions): Promise<FileInfo[]> {\n  const files: FileInfo[] = [];\n  const visited = new Set<string>();\n  const basePath = normalizePath(dirPath);\n  \n  // Load gitignore rules for the root directory if enabled\n  const gitignoreFilter = options.respectGitignore ? await loadGitignoreRules(dirPath) : null;\n\n  async function walkDirectory(currentPath: string): Promise<void> {\n    const normalizedPath = normalizePath(currentPath);\n\n    if (visited.has(normalizedPath)) {\n      return;\n    }\n    visited.add(normalizedPath);\n\n    try {\n      // Convert to relative path for gitignore matching\n      const relativePath = normalizedPath.startsWith(basePath) \n        ? normalizedPath.slice(basePath.length + 1)\n        : normalizedPath;\n        \n      if (shouldIgnoreFile(normalizedPath, relativePath, options.ignorePatterns, gitignoreFilter)) {\n        return;\n      }\n\n      if (await isDirectory(normalizedPath)) {\n        const entries = await fs.readdir(normalizedPath);\n\n        for (const entry of entries) {\n          const fullPath = join(normalizedPath, entry);\n          await walkDirectory(fullPath);\n        }\n      } else if (await isFile(normalizedPath)) {\n        if (!isSupportedFileType(normalizedPath)) {\n          return;\n        }\n\n        const stats = await fs.stat(normalizedPath);\n        if (stats.size > options.maxFileSize) {\n          return;\n        }\n\n        const fileInfo = await getFileInfo(normalizedPath);\n        files.push(fileInfo);\n      }\n    } catch (error) {\n      throw new IndexingError(`Failed to scan directory: ${normalizedPath}`, error as Error);\n    }\n  }\n\n  await walkDirectory(dirPath);\n  return files;\n}\n\nexport async function getFileMetadata(filePath: string): Promise<FileInfo> {\n  try {\n    return await getFileInfo(filePath);\n  } catch (error) {\n    throw new IndexingError(`Failed to get file metadata`, error as Error);\n  }\n}\n\nasync function shouldReprocessFile(filePath: string, existingRecord: FileRecord, config: Config): Promise<boolean> {\n  try {\n    const fs = await import('fs/promises');\n\n    // Try modtime check first (fast path)\n    const currentStats = await fs.stat(filePath);\n    const existingModTime = new Date(existingRecord.modifiedTime);\n\n    // If modtime is clearly older, likely unchanged\n    if (currentStats.mtime <= existingModTime) {\n      return false; // Skip processing\n    }\n\n    // If modtime suggests change, verify with hash\n    const currentFileInfo = await getFileInfo(filePath);\n    return currentFileInfo.hash !== existingRecord.hash;\n\n  } catch (modtimeError) {\n    // Graceful fallback: skip modtime, use hash only\n    if (config.verbose) {\n      console.log(`Warning: Could not check modification time for ${filePath}:`, modtimeError);\n    }\n    try {\n      const currentFileInfo = await getFileInfo(filePath);\n      return currentFileInfo.hash !== existingRecord.hash;\n    } catch (hashError) {\n      // If we can't hash either, assume changed to be safe\n      if (config.verbose) {\n        console.log(`Warning: Could not compute hash for ${filePath}:`, hashError);\n      }\n      return true;\n    }\n  }\n}\n\nexport async function indexDirectories(paths: string[], config: Config): Promise<IndexResult> {\n  let indexed = 0;\n  let skipped = 0;\n  let failed = 0;\n  let deleted = 0;\n  const errors: string[] = [];\n\n  const scanOptions: ScanOptions = {\n    ignorePatterns: config.indexing.ignorePatterns,\n    maxFileSize: config.indexing.maxFileSize,\n    respectGitignore: config.indexing.respectGitignore\n  };\n\n  // Initialize storage\n  const { sqlite, qdrant } = await initializeStorage(config);\n\n  // First pass: scan all directories to get total file count\n  let totalFiles = 0;\n  for (const path of paths) {\n    try {\n      if (config.verbose) {\n        console.log(`Scanning directory: ${path}`);\n      }\n      const files = await scanDirectory(path, scanOptions);\n      totalFiles += files.length;\n      if (config.verbose) {\n        console.log(`Found ${files.length} files to process in ${path}`);\n      }\n    } catch {\n      // Continue with other directories even if one fails to scan\n    }\n  }\n\n  if (!config.verbose && totalFiles > 0) {\n    // Add a blank line for spacing in the console output\n    console.log('');\n    console.log(`Found ${totalFiles} files to process (checking for changes...)`);\n  }\n\n  for (const path of paths) {\n    try {\n      // Mark directory as indexing\n      const normalizedPath = normalizePath(path);\n      await sqlite.upsertDirectory(normalizedPath, 'indexing');\n\n      const files = await scanDirectory(path, scanOptions);\n\n      // Track directory-specific counters\n      const dirStartIndexed = indexed;\n      const dirStartSkipped = skipped;\n\n      // Calculate progress interval for non-verbose updates\n      const progressInterval = totalFiles > 1000 ? 