@gettymade/roux 0.1.3 → 0.2.0

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../node_modules/string-similarity/src/index.js","../../src/cli/index.ts","../../src/cli/commands/init.ts","../../src/cli/commands/status.ts","../../src/providers/docstore/cache.ts","../../src/providers/vector/sqlite.ts","../../src/cli/commands/serve.ts","../../src/providers/docstore/index.ts","../../src/providers/docstore/parser.ts","../../src/graph/builder.ts","../../src/graph/operations.ts","../../src/providers/embedding/transformers.ts","../../src/core/graphcore.ts","../../src/mcp/server.ts","../../src/mcp/types.ts","../../src/mcp/truncate.ts","../../src/mcp/transforms.ts","../../src/mcp/handlers.ts","../../src/cli/commands/viz.ts"],"sourcesContent":["module.exports = {\n\tcompareTwoStrings:compareTwoStrings,\n\tfindBestMatch:findBestMatch\n};\n\nfunction compareTwoStrings(first, second) {\n\tfirst = first.replace(/\\s+/g, '')\n\tsecond = second.replace(/\\s+/g, '')\n\n\tif (first === second) return 1; // identical or empty\n\tif (first.length < 2 || second.length < 2) return 0; // if either is a 0-letter or 1-letter string\n\n\tlet firstBigrams = new Map();\n\tfor (let i = 0; i < first.length - 1; i++) {\n\t\tconst bigram = first.substring(i, i + 2);\n\t\tconst count = firstBigrams.has(bigram)\n\t\t\t? firstBigrams.get(bigram) + 1\n\t\t\t: 1;\n\n\t\tfirstBigrams.set(bigram, count);\n\t};\n\n\tlet intersectionSize = 0;\n\tfor (let i = 0; i < second.length - 1; i++) {\n\t\tconst bigram = second.substring(i, i + 2);\n\t\tconst count = firstBigrams.has(bigram)\n\t\t\t? firstBigrams.get(bigram)\n\t\t\t: 0;\n\n\t\tif (count > 0) {\n\t\t\tfirstBigrams.set(bigram, count - 1);\n\t\t\tintersectionSize++;\n\t\t}\n\t}\n\n\treturn (2.0 * intersectionSize) / (first.length + second.length - 2);\n}\n\nfunction findBestMatch(mainString, targetStrings) {\n\tif (!areArgsValid(mainString, targetStrings)) throw new Error('Bad arguments: First argument should be a string, second should be an array of strings');\n\t\n\tconst ratings = [];\n\tlet bestMatchIndex = 0;\n\n\tfor (let i = 0; i < targetStrings.length; i++) {\n\t\tconst currentTargetString = targetStrings[i];\n\t\tconst currentRating = compareTwoStrings(mainString, currentTargetString)\n\t\tratings.push({target: currentTargetString, rating: currentRating})\n\t\tif (currentRating > ratings[bestMatchIndex].rating) {\n\t\t\tbestMatchIndex = i\n\t\t}\n\t}\n\t\n\t\n\tconst bestMatch = ratings[bestMatchIndex]\n\t\n\treturn { ratings: ratings, bestMatch: bestMatch, bestMatchIndex: bestMatchIndex };\n}\n\nfunction areArgsValid(mainString, targetStrings) {\n\tif (typeof mainString !== 'string') return false;\n\tif (!Array.isArray(targetStrings)) return false;\n\tif (!targetStrings.length) return false;\n\tif (targetStrings.find( function (s) { return typeof s !== 'string'})) return false;\n\treturn true;\n}\n","#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { resolve } from 'node:path';\nimport { execFile } from 'node:child_process';\nimport { initCommand } from './commands/init.js';\nimport { statusCommand } from './commands/status.js';\nimport { serveCommand } from './commands/serve.js';\nimport { vizCommand } from './commands/viz.js';\n\nconst program = new Command();\n\nprogram\n  .name('roux')\n  .description('Graph Programming Interface for knowledge bases')\n  .version('0.1.0');\n\nprogram\n  .command('init')\n  .description('Initialize Roux in a directory')\n  .argument('[directory]', 'Directory to initialize', '.')\n  .action(async (directory: string) => {\n    const resolvedDir = resolve(directory);\n    const result = await initCommand(resolvedDir);\n\n    if (result.created) {\n      console.log(`Initialized Roux in ${resolvedDir}`);\n      console.log(`  Config: ${result.configPath}`);\n      if (result.hooksInstalled) {\n        console.log(`  Claude hooks: installed`);\n      }\n    } else {\n      if (result.hooksInstalled) {\n        console.log(`Upgraded Roux in ${resolvedDir}`);\n        console.log(`  Claude hooks: installed`);\n      } else {\n        console.log(`Already initialized: ${result.configPath}`);\n      }\n    }\n  });\n\nprogram\n  .command('status')\n  .description('Show graph statistics')\n  .argument('[directory]', 'Directory to check', '.')\n  .action(async (directory: string) => {\n    const resolvedDir = resolve(directory);\n\n    try {\n      const result = await statusCommand(resolvedDir);\n      console.log('Graph Status:');\n      console.log(`  Nodes: ${result.nodeCount}`);\n      console.log(`  Edges: ${result.edgeCount}`);\n      console.log(`  Embeddings: ${result.embeddingCount}/${result.nodeCount}`);\n      console.log(\n        `  Coverage: ${(result.embeddingCoverage * 100).toFixed(1)}%`\n      );\n    } catch (error) {\n      console.error(\n        error instanceof Error ? error.message : 'Unknown error'\n      );\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command('serve')\n  .description('Start MCP server with file watching')\n  .argument('[directory]', 'Directory to serve', '.')\n  .option('--no-watch', 'Disable file watching')\n  .action(async (directory: string, options: { watch: boolean }) => {\n    const resolvedDir = resolve(directory);\n\n    try {\n      console.log('Starting Roux server...');\n\n      const handle = await serveCommand(resolvedDir, {\n        watch: options.watch,\n        onProgress: (current, total) => {\n          process.stdout.write(\n            `\\r[${current}/${total}] Generating embeddings...`\n          );\n          if (current === total) {\n            console.log(' Done.');\n          }\n        },\n      });\n\n      console.log(`Serving ${handle.nodeCount} nodes`);\n      if (handle.isWatching) {\n        console.log('Watching for file changes...');\n      }\n\n      // Graceful shutdown\n      const shutdown = async () => {\n        console.log('\\nShutting down...');\n        await handle.stop();\n        process.exit(0);\n      };\n\n      process.on('SIGINT', shutdown);\n      process.on('SIGTERM', shutdown);\n\n      // Keep process alive\n      await new Promise(() => {});\n    } catch (error) {\n      console.error(\n        error instanceof Error ? error.message : 'Unknown error'\n      );\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command('viz')\n  .description('Generate graph visualization')\n  .argument('[directory]', 'Directory to visualize', '.')\n  .option('-o, --output <path>', 'Output file path')\n  .option('--open', 'Open in browser after generation')\n  .action(\n    async (directory: string, options: { output?: string; open?: boolean }) => {\n      const resolvedDir = resolve(directory);\n\n      try {\n        const result = await vizCommand(resolvedDir, {\n          output: options.output,\n          open: options.open,\n        });\n\n        console.log(\n          `Generated visualization: ${result.nodeCount} nodes, ${result.edgeCount} edges`\n        );\n        console.log(`  Output: ${result.outputPath}`);\n\n        if (result.shouldOpen) {\n          const openCmd =\n            process.platform === 'darwin'\n              ? 'open'\n              : process.platform === 'win32'\n                ? 'start'\n                : 'xdg-open';\n          execFile(openCmd, [result.outputPath]);\n        }\n      } catch (error) {\n        console.error(\n          error instanceof Error ? error.message : 'Unknown error'\n        );\n        process.exit(1);\n      }\n    }\n  );\n\nprogram.parse();\n","import { mkdir, writeFile, readFile, access } from 'node:fs/promises';\nimport { join } from 'node:path';\n\nexport interface InitResult {\n  created: boolean;\n  configPath: string;\n  hooksInstalled: boolean;\n}\n\ninterface McpServerConfig {\n  command?: string;\n  args?: string[];\n  env?: Record<string, string>;\n  type?: string;\n  url?: string;\n}\n\ninterface McpConfig {\n  mcpServers?: Record<string, McpServerConfig>;\n}\n\ninterface ClaudeHook {\n  type: string;\n  command: string;\n}\n\ninterface ClaudeHookEntry {\n  matcher: string;\n  hooks: ClaudeHook[];\n}\n\ninterface ClaudeSettings {\n  hooks?: {\n    PreToolUse?: ClaudeHookEntry[];\n    PostToolUse?: ClaudeHookEntry[];\n    [key: string]: ClaudeHookEntry[] | undefined;\n  };\n  [key: string]: unknown;\n}\n\nconst DEFAULT_CONFIG = `providers:\n  store:\n    type: docstore\n`;\n\nconst ROUX_MCP_CONFIG: McpServerConfig = {\n  command: 'npx',\n  args: ['roux', 'serve', '.'],\n  env: {},\n};\n\n/** Marker to identify roux's hook for idempotent updates */\nexport const HOOK_MARKER = 'roux-enforce-mcp';\n\n/** Hook command that rejects direct file operations on .md files */\nconst ENFORCE_MCP_HOOK_COMMAND = `node -e \"/* ${HOOK_MARKER} */ const d=JSON.parse(require('fs').readFileSync(0,'utf8'));const p=d.tool_input?.file_path||'';if(p.endsWith('.md')){console.error('Use mcp__roux__* tools for markdown files instead of Read/Edit/Write');process.exit(2)}\"`;\n\nconst ROUX_HOOK_ENTRY: ClaudeHookEntry = {\n  matcher: 'Read|Edit|Write',\n  hooks: [{ type: 'command', command: ENFORCE_MCP_HOOK_COMMAND }],\n};\n\nexport async function initCommand(directory: string): Promise<InitResult> {\n  const configPath = join(directory, 'roux.yaml');\n  const rouxDir = join(directory, '.roux');\n\n  // Check if already initialized\n  let configExists = false;\n  try {\n    await access(configPath);\n    configExists = true;\n  } catch {\n    // File doesn't exist\n  }\n\n  // Create .roux directory regardless\n  await mkdir(rouxDir, { recursive: true });\n\n  // Create/update MCP config\n  await updateMcpConfig(directory);\n\n  // Determine store type and update Claude hooks if docstore\n  const storeType = await getStoreType(directory, configExists);\n  let hooksInstalled = false;\n  if (storeType === 'docstore') {\n    hooksInstalled = await updateClaudeSettings(directory);\n  }\n\n  if (configExists) {\n    return { created: false, configPath, hooksInstalled };\n  }\n\n  // Create roux.yaml with minimal defaults\n  await writeFile(configPath, DEFAULT_CONFIG, 'utf-8');\n  return { created: true, configPath, hooksInstalled };\n}\n\nasync function updateMcpConfig(directory: string): Promise<void> {\n  const mcpPath = join(directory, '.mcp.json');\n\n  let config: McpConfig = {};\n\n  // Try to read existing config\n  try {\n    const content = await readFile(mcpPath, 'utf-8');\n    config = JSON.parse(content) as McpConfig;\n  } catch {\n    // File doesn't exist or invalid JSON — start fresh\n  }\n\n  // Ensure mcpServers object exists\n  if (!config.mcpServers) {\n    config.mcpServers = {};\n  }\n\n  // Add/update roux entry\n  config.mcpServers.roux = ROUX_MCP_CONFIG;\n\n  // Write back\n  await writeFile(mcpPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n}\n\nasync function getStoreType(\n  directory: string,\n  configExists: boolean\n): Promise<string> {\n  if (!configExists) {\n    return 'docstore'; // Default\n  }\n\n  try {\n    const configPath = join(directory, 'roux.yaml');\n    const content = await readFile(configPath, 'utf-8');\n    // Simple YAML parsing for store type\n    const typeMatch = content.match(/store:\\s*\\n\\s*type:\\s*(\\w+)/);\n    if (typeMatch?.[1]) {\n      return typeMatch[1];\n    }\n  } catch {\n    // Can't read config, assume default\n  }\n\n  return 'docstore';\n}\n\n/** Returns true if hooks were installed, false if skipped */\nasync function updateClaudeSettings(directory: string): Promise<boolean> {\n  const claudeDir = join(directory, '.claude');\n  const settingsPath = join(claudeDir, 'settings.json');\n\n  // Ensure .claude directory exists\n  await mkdir(claudeDir, { recursive: true });\n\n  let config: ClaudeSettings = {};\n  let existingContent: string | null = null;\n\n  // Try to read existing settings\n  try {\n    existingContent = await readFile(settingsPath, 'utf-8');\n    config = JSON.parse(existingContent) as ClaudeSettings;\n  } catch (err) {\n    if (existingContent !== null) {\n      // File exists but is malformed JSON — don't touch it\n      return false;\n    }\n    // File doesn't exist — start fresh\n  }\n\n  // Ensure hooks.PreToolUse array exists\n  if (!config.hooks) {\n    config.hooks = {};\n  }\n  if (!config.hooks.PreToolUse) {\n    config.hooks.PreToolUse = [];\n  }\n\n  // Check if our hook already exists\n  const hasRouxHook = config.hooks.PreToolUse.some((entry) =>\n    entry.hooks?.some((h) => h.command?.includes(HOOK_MARKER))\n  );\n\n  if (hasRouxHook) {\n    return false; // Already installed, don't duplicate\n  }\n\n  // Add our hook\n  config.hooks.PreToolUse.push(ROUX_HOOK_ENTRY);\n\n  // Write back\n  await writeFile(settingsPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n  return true;\n}\n","import { access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { Cache } from '../../providers/docstore/cache.js';\nimport { SqliteVectorProvider } from '../../providers/vector/sqlite.js';\n\nexport interface StatusResult {\n  nodeCount: number;\n  edgeCount: number;\n  embeddingCount: number;\n  embeddingCoverage: number;\n}\n\nexport async function statusCommand(directory: string): Promise<StatusResult> {\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  const cacheDir = join(directory, '.roux');\n  const cache = new Cache(cacheDir);\n  const vectorProvider = new SqliteVectorProvider(cacheDir);\n\n  try {\n    const stats = cache.getStats();\n    const embeddingCount = vectorProvider.getEmbeddingCount();\n\n    const embeddingCoverage =\n      stats.nodeCount === 0 ? 1 : embeddingCount / stats.nodeCount;\n\n    return {\n      nodeCount: stats.nodeCount,\n      edgeCount: stats.edgeCount,\n      embeddingCount,\n      embeddingCoverage,\n    };\n  } finally {\n    cache.close();\n    vectorProvider.close();\n  }\n}\n","import Database from 'better-sqlite3';\nimport { join } from 'node:path';\nimport { mkdirSync } from 'node:fs';\nimport stringSimilarity from 'string-similarity';\nimport type { Node, SourceRef } from '../../types/node.js';\nimport type {\n  TagMode,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../../types/provider.js';\n\nexport interface EmbeddingRecord {\n  model: string;\n  vector: number[];\n}\n\nexport interface CentralityRecord {\n  pagerank: number;\n  inDegree: number;\n  outDegree: number;\n  computedAt: number;\n}\n\ninterface NodeRow {\n  id: string;\n  title: string;\n  content: string;\n  tags: string;\n  outgoing_links: string;\n  properties: string;\n  source_type: string;\n  source_path: string;\n  source_modified: number;\n}\n\ninterface EmbeddingRow {\n  node_id: string;\n  model: string;\n  vector: Buffer;\n}\n\ninterface CentralityRow {\n  node_id: string;\n  pagerank: number;\n  in_degree: number;\n  out_degree: number;\n  computed_at: number;\n}\n\nexport class Cache {\n  private db: Database.Database;\n\n  constructor(cacheDir: string) {\n    mkdirSync(cacheDir, { recursive: true });\n    const dbPath = join(cacheDir, 'cache.db');\n    this.db = new Database(dbPath);\n    this.db.pragma('journal_mode = WAL');\n    this.initSchema();\n  }\n\n  private initSchema(): void {\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS nodes (\n        id TEXT PRIMARY KEY,\n        title TEXT,\n        content TEXT,\n        tags TEXT,\n        outgoing_links TEXT,\n        properties TEXT,\n        source_type TEXT,\n        source_path TEXT,\n        source_modified INTEGER\n      );\n\n      CREATE TABLE IF NOT EXISTS embeddings (\n        node_id TEXT PRIMARY KEY,\n        model TEXT,\n        vector BLOB,\n        FOREIGN KEY (node_id) REFERENCES nodes(id) ON DELETE CASCADE\n      );\n\n      CREATE TABLE IF NOT EXISTS centrality (\n        node_id TEXT PRIMARY KEY,\n        pagerank REAL,\n        in_degree INTEGER,\n        out_degree INTEGER,\n        computed_at INTEGER,\n        FOREIGN KEY (node_id) REFERENCES nodes(id) ON DELETE CASCADE\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_nodes_source_path ON nodes(source_path);\n    `);\n    // Enable foreign key enforcement for cascade deletes\n    this.db.pragma('foreign_keys = ON');\n  }\n\n  getTableNames(): string[] {\n    const rows = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='table'\")\n      .all() as Array<{ name: string }>;\n    return rows.map((r) => r.name);\n  }\n\n  upsertNode(\n    node: Node,\n    sourceType: string,\n    sourcePath: string,\n    sourceModified: number\n  ): void {\n    const stmt = this.db.prepare(`\n      INSERT INTO nodes (id, title, content, tags, outgoing_links, properties, source_type, source_path, source_modified)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)\n      ON CONFLICT(id) DO UPDATE SET\n        title = excluded.title,\n        content = excluded.content,\n        tags = excluded.tags,\n        outgoing_links = excluded.outgoing_links,\n        properties = excluded.properties,\n        source_type = excluded.source_type,\n        source_path = excluded.source_path,\n        source_modified = excluded.source_modified\n    `);\n\n    stmt.run(\n      node.id,\n      node.title,\n      node.content,\n      JSON.stringify(node.tags),\n      JSON.stringify(node.outgoingLinks),\n      JSON.stringify(node.properties),\n      sourceType,\n      sourcePath,\n      sourceModified\n    );\n  }\n\n  getNode(id: string): Node | null {\n    const row = this.db\n      .prepare('SELECT * FROM nodes WHERE id = ?')\n      .get(id) as NodeRow | undefined;\n\n    if (!row) return null;\n    return this.rowToNode(row);\n  }\n\n  getNodes(ids: string[]): Node[] {\n    if (ids.length === 0) return [];\n\n    // Fetch all nodes then order by input ids\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT * FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as NodeRow[];\n\n    const nodeMap = new Map<string, Node>();\n    for (const row of rows) {\n      nodeMap.set(row.id, this.rowToNode(row));\n    }\n\n    // Return in requested order\n    const result: Node[] = [];\n    for (const id of ids) {\n      const node = nodeMap.get(id);\n      if (node) result.push(node);\n    }\n    return result;\n  }\n\n  deleteNode(id: string): void {\n    this.db.prepare('DELETE FROM nodes WHERE id = ?').run(id);\n  }\n\n  getAllNodes(): Node[] {\n    const rows = this.db.prepare('SELECT * FROM nodes').all() as NodeRow[];\n    return rows.map((row) => this.rowToNode(row));\n  }\n\n  searchByTags(tags: string[], mode: TagMode): Node[] {\n    if (tags.length === 0) return [];\n\n    const allNodes = this.getAllNodes();\n    const lowerTags = tags.map((t) => t.toLowerCase());\n\n    return allNodes.filter((node) => {\n      const nodeTags = node.tags.map((t) => t.toLowerCase());\n      if (mode === 'any') {\n        return lowerTags.some((t) => nodeTags.includes(t));\n      } else {\n        return lowerTags.every((t) => nodeTags.includes(t));\n      }\n    });\n  }\n\n  getModifiedTime(sourcePath: string): number | null {\n    const row = this.db\n      .prepare('SELECT source_modified FROM nodes WHERE source_path = ?')\n      .get(sourcePath) as { source_modified: number } | undefined;\n\n    return row?.source_modified ?? null;\n  }\n\n  getNodeByPath(sourcePath: string): Node | null {\n    const row = this.db\n      .prepare('SELECT * FROM nodes WHERE source_path = ?')\n      .get(sourcePath) as NodeRow | undefined;\n\n    if (!row) return null;\n    return this.rowToNode(row);\n  }\n\n  getAllTrackedPaths(): Set<string> {\n    const rows = this.db\n      .prepare('SELECT source_path FROM nodes')\n      .all() as Array<{ source_path: string }>;\n\n    return new Set(rows.map((r) => r.source_path));\n  }\n\n  resolveTitles(ids: string[]): Map<string, string> {\n    if (ids.length === 0) return new Map();\n\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT id, title FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as Array<{ id: string; title: string }>;\n\n    const result = new Map<string, string>();\n    for (const row of rows) {\n      result.set(row.id, row.title);\n    }\n    return result;\n  }\n\n  nodesExist(ids: string[]): Map<string, boolean> {\n    if (ids.length === 0) return new Map();\n\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT id FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as Array<{ id: string }>;\n\n    const existingIds = new Set(rows.map((r) => r.id));\n    const result = new Map<string, boolean>();\n    for (const id of ids) {\n      result.set(id, existingIds.has(id));\n    }\n    return result;\n  }\n\n  listNodes(filter: ListFilter, options?: ListOptions): ListNodesResult {\n    const limit = Math.min(options?.limit ?? 100, 1000);\n    const offset = options?.offset ?? 0;\n\n    // Build query dynamically based on filters\n    const conditions: string[] = [];\n    const params: unknown[] = [];\n\n    if (filter.tag) {\n      // Case-insensitive tag match - tags stored as JSON array\n      conditions.push(\"EXISTS (SELECT 1 FROM json_each(tags) WHERE LOWER(json_each.value) = LOWER(?))\");\n      params.push(filter.tag);\n    }\n\n    if (filter.path) {\n      conditions.push(\"id LIKE ? || '%'\");\n      params.push(filter.path);\n    }\n\n    const whereClause = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n\n    // Get total count of matching nodes (without limit/offset)\n    const countQuery = `SELECT COUNT(*) as count FROM nodes ${whereClause}`;\n    const countRow = this.db.prepare(countQuery).get(...params) as { count: number };\n    const total = countRow.count;\n\n    // Get paginated results\n    const query = `SELECT id, title FROM nodes ${whereClause} LIMIT ? OFFSET ?`;\n    const rows = this.db.prepare(query).all(...params, limit, offset) as Array<{ id: string; title: string }>;\n\n    const nodes = rows.map((row) => ({ id: row.id, title: row.title }));\n    return { nodes, total };\n  }\n\n  resolveNodes(names: string[], options?: ResolveOptions): ResolveResult[] {\n    if (names.length === 0) return [];\n\n    const strategy = options?.strategy ?? 'fuzzy';\n    const threshold = options?.threshold ?? 0.7;\n\n    // Build filter without undefined values\n    const filter: ListFilter = {};\n    if (options?.tag) filter.tag = options.tag;\n    if (options?.path) filter.path = options.path;\n\n    // Get candidate nodes (applying tag/path filters)\n    const { nodes: candidates } = this.listNodes(filter, { limit: 1000 });\n\n    if (candidates.length === 0) {\n      return names.map((query) => ({ query, match: null, score: 0 }));\n    }\n\n    const candidateTitles = candidates.map((c) => c.title.toLowerCase());\n    const titleToId = new Map<string, string>();\n    for (const c of candidates) {\n      titleToId.set(c.title.toLowerCase(), c.id);\n    }\n\n    return names.map((query): ResolveResult => {\n      const queryLower = query.toLowerCase();\n\n      if (strategy === 'exact') {\n        // Exact case-insensitive title match\n        const matchedId = titleToId.get(queryLower);\n        if (matchedId) {\n          return { query, match: matchedId, score: 1 };\n        }\n        return { query, match: null, score: 0 };\n      }\n\n      // Fuzzy strategy using string-similarity\n      if (strategy === 'fuzzy') {\n        const result = stringSimilarity.findBestMatch(queryLower, candidateTitles);\n        const bestMatch = result.bestMatch;\n\n        if (bestMatch.rating >= threshold) {\n          // bestMatch.target is guaranteed to exist in titleToId since both come from candidates\n          const matchedId = titleToId.get(bestMatch.target)!;\n          return { query, match: matchedId, score: bestMatch.rating };\n        }\n        return { query, match: null, score: 0 };\n      }\n\n      // Semantic strategy - not supported at cache level, return no match\n      // DocStore will handle semantic by using embedding provider\n      return { query, match: null, score: 0 };\n    });\n  }\n\n  updateOutgoingLinks(nodeId: string, links: string[]): void {\n    this.db\n      .prepare('UPDATE nodes SET outgoing_links = ? WHERE id = ?')\n      .run(JSON.stringify(links), nodeId);\n  }\n\n  storeEmbedding(nodeId: string, vector: number[], model: string): void {\n    const buffer = Buffer.from(new Float32Array(vector).buffer);\n    this.db\n      .prepare(\n        `\n      INSERT INTO embeddings (node_id, model, vector)\n      VALUES (?, ?, ?)\n      ON CONFLICT(node_id) DO UPDATE SET\n        model = excluded.model,\n        vector = excluded.vector\n    `\n      )\n      .run(nodeId, model, buffer);\n  }\n\n  getEmbedding(nodeId: string): EmbeddingRecord | null {\n    const row = this.db\n      .prepare('SELECT model, vector FROM embeddings WHERE node_id = ?')\n      .get(nodeId) as EmbeddingRow | undefined;\n\n    if (!row) return null;\n\n    const float32 = new Float32Array(\n      row.vector.buffer,\n      row.vector.byteOffset,\n      row.vector.length / 4\n    );\n    return {\n      model: row.model,\n      vector: Array.from(float32),\n    };\n  }\n\n  storeCentrality(\n    nodeId: string,\n    pagerank: number,\n    inDegree: number,\n    outDegree: number,\n    computedAt: number\n  ): void {\n    this.db\n      .prepare(\n        `\n      INSERT INTO centrality (node_id, pagerank, in_degree, out_degree, computed_at)\n      VALUES (?, ?, ?, ?, ?)\n      ON CONFLICT(node_id) DO UPDATE SET\n        pagerank = excluded.pagerank,\n        in_degree = excluded.in_degree,\n        out_degree = excluded.out_degree,\n        computed_at = excluded.computed_at\n    `\n      )\n      .run(nodeId, pagerank, inDegree, outDegree, computedAt);\n  }\n\n  getCentrality(nodeId: string): CentralityRecord | null {\n    const row = this.db\n      .prepare('SELECT * FROM centrality WHERE node_id = ?')\n      .get(nodeId) as CentralityRow | undefined;\n\n    if (!row) return null;\n\n    return {\n      pagerank: row.pagerank,\n      inDegree: row.in_degree,\n      outDegree: row.out_degree,\n      computedAt: row.computed_at,\n    };\n  }\n\n  getStats(): { nodeCount: number; embeddingCount: number; edgeCount: number } {\n    const nodeCount = this.db\n      .prepare('SELECT COUNT(*) as count FROM nodes')\n      .get() as { count: number };\n\n    const embeddingCount = this.db\n      .prepare('SELECT COUNT(*) as count FROM embeddings')\n      .get() as { count: number };\n\n    // Sum all in_degree values to get edge count\n    const edgeSum = this.db\n      .prepare('SELECT SUM(in_degree) as total FROM centrality')\n      .get() as { total: number | null };\n\n    return {\n      nodeCount: nodeCount.count,\n      embeddingCount: embeddingCount.count,\n      edgeCount: edgeSum.total ?? 0,\n    };\n  }\n\n  clear(): void {\n    this.db.exec('DELETE FROM centrality');\n    this.db.exec('DELETE FROM embeddings');\n    this.db.exec('DELETE FROM nodes');\n  }\n\n  close(): void {\n    this.db.close();\n  }\n\n  private rowToNode(row: NodeRow): Node {\n    const sourceRef: SourceRef = {\n      type: row.source_type as SourceRef['type'],\n      path: row.source_path,\n      lastModified: new Date(row.source_modified),\n    };\n\n    return {\n      id: row.id,\n      title: row.title,\n      content: row.content,\n      tags: JSON.parse(row.tags) as string[],\n      outgoingLinks: JSON.parse(row.outgoing_links) as string[],\n      properties: JSON.parse(row.properties) as Record<string, unknown>,\n      sourceRef,\n    };\n  }\n}\n","import Database from 'better-sqlite3';\nimport type { Database as DatabaseType } from 'better-sqlite3';\nimport { join } from 'node:path';\nimport type { VectorProvider, VectorSearchResult } from '../../types/provider.js';\n\nexport class SqliteVectorProvider implements VectorProvider {\n  private db: DatabaseType;\n  private ownsDb: boolean;\n\n  constructor(pathOrDb: string | DatabaseType) {\n    if (typeof pathOrDb === 'string') {\n      this.db = new Database(join(pathOrDb, 'vectors.db'));\n      this.ownsDb = true;\n    } else {\n      this.db = pathOrDb;\n      this.ownsDb = false;\n    }\n    this.init();\n  }\n\n  private init(): void {\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS vectors (\n        id TEXT PRIMARY KEY,\n        model TEXT NOT NULL,\n        vector BLOB NOT NULL\n      )\n    `);\n  }\n\n  async store(id: string, vector: number[], model: string): Promise<void> {\n    if (vector.length === 0) {\n      throw new Error('Cannot store empty vector');\n    }\n    for (const v of vector) {\n      if (!Number.isFinite(v)) {\n        throw new Error(`Invalid vector value: ${v}`);\n      }\n    }\n\n    // Validate dimension consistency (exclude self for overwrites)\n    const existing = this.db\n      .prepare('SELECT LENGTH(vector) / 4 as dim FROM vectors WHERE id != ? LIMIT 1')\n      .get(id) as { dim: number } | undefined;\n\n    if (existing && existing.dim !== vector.length) {\n      throw new Error(\n        `Dimension mismatch: cannot store ${vector.length}-dim vector, existing vectors have ${existing.dim} dimensions`\n      );\n    }\n\n    const blob = Buffer.from(new Float32Array(vector).buffer);\n    this.db\n      .prepare(\n        `INSERT OR REPLACE INTO vectors (id, model, vector) VALUES (?, ?, ?)`\n      )\n      .run(id, model, blob);\n  }\n\n  async search(vector: number[], limit: number): Promise<VectorSearchResult[]> {\n    if (vector.length === 0) {\n      throw new Error('Cannot search with empty vector');\n    }\n    for (const v of vector) {\n      if (!Number.isFinite(v)) {\n        throw new Error(`Invalid vector value: ${v}`);\n      }\n    }\n    if (limit <= 0) {\n      return [];\n    }\n\n    const rows = this.db\n      .prepare('SELECT id, vector FROM vectors')\n      .all() as Array<{ id: string; vector: Buffer }>;\n\n    if (rows.length === 0) {\n      return [];\n    }\n\n    // Check dimension mismatch against first stored vector\n    const firstStoredDim = rows[0]!.vector.byteLength / 4;\n    if (vector.length !== firstStoredDim) {\n      throw new Error(\n        `Dimension mismatch: query has ${vector.length} dimensions, stored vectors have ${firstStoredDim}`\n      );\n    }\n\n    const queryVec = new Float32Array(vector);\n    const results: VectorSearchResult[] = [];\n\n    for (const row of rows) {\n      const storedVec = new Float32Array(\n        row.vector.buffer,\n        row.vector.byteOffset,\n        row.vector.byteLength / 4\n      );\n      const distance = cosineDistance(queryVec, storedVec);\n      results.push({ id: row.id, distance });\n    }\n\n    results.sort((a, b) => a.distance - b.distance);\n    return results.slice(0, limit);\n  }\n\n  async delete(id: string): Promise<void> {\n    this.db.prepare('DELETE FROM vectors WHERE id = ?').run(id);\n  }\n\n  async getModel(id: string): Promise<string | null> {\n    const row = this.db\n      .prepare('SELECT model FROM vectors WHERE id = ?')\n      .get(id) as { model: string } | undefined;\n    return row?.model ?? null;\n  }\n\n  hasEmbedding(id: string): boolean {\n    const row = this.db\n      .prepare('SELECT 1 FROM vectors WHERE id = ?')\n      .get(id);\n    return row !== undefined;\n  }\n\n  /** For testing: get table names */\n  getTableNames(): string[] {\n    const rows = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='table'\")\n      .all() as Array<{ name: string }>;\n    return rows.map((r) => r.name);\n  }\n\n  /** For testing: get vector blob size */\n  getVectorBlobSize(id: string): number | null {\n    const row = this.db\n      .prepare('SELECT LENGTH(vector) as size FROM vectors WHERE id = ?')\n      .get(id) as { size: number } | undefined;\n    return row?.size ?? null;\n  }\n\n  /** Get total number of stored embeddings */\n  getEmbeddingCount(): number {\n    const row = this.db\n      .prepare('SELECT COUNT(*) as count FROM vectors')\n      .get() as { count: number };\n    return row.count;\n  }\n\n  close(): void {\n    if (this.ownsDb) {\n      this.db.close();\n    }\n  }\n}\n\nfunction cosineDistance(a: Float32Array, b: Float32Array): number {\n  let dotProduct = 0;\n  let magnitudeA = 0;\n  let magnitudeB = 0;\n\n  for (let i = 0; i < a.length; i++) {\n    dotProduct += a[i]! * b[i]!;\n    magnitudeA += a[i]! * a[i]!;\n    magnitudeB += b[i]! * b[i]!;\n  }\n\n  magnitudeA = Math.sqrt(magnitudeA);\n  magnitudeB = Math.sqrt(magnitudeB);\n\n  if (magnitudeA === 0 || magnitudeB === 0) {\n    return 1; // No similarity for zero vectors\n  }\n\n  const similarity = dotProduct / (magnitudeA * magnitudeB);\n  return 1 - similarity;\n}\n","import { access, readFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { DocStore } from '../../providers/docstore/index.js';\nimport { TransformersEmbeddingProvider } from '../../providers/embedding/transformers.js';\nimport { GraphCoreImpl } from '../../core/graphcore.js';\nimport { McpServer, type TransportFactory } from '../../mcp/server.js';\nimport type { RouxConfig } from '../../types/config.js';\n\nexport interface ServeOptions {\n  watch?: boolean;\n  transportFactory?: TransportFactory;\n  onProgress?: (current: number, total: number) => void;\n}\n\nexport interface ServeHandle {\n  stop: () => Promise<void>;\n  isWatching: boolean;\n  nodeCount: number;\n}\n\nexport async function serveCommand(\n  directory: string,\n  options: ServeOptions = {}\n): Promise<ServeHandle> {\n  const { watch = true, transportFactory, onProgress } = options;\n\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  // Load config\n  const configContent = await readFile(configPath, 'utf-8');\n  const config = parseYaml(configContent) as RouxConfig;\n\n  // Create providers\n  const sourcePath = config.source?.path ?? '.';\n  const resolvedSourcePath = join(directory, sourcePath);\n  const cachePath = config.cache?.path ?? '.roux';\n  const resolvedCachePath = join(directory, cachePath);\n\n  const store = new DocStore(resolvedSourcePath, resolvedCachePath);\n  const embedding = new TransformersEmbeddingProvider(\n    config.providers?.embedding?.type === 'local'\n      ? config.providers.embedding.model\n      : undefined\n  );\n\n  // Sync cache\n  await store.sync();\n\n  // Generate embeddings for nodes without them\n  const allNodeIds = await store.getAllNodeIds();\n  const total = allNodeIds.length;\n\n  for (let i = 0; i < allNodeIds.length; i++) {\n    const id = allNodeIds[i]!;\n\n    if (!hasExistingEmbedding(store, id)) {\n      const node = await store.getNode(id);\n      if (node && node.content) {\n        const vector = await embedding.embed(node.content);\n        await store.storeEmbedding(id, vector, embedding.modelId());\n      }\n    }\n\n    if (onProgress) {\n      onProgress(i + 1, total);\n    }\n  }\n\n  // Create GraphCore\n  const core = new GraphCoreImpl();\n  core.registerStore(store);\n  core.registerEmbedding(embedding);\n\n  // Start MCP server\n  const mcpServer = new McpServer({\n    core,\n    store,\n    hasEmbedding: true,\n  });\n\n  await mcpServer.start(transportFactory);\n\n  // Start file watcher if enabled\n  if (watch) {\n    try {\n      await store.startWatching(async (changedIds) => {\n        // Generate embeddings for changed nodes\n        for (const id of changedIds) {\n          const node = await store.getNode(id);\n          if (node && node.content) {\n            const vector = await embedding.embed(node.content);\n            await store.storeEmbedding(id, vector, embedding.modelId());\n          }\n        }\n      });\n    } catch (err) {\n      console.warn(\n        'File watching disabled:',\n        (err as Error).message || 'Unknown error'\n      );\n    }\n  }\n\n  return {\n    stop: async () => {\n      store.stopWatching();\n      store.close();\n      await mcpServer.close();\n    },\n    isWatching: store.isWatching(),\n    nodeCount: allNodeIds.length,\n  };\n}\n\nfunction hasExistingEmbedding(store: DocStore, id: string): boolean {\n  return store.hasEmbedding(id);\n}\n","import { readFile, writeFile, stat, readdir, mkdir, rm } from 'node:fs/promises';\nimport { join, relative, dirname, resolve } from 'node:path';\nimport { watch, type FSWatcher } from 'chokidar';\nimport type { DirectedGraph } from 'graphology';\nimport type { Node } from '../../types/node.js';\nimport type {\n  StoreProvider,\n  NeighborOptions,\n  Metric,\n  TagMode,\n  VectorSearchResult,\n  VectorProvider,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../../types/provider.js';\nimport { Cache } from './cache.js';\nimport { SqliteVectorProvider } from '../vector/sqlite.js';\nimport {\n  parseMarkdown,\n  extractWikiLinks,\n  normalizeId,\n  titleFromPath,\n  serializeToMarkdown,\n} from './parser.js';\nimport { buildGraph } from '../../graph/builder.js';\nimport {\n  getNeighborIds,\n  findPath as graphFindPath,\n  getHubs as graphGetHubs,\n  computeCentrality,\n} from '../../graph/operations.js';\n\nexport class DocStore implements StoreProvider {\n  private cache: Cache;\n  private sourceRoot: string;\n  private graph: DirectedGraph | null = null;\n  private vectorProvider: VectorProvider;\n  private ownsVectorProvider: boolean;\n\n  private watcher: FSWatcher | null = null;\n  private debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  private pendingChanges: Map<string, 'add' | 'change' | 'unlink'> = new Map();\n  private onChangeCallback: ((changedIds: string[]) => void) | undefined;\n\n  constructor(\n    sourceRoot: string,\n    cacheDir: string,\n    vectorProvider?: VectorProvider\n  ) {\n    this.sourceRoot = sourceRoot;\n    this.cache = new Cache(cacheDir);\n    this.ownsVectorProvider = !vectorProvider;\n    this.vectorProvider = vectorProvider ?? new SqliteVectorProvider(cacheDir);\n  }\n\n  async sync(): Promise<void> {\n    const currentPaths = await this.collectMarkdownFiles(this.sourceRoot);\n    const trackedPaths = this.cache.getAllTrackedPaths();\n\n    // Process new/modified files\n    for (const filePath of currentPaths) {\n      try {\n        const mtime = await this.getFileMtime(filePath);\n        const cachedMtime = this.cache.getModifiedTime(filePath);\n\n        if (cachedMtime === null || mtime > cachedMtime) {\n          const node = await this.fileToNode(filePath);\n          this.cache.upsertNode(node, 'file', filePath, mtime);\n        }\n      } catch (err) {\n        // File may have been deleted between readdir and stat — skip it\n        if ((err as NodeJS.ErrnoException).code === 'ENOENT') {\n          continue;\n        }\n        throw err;\n      }\n    }\n\n    // Remove deleted files\n    const currentSet = new Set(currentPaths);\n    for (const tracked of trackedPaths) {\n      if (!currentSet.has(tracked)) {\n        const node = this.cache.getNodeByPath(tracked);\n        if (node) {\n          this.cache.deleteNode(node.id);\n        }\n      }\n    }\n\n    // Resolve wiki-links after all nodes are cached\n    const filenameIndex = this.buildFilenameIndex();\n    this.resolveOutgoingLinks(filenameIndex);\n\n    // Rebuild graph from all nodes\n    this.rebuildGraph();\n  }\n\n  async createNode(node: Node): Promise<void> {\n    const normalizedId = normalizeId(node.id);\n    this.validatePathWithinSource(normalizedId);\n\n    const existing = this.cache.getNode(normalizedId);\n    if (existing) {\n      throw new Error(`Node already exists: ${normalizedId}`);\n    }\n\n    const filePath = join(this.sourceRoot, normalizedId);\n    const dir = dirname(filePath);\n    await mkdir(dir, { recursive: true });\n\n    const parsed = {\n      title: node.title,\n      tags: node.tags,\n      properties: node.properties,\n      content: node.content,\n    };\n    const markdown = serializeToMarkdown(parsed);\n    await writeFile(filePath, markdown, 'utf-8');\n\n    const mtime = await this.getFileMtime(filePath);\n    const normalizedNode = { ...node, id: normalizedId };\n    this.cache.upsertNode(normalizedNode, 'file', filePath, mtime);\n\n    // Rebuild graph to include new node\n    this.rebuildGraph();\n  }\n\n  async updateNode(id: string, updates: Partial<Node>): Promise<void> {\n    const normalizedId = normalizeId(id);\n    const existing = this.cache.getNode(normalizedId);\n    if (!existing) {\n      throw new Error(`Node not found: ${id}`);\n    }\n\n    // If content is updated, reparse wiki-links\n    let outgoingLinks = updates.outgoingLinks;\n    if (updates.content !== undefined && outgoingLinks === undefined) {\n      const rawLinks = extractWikiLinks(updates.content);\n      outgoingLinks = rawLinks.map((link) => this.normalizeWikiLink(link));\n    }\n\n    const updated: Node = {\n      ...existing,\n      ...updates,\n      outgoingLinks: outgoingLinks ?? existing.outgoingLinks,\n      id: existing.id, // ID cannot be changed\n    };\n\n    const filePath = join(this.sourceRoot, existing.id);\n    const parsed = {\n      title: updated.title,\n      tags: updated.tags,\n      properties: updated.properties,\n      content: updated.content,\n    };\n    const markdown = serializeToMarkdown(parsed);\n    await writeFile(filePath, markdown, 'utf-8');\n\n    const mtime = await this.getFileMtime(filePath);\n    this.cache.upsertNode(updated, 'file', filePath, mtime);\n\n    // Rebuild graph if links changed\n    if (outgoingLinks !== undefined || updates.outgoingLinks !== undefined) {\n      this.rebuildGraph();\n    }\n  }\n\n  async deleteNode(id: string): Promise<void> {\n    const normalizedId = normalizeId(id);\n    const existing = this.cache.getNode(normalizedId);\n    if (!existing) {\n      throw new Error(`Node not found: ${id}`);\n    }\n\n    const filePath = join(this.sourceRoot, existing.id);\n    await rm(filePath);\n    this.cache.deleteNode(existing.id);\n    await this.vectorProvider.delete(existing.id);\n\n    // Rebuild graph without deleted node\n    this.rebuildGraph();\n  }\n\n  async getNode(id: string): Promise<Node | null> {\n    // Normalize ID for case-insensitive lookup\n    const normalizedId = normalizeId(id);\n    return this.cache.getNode(normalizedId);\n  }\n\n  async getNodes(ids: string[]): Promise<Node[]> {\n    const normalizedIds = ids.map(normalizeId);\n    return this.cache.getNodes(normalizedIds);\n  }\n\n  async getAllNodeIds(): Promise<string[]> {\n    const nodes = this.cache.getAllNodes();\n    return nodes.map((n) => n.id);\n  }\n\n  async searchByTags(tags: string[], mode: TagMode): Promise<Node[]> {\n    return this.cache.searchByTags(tags, mode);\n  }\n\n  async getRandomNode(tags?: string[]): Promise<Node | null> {\n    let candidates: Node[];\n\n    if (tags && tags.length > 0) {\n      candidates = await this.searchByTags(tags, 'any');\n    } else {\n      candidates = this.cache.getAllNodes();\n    }\n\n    if (candidates.length === 0) {\n      return null;\n    }\n\n    const randomIndex = Math.floor(Math.random() * candidates.length);\n    // Safe: randomIndex is always 0 to length-1 when length > 0\n    return candidates[randomIndex]!;\n  }\n\n  async resolveTitles(ids: string[]): Promise<Map<string, string>> {\n    return this.cache.resolveTitles(ids);\n  }\n\n  async listNodes(\n    filter: ListFilter,\n    options?: ListOptions\n  ): Promise<ListNodesResult> {\n    return this.cache.listNodes(filter, options);\n  }\n\n  async resolveNodes(\n    names: string[],\n    options?: ResolveOptions\n  ): Promise<ResolveResult[]> {\n    // For exact and fuzzy, delegate to cache\n    const strategy = options?.strategy ?? 