50 : 10;\n\n      for (const file of files) {\n        try {\n          // Check if file already exists and needs reprocessing\n          const existingFile = await sqlite.getFile(file.path);\n\n          if (existingFile) {\n            const needsReprocessing = await shouldReprocessFile(file.path, existingFile, config);\n            if (!needsReprocessing) {\n              skipped++;\n              if (config.verbose) {\n                console.log(`  Skipped: ${file.path} (unchanged)`);\n              }\n              // Show periodic progress in non-verbose mode\n              if (!config.verbose && (indexed + skipped) % progressInterval === 0) {\n                console.log(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);\n              }\n              continue; // Skip unchanged file\n            }\n\n            // File changed - clean up old vectors first\n            await qdrant.deletePointsByFilePath(file.path);\n          }\n\n          const rawContent = await fs.readFile(file.path, 'utf-8');\n\n          // Skip non-UTF-8 files (Node.js inserts U+FFFD for invalid byte sequences)\n          if (rawContent.includes('\\uFFFD')) {\n            log('warning', 'Skipping non-UTF-8 file', { path: file.path });\n            await sqlite.upsertFile(file, [], ['Skipped: file appears to be non-UTF-8 encoded']);\n            skipped++;\n            continue;\n          }\n\n          // Normalize CRLF to LF for consistent chunk boundaries\n          const content = rawContent.replace(/\\r\\n/g, '\\n');\n          const chunks = chunkText(content, config.indexing.chunkSize, config.indexing.chunkOverlap);\n\n          // Store file metadata in SQLite\n          await sqlite.upsertFile(file, chunks);\n\n          // Generate embeddings and store in Qdrant\n          for (let i = 0; i < chunks.length; i++) {\n            const chunk = chunks[i];\n            const embedding = await generateEmbedding(chunk.content, config);\n            // Generate a unique integer ID by combining hash and chunk index\n            const hashNum = parseInt(file.hash.slice(0, 8), 16);\n            const pointId = (hashNum % 1000000) * 1000 + parseInt(chunk.id);\n            const point = {\n              id: pointId,\n              vector: embedding,\n              payload: {\n                filePath: file.path,\n                chunkId: chunk.id,\n                fileHash: file.hash,\n                content: chunk.content,\n                parentDirectories: file.parentDirs\n              }\n            };\n            await qdrant.upsertPoints([point]);\n          }\n\n          indexed++;\n          if (config.verbose) {\n            console.log(`  Indexed: ${file.path} (${chunks.length} chunks)`);\n          }\n          // Show periodic progress in non-verbose mode\n          if (!config.verbose && (indexed + skipped) % progressInterval === 0) {\n            console.log(`Progress: ${indexed + skipped}/${totalFiles} files (${skipped} skipped as unchanged)...`);\n          }\n        } catch (error) {\n          const errorMessage = error instanceof Error ? error.message : String(error);\n          const causeMessage = error instanceof Error && error.cause ? `: ${(error.cause as Error).message}` : '';\n          const fullError = `Failed to process ${file.path}: ${errorMessage}${causeMessage}`;\n          errors.push(fullError);\n          failed++;\n\n          // Print error immediately during processing (not just in verbose mode)\n          console.error(`❌ ${fullError}`);\n        }\n      }\n\n      // Clean up deleted files from this directory\n      const indexedFiles = await sqlite.getFilesByDirectory(normalizedPath);\n      const existingFilePaths = new Set(files.map(f => f.path));\n      const deletedFiles = indexedFiles.filter(f => !existingFilePaths.has(f.path));\n\n      for (const deletedFile of deletedFiles) {\n        try {\n          // Remove from Qdrant\n          await qdrant.deletePointsByFilePath(deletedFile.path);\n          \n          // Remove from SQLite\n          await sqlite.deleteFile(deletedFile.path);\n          \n          deleted++;\n          if (config.verbose) {\n            console.log(`  Cleaned up deleted file: ${deletedFile.path}`);\n          }\n        } catch (error) {\n          const errorMessage = error instanceof Error ? error.message : String(error);\n          const fullError = `Failed to clean up deleted file ${deletedFile.path}: ${errorMessage}`;\n          errors.push(fullError);\n          failed++;\n          \n          console.error(`❌ ${fullError}`);\n        }\n      }\n\n      // Mark directory as completed if no errors for this directory\n      const directoryErrors = errors.filter(err => err.includes(path));\n      const directoryStatus = directoryErrors.length > 0 ? 'failed' : 'completed';\n      await sqlite.upsertDirectory(normalizedPath, directoryStatus);\n\n      // Show directory completion\n      const dirFiles = files.length;\n      const dirIndexed = indexed - dirStartIndexed;\n      const dirSkipped = skipped - dirStartSkipped;\n      if (config.verbose) {\n        console.log(`Directory ${path} completed: ${dirIndexed} indexed, ${dirSkipped} skipped`);\n      } else {\n        console.log(`Directory ${path} completed: ${dirFiles} files processed`);\n      }\n\n    } catch (error) {\n      const normalizedPath = normalizePath(path);\n      await sqlite.upsertDirectory(normalizedPath, 'failed');\n      errors.push(`Failed to scan directory ${path}: ${(error as Error).message}`);\n    }\n  }\n\n  return { indexed, skipped, failed, deleted, errors 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