'fuzzy';\n    if (strategy === 'exact' || strategy === 'fuzzy') {\n      return this.cache.resolveNodes(names, options);\n    }\n\n    // Semantic strategy: use vector search\n    // This requires embedding provider which DocStore doesn't have direct access to\n    // Return unmatched for now - GraphCore will handle semantic with embedding provider\n    return names.map((query) => ({ query, match: null, score: 0 }));\n  }\n\n  async nodesExist(ids: string[]): Promise<Map<string, boolean>> {\n    const normalizedIds = ids.map(normalizeId);\n    return this.cache.nodesExist(normalizedIds);\n  }\n\n  async getNeighbors(id: string, options: NeighborOptions): Promise<Node[]> {\n    this.ensureGraph();\n    const neighborIds = getNeighborIds(this.graph!, id, options);\n    return this.cache.getNodes(neighborIds);\n  }\n\n  async findPath(source: string, target: string): Promise<string[] | null> {\n    this.ensureGraph();\n    return graphFindPath(this.graph!, source, target);\n  }\n\n  async getHubs(metric: Metric, limit: number): Promise<Array<[string, number]>> {\n    this.ensureGraph();\n    return graphGetHubs(this.graph!, metric, limit);\n  }\n\n  async storeEmbedding(\n    id: string,\n    vector: number[],\n    model: string\n  ): Promise<void> {\n    return this.vectorProvider.store(id, vector, model);\n  }\n\n  async searchByVector(\n    vector: number[],\n    limit: number\n  ): Promise<VectorSearchResult[]> {\n    return this.vectorProvider.search(vector, limit);\n  }\n\n  hasEmbedding(id: string): boolean {\n    return this.vectorProvider.hasEmbedding(id);\n  }\n\n  close(): void {\n    this.stopWatching();\n    this.cache.close();\n    if (this.ownsVectorProvider && 'close' in this.vectorProvider) {\n      (this.vectorProvider as { close: () => void }).close();\n    }\n  }\n\n  startWatching(onChange?: (changedIds: string[]) => void): Promise<void> {\n    if (this.watcher) {\n      throw new Error('Already watching. Call stopWatching() first.');\n    }\n\n    this.onChangeCallback = onChange;\n\n    return new Promise((resolve, reject) => {\n      this.watcher = watch(this.sourceRoot, {\n        ignoreInitial: true,\n        ignored: [...DocStore.EXCLUDED_DIRS].map((dir) => `**/${dir}/**`),\n        awaitWriteFinish: {\n          stabilityThreshold: 100,\n        },\n        followSymlinks: false,\n      });\n\n      this.watcher\n        .on('ready', () => resolve())\n        .on('add', (path) => this.queueChange(path, 'add'))\n        .on('change', (path) => this.queueChange(path, 'change'))\n        .on('unlink', (path) => this.queueChange(path, 'unlink'))\n        .on('error', (err) => {\n          if ((err as NodeJS.ErrnoException).code === 'EMFILE') {\n            console.error(\n              'File watcher hit file descriptor limit. ' +\n                'Try: ulimit -n 65536 or reduce watched files.'\n            );\n          }\n          reject(err);\n        });\n    });\n  }\n\n  stopWatching(): void {\n    if (this.debounceTimer) {\n      clearTimeout(this.debounceTimer);\n      this.debounceTimer = null;\n    }\n    this.pendingChanges.clear();\n\n    if (this.watcher) {\n      this.watcher.close();\n      this.watcher = null;\n    }\n  }\n\n  isWatching(): boolean {\n    return this.watcher !== null;\n  }\n\n  private queueChange(filePath: string, event: 'add' | 'change' | 'unlink'): void {\n    const relativePath = relative(this.sourceRoot, filePath);\n    const id = normalizeId(relativePath);\n\n    // Check exclusions\n    if (!filePath.endsWith('.md')) {\n      return;\n    }\n\n    // Check if path contains any excluded directory\n    const pathParts = relativePath.split('/');\n    for (const part of pathParts) {\n      if (DocStore.EXCLUDED_DIRS.has(part)) {\n        return;\n      }\n    }\n\n    // Apply coalescing rules\n    const existing = this.pendingChanges.get(id);\n\n    if (existing) {\n      if (existing === 'add' && event === 'change') {\n        // add + change = add (keep as add)\n        return;\n      } else if (existing === 'add' && event === 'unlink') {\n        // add + unlink = remove from queue\n        this.pendingChanges.delete(id);\n      } else if (existing === 'change' && event === 'unlink') {\n        // change + unlink = unlink\n        this.pendingChanges.set(id, 'unlink');\n      }\n      // change + change = change (already set, no action needed)\n    } else {\n      this.pendingChanges.set(id, event);\n    }\n\n    // Reset debounce timer\n    if (this.debounceTimer) {\n      clearTimeout(this.debounceTimer);\n    }\n\n    this.debounceTimer = setTimeout(() => {\n      this.processQueue();\n    }, 1000);\n  }\n\n  private async processQueue(): Promise<void> {\n    const changes = new Map(this.pendingChanges);\n    this.pendingChanges.clear();\n    this.debounceTimer = null;\n\n    const processedIds: string[] = [];\n\n    for (const [id, event] of changes) {\n      try {\n        if (event === 'unlink') {\n          const existing = this.cache.getNode(id);\n          if (existing) {\n            this.cache.deleteNode(id);\n            await this.vectorProvider.delete(id);\n            processedIds.push(id);\n          }\n        } else {\n          // add or change\n          const filePath = join(this.sourceRoot, id);\n          const node = await this.fileToNode(filePath);\n          const mtime = await this.getFileMtime(filePath);\n          this.cache.upsertNode(node, 'file', filePath, mtime);\n          processedIds.push(id);\n        }\n      } catch (err) {\n        console.warn(`Failed to process file change for ${id}:`, err);\n      }\n    }\n\n    // Resolve wiki-links and rebuild graph after processing all changes\n    if (processedIds.length > 0) {\n      const filenameIndex = this.buildFilenameIndex();\n      this.resolveOutgoingLinks(filenameIndex);\n      this.rebuildGraph();\n    }\n\n    // Call callback if provided\n    if (this.onChangeCallback && processedIds.length > 0) {\n      this.onChangeCallback(processedIds);\n    }\n  }\n\n  private buildFilenameIndex(): Map<string, string[]> {\n    const index = new Map<string, string[]>();\n    for (const node of this.cache.getAllNodes()) {\n      const basename = node.id.split('/').pop()!;\n      const existing = index.get(basename) ?? [];\n      existing.push(node.id);\n      index.set(basename, existing);\n    }\n    // Sort each array alphabetically for deterministic first-match\n    for (const paths of index.values()) {\n      paths.sort();\n    }\n    return index;\n  }\n\n  private resolveOutgoingLinks(filenameIndex: Map<string, string[]>): void {\n    // Build set of valid node IDs for quick lookup\n    const validNodeIds = new Set<string>();\n    for (const paths of filenameIndex.values()) {\n      for (const path of paths) {\n        validNodeIds.add(path);\n      }\n    }\n\n    for (const node of this.cache.getAllNodes()) {\n      const resolved = node.outgoingLinks.map((link) => {\n        // If link already exists as a valid node ID, keep it\n        if (validNodeIds.has(link)) {\n          return link;\n        }\n        // Only resolve bare filenames (no path separators)\n        // Partial paths like \"folder/target.md\" stay literal\n        if (link.includes('/')) {\n          return link;\n        }\n        // Try basename lookup for bare filenames\n        const matches = filenameIndex.get(link);\n        if (matches && matches.length > 0) {\n          return matches[0]!;\n        }\n        return link;\n      });\n\n      // Only update if something changed\n      if (resolved.some((r, i) => r !== node.outgoingLinks[i])) {\n        this.cache.updateOutgoingLinks(node.id, resolved);\n      }\n    }\n  }\n\n  private ensureGraph(): void {\n    if (!this.graph) {\n      this.rebuildGraph();\n    }\n  }\n\n  private rebuildGraph(): void {\n    const nodes = this.cache.getAllNodes();\n    this.graph = buildGraph(nodes);\n\n    // Cache centrality metrics\n    const centrality = computeCentrality(this.graph);\n    const now = Date.now();\n    for (const [id, metrics] of centrality) {\n      this.cache.storeCentrality(id, 0, metrics.inDegree, metrics.outDegree, now);\n    }\n  }\n\n  private static readonly EXCLUDED_DIRS = new Set(['.roux', 'node_modules', '.git', '.obsidian']);\n\n  private async collectMarkdownFiles(dir: string): Promise<string[]> {\n    const results: string[] = [];\n\n    let entries;\n    try {\n      entries = await readdir(dir, { withFileTypes: true });\n    } catch {\n      // Directory doesn't exist yet\n      return results;\n    }\n\n    for (const entry of entries) {\n      const fullPath = join(dir, entry.name);\n\n      if (entry.isDirectory()) {\n        // Skip excluded directories\n        if (DocStore.EXCLUDED_DIRS.has(entry.name)) {\n          continue;\n        }\n        const nested = await this.collectMarkdownFiles(fullPath);\n        results.push(...nested);\n      } else if (entry.isFile() && entry.name.endsWith('.md')) {\n        results.push(fullPath);\n      }\n    }\n\n    return results;\n  }\n\n  private async getFileMtime(filePath: string): Promise<number> {\n    const stats = await stat(filePath);\n    return stats.mtimeMs;\n  }\n\n  private async fileToNode(filePath: string): Promise<Node> {\n    const raw = await readFile(filePath, 'utf-8');\n    const parsed = parseMarkdown(raw);\n\n    const relativePath = relative(this.sourceRoot, filePath);\n    const id = normalizeId(relativePath);\n\n    // Derive title from path if not in frontmatter\n    const title = parsed.title ?? titleFromPath(id);\n\n    // Extract and normalize wiki links\n    const rawLinks = extractWikiLinks(parsed.content);\n    const outgoingLinks = rawLinks.map((link) => this.normalizeWikiLink(link));\n\n    return {\n      id,\n      title,\n      content: parsed.content,\n      tags: parsed.tags,\n      outgoingLinks,\n      properties: parsed.properties,\n      sourceRef: {\n        type: 'file',\n        path: filePath,\n        lastModified: new Date(await this.getFileMtime(filePath)),\n      },\n    };\n  }\n\n  /**\n   * Normalize a wiki-link target to an ID.\n   * - If it has a file extension, normalize as-is\n   * - If no extension, add .md\n   * - Lowercase, forward slashes\n   */\n  private normalizeWikiLink(target: string): string {\n    let normalized = target.toLowerCase().replace(/\\\\/g, '/');\n\n    // Add .md if no file extension present\n    // File extension = dot followed by 1-4 alphanumeric chars at end\n    if (!this.hasFileExtension(normalized)) {\n      normalized += '.md';\n    }\n\n    return normalized;\n  }\n\n  private hasFileExtension(path: string): boolean {\n    // Match common file extensions: .md, .txt, .png, .json, etc.\n    // Extension must contain at least one letter (to exclude .2024, .123, etc.)\n    const match = path.match(/\\.([a-z0-9]{1,4})$/i);\n    if (!match?.[1]) return false;\n    // Require at least one letter in the extension\n    return /[a-z]/i.test(match[1]);\n  }\n\n  private validatePathWithinSource(id: string): void {\n    const resolvedPath = resolve(this.sourceRoot, id);\n    const resolvedRoot = resolve(this.sourceRoot);\n\n    if (!resolvedPath.startsWith(resolvedRoot + '/')) {\n      throw new Error(`Path traversal detected: ${id} resolves outside source root`);\n    }\n  }\n}\n\nexport { Cache } from './cache.js';\nexport {\n  parseMarkdown,\n  extractWikiLinks,\n  normalizeId,\n  titleFromPath,\n  serializeToMarkdown,\n} from './parser.js';\n","import matter from 'gray-matter';\n\nexport interface ParsedMarkdown {\n  title: string | undefined;\n  tags: string[];\n  properties: Record<string, unknown>;\n  content: string;\n}\n\n/**\n * Parse markdown with YAML frontmatter.\n * Handles missing/malformed frontmatter gracefully.\n */\nexport function parseMarkdown(raw: string): ParsedMarkdown {\n  let parsed: matter.GrayMatterFile<string>;\n  try {\n    parsed = matter(raw);\n  } catch {\n    // Malformed frontmatter - return content as-is\n    return {\n      title: undefined,\n      tags: [],\n      properties: {},\n      content: raw,\n    };\n  }\n\n  const data = parsed.data as Record<string, unknown>;\n\n  // Extract title\n  const title = typeof data['title'] === 'string' ? data['title'] : undefined;\n\n  // Extract tags - must be an array of strings\n  let tags: string[] = [];\n  if (Array.isArray(data['tags'])) {\n    tags = data['tags'].filter((t): t is string => typeof t === 'string');\n  }\n\n  // Extract other properties (excluding title and tags)\n  const properties: Record<string, unknown> = {};\n  for (const [key, value] of Object.entries(data)) {\n    if (key !== 'title' && key !== 'tags') {\n      properties[key] = value;\n    }\n  }\n\n  return {\n    title,\n    tags,\n    properties,\n    content: parsed.content.trim(),\n  };\n}\n\n/**\n * Extract wiki-link targets from markdown content.\n * Ignores links inside code blocks and inline code.\n * Deduplicates results.\n */\nexport function extractWikiLinks(content: string): string[] {\n  // Remove code blocks first\n  const withoutCodeBlocks = content.replace(/```[\\s\\S]*?```/g, '');\n\n  // Remove inline code\n  const withoutInlineCode = withoutCodeBlocks.replace(/`[^`]+`/g, '');\n\n  // Match wiki links: [[target]] or [[target|display]]\n  const linkRegex = /\\[\\[([^\\]|]+)(?:\\|[^\\]]+)?\\]\\]/g;\n  const seen = new Set<string>();\n  const links: string[] = [];\n\n  let match;\n  while ((match = linkRegex.exec(withoutInlineCode)) !== null) {\n    const target = match[1]?.trim();\n    if (target && !seen.has(target)) {\n      seen.add(target);\n      links.push(target);\n    }\n  }\n\n  return links;\n}\n\n/**\n * Normalize a file path to a consistent ID format.\n * - Lowercased\n * - Forward slashes only\n * - Preserves extension\n */\nexport function normalizeId(path: string): string {\n  return path.toLowerCase().replace(/\\\\/g, '/');\n}\n\n/**\n * Derive a human-readable title from a file path.\n * - Removes directory prefix\n * - Removes extension\n * - Replaces hyphens/underscores with spaces\n * - Title-cases words\n */\nexport function titleFromPath(path: string): string {\n  // Get filename without directory\n  const parts = path.split(/[/\\\\]/);\n  // parts is always non-empty (even '' splits to [''])\n  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion\n  const filename = parts.at(-1)!;\n\n  // Remove extension\n  const withoutExt = filename.replace(/\\.[^.]+$/, '');\n\n  // Replace hyphens and underscores with spaces, collapse multiples\n  const spaced = withoutExt.replace(/[-_]+/g, ' ').toLowerCase();\n\n  // Title-case each word\n  return spaced\n    .split(' ')\n    .filter((w) => w.length > 0)\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\n    .join(' ');\n}\n\n/**\n * Serialize parsed markdown back to a string with YAML frontmatter.\n * Omits frontmatter if no metadata is present.\n */\nexport function serializeToMarkdown(parsed: ParsedMarkdown): string {\n  const hasFrontmatter =\n    parsed.title !== undefined ||\n    parsed.tags.length > 0 ||\n    Object.keys(parsed.properties).length > 0;\n\n  if (!hasFrontmatter) {\n    return parsed.content;\n  }\n\n  // Build frontmatter object\n  const frontmatter: Record<string, unknown> = {};\n\n  if (parsed.title !== undefined) {\n    frontmatter['title'] = parsed.title;\n  }\n\n  if (parsed.tags.length > 0) {\n    frontmatter['tags'] = parsed.tags;\n  }\n\n  // Add other properties\n  for (const [key, value] of Object.entries(parsed.properties)) {\n    frontmatter[key] = value;\n  }\n\n  // Use gray-matter to stringify\n  return matter.stringify(parsed.content, frontmatter);\n}\n","import { DirectedGraph } from 'graphology';\nimport type { Node } from '../types/node.js';\n\n/**\n * Build a directed graph from an array of nodes.\n * Edges are derived from each node's outgoingLinks.\n * Links to non-existent nodes are ignored.\n */\nexport function buildGraph(nodes: Node[]): DirectedGraph {\n  const graph = new DirectedGraph();\n\n  // First pass: add all nodes\n  const nodeIds = new Set<string>();\n  for (const node of nodes) {\n    graph.addNode(node.id);\n    nodeIds.add(node.id);\n  }\n\n  // Second pass: add edges (only to existing nodes)\n  for (const node of nodes) {\n    const seen = new Set<string>();\n    for (const target of node.outgoingLinks) {\n      // Skip if target doesn't exist or we've already added this edge\n      if (!nodeIds.has(target) || seen.has(target)) {\n        continue;\n      }\n      seen.add(target);\n      graph.addDirectedEdge(node.id, target);\n    }\n  }\n\n  return graph;\n}\n","import type { DirectedGraph } from 'graphology';\nimport { bidirectional } from 'graphology-shortest-path';\nimport type {\n  NeighborOptions,\n  Metric,\n  CentralityMetrics,\n} from '../types/provider.js';\n\n/**\n * Get neighbor IDs based on direction.\n * Returns empty array if node doesn't exist.\n */\nexport function getNeighborIds(\n  graph: DirectedGraph,\n  id: string,\n  options: NeighborOptions\n): string[] {\n  if (!graph.hasNode(id)) {\n    return [];\n  }\n\n  let neighbors: string[];\n\n  switch (options.direction) {\n    case 'in':\n      neighbors = graph.inNeighbors(id);\n      break;\n    case 'out':\n      neighbors = graph.outNeighbors(id);\n      break;\n    case 'both':\n      neighbors = graph.neighbors(id);\n      break;\n  }\n\n  if (options.limit !== undefined) {\n    if (options.limit <= 0) {\n      return [];\n    }\n    if (options.limit < neighbors.length) {\n      return neighbors.slice(0, options.limit);\n    }\n  }\n\n  return neighbors;\n}\n\n/**\n * Find shortest path between two nodes.\n * Returns array of node IDs or null if no path exists.\n */\nexport function findPath(\n  graph: DirectedGraph,\n  source: string,\n  target: string\n): string[] | null {\n  if (!graph.hasNode(source) || !graph.hasNode(target)) {\n    return null;\n  }\n\n  if (source === target) {\n    return [source];\n  }\n\n  const path = bidirectional(graph, source, target);\n  return path;\n}\n\n/**\n * Get top nodes by centrality metric.\n * Returns array of [id, score] tuples sorted descending.\n */\nexport function getHubs(\n  graph: DirectedGraph,\n  metric: Metric,\n  limit: number\n): Array<[string, number]> {\n  if (limit <= 0) {\n    return [];\n  }\n\n  const scores: Array<[string, number]> = [];\n\n  graph.forEachNode((id) => {\n    let score: number;\n    switch (metric) {\n      case 'in_degree':\n        score = graph.inDegree(id);\n        break;\n      case 'out_degree':\n        score = graph.outDegree(id);\n        break;\n      case 'pagerank':\n        // PageRank is post-MVP, use in_degree as fallback\n        score = graph.inDegree(id);\n        break;\n    }\n    scores.push([id, score]);\n  });\n\n  scores.sort((a, b) => b[1] - a[1]);\n  return scores.slice(0, limit);\n}\n\n/**\n * Compute centrality metrics for all nodes.\n * For MVP, computes in_degree and out_degree only.\n */\nexport function computeCentrality(\n  graph: DirectedGraph\n): Map<string, CentralityMetrics> {\n  const result = new Map<string, CentralityMetrics>();\n\n  graph.forEachNode((id) => {\n    result.set(id, {\n      inDegree: graph.inDegree(id),\n      outDegree: graph.outDegree(id),\n    });\n  });\n\n  return result;\n}\n","import { pipeline, type FeatureExtractionPipeline } from '@xenova/transformers';\nimport type { EmbeddingProvider } from '../../types/provider.js';\n\nconst DEFAULT_MODEL = 'Xenova/all-MiniLM-L6-v2';\nconst DEFAULT_DIMENSIONS = 384;\n\nexport class TransformersEmbeddingProvider implements EmbeddingProvider {\n  private model: string;\n  private dims: number;\n  private pipe: FeatureExtractionPipeline | null = null;\n\n  constructor(model = DEFAULT_MODEL, dimensions = DEFAULT_DIMENSIONS) {\n    this.model = model;\n    this.dims = dimensions;\n  }\n\n  private async getPipeline(): Promise<FeatureExtractionPipeline> {\n    if (!this.pipe) {\n      this.pipe = await pipeline('feature-extraction', this.model);\n    }\n    return this.pipe;\n  }\n\n  async embed(text: string): Promise<number[]> {\n    const pipe = await this.getPipeline();\n    const output = await pipe(text, { pooling: 'mean', normalize: true });\n    return Array.from(output.data as Float32Array);\n  }\n\n  async embedBatch(texts: string[]): Promise<number[][]> {\n    if (texts.length === 0) {\n      return [];\n    }\n    return Promise.all(texts.map((t) => this.embed(t)));\n  }\n\n  dimensions(): number {\n    return this.dims;\n  }\n\n  modelId(): string {\n    return this.model;\n  }\n}\n","import type { Node, NodeWithContext } from '../types/node.js';\nimport type {\n  GraphCore,\n  SearchOptions,\n} from '../types/graphcore.js';\nimport type {\n  StoreProvider,\n  EmbeddingProvider,\n  Metric,\n  TagMode,\n  NeighborOptions,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../types/provider.js';\nimport type { RouxConfig } from '../types/config.js';\nimport { DocStore } from '../providers/docstore/index.js';\nimport { TransformersEmbeddingProvider } from '../providers/embedding/transformers.js';\n\nexport class GraphCoreImpl implements GraphCore {\n  private store: StoreProvider | null = null;\n  private embedding: EmbeddingProvider | null = null;\n\n  registerStore(provider: StoreProvider): void {\n    if (!provider) {\n      throw new Error('Store provider is required');\n    }\n    this.store = provider;\n  }\n\n  registerEmbedding(provider: EmbeddingProvider): void {\n    if (!provider) {\n      throw new Error('Embedding provider is required');\n    }\n    this.embedding = provider;\n  }\n\n  private requireStore(): StoreProvider {\n    if (!this.store) {\n      throw new Error('StoreProvider not registered');\n    }\n    return this.store;\n  }\n\n  private requireEmbedding(): EmbeddingProvider {\n    if (!this.embedding) {\n      throw new Error('EmbeddingProvider not registered');\n    }\n    return this.embedding;\n  }\n\n  async search(query: string, options?: SearchOptions): Promise<Node[]> {\n    const store = this.requireStore();\n    const embedding = this.requireEmbedding();\n\n    const limit = options?.limit ?? 10;\n    const vector = await embedding.embed(query);\n    const results = await store.searchByVector(vector, limit);\n\n    // Results are already sorted by distance ascending\n    const ids = results.map((r) => r.id);\n    return store.getNodes(ids);\n  }\n\n  async getNode(id: string, depth?: number): Promise<NodeWithContext | null> {\n    const store = this.requireStore();\n    const node = await store.getNode(id);\n\n    if (!node) {\n      return null;\n    }\n\n    if (!depth || depth === 0) {\n      return node;\n    }\n\n    // Fetch neighbors for context\n    const [incomingNeighbors, outgoingNeighbors] = await Promise.all([\n      store.getNeighbors(id, { direction: 'in' }),\n      store.getNeighbors(id, { direction: 'out' }),\n    ]);\n\n    // Deduplicate neighbors (same node could be both incoming and outgoing)\n    const neighborMap = new Map<string, Node>();\n    for (const n of [...incomingNeighbors, ...outgoingNeighbors]) {\n      neighborMap.set(n.id, n);\n    }\n\n    const result: NodeWithContext = {\n      ...node,\n      neighbors: Array.from(neighborMap.values()),\n      incomingCount: incomingNeighbors.length,\n      outgoingCount: outgoingNeighbors.length,\n    };\n\n    return result;\n  }\n\n  async createNode(partial: Partial<Node>): Promise<Node> {\n    const store = this.requireStore();\n\n    if (!partial.id || partial.id.trim() === '') {\n      throw new Error('Node id is required and cannot be empty');\n    }\n    if (!partial.title) {\n      throw new Error('Node title is required');\n    }\n\n    const node: Node = {\n      id: partial.id,\n      title: partial.title,\n      content: partial.content ?? '',\n      tags: partial.tags ?? [],\n      outgoingLinks: partial.outgoingLinks ?? [],\n      properties: partial.properties ?? {},\n      ...(partial.sourceRef && { sourceRef: partial.sourceRef }),\n    };\n\n    await store.createNode(node);\n    return (await store.getNode(node.id)) ?? node;\n  }\n\n  async updateNode(id: string, updates: Partial<Node>): Promise<Node> {\n    const store = this.requireStore();\n    await store.updateNode(id, updates);\n    const updated = await store.getNode(id);\n    if (!updated) {\n      throw new Error(`Node not found after update: ${id}`);\n    }\n    return updated;\n  }\n\n  async deleteNode(id: string): Promise<boolean> {\n    const store = this.requireStore();\n    try {\n      await store.deleteNode(id);\n      return true;\n    } catch (err) {\n      // Only swallow \"not found\" errors - propagate everything else\n      if (err instanceof Error && /not found/i.test(err.message)) {\n        return false;\n      }\n      throw err;\n    }\n  }\n\n  async getNeighbors(id: string, options: NeighborOptions): Promise<Node[]> {\n    const store = this.requireStore();\n    return store.getNeighbors(id, options);\n  }\n\n  async findPath(source: string, target: string): Promise<string[] | null> {\n    const store = this.requireStore();\n    return store.findPath(source, target);\n  }\n\n  async getHubs(\n    metric: Metric,\n    limit: number\n  ): Promise<Array<[string, number]>> {\n    const store = this.requireStore();\n    return store.getHubs(metric, limit);\n  }\n\n  async searchByTags(\n    tags: string[],\n    mode: TagMode,\n    limit?: number\n  ): Promise<Node[]> {\n    const store = this.requireStore();\n    const results = await store.searchByTags(tags, mode);\n    if (limit !== undefined) {\n      return results.slice(0, limit);\n    }\n    return results;\n  }\n\n  async getRandomNode(tags?: string[]): Promise<Node | null> {\n    const store = this.requireStore();\n    return store.getRandomNode(tags);\n  }\n\n  async listNodes(\n    filter: ListFilter,\n    options?: ListOptions\n  ): Promise<ListNodesResult> {\n    return this.requireStore().listNodes(filter, options);\n  }\n\n  async resolveNodes(\n    names: string[],\n    options?: ResolveOptions\n  ): Promise<ResolveResult[]> {\n    const store = this.requireStore();\n    const strategy = options?.strategy ?? 'fuzzy';\n\n    // Semantic strategy requires embedding provider\n    if (strategy === 'semantic') {\n      if (!this.embedding) {\n        throw new Error('Semantic resolution requires EmbeddingProvider');\n      }\n\n      // Build filter without undefined values\n      const filter: ListFilter = {};\n      if (options?.tag) filter.tag = options.tag;\n      if (options?.path) filter.path = options.path;\n\n      // Get candidates from store with filters\n      const { nodes: candidates } = await store.listNodes(filter, { limit: 1000 });\n\n      if (candidates.length === 0 || names.length === 0) {\n        return names.map((query) => ({ query, match: null, score: 0 }));\n      }\n\n      const threshold = options?.threshold ?? 0.7;\n\n      // Embed all queries in batch\n      const queryVectors = await this.embedding.embedBatch(names);\n\n      // Embed all candidate titles in batch\n      const candidateTitles = candidates.map((c) => c.title);\n      const candidateVectors = await this.embedding.embedBatch(candidateTitles);\n\n      // Validate dimensions match\n      if (queryVectors.length > 0 && candidateVectors.length > 0) {\n        const queryDim = queryVectors[0]!.length;\n        const candidateDim = candidateVectors[0]!.length;\n        if (queryDim !== candidateDim) {\n          throw new Error(\n            `Embedding dimension mismatch: query=${queryDim}, candidate=${candidateDim}`\n          );\n        }\n      }\n\n      // For each query, find best matching candidate by cosine similarity\n      return names.map((query, qIdx): ResolveResult => {\n        const queryVector = queryVectors[qIdx]!;\n        let bestScore = 0;\n        let bestMatch: string | null = null;\n\n        for (let cIdx = 0; cIdx < candidates.length; cIdx++) {\n          const similarity = this.cosineSimilarity(queryVector, candidateVectors[cIdx]!);\n          if (similarity > bestScore) {\n            bestScore = similarity;\n            bestMatch = candidates[cIdx]!.id;\n          }\n        }\n\n        if (bestScore >= threshold) {\n          return { query, match: bestMatch, score: bestScore };\n        }\n        return { query, match: null, score: 0 };\n      });\n    }\n\n    // Exact and fuzzy delegate to store\n    return store.resolveNodes(names, options);\n  }\n\n  private cosineSimilarity(a: number[], b: number[]): number {\n    let dotProduct = 0;\n    let normA = 0;\n    let normB = 0;\n    for (let i = 0; i < a.length; i++) {\n      dotProduct += a[i]! * b[i]!;\n      normA += a[i]! * a[i]!;\n      normB += b[i]! * b[i]!;\n    }\n    if (normA === 0 || normB === 0) return 0;\n    return dotProduct / (Math.sqrt(normA) * Math.sqrt(normB));\n  }\n\n  static fromConfig(config: RouxConfig): GraphCoreImpl {\n    if (!config.providers?.store) {\n      throw new Error('StoreProvider configuration is required');\n    }\n\n    const core = new GraphCoreImpl();\n\n    // Create store based on config\n    if (config.providers.store.type === 'docstore') {\n      const sourcePath = config.source?.path ?? '.';\n      const cachePath = config.cache?.path ?? '.roux';\n      const store = new DocStore(sourcePath, cachePath);\n      core.registerStore(store);\n    } else {\n      throw new Error(\n        `Unsupported store provider type: ${config.providers.store.type}. Supported: docstore`\n      );\n    }\n\n    // Create embedding provider (defaults to local transformers)\n    const embeddingConfig = config.providers.embedding;\n    if (!embeddingConfig || embeddingConfig.type === 'local') {\n      const model = embeddingConfig?.model;\n      const embedding = new TransformersEmbeddingProvider(model);\n      core.registerEmbedding(embedding);\n    } else {\n      throw new Error(\n        `Unsupported embedding provider type: ${embeddingConfig.type}. Supported: local`\n      );\n    }\n\n    return core;\n  }\n}\n","import { Server } from '@modelcontextprotocol/sdk/server/index.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport {\n  CallToolRequestSchema,\n  ListToolsRequestSchema,\n  type Tool,\n} from '@modelcontextprotocol/sdk/types.js';\n\nimport type { GraphCore } from '../types/graphcore.js';\nimport type { StoreProvider } from '../types/provider.js';\nimport { McpError } from './types.js';\nimport { dispatchTool, type HandlerContext } from './handlers.js';\n\nexport interface McpServerOptions {\n  /** GraphCore instance for operations */\n  core: GraphCore;\n  /** StoreProvider for link resolution and direct store access */\n  store: StoreProvider;\n  /** Whether embedding provider is available (enables search tool) */\n  hasEmbedding: boolean;\n}\n\n/** MCP Transport interface for server connection. */\nexport interface McpTransport {\n  start?(): Promise<void>;\n  close?(): Promise<void>;\n}\n\n/** Factory function to create a transport. Defaults to StdioServerTransport. */\nexport type TransportFactory = () => McpTransport;\n\n/** Tool input schemas as JSON Schema objects */\nconst TOOL_SCHEMAS = {\n  search: {\n    type: 'object',\n    properties: {\n      query: {\n        type: 'string',\n        description: 'Natural language search query',\n      },\n      limit: {\n        type: 'integer',\n        minimum: 1,\n        maximum: 50,\n        default: 10,\n        description: 'Maximum results to return',\n      },\n      include_content: {\n        type: 'boolean',\n        default: false,\n        description:\n          'Include node content in results. Default false returns metadata only (id, title, tags, properties, links). Set true to include truncated content.',\n      },\n    },\n    required: ['query'],\n  },\n\n  get_node: {\n    type: 'object',\n    properties: {\n      id: {\n        type: 'string',\n        description:\n          'Node ID (file path for DocStore). ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n      depth: {\n        type: 'integer',\n        minimum: 0,\n        maximum: 1,\n        default: 0,\n        description: '0 = node only, 1 = include neighbors',\n      },\n    },\n    required: ['id'],\n  },\n\n  get_neighbors: {\n    type: 'object',\n    properties: {\n      id: {\n        type: 'string',\n        description:\n          'Source node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n      direction: {\n        type: 'string',\n        enum: ['in', 'out', 'both'],\n        default: 'both',\n        description: 'in = nodes linking here, out = nodes linked to, both = all',\n      },\n      limit: {\n        type: 'integer',\n        minimum: 1,\n        maximum: 50,\n        default: 20,\n        description: 'Maximum neighbors to return',\n      },\n      include_content: {\n        type: 'boolean',\n        default: false,\n        description:\n          'Include node content in results. Default false returns metadata only (id, title, tags, properties, links). Set true to include truncated content.',\n      },\n    },\n    required: ['id'],\n  },\n\n  find_path: {\n    type: 'object',\n    properties: {\n      source: {\n        type: 'string',\n        description:\n          'Start node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n      target: {\n        type: 'string',\n        description:\n          'End node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n    },\n    required: ['source', 'target'],\n  },\n\n  get_hubs: {\n    type: 'object',\n    properties: {\n      metric: {\n        type: 'string',\n        enum: ['in_degree', 'out_degree'],\n        default: 'in_degree',\n        description: 'Centrality metric',\n      },\n      limit: {\n        type: 'integer',\n        minimum: 1,\n        maximum: 50,\n        default: 10,\n        description: 'Maximum results',\n      },\n    },\n  },\n\n  search_by_tags: {\n    type: 'object',\n    properties: {\n      tags: {\n        type: 'array',\n        items: { type: 'string' },\n        minItems: 1,\n        description: 'Tags to match',\n      },\n      mode: {\n        type: 'string',\n        enum: ['any', 'all'],\n        default: 'any',\n        description: 'any = OR matching, all = AND matching',\n      },\n      limit: {\n        type: 'integer',\n        minimum: 1,\n        maximum: 100,\n        default: 20,\n        description: 'Maximum results',\n      },\n    },\n    required: ['tags'],\n  },\n\n  random_node: {\n    type: 'object',\n    properties: {\n      tags: {\n        type: 'array',\n        items: { type: 'string' },\n        description: 'Optional: limit to nodes with these tags (any match)',\n      },\n    },\n  },\n\n  create_node: {\n    type: 'object',\n    properties: {\n      title: {\n        type: 'string',\n        description:\n          'Node title (becomes filename for DocStore). Returned ID will be normalized to lowercase.',\n      },\n      content: {\n        type: 'string',\n        description: 'Full text content (markdown)',\n      },\n      tags: {\n        type: 'array',\n        items: { type: 'string' },\n        default: [],\n        description: 'Classification tags',\n      },\n      directory: {\n        type: 'string',\n        description: \"Optional: subdirectory path (e.g., 'notes/drafts')\",\n      },\n    },\n    required: ['title', 'content'],\n  },\n\n  update_node: {\n    type: 'object',\n    properties: {\n      id: {\n        type: 'string',\n        description:\n          'Node ID to update. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n      title: {\n        type: 'string',\n        description: 'New title (renames file for DocStore)',\n      },\n      content: {\n        type: 'string',\n        description: 'New content (replaces entirely)',\n      },\n      tags: {\n        type: 'array',\n        items: { type: 'string' },\n        description: 'New tags (replaces existing)',\n      },\n    },\n    required: ['id'],\n  },\n\n  delete_node: {\n    type: 'object',\n    properties: {\n      id: {\n        type: 'string',\n        description:\n          'Node ID to delete. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n    },\n    required: ['id'],\n  },\n\n  list_nodes: {\n    type: 'object',\n    properties: {\n      tag: {\n        type: 'string',\n        description:\n          'Filter by tag from the \"tags\" frontmatter array (case-insensitive). Does NOT search other frontmatter fields like \"type\" or \"category\".',\n      },\n      path: {\n        type: 'string',\n        description: 'Filter by path prefix (startsWith, case-insensitive)',\n      },\n      limit: {\n        type: 'integer',\n        minimum: 1,\n        maximum: 1000,\n        default: 100,\n        description: 'Maximum results to return',\n      },\n      offset: {\n        type: 'integer',\n        minimum: 0,\n        default: 0,\n        description: 'Skip this many results (for pagination)',\n      },\n    },\n  },\n\n  resolve_nodes: {\n    type: 'object',\n    properties: {\n      names: {\n        type: 'array',\n        items: { type: 'string' },\n        description: 'Names to resolve to existing nodes',\n      },\n      strategy: {\n        type: 'string',\n        enum: ['exact', 'fuzzy', 'semantic'],\n        default: 'fuzzy',\n        description:\n          'How to match names to nodes. \"exact\": case-insensitive title equality. \"fuzzy\": string similarity (Dice coefficient) — use for typos, misspellings, partial matches. \"semantic\": embedding cosine similarity — use for synonyms or related concepts (NOT typos). Misspellings embed poorly because they produce unrelated vectors.',\n      },\n      threshold: {\n        type: 'number',\n        minimum: 0,\n        maximum: 1,\n        default: 0.7,\n        description:\n          'Minimum similarity score (0-1). Lower values match more loosely. For typo tolerance, use fuzzy with threshold 0.5-0.6. Ignored for exact strategy.',\n      },\n      tag: {\n        type: 'string',\n        description:\n          'Filter candidates by tag from \"tags\" frontmatter array (case-insensitive)',\n      },\n      path: {\n        type: 'string',\n        description: 'Filter candidates by path prefix (case-insensitive)',\n      },\n    },\n    required: ['names'],\n  },\n\n  nodes_exist: {\n    type: 'object',\n    properties: {\n      ids: {\n        type: 'array',\n        items: { type: 'string' },\n        description:\n          'Node IDs to check existence. IDs are normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n      },\n    },\n    required: ['ids'],\n  },\n} as const;\n\n/** Tool definitions for MCP protocol */\nexport function getToolDefinitions(hasEmbedding: boolean): Tool[] {\n  const tools: Tool[] = [\n    {\n      name: 'get_node',\n      description:\n        'Retrieve a single node by ID with optional neighbor context',\n      inputSchema: TOOL_SCHEMAS.get_node,\n    },\n    {\n      name: 'get_neighbors',\n      description: 'Get nodes linked to or from a specific node',\n      inputSchema: TOOL_SCHEMAS.get_neighbors,\n    },\n    {\n      name: 'find_path',\n      description: 'Find the shortest path between two nodes',\n      inputSchema: TOOL_SCHEMAS.find_path,\n    },\n    {\n      name: 'get_hubs',\n      description: 'Get the most central nodes by graph metric',\n      inputSchema: TOOL_SCHEMAS.get_hubs,\n    },\n    {\n      name: 'search_by_tags',\n      description: 'Filter nodes by tags (AND or OR matching)',\n      inputSchema: TOOL_SCHEMAS.search_by_tags,\n    },\n    {\n      name: 'random_node',\n      description: 'Get a random node for discovery, optionally filtered by tags',\n      inputSchema: TOOL_SCHEMAS.random_node,\n    },\n    {\n      name: 'create_node',\n      description: 'Create a new node (writes file for DocStore)',\n      inputSchema: TOOL_SCHEMAS.create_node,\n    },\n    {\n      name: 'update_node',\n      description:\n        'Update an existing node. Title changes rejected if incoming links exist.',\n      inputSchema: TOOL_SCHEMAS.update_node,\n    },\n    {\n      name: 'delete_node',\n      description: 'Delete a node by ID',\n      inputSchema: TOOL_SCHEMAS.delete_node,\n    },\n    {\n      name: 'list_nodes',\n      description:\n        'List nodes with optional filters and pagination. Tag filter searches the \"tags\" frontmatter array only. All IDs returned are lowercase.',\n      inputSchema: TOOL_SCHEMAS.list_nodes,\n    },\n    {\n      name: 'resolve_nodes',\n      description:\n        'Batch resolve names to existing node IDs. Strategy selection: \"exact\" for known titles, \"fuzzy\" for typos/misspellings (e.g., \"chikken\" -> \"chicken\"), \"semantic\" for synonyms/concepts (e.g., \"poultry leg meat\" -> \"chicken thigh\"). Semantic does NOT handle typos — misspellings produce garbage embeddings.',\n      inputSchema: TOOL_SCHEMAS.resolve_nodes,\n    },\n    {\n      name: 'nodes_exist',\n      description:\n        'Batch check if node IDs exist. IDs are normalized to lowercase before checking.',\n      inputSchema: TOOL_SCHEMAS.nodes_exist,\n    },\n  ];\n\n  if (hasEmbedding) {\n    tools.unshift({\n      name: 'search',\n      description: 'Semantic similarity search across all nodes',\n      inputSchema: TOOL_SCHEMAS.search,\n    });\n  }\n\n  return tools;\n}\n\nexport class McpServer {\n  private server: Server;\n  private ctx: HandlerContext;\n\n  constructor(options: McpServerOptions) {\n    this.ctx = {\n      core: options.core,\n      store: options.store,\n      hasEmbedding: options.hasEmbedding,\n    };\n\n    this.server = new Server(\n      { name: 'roux', version: '0.1.0' },\n      { capabilities: { tools: {} } }\n    );\n\n    this.setupHandlers();\n  }\n\n  /* v8 ignore start - MCP SDK callbacks tested via integration in Phase 11 */\n  private setupHandlers(): void {\n    this.server.setRequestHandler(ListToolsRequestSchema, async () => ({\n      tools: getToolDefinitions(this.ctx.hasEmbedding),\n    }));\n\n    this.server.setRequestHandler(CallToolRequestSchema, async (request) => {\n      const { name, arguments: args } = request.params;\n\n      try {\n        const result = await dispatchTool(this.ctx, name, args ?? {});\n        return {\n          content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],\n        };\n      } catch (error) {\n        if (error instanceof McpError) {\n          return {\n            content: [\n              { type: 'text', text: JSON.stringify(error.toResponse()) },\n            ],\n            isError: true,\n          };\n        }\n        const mcpError = new McpError(\n          'PROVIDER_ERROR',\n          error instanceof Error ? error.message : 'Unknown error'\n        );\n        return {\n          content: [\n            { type: 'text', text: JSON.stringify(mcpError.toResponse()) },\n          ],\n          isError: true,\n        };\n      }\n    });\n  }\n  /* v8 ignore stop */\n\n  /**\n   * Start the server with optional transport factory.\n   * @param transportFactory Factory to create transport. Defaults to StdioServerTransport.\n   */\n  async start(transportFactory?: TransportFactory): Promise<void> {\n    /* v8 ignore start - Default stdio transport tested via integration */\n    const transport = transportFactory\n      ? transportFactory()\n      : new StdioServerTransport();\n    /* v8 ignore stop */\n    await this.server.connect(transport as Parameters<typeof this.server.connect>[0]);\n  }\n\n  async close(): Promise<void> {\n    await this.server.close();\n  }\n}\n\n/**\n * Create and start an MCP server.\n * @param options Server configuration\n * @param transportFactory Optional transport factory for testing\n */\nexport async function createMcpServer(\n  options: McpServerOptions,\n  transportFactory?: TransportFactory\n): Promise<McpServer> {\n  const server = new McpServer(options);\n  await server.start(transportFactory);\n  return server;\n}\n","import type { LinkInfo } from '../types/provider.js';\n\n/** Link with resolved human-readable title. Re-export for MCP layer. */\nexport type { LinkInfo };\n\n/** Metadata-only response for browsing operations (search, get_neighbors). */\nexport interface NodeMetadataResponse {\n  id: string;\n  title: string;\n  tags: string[];\n  links: LinkInfo[];\n  properties: Record<string, unknown>;\n}\n\n/** Full response including content (for get_node, create, update, etc.). */\nexport interface NodeResponse extends NodeMetadataResponse {\n  content: string;\n}\n\n/** Extended response for get_node with depth > 0. */\nexport interface NodeWithContextResponse extends NodeResponse {\n  incomingNeighbors: NodeResponse[];\n  outgoingNeighbors: NodeResponse[];\n  incomingCount: number;\n  outgoingCount: number;\n}\n\n/** Search results include similarity score. Content optional based on include_content param. */\nexport interface SearchResultResponse extends NodeMetadataResponse {\n  score: number;\n  content?: string;\n}\n\n/** Hub results pair ID with metric value. */\nexport interface HubResponse {\n  id: string;\n  title: string;\n  score: number;\n}\n\n/** Path results are ordered node IDs. */\nexport interface PathResponse {\n  path: string[];\n  length: number;\n}\n\n/** Delete operation result. */\nexport interface DeleteResponse {\n  deleted: boolean;\n}\n\n/** Standard error response shape. */\nexport interface ErrorResponse {\n  error: {\n    code: ErrorCode;\n    message: string;\n  };\n}\n\n/** Known error codes. */\nexport type ErrorCode =\n  | 'INVALID_PARAMS'\n  | 'NODE_EXISTS'\n  | 'NODE_NOT_FOUND'\n  | 'LINK_INTEGRITY'\n  | 'PROVIDER_ERROR';\n\n/** Custom error class for MCP operations. */\nexport class McpError extends Error {\n  constructor(\n    public readonly code: ErrorCode,\n    message: string\n  ) {\n    super(message);\n    this.name = 'McpError';\n  }\n\n  toResponse(): ErrorResponse {\n    return {\n      error: {\n        code: this.code,\n        message: this.message,\n      },\n    };\n  }\n}\n","/** Content truncation limits by context. */\nexport const TRUNCATION_LIMITS = {\n  /** Primary node (get_node, single result) */\n  primary: 10_000,\n  /** List results (search, neighbors) */\n  list: 500,\n  /** Neighbor nodes in context */\n  neighbor: 200,\n} as const;\n\nexport type TruncationContext = keyof typeof TRUNCATION_LIMITS;\n\nconst TRUNCATION_SUFFIX = '... [truncated]';\n\n/**\n * Truncate content to limit, appending suffix if truncated.\n * Returns original content if within limit.\n */\nexport function truncateContent(\n  content: string,\n  context: TruncationContext\n): string {\n  const limit = TRUNCATION_LIMITS[context];\n\n  if (content.length <= limit) {\n    return content;\n  }\n\n  // Account for suffix length when truncating, guard against negative\n  const truncatedLength = Math.max(0, limit - TRUNCATION_SUFFIX.length);\n  return content.slice(0, truncatedLength) + TRUNCATION_SUFFIX;\n}\n\n/**\n * Check if content was truncated (ends with truncation suffix).\n */\nexport function isTruncated(content: string): boolean {\n  return content.endsWith(TRUNCATION_SUFFIX);\n}\n","import type { Node } from '../types/node.js';\nimport type { LinkInfo, StoreProvider } from '../types/provider.js';\nimport type {\n  NodeResponse,\n  NodeMetadataResponse,\n  NodeWithContextResponse,\n  SearchResultResponse,\n  HubResponse,\n  PathResponse,\n} from './types.js';\nimport { truncateContent, type TruncationContext } from './truncate.js';\n\n/** Maximum neighbors to include in NodeWithContextResponse. */\nexport const MAX_NEIGHBORS = 20;\n\n/** Maximum links to resolve titles for (prevents OOM on nodes with massive link counts). */\nexport const MAX_LINKS_TO_RESOLVE = 100;\n\n/**\n * Transform a Node to NodeResponse, resolving link titles.\n */\nexport async function nodeToResponse(\n  node: Node,\n  store: StoreProvider,\n  truncation: TruncationContext\n): Promise<NodeResponse> {\n  // Limit links to prevent OOM on nodes with massive outgoing link counts\n  const linksToResolve = node.outgoingLinks.slice(0, MAX_LINKS_TO_RESOLVE);\n  const titles = await store.resolveTitles(linksToResolve);\n\n  const links: LinkInfo[] = linksToResolve.map((id) => ({\n    id,\n    title: titles.get(id) ?? id,\n  }));\n\n  return {\n    id: node.id,\n    title: node.title,\n    content: truncateContent(node.content, truncation),\n    tags: node.tags,\n    links,\n    properties: node.properties,\n  };\n}\n\n/**\n * Transform multiple nodes to responses, resolving all link titles in batch.\n * When includeContent is false, returns NodeMetadataResponse[] (no content field).\n * When includeContent is true, returns NodeResponse[] (with truncated content).\n */\nexport async function nodesToResponses(\n  nodes: Node[],\n  store: StoreProvider,\n  truncation: TruncationContext,\n  includeContent: boolean\n): Promise<NodeResponse[] | NodeMetadataResponse[]> {\n  // Collect unique link IDs, limiting per-node to prevent OOM\n  const allLinkIds = new Set<string>();\n  const nodeLinkLimits = new Map<string, string[]>();\n\n  for (const node of nodes) {\n    const limitedLinks = node.outgoingLinks.slice(0, MAX_LINKS_TO_RESOLVE);\n    nodeLinkLimits.set(node.id, limitedLinks);\n    for (const linkId of limitedLinks) {\n      allLinkIds.add(linkId);\n    }\n  }\n\n  // Batch resolve titles\n  const titles = await store.resolveTitles(Array.from(allLinkIds));\n\n  // Transform nodes using limited links\n  return nodes.map((node) => {\n    // Defensive fallback - all node IDs are populated in the loop above\n    const limitedLinks = nodeLinkLimits.get(node.id) /* v8 ignore next */ ?? [];\n    const base: NodeMetadataResponse = {\n      id: node.id,\n      title: node.title,\n      tags: node.tags,\n      links: limitedLinks.map((id) => ({\n        id,\n        title: titles.get(id) ?? id,\n      })),\n      properties: node.properties,\n    };\n\n    if (includeContent) {\n      return {\n        ...base,\n        content: truncateContent(node.content, truncation),\n      } as NodeResponse;\n    }\n\n    return base;\n  });\n}\n\n/**\n * Transform a Node with neighbor context to NodeWithContextResponse.\n */\nexport async function nodeToContextResponse(\n  node: Node,\n  incomingNeighbors: Node[],\n  outgoingNeighbors: Node[],\n  store: StoreProvider\n): Promise<NodeWithContextResponse> {\n  // Get primary node response\n  const primary = await nodeToResponse(node, store, 'primary');\n\n  // Limit neighbors\n  const limitedIncoming = incomingNeighbors.slice(0, MAX_NEIGHBORS);\n  const limitedOutgoing = outgoingNeighbors.slice(0, MAX_NEIGHBORS);\n\n  // Transform neighbors with neighbor truncation\n  // Context responses always include content (truncated for neighbors)\n  const [incomingResponses, outgoingResponses] = await Promise.all([\n    nodesToResponses(limitedIncoming, store, 'neighbor', true) as Promise<NodeResponse[]>,\n    nodesToResponses(limitedOutgoing, store, 'neighbor', true) as Promise<NodeResponse[]>,\n  ]);\n\n  return {\n    ...primary,\n    incomingNeighbors: incomingResponses,\n    outgoingNeighbors: outgoingResponses,\n    incomingCount: incomingNeighbors.length,\n    outgoingCount: outgoingNeighbors.length,\n  };\n}\n\n/**\n * Transform search results with scores.\n * When includeContent is false, content field is omitted.\n * When includeContent is true, content is truncated and included.\n */\nexport async function nodesToSearchResults(\n  nodes: Node[],\n  scores: Map<string, number>,\n  store: StoreProvider,\n  includeContent: boolean\n): Promise<SearchResultResponse[]> {\n  const responses = await nodesToResponses(nodes, store, 'list', includeContent);\n\n  return responses.map((response) => ({\n    ...response,\n    score: scores.get(response.id) ?? 0,\n  }));\n}\n\n/**\n * Transform hub results (id, score pairs) to HubResponse[].\n */\nexport async function hubsToResponses(\n  hubs: Array<[string, number]>,\n  store: StoreProvider\n): Promise<HubResponse[]> {\n  const ids = hubs.map(([id]) => id);\n  const titles = await store.resolveTitles(ids);\n\n  return hubs.map(([id, score]) => ({\n    id,\n    title: titles.get(id) ?? id,\n    score,\n  }));\n}\n\n/**\n * Transform a path (array of node IDs) to PathResponse.\n */\nexport function pathToResponse(path: string[]): PathResponse {\n  return {\n    path,\n    length: path.length - 1,\n  };\n}\n","import type { GraphCore } from '../types/graphcore.js';\nimport type {\n  StoreProvider,\n  Metric,\n  TagMode,\n  ListFilter,\n  ResolveOptions,\n  ResolveStrategy,\n  NodeSummary,\n  ResolveResult,\n} from '../types/provider.js';\nimport type { Node } from '../types/node.js';\nimport {\n  McpError,\n  type NodeResponse,\n  type NodeMetadataResponse,\n  type NodeWithContextResponse,\n  type SearchResultResponse,\n  type HubResponse,\n  type PathResponse,\n  type DeleteResponse,\n} from './types.js';\nimport {\n  nodeToResponse,\n  nodesToResponses,\n  nodeToContextResponse,\n  nodesToSearchResults,\n  hubsToResponses,\n  pathToResponse,\n} from './transforms.js';\n\nexport interface HandlerContext {\n  core: GraphCore;\n  store: StoreProvider;\n  hasEmbedding: boolean;\n}\n\nfunction coerceLimit(value: unknown, defaultValue: number): number {\n  if (value === undefined || value === null) {\n    return defaultValue;\n  }\n  const num = Number(value);\n  if (Number.isNaN(num)) {\n    return defaultValue;\n  }\n  const floored = Math.floor(num);\n  if (floored < 1) {\n    throw new McpError('INVALID_PARAMS', 'limit must be at least 1');\n  }\n  return floored;\n}\n\nfunction coerceOffset(value: unknown, defaultValue: number): number {\n  if (value === undefined || value === null) {\n    return defaultValue;\n  }\n  const num = Number(value);\n  if (Number.isNaN(num)) {\n    return defaultValue;\n  }\n  const floored = Math.floor(num);\n  if (floored < 0) {\n    throw new McpError('INVALID_PARAMS', 'offset must be at least 0');\n  }\n  return floored;\n}\n\nexport interface ListNodesResponse {\n  nodes: NodeSummary[];\n  total: number;\n}\n\nexport interface NodesExistResponse {\n  [id: string]: boolean;\n}\n\nexport type ToolResult =\n  | NodeResponse\n  | NodeMetadataResponse\n  | NodeWithContextResponse\n  | SearchResultResponse[]\n  | NodeResponse[]\n  | NodeMetadataResponse[]\n  | HubResponse[]\n  | PathResponse\n  | DeleteResponse\n  | ListNodesResponse\n  | ResolveResult[]\n  | NodesExistResponse\n  | null;\n\nexport async function handleSearch(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<SearchResultResponse[]> {\n  if (!ctx.hasEmbedding) {\n    throw new McpError('PROVIDER_ERROR', 'Search requires embedding provider');\n  }\n\n  const query = args.query;\n  const limit = coerceLimit(args.limit, 10);\n  const includeContent = args.include_content === true;\n\n  if (typeof query !== 'string' || query.trim() === '') {\n    throw new McpError('INVALID_PARAMS', 'query is required and must be a non-empty string');\n  }\n\n  const nodes = await ctx.core.search(query, { limit });\n\n  // Approximate scores for display. Results are sorted by actual similarity (distance-based).\n  // Score is a UI hint (higher = better match), not the raw similarity metric.\n  const scores = new Map<string, number>();\n  nodes.forEach((node, index) => {\n    scores.set(node.id, Math.max(0, 1 - index * 0.05));\n  });\n\n  return nodesToSearchResults(nodes, scores, ctx.store, includeContent);\n}\n\nfunction coerceDepth(value: unknown): number {\n  if (value === undefined || value === null) {\n    return 0;\n  }\n  const num = Number(value);\n  if (Number.isNaN(num)) {\n    return 0;\n  }\n  return num >= 1 ? 1 : 0;\n}\n\nexport async function handleGetNode(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse | NodeWithContextResponse | null> {\n  const id = args.id as string;\n  const depth = coerceDepth(args.depth);\n\n  if (!id || typeof id !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'id is required and must be a string');\n  }\n\n  const node = await ctx.core.getNode(id, depth);\n  if (!node) {\n    return null;\n  }\n\n  if (depth === 0) {\n    return nodeToResponse(node, ctx.store, 'primary');\n  }\n\n  const [incomingNeighbors, outgoingNeighbors] = await Promise.all([\n    ctx.core.getNeighbors(id, { direction: 'in' }),\n    ctx.core.getNeighbors(id, { direction: 'out' }),\n  ]);\n\n  return nodeToContextResponse(node, incomingNeighbors, outgoingNeighbors, ctx.store);\n}\n\nconst VALID_DIRECTIONS = ['in', 'out', 'both'] as const;\n\nexport async function handleGetNeighbors(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse[] | NodeMetadataResponse[]> {\n  const id = args.id as string;\n  const directionRaw = args.direction ?? 'both';\n  const limit = coerceLimit(args.limit, 20);\n  const includeContent = args.include_content === true;\n\n  if (!id || typeof id !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'id is required and must be a string');\n  }\n\n  if (!VALID_DIRECTIONS.includes(directionRaw as (typeof VALID_DIRECTIONS)[number])) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      `direction must be one of: ${VALID_DIRECTIONS.join(', ')}`\n    );\n  }\n  const direction = directionRaw as 'in' | 'out' | 'both';\n\n  const neighbors = await ctx.core.getNeighbors(id, { direction, limit });\n  return nodesToResponses(neighbors, ctx.store, 'list', includeContent);\n}\n\nexport async function handleFindPath(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<PathResponse | null> {\n  const source = args.source as string;\n  const target = args.target as string;\n\n  if (!source || typeof source !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'source is required and must be a string');\n  }\n  if (!target || typeof target !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'target is required and must be a string');\n  }\n\n  const path = await ctx.core.findPath(source, target);\n  if (!path) {\n    return null;\n  }\n\n  return pathToResponse(path);\n}\n\nconst VALID_METRICS = ['pagerank', 'in_degree', 'out_degree'] as const;\n\nexport async function handleGetHubs(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<HubResponse[]> {\n  const metricRaw = args.metric ?? 'in_degree';\n  const limit = coerceLimit(args.limit, 10);\n\n  if (!VALID_METRICS.includes(metricRaw as Metric)) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      `metric must be one of: ${VALID_METRICS.join(', ')}`\n    );\n  }\n  const metric = metricRaw as Metric;\n\n  const hubs = await ctx.core.getHubs(metric, limit);\n  return hubsToResponses(hubs, ctx.store);\n}\n\nconst VALID_TAG_MODES = ['any', 'all'] as const;\n\nexport async function handleSearchByTags(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse[]> {\n  const tags = args.tags;\n  const modeRaw = args.mode ?? 'any';\n  const limit = coerceLimit(args.limit, 20);\n\n  if (!Array.isArray(tags) || tags.length === 0) {\n    throw new McpError('INVALID_PARAMS', 'tags is required and must be a non-empty array');\n  }\n\n  // Validate all elements are strings\n  if (!tags.every((t) => typeof t === 'string')) {\n    throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n  }\n\n  if (!VALID_TAG_MODES.includes(modeRaw as TagMode)) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      `mode must be one of: ${VALID_TAG_MODES.join(', ')}`\n    );\n  }\n  const mode = modeRaw as TagMode;\n\n  const nodes = await ctx.core.searchByTags(tags, mode, limit);\n  // searchByTags always includes content (not a browsing operation like search/get_neighbors)\n  return nodesToResponses(nodes, ctx.store, 'list', true) as Promise<NodeResponse[]>;\n}\n\nexport async function handleRandomNode(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse | null> {\n  const tags = args.tags;\n\n  if (tags !== undefined) {\n    if (!Array.isArray(tags) || !tags.every((t) => typeof t === 'string')) {\n      throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n    }\n  }\n\n  const node = await ctx.core.getRandomNode(tags as string[] | undefined);\n  if (!node) {\n    return null;\n  }\n\n  return nodeToResponse(node, ctx.store, 'primary');\n}\n\nexport async function handleCreateNode(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse> {\n  const title = args.title as string;\n  const content = args.content as string;\n  const tagsRaw = args.tags;\n  const directory = args.directory as string | undefined;\n\n  if (!title || typeof title !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'title is required and must be a string');\n  }\n  if (!content || typeof content !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'content is required and must be a string');\n  }\n\n  let tags: string[] = [];\n  if (tagsRaw !== undefined) {\n    if (!Array.isArray(tagsRaw) || !tagsRaw.every((t) => typeof t === 'string')) {\n      throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n    }\n    tags = tagsRaw;\n  }\n\n  const filename = sanitizeFilename(title) + '.md';\n  const id = directory ? `${directory}/${filename}` : filename;\n\n  const existing = await ctx.core.getNode(id);\n  if (existing) {\n    throw new McpError('NODE_EXISTS', `Node already exists: ${id}`);\n  }\n\n  const node = await ctx.core.createNode({\n    id,\n    title,\n    content,\n    tags,\n  });\n\n  return nodeToResponse(node, ctx.store, 'primary');\n}\n\nexport async function handleUpdateNode(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse> {\n  const id = args.id as string;\n  const title = args.title as string | undefined;\n  const content = args.content as string | undefined;\n  const tagsRaw = args.tags;\n\n  if (!id || typeof id !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'id is required and must be a string');\n  }\n\n  if (title === undefined && content === undefined && tagsRaw === undefined) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      'At least one of title, content, or tags must be provided'\n    );\n  }\n\n  let tags: string[] | undefined;\n  if (tagsRaw !== undefined) {\n    if (!Array.isArray(tagsRaw) || !tagsRaw.every((t) => typeof t === 'string')) {\n      throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n    }\n    tags = tagsRaw;\n  }\n\n  const existing = await ctx.core.getNode(id);\n  if (!existing) {\n    throw new McpError('NODE_NOT_FOUND', `Node not found: ${id}`);\n  }\n\n  if (title !== undefined && title !== existing.title) {\n    const incomingNeighbors = await ctx.core.getNeighbors(id, { direction: 'in' });\n    if (incomingNeighbors.length > 0) {\n      throw new McpError(\n        'LINK_INTEGRITY',\n        `Cannot rename node with ${incomingNeighbors.length} incoming links`\n      );\n    }\n  }\n\n  const updates: Partial<Node> = {};\n  if (title !== undefined) updates.title = title;\n  if (content !== undefined) updates.content = content;\n  if (tags !== undefined) updates.tags = tags;\n\n  const updated = await ctx.core.updateNode(id, updates);\n  return nodeToResponse(updated, ctx.store, 'primary');\n}\n\nexport async function handleDeleteNode(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<DeleteResponse> {\n  const id = args.id as string;\n\n  if (!id || typeof id !== 'string') {\n    throw new McpError('INVALID_PARAMS', 'id is required and must be a string');\n  }\n\n  const deleted = await ctx.core.deleteNode(id);\n  return { deleted };\n}\n\nconst VALID_STRATEGIES = ['exact', 'fuzzy', 'semantic'] as const;\n\nexport async function handleListNodes(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<ListNodesResponse> {\n  const tag = args.tag as string | undefined;\n  const path = args.path as string | undefined;\n  const limit = coerceLimit(args.limit, 100);\n  const offset = coerceOffset(args.offset, 0);\n\n  const filter: ListFilter = {};\n  if (tag) filter.tag = tag;\n  if (path) filter.path = path;\n\n  return ctx.core.listNodes(filter, { limit, offset });\n}\n\nexport async function handleResolveNodes(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<ResolveResult[]> {\n  const names = args.names;\n  const strategy = args.strategy as ResolveStrategy | undefined;\n  const threshold = args.threshold as number | undefined;\n  const tag = args.tag as string | undefined;\n  const path = args.path as string | undefined;\n\n  if (!Array.isArray(names)) {\n    throw new McpError('INVALID_PARAMS', 'names is required and must be an array');\n  }\n\n  if (strategy !== undefined && !VALID_STRATEGIES.includes(strategy as ResolveStrategy)) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      `strategy must be one of: ${VALID_STRATEGIES.join(', ')}`\n    );\n  }\n\n  if (strategy === 'semantic' && !ctx.hasEmbedding) {\n    throw new McpError('PROVIDER_ERROR', 'Semantic resolution requires embedding provider');\n  }\n\n  const options: ResolveOptions = {};\n  if (strategy) options.strategy = strategy;\n  if (threshold !== undefined) options.threshold = threshold;\n  if (tag) options.tag = tag;\n  if (path) options.path = path;\n\n  return ctx.core.resolveNodes(names as string[], options);\n}\n\nexport async function handleNodesExist(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodesExistResponse> {\n  const ids = args.ids;\n\n  if (!Array.isArray(ids)) {\n    throw new McpError('INVALID_PARAMS', 'ids is required and must be an array');\n  }\n\n  const result = await ctx.store.nodesExist(ids as string[]);\n\n  // Convert Map to plain object\n  const response: NodesExistResponse = {};\n  for (const [id, exists] of result) {\n    response[id] = exists;\n  }\n  return response;\n}\n\nexport function sanitizeFilename(title: string): string {\n  const sanitized = title\n    .toLowerCase()\n    .replace(/[^a-z0-9\\s-]/g, '')\n    .replace(/\\s+/g, '-')\n    .replace(/-+/g, '-')\n    .replace(/^-+|-+$/g, '');\n\n  return sanitized || 'untitled';\n}\n\nexport async function dispatchTool(\n  ctx: HandlerContext,\n  name: string,\n  args: Record<string, unknown>\n): Promise<ToolResult> {\n  switch (name) {\n    case 'search':\n      return handleSearch(ctx, args);\n    case 'get_node':\n      return handleGetNode(ctx, args);\n    case 'get_neighbors':\n      return handleGetNeighbors(ctx, args);\n    case 'find_path':\n      return handleFindPath(ctx, args);\n    case 'get_hubs':\n      return handleGetHubs(ctx, args);\n    case 'search_by_tags':\n      return handleSearchByTags(ctx, args);\n    case 'random_node':\n      return handleRandomNode(ctx, args);\n    case 'create_node':\n      return handleCreateNode(ctx, args);\n    case 'update_node':\n      return handleUpdateNode(ctx, args);\n    case 'delete_node':\n      return handleDeleteNode(ctx, args);\n    case 'list_nodes':\n      return handleListNodes(ctx, args);\n    case 'resolve_nodes':\n      return handleResolveNodes(ctx, args);\n    case 'nodes_exist':\n      return handleNodesExist(ctx, args);\n    default:\n      throw new McpError('INVALID_PARAMS', `Unknown tool: ${name}`);\n  }\n}\n","import { access, writeFile, mkdir } from 'node:fs/promises';\nimport { join, dirname } from 'node:path';\nimport { Cache } from '../../providers/docstore/cache.js';\n\nexport interface VizOptions {\n  output?: string | undefined;\n  open?: boolean | undefined;\n}\n\nexport interface VizResult {\n  outputPath: string;\n  nodeCount: number;\n  edgeCount: number;\n  shouldOpen: boolean;\n}\n\ninterface GraphNode {\n  id: string;\n  title: string;\n  inDegree: number;\n}\n\ninterface GraphEdge {\n  source: string;\n  target: string;\n}\n\nexport async function vizCommand(\n  directory: string,\n  options: VizOptions = {}\n): Promise<VizResult> {\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  const cacheDir = join(directory, '.roux');\n  const outputPath = options.output ?? join(cacheDir, 'graph.html');\n\n  const cache = new Cache(cacheDir);\n\n  try {\n    const nodes = cache.getAllNodes();\n    const graphNodes: GraphNode[] = [];\n    const graphEdges: GraphEdge[] = [];\n\n    // Build set of existing node IDs for edge filtering\n    const existingNodeIds = new Set(nodes.map((n) => n.id));\n\n    // Build node list with degree info\n    for (const node of nodes) {\n      const centrality = cache.getCentrality(node.id);\n      graphNodes.push({\n        id: node.id,\n        title: node.title,\n        inDegree: centrality?.inDegree ?? 0,\n      });\n\n      // Build edges from outgoing links, filtering to existing targets only\n      for (const target of node.outgoingLinks) {\n        if (existingNodeIds.has(target)) {\n          graphEdges.push({\n            source: node.id,\n            target,\n          });\n        }\n      }\n    }\n\n    // Generate HTML\n    const html = generateHtml(graphNodes, graphEdges);\n\n    // Ensure output directory exists\n    await mkdir(dirname(outputPath), { recursive: true });\n    await writeFile(outputPath, html, 'utf-8');\n\n    return {\n      outputPath,\n      nodeCount: graphNodes.length,\n      edgeCount: graphEdges.length,\n      shouldOpen: options.open ?? false,\n    };\n  } finally {\n    cache.close();\n  }\n}\n\nfunction generateHtml(nodes: GraphNode[], edges: GraphEdge[]): string {\n  const nodesJson = JSON.stringify(nodes);\n  const edgesJson = JSON.stringify(edges);\n\n  return `<!DOCTYPE html>\n<html lang=\"en\">\n<head>\n  <meta charset=\"UTF-8\">\n  <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">\n  <title>Roux Graph Visualization</title>\n  <script src=\"https://d3js.org/d3.v7.min.js\"></script>\n  <style>\n    * { margin: 0; padding: 0; box-sizing: border-box; }\n    body { font-family: system-ui, sans-serif; background: #1a1a2e; overflow: hidden; }\n    svg { display: block; width: 100vw; height: 100vh; }\n    .node circle { cursor: pointer; }\n    .node text { fill: #e0e0e0; font-size: 10px; pointer-events: none; }\n    .link { stroke: #4a4a6a; stroke-opacity: 0.6; fill: none; }\n    .tooltip {\n      position: absolute;\n      background: #16213e;\n      color: #e0e0e0;\n      padding: 8px 12px;\n      border-radius: 4px;\n      font-size: 12px;\n      pointer-events: none;\n      opacity: 0;\n      transition: opacity 0.2s;\n      border: 1px solid #4a4a6a;\n    }\n  </style>\n</head>\n<body>\n  <div class=\"tooltip\" id=\"tooltip\"></div>\n  <svg></svg>\n  <script>\n    const nodes = ${nodesJson};\n    const links = ${edgesJson};\n\n    const width = window.innerWidth;\n    const height = window.innerHeight;\n\n    const svg = d3.select(\"svg\")\n      .attr(\"viewBox\", [0, 0, width, height]);\n\n    const g = svg.append(\"g\");\n\n    // Zoom behavior\n    svg.call(d3.zoom()\n      .scaleExtent([0.1, 4])\n      .on(\"zoom\", (event) => g.attr(\"transform\", event.transform)));\n\n    // Node size based on in-degree\n    const maxDegree = Math.max(1, ...nodes.map(n => n.inDegree));\n    const nodeRadius = d => 5 + (d.inDegree / maxDegree) * 15;\n\n    // Force simulation\n    const simulation = d3.forceSimulation(nodes)\n      .force(\"link\", d3.forceLink(links).id(d => d.id).distance(100))\n      .force(\"charge\", d3.forceManyBody().strength(-200))\n      .force(\"center\", d3.forceCenter(width / 2, height / 2))\n      .force(\"collision\", d3.forceCollide().radius(d => nodeRadius(d) + 5));\n\n    // Draw links with arrows\n    svg.append(\"defs\").append(\"marker\")\n      .attr(\"id\", \"arrow\")\n      .attr(\"viewBox\", \"0 -5 10 10\")\n      .attr(\"refX\", 20)\n      .attr(\"refY\", 0)\n      .attr(\"markerWidth\", 6)\n      .attr(\"markerHeight\", 6)\n      .attr(\"orient\", \"auto\")\n      .append(\"path\")\n      .attr(\"fill\", \"#4a4a6a\")\n      .attr(\"d\", \"M0,-5L10,0L0,5\");\n\n    const link = g.append(\"g\")\n      .selectAll(\"line\")\n      .data(links)\n      .join(\"line\")\n      .attr(\"class\", \"link\")\n      .attr(\"marker-end\", \"url(#arrow)\");\n\n    // Draw nodes\n    const node = g.append(\"g\")\n      .selectAll(\".node\")\n      .data(nodes)\n      .join(\"g\")\n      .attr(\"class\", \"node\")\n      .call(d3.drag()\n        .on(\"start\", dragstarted)\n        .on(\"drag\", dragged)\n        .on(\"end\", dragended));\n\n    node.append(\"circle\")\n      .attr(\"r\", nodeRadius)\n      .attr(\"fill\", \"#0f4c75\")\n      .attr(\"stroke\", \"#3282b8\")\n      .attr(\"stroke-width\", 2);\n\n    node.append(\"text\")\n      .attr(\"dx\", d => nodeRadius(d) + 5)\n      .attr(\"dy\", 4)\n      .text(d => d.title.length > 20 ? d.title.slice(0, 17) + \"...\" : d.title);\n\n    // Tooltip\n    const tooltip = d3.select(\"#tooltip\");\n    node\n      .on(\"mouseover\", (event, d) => {\n        tooltip\n          .style(\"opacity\", 1)\n          .html(\\`<strong>\\${d.title}</strong><br>ID: \\${d.id}<br>Incoming links: \\${d.inDegree}\\`);\n      })\n      .on(\"mousemove\", (event) => {\n        tooltip\n          .style(\"left\", (event.pageX + 10) + \"px\")\n          .style(\"top\", (event.pageY - 10) + \"px\");\n      })\n      .on(\"mouseout\", () => tooltip.style(\"opacity\", 0));\n\n    // Simulation tick\n    simulation.on(\"tick\", () => {\n      link\n        .attr(\"x1\", d => d.source.x)\n        .attr(\"y1\", d => d.source.y)\n        .attr(\"x2\", d => d.target.x)\n        .attr(\"y2\", d => d.target.y);\n\n      node.attr(\"transform\", d => \\`translate(\\${d.x},\\${d.y})\\`);\n    });\n\n    function dragstarted(event, d) {\n      if (!event.active) simulation.alphaTarget(0.3).restart();\n      d.fx = d.x;\n      d.fy = d.y;\n    }\n\n    function dragged(event, d) {\n      d.fx = event.x;\n      d.fy = event.y;\n    }\n\n    function dragended(event, d) {\n      if 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+{"version":3,"sources":["../../node_modules/string-similarity/src/index.js","../../src/cli/index.ts","../../src/cli/commands/init.ts","../../src/cli/commands/status.ts","../../src/providers/docstore/cache.ts","../../src/providers/docstore/cache/centrality.ts","../../src/providers/store/resolve.ts","../../src/providers/vector/sqlite.ts","../../src/utils/heap.ts","../../src/utils/math.ts","../../src/cli/commands/serve.ts","../../src/providers/docstore/index.ts","../../src/graph/builder.ts","../../src/graph/traversal.ts","../../src/graph/analysis.ts","../../src/graph/manager.ts","../../src/providers/store/index.ts","../../src/providers/docstore/parser.ts","../../src/providers/docstore/normalize.ts","../../src/providers/docstore/watcher.ts","../../src/providers/docstore/constants.ts","../../src/providers/docstore/links.ts","../../src/providers/docstore/file-operations.ts","../../src/providers/docstore/id.ts","../../src/providers/docstore/reader-registry.ts","../../src/providers/docstore/readers/markdown.ts","../../src/providers/embedding/transformers.ts","../../src/types/provider.ts","../../src/core/graphcore.ts","../../src/mcp/server.ts","../../src/types/config.ts","../../src/index.ts","../../src/mcp/types.ts","../../src/mcp/handlers/search.ts","../../src/mcp/validation.ts","../../src/mcp/truncate.ts","../../src/mcp/transforms.ts","../../src/mcp/handlers/get_node.ts","../../src/mcp/handlers/get_neighbors.ts","../../src/mcp/handlers/find_path.ts","../../src/mcp/handlers/get_hubs.ts","../../src/mcp/handlers/search_by_tags.ts","../../src/mcp/handlers/random_node.ts","../../src/mcp/handlers/create_node.ts","../../src/mcp/handlers/update_node.ts","../../src/mcp/handlers/delete_node.ts","../../src/mcp/handlers/list_nodes.ts","../../src/mcp/handlers/resolve_nodes.ts","../../src/mcp/handlers/nodes_exist.ts","../../src/mcp/handlers/index.ts","../../src/cli/commands/viz.ts"],"sourcesContent":["module.exports = {\n\tcompareTwoStrings:compareTwoStrings,\n\tfindBestMatch:findBestMatch\n};\n\nfunction compareTwoStrings(first, second) {\n\tfirst = first.replace(/\\s+/g, '')\n\tsecond = second.replace(/\\s+/g, '')\n\n\tif (first === second) return 1; // identical or empty\n\tif (first.length < 2 || second.length < 2) return 0; // if either is a 0-letter or 1-letter string\n\n\tlet firstBigrams = new Map();\n\tfor (let i = 0; i < first.length - 1; i++) {\n\t\tconst bigram = first.substring(i, i + 2);\n\t\tconst count = firstBigrams.has(bigram)\n\t\t\t? firstBigrams.get(bigram) + 1\n\t\t\t: 1;\n\n\t\tfirstBigrams.set(bigram, count);\n\t};\n\n\tlet intersectionSize = 0;\n\tfor (let i = 0; i < second.length - 1; i++) {\n\t\tconst bigram = second.substring(i, i + 2);\n\t\tconst count = firstBigrams.has(bigram)\n\t\t\t? firstBigrams.get(bigram)\n\t\t\t: 0;\n\n\t\tif (count > 0) {\n\t\t\tfirstBigrams.set(bigram, count - 1);\n\t\t\tintersectionSize++;\n\t\t}\n\t}\n\n\treturn (2.0 * intersectionSize) / (first.length + second.length - 2);\n}\n\nfunction findBestMatch(mainString, targetStrings) {\n\tif (!areArgsValid(mainString, targetStrings)) throw new Error('Bad arguments: First argument should be a string, second should be an array of strings');\n\t\n\tconst ratings = [];\n\tlet bestMatchIndex = 0;\n\n\tfor (let i = 0; i < targetStrings.length; i++) {\n\t\tconst currentTargetString = targetStrings[i];\n\t\tconst currentRating = compareTwoStrings(mainString, currentTargetString)\n\t\tratings.push({target: currentTargetString, rating: currentRating})\n\t\tif (currentRating > ratings[bestMatchIndex].rating) {\n\t\t\tbestMatchIndex = i\n\t\t}\n\t}\n\t\n\t\n\tconst bestMatch = ratings[bestMatchIndex]\n\t\n\treturn { ratings: ratings, bestMatch: bestMatch, bestMatchIndex: bestMatchIndex };\n}\n\nfunction areArgsValid(mainString, targetStrings) {\n\tif (typeof mainString !== 'string') return false;\n\tif (!Array.isArray(targetStrings)) return false;\n\tif (!targetStrings.length) return false;\n\tif (targetStrings.find( function (s) { return typeof s !== 'string'})) return false;\n\treturn true;\n}\n","#!/usr/bin/env node\n\nimport { Command } from 'commander';\nimport { resolve } from 'node:path';\nimport { execFile } from 'node:child_process';\nimport { initCommand } from './commands/init.js';\nimport { statusCommand } from './commands/status.js';\nimport { serveCommand } from './commands/serve.js';\nimport { vizCommand } from './commands/viz.js';\nimport { VERSION } from '../index.js';\n\nfunction handleCliError(error: unknown): never {\n  console.error(error instanceof Error ? error.message : 'Unknown error');\n  process.exit(1);\n}\n\nconst program = new Command();\n\nprogram\n  .name('roux')\n  .description('Graph Programming Interface for knowledge bases')\n  .version(VERSION);\n\nprogram\n  .command('init')\n  .description('Initialize Roux in a directory')\n  .argument('[directory]', 'Directory to initialize', '.')\n  .action(async (directory: string) => {\n    const resolvedDir = resolve(directory);\n    const result = await initCommand(resolvedDir);\n\n    if (result.created) {\n      console.log(`Initialized Roux in ${resolvedDir}`);\n      console.log(`  Config: ${result.configPath}`);\n      if (result.hooksInstalled) {\n        console.log(`  Claude hooks: installed`);\n      }\n    } else {\n      if (result.hooksInstalled) {\n        console.log(`Upgraded Roux in ${resolvedDir}`);\n        console.log(`  Claude hooks: installed`);\n      } else {\n        console.log(`Already initialized: ${result.configPath}`);\n      }\n    }\n  });\n\nprogram\n  .command('status')\n  .description('Show graph statistics')\n  .argument('[directory]', 'Directory to check', '.')\n  .action(async (directory: string) => {\n    const resolvedDir = resolve(directory);\n\n    try {\n      const result = await statusCommand(resolvedDir);\n      console.log('Graph Status:');\n      console.log(`  Nodes: ${result.nodeCount}`);\n      console.log(`  Edges: ${result.edgeCount}`);\n      console.log(`  Embeddings: ${result.embeddingCount}/${result.nodeCount}`);\n      console.log(\n        `  Coverage: ${(result.embeddingCoverage * 100).toFixed(1)}%`\n      );\n    } catch (error) {\n      handleCliError(error);\n    }\n  });\n\nprogram\n  .command('serve')\n  .description('Start MCP server with file watching')\n  .argument('[directory]', 'Directory to serve', '.')\n  .option('--no-watch', 'Disable file watching')\n  .action(async (directory: string, options: { watch: boolean }) => {\n    const resolvedDir = resolve(directory);\n\n    try {\n      console.log('Starting Roux server...');\n\n      const handle = await serveCommand(resolvedDir, {\n        watch: options.watch,\n        onProgress: (current, total) => {\n          process.stdout.write(\n            `\\r[${current}/${total}] Generating embeddings...`\n          );\n          if (current === total) {\n            console.log(' Done.');\n          }\n        },\n      });\n\n      console.log(`Serving ${handle.nodeCount} nodes`);\n      if (handle.isWatching) {\n        console.log('Watching for file changes...');\n      }\n\n      // Graceful shutdown\n      const shutdown = async () => {\n        console.log('\\nShutting down...');\n        await handle.stop();\n        process.exit(0);\n      };\n\n      process.on('SIGINT', shutdown);\n      process.on('SIGTERM', shutdown);\n\n      // Keep process alive\n      await new Promise(() => {});\n    } catch (error) {\n      handleCliError(error);\n    }\n  });\n\nprogram\n  .command('viz')\n  .description('Generate graph visualization')\n  .argument('[directory]', 'Directory to visualize', '.')\n  .option('-o, --output <path>', 'Output file path')\n  .option('--open', 'Open in browser after generation')\n  .action(\n    async (directory: string, options: { output?: string; open?: boolean }) => {\n      const resolvedDir = resolve(directory);\n\n      try {\n        const result = await vizCommand(resolvedDir, {\n          output: options.output,\n          open: options.open,\n        });\n\n        console.log(\n          `Generated visualization: ${result.nodeCount} nodes, ${result.edgeCount} edges`\n        );\n        console.log(`  Output: ${result.outputPath}`);\n\n        if (result.shouldOpen) {\n          const openCmd =\n            process.platform === 'darwin'\n              ? 'open'\n              : process.platform === 'win32'\n                ? 'start'\n                : 'xdg-open';\n          execFile(openCmd, [result.outputPath]);\n        }\n      } catch (error) {\n        handleCliError(error);\n      }\n    }\n  );\n\nprogram.parse();\n","import { mkdir, writeFile, readFile, access } from 'node:fs/promises';\nimport { join } from 'node:path';\n\nexport interface InitResult {\n  created: boolean;\n  configPath: string;\n  hooksInstalled: boolean;\n}\n\ninterface McpServerConfig {\n  command?: string;\n  args?: string[];\n  env?: Record<string, string>;\n  type?: string;\n  url?: string;\n}\n\ninterface McpConfig {\n  mcpServers?: Record<string, McpServerConfig>;\n}\n\ninterface ClaudeHook {\n  type: string;\n  command: string;\n}\n\ninterface ClaudeHookEntry {\n  matcher: string;\n  hooks: ClaudeHook[];\n}\n\ninterface ClaudeSettings {\n  hooks?: {\n    PreToolUse?: ClaudeHookEntry[];\n    PostToolUse?: ClaudeHookEntry[];\n    [key: string]: ClaudeHookEntry[] | undefined;\n  };\n  [key: string]: unknown;\n}\n\nconst DEFAULT_CONFIG = `providers:\n  store:\n    type: docstore\n`;\n\nconst ROUX_MCP_CONFIG: McpServerConfig = {\n  command: 'npx',\n  args: ['roux', 'serve', '.'],\n  env: {},\n};\n\n/** Marker to identify roux's hook for idempotent updates */\nexport const HOOK_MARKER = 'roux-enforce-mcp';\n\n/** Hook command that rejects direct file operations on .md files */\nconst ENFORCE_MCP_HOOK_COMMAND = `node -e \"/* ${HOOK_MARKER} */ const d=JSON.parse(require('fs').readFileSync(0,'utf8'));const p=d.tool_input?.file_path||'';if(p.endsWith('.md')){console.error('Use mcp__roux__* tools for markdown files instead of Read/Edit/Write');process.exit(2)}\"`;\n\nconst ROUX_HOOK_ENTRY: ClaudeHookEntry = {\n  matcher: 'Read|Edit|Write',\n  hooks: [{ type: 'command', command: ENFORCE_MCP_HOOK_COMMAND }],\n};\n\nexport async function initCommand(directory: string): Promise<InitResult> {\n  const configPath = join(directory, 'roux.yaml');\n  const rouxDir = join(directory, '.roux');\n\n  // Check if already initialized\n  let configExists = false;\n  try {\n    await access(configPath);\n    configExists = true;\n  } catch {\n    // File doesn't exist\n  }\n\n  // Create .roux directory regardless\n  await mkdir(rouxDir, { recursive: true });\n\n  // Create/update MCP config\n  await updateMcpConfig(directory);\n\n  // Determine store type and update Claude hooks if docstore\n  const storeType = await getStoreType(directory, configExists);\n  let hooksInstalled = false;\n  if (storeType === 'docstore') {\n    hooksInstalled = await updateClaudeSettings(directory);\n  }\n\n  if (configExists) {\n    return { created: false, configPath, hooksInstalled };\n  }\n\n  // Create roux.yaml with minimal defaults\n  await writeFile(configPath, DEFAULT_CONFIG, 'utf-8');\n  return { created: true, configPath, hooksInstalled };\n}\n\nasync function updateMcpConfig(directory: string): Promise<void> {\n  const mcpPath = join(directory, '.mcp.json');\n\n  let config: McpConfig = {};\n\n  // Try to read existing config\n  try {\n    const content = await readFile(mcpPath, 'utf-8');\n    config = JSON.parse(content) as McpConfig;\n  } catch {\n    // File doesn't exist or invalid JSON — start fresh\n  }\n\n  // Ensure mcpServers object exists\n  if (!config.mcpServers) {\n    config.mcpServers = {};\n  }\n\n  // Add/update roux entry\n  config.mcpServers.roux = ROUX_MCP_CONFIG;\n\n  // Write back\n  await writeFile(mcpPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n}\n\nasync function getStoreType(\n  directory: string,\n  configExists: boolean\n): Promise<string> {\n  if (!configExists) {\n    return 'docstore'; // Default\n  }\n\n  try {\n    const configPath = join(directory, 'roux.yaml');\n    const content = await readFile(configPath, 'utf-8');\n    // Simple YAML parsing for store type\n    const typeMatch = content.match(/store:\\s*\\n\\s*type:\\s*(\\w+)/);\n    if (typeMatch?.[1]) {\n      return typeMatch[1];\n    }\n  } catch {\n    // Can't read config, assume default\n  }\n\n  return 'docstore';\n}\n\n/** Returns true if hooks were installed, false if skipped */\nasync function updateClaudeSettings(directory: string): Promise<boolean> {\n  const claudeDir = join(directory, '.claude');\n  const settingsPath = join(claudeDir, 'settings.json');\n\n  // Ensure .claude directory exists\n  await mkdir(claudeDir, { recursive: true });\n\n  let config: ClaudeSettings = {};\n  let existingContent: string | null = null;\n\n  // Try to read existing settings\n  try {\n    existingContent = await readFile(settingsPath, 'utf-8');\n    config = JSON.parse(existingContent) as ClaudeSettings;\n  } catch (err) {\n    if (existingContent !== null) {\n      // File exists but is malformed JSON — don't touch it\n      return false;\n    }\n    // File doesn't exist — start fresh\n  }\n\n  // Ensure hooks.PreToolUse array exists\n  if (!config.hooks) {\n    config.hooks = {};\n  }\n  if (!config.hooks.PreToolUse) {\n    config.hooks.PreToolUse = [];\n  }\n\n  // Check if our hook already exists\n  const hasRouxHook = config.hooks.PreToolUse.some((entry) =>\n    entry.hooks?.some((h) => h.command?.includes(HOOK_MARKER))\n  );\n\n  if (hasRouxHook) {\n    return false; // Already installed, don't duplicate\n  }\n\n  // Add our hook\n  config.hooks.PreToolUse.push(ROUX_HOOK_ENTRY);\n\n  // Write back\n  await writeFile(settingsPath, JSON.stringify(config, null, 2) + '\\n', 'utf-8');\n  return true;\n}\n","import { access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { Cache } from '../../providers/docstore/cache.js';\nimport { SqliteVectorIndex } from '../../providers/vector/sqlite.js';\n\nexport interface StatusResult {\n  nodeCount: number;\n  edgeCount: number;\n  embeddingCount: number;\n  embeddingCoverage: number;\n}\n\nexport async function statusCommand(directory: string): Promise<StatusResult> {\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  const cacheDir = join(directory, '.roux');\n  const cache = new Cache(cacheDir);\n  const vectorProvider = new SqliteVectorIndex(cacheDir);\n\n  try {\n    const stats = cache.getStats();\n    const embeddingCount = vectorProvider.getEmbeddingCount();\n\n    const embeddingCoverage =\n      stats.nodeCount === 0 ? 1 : embeddingCount / stats.nodeCount;\n\n    return {\n      nodeCount: stats.nodeCount,\n      edgeCount: stats.edgeCount,\n      embeddingCount,\n      embeddingCoverage,\n    };\n  } finally {\n    cache.close();\n    vectorProvider.close();\n  }\n}\n","import Database from 'better-sqlite3';\nimport { join } from 'node:path';\nimport { mkdirSync } from 'node:fs';\nimport type { Node, SourceRef } from '../../types/node.js';\nimport type {\n  TagMode,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../../types/provider.js';\nimport {\n  type CentralityRecord,\n  initCentralitySchema,\n  storeCentrality,\n  getCentrality,\n  resolveNames,\n} from './cache/index.js';\n\nexport type { CentralityRecord };\n\ninterface NodeRow {\n  id: string;\n  title: string;\n  content: string;\n  tags: string;\n  outgoing_links: string;\n  properties: string;\n  source_type: string;\n  source_path: string;\n  source_modified: number;\n}\n\n\nexport class Cache {\n  private db: Database.Database;\n\n  constructor(cacheDir: string) {\n    mkdirSync(cacheDir, { recursive: true });\n    const dbPath = join(cacheDir, 'cache.db');\n    this.db = new Database(dbPath);\n    this.db.pragma('journal_mode = WAL');\n    this.initSchema();\n  }\n\n  private initSchema(): void {\n    // Create nodes table (core schema owned by Cache)\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS nodes (\n        id TEXT PRIMARY KEY,\n        title TEXT,\n        content TEXT,\n        tags TEXT,\n        outgoing_links TEXT,\n        properties TEXT,\n        source_type TEXT,\n        source_path TEXT,\n        source_modified INTEGER\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_nodes_source_path ON nodes(source_path);\n    `);\n\n    // Delegate centrality schema to its module\n    initCentralitySchema(this.db);\n\n    // Enable foreign key enforcement for cascade deletes\n    this.db.pragma('foreign_keys = ON');\n  }\n\n  getTableNames(): string[] {\n    const rows = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='table'\")\n      .all() as Array<{ name: string }>;\n    return rows.map((r) => r.name);\n  }\n\n  upsertNode(\n    node: Node,\n    sourceType: string,\n    sourcePath: string,\n    sourceModified: number\n  ): void {\n    const stmt = this.db.prepare(`\n      INSERT INTO nodes (id, title, content, tags, outgoing_links, properties, source_type, source_path, source_modified)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)\n      ON CONFLICT(id) DO UPDATE SET\n        title = excluded.title,\n        content = excluded.content,\n        tags = excluded.tags,\n        outgoing_links = excluded.outgoing_links,\n        properties = excluded.properties,\n        source_type = excluded.source_type,\n        source_path = excluded.source_path,\n        source_modified = excluded.source_modified\n    `);\n\n    stmt.run(\n      node.id,\n      node.title,\n      node.content,\n      JSON.stringify(node.tags),\n      JSON.stringify(node.outgoingLinks),\n      JSON.stringify(node.properties),\n      sourceType,\n      sourcePath,\n      sourceModified\n    );\n  }\n\n  getNode(id: string): Node | null {\n    const row = this.db\n      .prepare('SELECT * FROM nodes WHERE id = ?')\n      .get(id) as NodeRow | undefined;\n\n    if (!row) return null;\n    return this.rowToNode(row);\n  }\n\n  getNodes(ids: string[]): Node[] {\n    if (ids.length === 0) return [];\n\n    // Fetch all nodes then order by input ids\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT * FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as NodeRow[];\n\n    const nodeMap = new Map<string, Node>();\n    for (const row of rows) {\n      nodeMap.set(row.id, this.rowToNode(row));\n    }\n\n    // Return in requested order\n    const result: Node[] = [];\n    for (const id of ids) {\n      const node = nodeMap.get(id);\n      if (node) result.push(node);\n    }\n    return result;\n  }\n\n  deleteNode(id: string): void {\n    this.db.prepare('DELETE FROM nodes WHERE id = ?').run(id);\n  }\n\n  getAllNodes(): Node[] {\n    const rows = this.db.prepare('SELECT * FROM nodes').all() as NodeRow[];\n    return rows.map((row) => this.rowToNode(row));\n  }\n\n  searchByTags(tags: string[], mode: TagMode, limit?: number): Node[] {\n    if (tags.length === 0) return [];\n\n    const lowerTags = tags.map((t) => t.toLowerCase());\n\n    // Build SQL query with tag filtering in the database\n    // Tags are stored as JSON array, so we use json_each to search\n    let query: string;\n    const params: unknown[] = [];\n\n    if (mode === 'any') {\n      // Match nodes that have ANY of the specified tags\n      const tagConditions = lowerTags.map(() =>\n        \"EXISTS (SELECT 1 FROM json_each(tags) WHERE LOWER(json_each.value) = ?)\"\n      ).join(' OR ');\n      query = `SELECT * FROM nodes WHERE ${tagConditions}`;\n      params.push(...lowerTags);\n    } else {\n      // Match nodes that have ALL of the specified tags\n      const tagConditions = lowerTags.map(() =>\n        \"EXISTS (SELECT 1 FROM json_each(tags) WHERE LOWER(json_each.value) = ?)\"\n      ).join(' AND ');\n      query = `SELECT * FROM nodes WHERE ${tagConditions}`;\n      params.push(...lowerTags);\n    }\n\n    if (limit !== undefined) {\n      query += ' LIMIT ?';\n      params.push(limit);\n    }\n\n    const rows = this.db.prepare(query).all(...params) as NodeRow[];\n    return rows.map((row) => this.rowToNode(row));\n  }\n\n  getModifiedTime(sourcePath: string): number | null {\n    const row = this.db\n      .prepare('SELECT source_modified FROM nodes WHERE source_path = ?')\n      .get(sourcePath) as { source_modified: number } | undefined;\n\n    return row?.source_modified ?? null;\n  }\n\n  getNodeByPath(sourcePath: string): Node | null {\n    // Case-insensitive path lookup for cross-platform compatibility\n    const row = this.db\n      .prepare('SELECT * FROM nodes WHERE LOWER(source_path) = LOWER(?)')\n      .get(sourcePath) as NodeRow | undefined;\n\n    if (!row) return null;\n    return this.rowToNode(row);\n  }\n\n  getAllTrackedPaths(): Set<string> {\n    const rows = this.db\n      .prepare('SELECT source_path FROM nodes')\n      .all() as Array<{ source_path: string }>;\n\n    return new Set(rows.map((r) => r.source_path));\n  }\n\n  updateSourcePath(id: string, newPath: string): void {\n    this.db\n      .prepare('UPDATE nodes SET source_path = ? WHERE id = ?')\n      .run(newPath, id);\n  }\n\n  getIdByPath(sourcePath: string): string | null {\n    const row = this.db\n      .prepare('SELECT id FROM nodes WHERE source_path = ?')\n      .get(sourcePath) as { id: string } | undefined;\n\n    return row?.id ?? null;\n  }\n\n  resolveTitles(ids: string[]): Map<string, string> {\n    if (ids.length === 0) return new Map();\n\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT id, title FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as Array<{ id: string; title: string }>;\n\n    const result = new Map<string, string>();\n    for (const row of rows) {\n      result.set(row.id, row.title);\n    }\n    return result;\n  }\n\n  nodesExist(ids: string[]): Map<string, boolean> {\n    if (ids.length === 0) return new Map();\n\n    const placeholders = ids.map(() => '?').join(',');\n    const rows = this.db\n      .prepare(`SELECT id FROM nodes WHERE id IN (${placeholders})`)\n      .all(...ids) as Array<{ id: string }>;\n\n    const existingIds = new Set(rows.map((r) => r.id));\n    const result = new Map<string, boolean>();\n    for (const id of ids) {\n      result.set(id, existingIds.has(id));\n    }\n    return result;\n  }\n\n  listNodes(filter: ListFilter, options?: ListOptions): ListNodesResult {\n    const limit = Math.min(options?.limit ?? 100, 1000);\n    const offset = options?.offset ?? 0;\n\n    // Build query dynamically based on filters\n    const conditions: string[] = [];\n    const params: unknown[] = [];\n\n    if (filter.tag) {\n      // Case-insensitive tag match - tags stored as JSON array\n      conditions.push(\"EXISTS (SELECT 1 FROM json_each(tags) WHERE LOWER(json_each.value) = LOWER(?))\");\n      params.push(filter.tag);\n    }\n\n    if (filter.path) {\n      // Filter by source_path since node id is now a stable nanoid\n      conditions.push(\"LOWER(source_path) LIKE '%' || LOWER(?) || '%'\");\n      params.push(filter.path);\n    }\n\n    const whereClause = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n\n    // Get total count of matching nodes (without limit/offset)\n    const countQuery = `SELECT COUNT(*) as count FROM nodes ${whereClause}`;\n    const countRow = this.db.prepare(countQuery).get(...params) as { count: number };\n    const total = countRow.count;\n\n    // Get paginated results\n    const query = `SELECT id, title FROM nodes ${whereClause} LIMIT ? OFFSET ?`;\n    const rows = this.db.prepare(query).all(...params, limit, offset) as Array<{ id: string; title: string }>;\n\n    const nodes = rows.map((row) => ({ id: row.id, title: row.title }));\n    return { nodes, total };\n  }\n\n  resolveNodes(names: string[], options?: ResolveOptions): ResolveResult[] {\n    if (names.length === 0) return [];\n\n    const strategy = options?.strategy ?? 'fuzzy';\n    const threshold = options?.threshold ?? 0.7;\n\n    // Build filter without undefined values\n    const filter: ListFilter = {};\n    if (options?.tag) filter.tag = options.tag;\n    if (options?.path) filter.path = options.path;\n\n    // Get candidate nodes (applying tag/path filters)\n    const { nodes: candidates } = this.listNodes(filter, { limit: 1000 });\n\n    return resolveNames(names, candidates, { strategy, threshold });\n  }\n\n  updateOutgoingLinks(nodeId: string, links: string[]): void {\n    this.db\n      .prepare('UPDATE nodes SET outgoing_links = ? WHERE id = ?')\n      .run(JSON.stringify(links), nodeId);\n  }\n\n  storeCentrality(\n    nodeId: string,\n    pagerank: number,\n    inDegree: number,\n    outDegree: number,\n    computedAt: number\n  ): void {\n    storeCentrality(this.db, nodeId, pagerank, inDegree, outDegree, computedAt);\n  }\n\n  getCentrality(nodeId: string): CentralityRecord | null {\n    return getCentrality(this.db, nodeId);\n  }\n\n  getStats(): { nodeCount: number; edgeCount: number } {\n    const nodeCount = this.db\n      .prepare('SELECT COUNT(*) as count FROM nodes')\n      .get() as { count: number };\n\n    // Sum all in_degree values to get edge count\n    const edgeSum = this.db\n      .prepare('SELECT SUM(in_degree) as total FROM centrality')\n      .get() as { total: number | null };\n\n    return {\n      nodeCount: nodeCount.count,\n      edgeCount: edgeSum.total ?? 0,\n    };\n  }\n\n  clear(): void {\n    this.db.exec('DELETE FROM centrality');\n    this.db.exec('DELETE FROM nodes');\n  }\n\n  close(): void {\n    this.db.close();\n  }\n\n  private rowToNode(row: NodeRow): Node {\n    const sourceRef: SourceRef = {\n      type: row.source_type as SourceRef['type'],\n      path: row.source_path,\n      lastModified: new Date(row.source_modified),\n    };\n\n    return {\n      id: row.id,\n      title: row.title,\n      content: row.content,\n      tags: JSON.parse(row.tags) as string[],\n      outgoingLinks: JSON.parse(row.outgoing_links) as string[],\n      properties: JSON.parse(row.properties) as Record<string, unknown>,\n      sourceRef,\n    };\n  }\n}\n","import type Database from 'better-sqlite3';\n\nexport interface CentralityRecord {\n  pagerank: number;\n  inDegree: number;\n  outDegree: number;\n  computedAt: number;\n}\n\nexport function initCentralitySchema(db: Database.Database): void {\n  db.exec(`\n    CREATE TABLE IF NOT EXISTS centrality (\n      node_id TEXT PRIMARY KEY,\n      pagerank REAL,\n      in_degree INTEGER,\n      out_degree INTEGER,\n      computed_at INTEGER,\n      FOREIGN KEY (node_id) REFERENCES nodes(id) ON DELETE CASCADE\n    )\n  `);\n}\n\ninterface CentralityRow {\n  node_id: string;\n  pagerank: number;\n  in_degree: number;\n  out_degree: number;\n  computed_at: number;\n}\n\nexport function storeCentrality(\n  db: Database.Database,\n  nodeId: string,\n  pagerank: number,\n  inDegree: number,\n  outDegree: number,\n  computedAt: number\n): void {\n  db.prepare(\n    `\n    INSERT INTO centrality (node_id, pagerank, in_degree, out_degree, computed_at)\n    VALUES (?, ?, ?, ?, ?)\n    ON CONFLICT(node_id) DO UPDATE SET\n      pagerank = excluded.pagerank,\n      in_degree = excluded.in_degree,\n      out_degree = excluded.out_degree,\n      computed_at = excluded.computed_at\n  `\n  ).run(nodeId, pagerank, inDegree, outDegree, computedAt);\n}\n\nexport function getCentrality(\n  db: Database.Database,\n  nodeId: string\n): CentralityRecord | null {\n  const row = db\n    .prepare('SELECT * FROM centrality WHERE node_id = ?')\n    .get(nodeId) as CentralityRow | undefined;\n\n  if (!row) return null;\n\n  return {\n    pagerank: row.pagerank,\n    inDegree: row.in_degree,\n    outDegree: row.out_degree,\n    computedAt: row.computed_at,\n  };\n}\n","import stringSimilarity from 'string-similarity';\nimport type { ResolveResult, ResolveStrategy } from '../../types/provider.js';\n\nexport interface Candidate {\n  id: string;\n  title: string;\n}\n\nexport interface ResolveMatchOptions {\n  strategy: ResolveStrategy;\n  threshold: number;\n}\n\n/**\n * Resolve names to node IDs using exact or fuzzy matching.\n * Semantic strategy returns no matches (handled at higher level with embeddings).\n */\nexport function resolveNames(\n  names: string[],\n  candidates: Candidate[],\n  options: ResolveMatchOptions\n): ResolveResult[] {\n  if (names.length === 0) return [];\n\n  const { strategy, threshold } = options;\n\n  if (candidates.length === 0) {\n    return names.map((query) => ({ query, match: null, score: 0 }));\n  }\n\n  const candidateTitles = candidates.map((c) => c.title.toLowerCase());\n  const titleToId = new Map<string, string>();\n  for (const c of candidates) {\n    titleToId.set(c.title.toLowerCase(), c.id);\n  }\n\n  return names.map((query): ResolveResult => {\n    const queryLower = query.toLowerCase();\n\n    if (strategy === 'exact') {\n      const matchedId = titleToId.get(queryLower);\n      if (matchedId) {\n        return { query, match: matchedId, score: 1 };\n      }\n      return { query, match: null, score: 0 };\n    }\n\n    if (strategy === 'fuzzy') {\n      const result = stringSimilarity.findBestMatch(queryLower, candidateTitles);\n      const bestMatch = result.bestMatch;\n\n      if (bestMatch.rating >= threshold) {\n        const matchedId = titleToId.get(bestMatch.target)!;\n        return { query, match: matchedId, score: bestMatch.rating };\n      }\n      return { query, match: null, score: 0 };\n    }\n\n    // Semantic strategy - not supported at this level\n    return { query, match: null, score: 0 };\n  });\n}\n","import Database from 'better-sqlite3';\nimport type { Database as DatabaseType } from 'better-sqlite3';\nimport { join } from 'node:path';\nimport type { VectorIndex, VectorSearchResult } from '../../types/provider.js';\nimport { MinHeap } from '../../utils/heap.js';\nimport { cosineDistance } from '../../utils/math.js';\n\nexport class SqliteVectorIndex implements VectorIndex {\n  private db: DatabaseType;\n  private ownsDb: boolean;\n  private modelMismatchWarned = false;\n\n  constructor(pathOrDb: string | DatabaseType) {\n    if (typeof pathOrDb === 'string') {\n      this.db = new Database(join(pathOrDb, 'vectors.db'));\n      this.ownsDb = true;\n    } else {\n      this.db = pathOrDb;\n      this.ownsDb = false;\n    }\n    this.init();\n  }\n\n  private init(): void {\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS vectors (\n        id TEXT PRIMARY KEY,\n        model TEXT NOT NULL,\n        vector BLOB NOT NULL\n      )\n    `);\n  }\n\n  async store(id: string, vector: number[], model: string): Promise<void> {\n    if (vector.length === 0) {\n      throw new Error('Cannot store empty vector');\n    }\n    for (const v of vector) {\n      if (!Number.isFinite(v)) {\n        throw new Error(`Invalid vector value: ${v}`);\n      }\n    }\n\n    // Validate dimension consistency (exclude self for overwrites)\n    const existing = this.db\n      .prepare('SELECT LENGTH(vector) / 4 as dim FROM vectors WHERE id != ? LIMIT 1')\n      .get(id) as { dim: number } | undefined;\n\n    if (existing && existing.dim !== vector.length) {\n      throw new Error(\n        `Dimension mismatch: cannot store ${vector.length}-dim vector, existing vectors have ${existing.dim} dimensions`\n      );\n    }\n\n    const blob = Buffer.from(new Float32Array(vector).buffer);\n    this.db\n      .prepare(\n        `INSERT OR REPLACE INTO vectors (id, model, vector) VALUES (?, ?, ?)`\n      )\n      .run(id, model, blob);\n  }\n\n  async search(vector: number[], limit: number): Promise<VectorSearchResult[]> {\n    if (vector.length === 0) {\n      throw new Error('Cannot search with empty vector');\n    }\n    for (const v of vector) {\n      if (!Number.isFinite(v)) {\n        throw new Error(`Invalid vector value: ${v}`);\n      }\n    }\n    if (limit <= 0) {\n      return [];\n    }\n\n    // Warn once if index contains mixed models\n    if (!this.modelMismatchWarned) {\n      const models = this.db\n        .prepare('SELECT DISTINCT model FROM vectors')\n        .all() as Array<{ model: string }>;\n      if (models.length > 1) {\n        console.warn(\n          `Vector index contains embeddings from multiple models: ${models.map((m) => m.model).join(', ')}. ` +\n            'Search results may be unreliable. Re-sync to re-embed all documents with current model.'\n        );\n        this.modelMismatchWarned = true;\n      }\n    }\n\n    const queryVec = new Float32Array(vector);\n    const stmt = this.db.prepare('SELECT id, vector FROM vectors');\n\n    // Max-heap by distance: largest distance at root for efficient eviction\n    const heap = new MinHeap<VectorSearchResult>(\n      (a, b) => b.distance - a.distance\n    );\n\n    let dimensionChecked = false;\n\n    for (const row of stmt.iterate() as IterableIterator<{\n      id: string;\n      vector: Buffer;\n    }>) {\n      // Check dimension mismatch against first stored vector\n      if (!dimensionChecked) {\n        const storedDim = row.vector.byteLength / 4;\n        if (vector.length !== storedDim) {\n          throw new Error(\n            `Dimension mismatch: query has ${vector.length} dimensions, stored vectors have ${storedDim}`\n          );\n        }\n        dimensionChecked = true;\n      }\n\n      const storedVec = new Float32Array(\n        row.vector.buffer,\n        row.vector.byteOffset,\n        row.vector.byteLength / 4\n      );\n      const distance = cosineDistance(queryVec, storedVec);\n\n      if (heap.size() < limit) {\n        heap.push({ id: row.id, distance });\n      } else if (distance < heap.peek()!.distance) {\n        heap.pop();\n        heap.push({ id: row.id, distance });\n      }\n    }\n\n    // Extract and sort by distance ascending\n    return heap.toArray().sort((a, b) => a.distance - b.distance);\n  }\n\n  async delete(id: string): Promise<void> {\n    this.db.prepare('DELETE FROM vectors WHERE id = ?').run(id);\n  }\n\n  async getModel(id: string): Promise<string | null> {\n    const row = this.db\n      .prepare('SELECT model FROM vectors WHERE id = ?')\n      .get(id) as { model: string } | undefined;\n    return row?.model ?? null;\n  }\n\n  hasEmbedding(id: string): boolean {\n    const row = this.db\n      .prepare('SELECT 1 FROM vectors WHERE id = ?')\n      .get(id);\n    return row !== undefined;\n  }\n\n  /** For testing: get table names */\n  getTableNames(): string[] {\n    const rows = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='table'\")\n      .all() as Array<{ name: string }>;\n    return rows.map((r) => r.name);\n  }\n\n  /** For testing: get vector blob size */\n  getVectorBlobSize(id: string): number | null {\n    const row = this.db\n      .prepare('SELECT LENGTH(vector) as size FROM vectors WHERE id = ?')\n      .get(id) as { size: number } | undefined;\n    return row?.size ?? null;\n  }\n\n  /** Get total number of stored embeddings */\n  getEmbeddingCount(): number {\n    const row = this.db\n      .prepare('SELECT COUNT(*) as count FROM vectors')\n      .get() as { count: number };\n    return row.count;\n  }\n\n  close(): void {\n    if (this.ownsDb) {\n      this.db.close();\n    }\n  }\n}\n","type Comparator<T> = (a: T, b: T) => number;\n\n/**\n * Min-heap implementation for top-k selection.\n * The smallest element (by comparator) is always at the root.\n */\nexport class MinHeap<T> {\n  private data: T[] = [];\n  private compare: Comparator<T>;\n\n  constructor(comparator: Comparator<T>) {\n    this.compare = comparator;\n  }\n\n  size(): number {\n    return this.data.length;\n  }\n\n  peek(): T | undefined {\n    return this.data[0];\n  }\n\n  push(value: T): void {\n    this.data.push(value);\n    this.bubbleUp(this.data.length - 1);\n  }\n\n  pop(): T | undefined {\n    if (this.data.length === 0) return undefined;\n    if (this.data.length === 1) return this.data.pop();\n\n    const min = this.data[0];\n    this.data[0] = this.data.pop()!;\n    this.bubbleDown(0);\n    return min;\n  }\n\n  toArray(): T[] {\n    return [...this.data];\n  }\n\n  private bubbleUp(index: number): void {\n    while (index > 0) {\n      const parentIndex = Math.floor((index - 1) / 2);\n      if (this.compare(this.data[index]!, this.data[parentIndex]!) >= 0) {\n        break;\n      }\n      this.swap(index, parentIndex);\n      index = parentIndex;\n    }\n  }\n\n  private bubbleDown(index: number): void {\n    const length = this.data.length;\n    while (true) {\n      const leftChild = 2 * index + 1;\n      const rightChild = 2 * index + 2;\n      let smallest = index;\n\n      if (leftChild < length && this.compare(this.data[leftChild]!, this.data[smallest]!) < 0) {\n        smallest = leftChild;\n      }\n      if (rightChild < length && this.compare(this.data[rightChild]!, this.data[smallest]!) < 0) {\n        smallest = rightChild;\n      }\n\n      if (smallest === index) break;\n\n      this.swap(index, smallest);\n      index = smallest;\n    }\n  }\n\n  private swap(i: number, j: number): void {\n    const temp = this.data[i]!;\n    this.data[i] = this.data[j]!;\n    this.data[j] = temp;\n  }\n}\n","type VectorLike = ArrayLike<number>;\n\n/**\n * Compute cosine similarity between two vectors.\n * Returns value in range [-1, 1] where 1 = identical direction, 0 = orthogonal, -1 = opposite.\n * Returns 0 if either vector has zero magnitude.\n * Throws if either vector is empty or dimensions differ.\n */\nexport function cosineSimilarity(a: VectorLike, b: VectorLike): number {\n  if (a.length === 0 || b.length === 0) {\n    throw new Error('Cannot compute similarity for empty vector');\n  }\n  if (a.length !== b.length) {\n    throw new Error(`Dimension mismatch: ${a.length} vs ${b.length}`);\n  }\n\n  let dotProduct = 0;\n  let normA = 0;\n  let normB = 0;\n\n  for (let i = 0; i < a.length; i++) {\n    dotProduct += a[i]! * b[i]!;\n    normA += a[i]! * a[i]!;\n    normB += b[i]! * b[i]!;\n  }\n\n  if (normA === 0 || normB === 0) return 0;\n\n  return dotProduct / (Math.sqrt(normA) * Math.sqrt(normB));\n}\n\n/**\n * Compute cosine distance between two vectors.\n * Returns value in range [0, 2] where 0 = identical direction, 1 = orthogonal, 2 = opposite.\n * Returns 1 if either vector has zero magnitude.\n */\nexport function cosineDistance(a: VectorLike, b: VectorLike): number {\n  const similarity = cosineSimilarity(a, b);\n  if (similarity === 0 && (isZeroVector(a) || isZeroVector(b))) {\n    return 1;\n  }\n  return 1 - similarity;\n}\n\nfunction isZeroVector(v: VectorLike): boolean {\n  for (let i = 0; i < v.length; i++) {\n    if (v[i] !== 0) return false;\n  }\n  return true;\n}\n","import { access, readFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { DocStore } from '../../providers/docstore/index.js';\nimport { TransformersEmbedding } from '../../providers/embedding/transformers.js';\nimport { GraphCoreImpl } from '../../core/graphcore.js';\nimport { McpServer, type TransportFactory } from '../../mcp/server.js';\nimport { DEFAULT_NAMING, type RouxConfig } from '../../types/config.js';\n\nexport interface ServeOptions {\n  watch?: boolean;\n  transportFactory?: TransportFactory;\n  onProgress?: (current: number, total: number) => void;\n}\n\nexport interface ServeHandle {\n  stop: () => Promise<void>;\n  isWatching: boolean;\n  nodeCount: number;\n}\n\nexport async function serveCommand(\n  directory: string,\n  options: ServeOptions = {}\n): Promise<ServeHandle> {\n  const { watch = true, transportFactory, onProgress } = options;\n\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  // Load config\n  const configContent = await readFile(configPath, 'utf-8');\n  const config = parseYaml(configContent) as RouxConfig;\n\n  // Create providers\n  const sourcePath = config.source?.path ?? '.';\n  const resolvedSourcePath = join(directory, sourcePath);\n  const cachePath = config.cache?.path ?? '.roux';\n  const resolvedCachePath = join(directory, cachePath);\n\n  const store = new DocStore({ sourceRoot: resolvedSourcePath, cacheDir: resolvedCachePath });\n  const embeddingModel =\n    config.providers?.embedding?.type === 'local'\n      ? config.providers.embedding.model\n      : undefined;\n  const embedding = new TransformersEmbedding(\n    embeddingModel ? { model: embeddingModel } : {}\n  );\n\n  // Create GraphCore and register providers (store.onRegister calls sync)\n  const core = new GraphCoreImpl();\n  await core.registerStore(store);\n  await core.registerEmbedding(embedding);\n\n  // Generate embeddings for nodes without them\n  const allNodeIds = await store.getAllNodeIds();\n  const total = allNodeIds.length;\n\n  for (let i = 0; i < allNodeIds.length; i++) {\n    const id = allNodeIds[i]!;\n\n    if (!hasExistingEmbedding(store, id)) {\n      const node = await store.getNode(id);\n      if (node && node.content) {\n        const vector = await embedding.embed(node.content);\n        await store.storeEmbedding(id, vector, embedding.modelId());\n      }\n    }\n\n    if (onProgress) {\n      onProgress(i + 1, total);\n    }\n  }\n\n  // Resolve naming conventions\n  const naming = { ...DEFAULT_NAMING, ...config.naming };\n\n  // Start MCP server\n  const mcpServer = new McpServer({\n    core,\n    store,\n    hasEmbedding: true,\n    naming,\n  });\n\n  try {\n    await mcpServer.start(transportFactory);\n  } catch (err) {\n    // Clean up providers on MCP server start failure\n    await core.destroy();\n    throw err;\n  }\n\n  // Start file watcher if enabled\n  if (watch) {\n    try {\n      await store.startWatching(async (changedIds) => {\n        // Generate embeddings for changed nodes\n        for (const id of changedIds) {\n          try {\n            const node = await store.getNode(id);\n            if (node && node.content) {\n              const vector = await embedding.embed(node.content);\n              await store.storeEmbedding(id, vector, embedding.modelId());\n            }\n          } catch (err) {\n            // Log warning but continue processing other changed files\n            console.warn(\n              'Failed to generate embedding for',\n              id,\n              ':',\n              (err as Error).message || 'Unknown error'\n            );\n          }\n        }\n      });\n    } catch (err) {\n      console.warn(\n        'File watching disabled:',\n        (err as Error).message || 'Unknown error'\n      );\n    }\n  }\n\n  return {\n    stop: async () => {\n      await core.destroy();\n      await mcpServer.close();\n    },\n    isWatching: store.isWatching(),\n    nodeCount: allNodeIds.length,\n  };\n}\n\nfunction hasExistingEmbedding(store: DocStore, id: string): boolean {\n  return store.hasEmbedding(id);\n}\n","import { writeFile, mkdir, rm, stat } from 'node:fs/promises';\nimport { mkdirSync } from 'node:fs';\nimport { join, relative, dirname, extname } from 'node:path';\nimport type { Node, NodeUpdates } from '../../types/node.js';\nimport type {\n  TagMode,\n  VectorIndex,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n  CentralityMetrics,\n} from '../../types/provider.js';\nimport { StoreProvider } from '../store/index.js';\nimport { Cache } from './cache.js';\nimport { SqliteVectorIndex } from '../vector/sqlite.js';\nimport {\n  parseMarkdown,\n  extractWikiLinks,\n  normalizeId,\n  serializeToMarkdown,\n} from './parser.js';\nimport { FileWatcher, type FileEventType } from './watcher.js';\nimport {\n  normalizeWikiLink,\n  buildFilenameIndex,\n  resolveLinks,\n} from './links.js';\nimport {\n  getFileMtime,\n  validatePathWithinSource,\n  collectFiles,\n  readFileContent,\n} from './file-operations.js';\nimport { ReaderRegistry } from './reader-registry.js';\nimport type { FileContext } from './types.js';\nimport { MarkdownReader } from './readers/index.js';\nimport { generateId } from './id.js';\n\n/**\n * Create a registry with default readers pre-registered.\n * Returns a new instance each call.\n */\nfunction createDefaultRegistry(): ReaderRegistry {\n  const registry = new ReaderRegistry();\n  registry.register(new MarkdownReader());\n  return registry;\n}\n\nexport interface DocStoreOptions {\n  sourceRoot: string;\n  cacheDir: string;\n  id?: string;\n  vectorIndex?: VectorIndex;\n  registry?: ReaderRegistry;\n  /** Optional FileWatcher instance. If provided, DocStore uses it instead of creating one. */\n  fileWatcher?: FileWatcher;\n}\n\nexport class DocStore extends StoreProvider {\n  readonly id: string;\n  private cache: Cache;\n  private sourceRoot: string;\n  private ownsVectorIndex: boolean;\n  private registry: ReaderRegistry;\n\n  private fileWatcher: FileWatcher | null = null;\n  private onChangeCallback: ((changedIds: string[]) => void) | undefined;\n\n  constructor(options: DocStoreOptions) {\n    const {\n      sourceRoot,\n      cacheDir,\n      id = 'docstore',\n      vectorIndex,\n      registry,\n      fileWatcher,\n    } = options;\n\n    const ownsVector = !vectorIndex;\n    // Ensure cacheDir exists before SqliteVectorIndex tries to open a DB inside it\n    if (!vectorIndex) mkdirSync(cacheDir, { recursive: true });\n    const vi = vectorIndex ?? new SqliteVectorIndex(cacheDir);\n    super({ vectorIndex: vi });\n\n    this.id = id;\n    this.sourceRoot = sourceRoot;\n    this.cache = new Cache(cacheDir);\n    this.ownsVectorIndex = ownsVector;\n    this.registry = registry ?? createDefaultRegistry();\n    this.fileWatcher = fileWatcher ?? null;\n  }\n\n  async sync(): Promise<void> {\n    // Pause watcher during sync to avoid processing our own writes\n    if (this.fileWatcher?.isWatching()) {\n      this.fileWatcher.pause();\n    }\n\n    try {\n      const extensions = this.registry.getExtensions();\n      const currentPaths = await collectFiles(this.sourceRoot, extensions);\n      const trackedPaths = this.cache.getAllTrackedPaths();\n\n      // Track IDs seen during this sync for duplicate detection\n      const seenIds = new Map<string, string>(); // id -> first file path\n\n      // Process new/modified files\n      for (const filePath of currentPaths) {\n        try {\n          const mtime = await getFileMtime(filePath);\n          const cachedMtime = this.cache.getModifiedTime(filePath);\n\n          if (cachedMtime === null || mtime > cachedMtime) {\n            const { node, needsIdWrite, newMtime } = await this.parseAndMaybeWriteId(filePath, mtime);\n\n            // Check for duplicate ID\n            const existingPath = seenIds.get(node.id);\n            if (existingPath) {\n              console.warn(\n                `Duplicate ID ${node.id} found in ${filePath} (first seen in ${existingPath}):`,\n                new Error('Skipping duplicate')\n              );\n              continue;\n            }\n\n            seenIds.set(node.id, filePath);\n\n            // Use new mtime if we wrote back, otherwise original\n            const finalMtime = needsIdWrite ? (newMtime ?? mtime) : mtime;\n            this.cache.upsertNode(node, 'file', filePath, finalMtime);\n          } else {\n            // Even if not modified, track the ID for duplicate detection\n            const existingNode = this.cache.getNodeByPath(filePath);\n            if (existingNode) {\n              const existingPath = seenIds.get(existingNode.id);\n              if (existingPath) {\n                console.warn(\n                  `Duplicate ID ${existingNode.id} found in ${filePath} (first seen in ${existingPath}):`,\n                  new Error('Skipping duplicate')\n                );\n                // Remove from cache since we're skipping this one\n                this.cache.deleteNode(existingNode.id);\n              } else {\n                seenIds.set(existingNode.id, filePath);\n              }\n            }\n          }\n        } catch (err) {\n          // File may have been deleted between readdir and stat — skip silently\n          if ((err as NodeJS.ErrnoException).code === 'ENOENT') {\n            continue;\n          }\n          // All other errors (parse failures, read errors): log and skip file\n          // Graceful degradation - one bad file shouldn't crash the entire sync\n          console.warn(`Failed to process file ${filePath}:`, err);\n          continue;\n        }\n      }\n\n      // Remove deleted files\n      const currentSet = new Set(currentPaths);\n      for (const tracked of trackedPaths) {\n        if (!currentSet.has(tracked)) {\n          const node = this.cache.getNodeByPath(tracked);\n          if (node) {\n            this.cache.deleteNode(node.id);\n          }\n        }\n      }\n\n      // Resolve wiki-links after all nodes are cached\n      this.resolveAllLinks();\n\n      // Rebuild graph from all nodes\n      await this.syncGraph();\n    } finally {\n      // Always resume watcher, even if sync fails\n      if (this.fileWatcher?.isWatching()) {\n        this.fileWatcher.resume();\n      }\n    }\n  }\n\n  async createNode(node: Node): Promise<void> {\n    // Use node.id as file path, not as the stable ID\n    const normalizedPath = normalizeId(node.id);\n    validatePathWithinSource(this.sourceRoot, normalizedPath);\n\n    const existingByPath = this.cache.getNodeByPath(join(this.sourceRoot, normalizedPath));\n    if (existingByPath) {\n      throw new Error(`Node already exists: ${normalizedPath}`);\n    }\n\n    const filePath = join(this.sourceRoot, normalizedPath);\n    const dir = dirname(filePath);\n    await mkdir(dir, { recursive: true });\n\n    // Generate fresh stable ID\n    const stableId = generateId();\n\n    const rawLinks = extractWikiLinks(node.content);\n    const parsed = {\n      id: stableId,\n      title: node.title,\n      tags: node.tags,\n      properties: node.properties,\n      content: node.content,\n      rawLinks,\n    };\n    const markdown = serializeToMarkdown(parsed);\n    await writeFile(filePath, markdown, 'utf-8');\n\n    // Extract wikilinks from content\n    let outgoingLinks = node.outgoingLinks;\n    if (node.content && (!outgoingLinks || outgoingLinks.length === 0)) {\n      outgoingLinks = rawLinks.map((link) => normalizeWikiLink(link));\n    }\n\n    const mtime = await getFileMtime(filePath);\n    const createdNode: Node = {\n      ...node,\n      id: stableId,\n      outgoingLinks,\n      sourceRef: {\n        type: 'file',\n        path: filePath,\n        lastModified: new Date(mtime),\n      },\n    };\n    this.cache.upsertNode(createdNode, 'file', filePath, mtime);\n\n    // Resolve wikilinks and rebuild graph\n    this.resolveAllLinks();\n    await this.syncGraph();\n  }\n\n  async updateNode(id: string, updates: NodeUpdates): Promise<void> {\n    // Try to find node by ID directly, by normalized path, or by source path\n    let existing = this.cache.getNode(id);\n    if (!existing) {\n      const normalizedId = normalizeId(id);\n      existing = this.cache.getNode(normalizedId);\n    }\n    if (!existing && (id.includes('.') || id.includes('/'))) {\n      const fullPath = join(this.sourceRoot, normalizeId(id));\n      existing = this.cache.getNodeByPath(fullPath);\n    }\n    if (!existing) {\n      throw new Error(`Node not found: ${id}`);\n    }\n\n    // Strip id from updates if present - original ID must be preserved\n    const { ...safeUpdates } = updates;\n\n    // Derive outgoingLinks from content (new or existing)\n    const contentForLinks = safeUpdates.content ?? existing.content;\n    const rawLinks = extractWikiLinks(contentForLinks);\n    const outgoingLinks = rawLinks.map((link) => normalizeWikiLink(link));\n\n    const updated: Node = {\n      ...existing,\n      ...safeUpdates,\n      outgoingLinks,\n      id: existing.id, // Preserve original ID\n    };\n\n    // Get file path from sourceRef (stable ID means path may differ from id)\n    const filePath = existing.sourceRef?.path ?? join(this.sourceRoot, existing.id);\n\n    const parsed = {\n      id: existing.id, // Write the stable ID back to frontmatter\n      title: updated.title,\n      tags: updated.tags,\n      properties: updated.properties,\n      content: updated.content,\n      rawLinks,\n    };\n    const markdown = serializeToMarkdown(parsed);\n    await writeFile(filePath, markdown, 'utf-8');\n\n    const mtime = await getFileMtime(filePath);\n    this.cache.upsertNode(updated, 'file', filePath, mtime);\n\n    // Resolve wikilinks and rebuild graph\n    this.resolveAllLinks();\n    await this.syncGraph();\n  }\n\n  async deleteNode(id: string): Promise<void> {\n    // Try to find node by ID directly, by normalized path, or by source path\n    let existing = this.cache.getNode(id);\n    if (!existing) {\n      const normalizedId = normalizeId(id);\n      existing = this.cache.getNode(normalizedId);\n    }\n    if (!existing && (id.includes('.') || id.includes('/'))) {\n      const fullPath = join(this.sourceRoot, normalizeId(id));\n      existing = this.cache.getNodeByPath(fullPath);\n    }\n    if (!existing) {\n      throw new Error(`Node not found: ${id}`);\n    }\n\n    // Get file path from sourceRef\n    const filePath = existing.sourceRef?.path ?? join(this.sourceRoot, existing.id);\n    await rm(filePath);\n    this.cache.deleteNode(existing.id);\n    if (this.vectorIndex) await this.vectorIndex.delete(existing.id);\n\n    // Rebuild graph without deleted node\n    await this.syncGraph();\n  }\n\n  async getNode(id: string): Promise<Node | null> {\n    // Try exact ID first (stable IDs are case-sensitive)\n    let node = this.cache.getNode(id);\n    if (node) return node;\n\n    // Fall back to normalized ID for path-based lookups\n    const normalizedId = normalizeId(id);\n    if (normalizedId !== id) {\n      node = this.cache.getNode(normalizedId);\n      if (node) return node;\n    }\n\n    // Try lookup by source path (for backwards compatibility with path-based queries)\n    if (id.includes('.') || id.includes('/')) {\n      const fullPath = join(this.sourceRoot, normalizedId);\n      node = this.cache.getNodeByPath(fullPath);\n    }\n\n    return node;\n  }\n\n  async getNodes(ids: string[]): Promise<Node[]> {\n    // Use getNode for each to leverage path-based fallback\n    const results: Node[] = [];\n    for (const id of ids) {\n      const node = await this.getNode(id);\n      if (node) results.push(node);\n    }\n    return results;\n  }\n\n  async getAllNodeIds(): Promise<string[]> {\n    const nodes = this.cache.getAllNodes();\n    return nodes.map((n) => n.id);\n  }\n\n  async searchByTags(tags: string[], mode: TagMode, limit?: number): Promise<Node[]> {\n    return this.cache.searchByTags(tags, mode, limit);\n  }\n\n  async resolveTitles(ids: string[]): Promise<Map<string, string>> {\n    return this.cache.resolveTitles(ids);\n  }\n\n  async listNodes(\n    filter: ListFilter,\n    options?: ListOptions\n  ): Promise<ListNodesResult> {\n    return this.cache.listNodes(filter, options);\n  }\n\n  async resolveNodes(\n    names: string[],\n    options?: ResolveOptions\n  ): Promise<ResolveResult[]> {\n    // For exact and fuzzy, delegate to cache\n    const strategy = options?.strategy ?? 'fuzzy';\n    if (strategy === 'exact' || strategy === 'fuzzy') {\n      return this.cache.resolveNodes(names, options);\n    }\n\n    // Semantic strategy: use vector search\n    // This requires embedding provider which DocStore doesn't have direct access to\n    // Return unmatched for now - GraphCore will handle semantic with embedding provider\n    return names.map((query) => ({ query, match: null, score: 0 }));\n  }\n\n  async nodesExist(ids: string[]): Promise<Map<string, boolean>> {\n    const result = new Map<string, boolean>();\n    for (const id of ids) {\n      const node = await this.getNode(id);\n      // Use normalized ID as key for consistency\n      result.set(normalizeId(id), node !== null);\n    }\n    return result;\n  }\n\n  hasEmbedding(id: string): boolean {\n    if (!this.vectorIndex) return false;\n    return this.vectorIndex.hasEmbedding(id);\n  }\n\n  close(): void {\n    this.stopWatching();\n    this.cache.close();\n    if (this.ownsVectorIndex && this.vectorIndex && 'close' in this.vectorIndex) {\n      (this.vectorIndex as { close: () => void }).close();\n    }\n  }\n\n  // Lifecycle hooks\n\n  async onRegister(): Promise<void> {\n    await this.sync();\n  }\n\n  async onUnregister(): Promise<void> {\n    this.close();\n  }\n\n  startWatching(onChange?: (changedIds: string[]) => void): Promise<void> {\n    if (this.fileWatcher?.isWatching()) {\n      throw new Error('Already watching. Call stopWatching() first.');\n    }\n\n    this.onChangeCallback = onChange;\n\n    if (!this.fileWatcher) {\n      this.fileWatcher = new FileWatcher({\n        root: this.sourceRoot,\n        extensions: this.registry.getExtensions(),\n        onBatch: (events) => this.handleWatcherBatch(events),\n      });\n    }\n\n    return this.fileWatcher.start();\n  }\n\n  stopWatching(): void {\n    if (this.fileWatcher) {\n      this.fileWatcher.stop();\n    }\n  }\n\n  isWatching(): boolean {\n    return this.fileWatcher?.isWatching() ?? false;\n  }\n\n  private async handleWatcherBatch(events: Map<string, FileEventType>): Promise<void> {\n    // Pause watcher during batch processing to avoid triggering events from ID writebacks\n    this.fileWatcher?.pause();\n\n    const processedIds: string[] = [];\n\n    try {\n      for (const [pathId, event] of events) {\n        // pathId is the normalized file path from the watcher (e.g., \"folder/file.md\")\n        const filePath = join(this.sourceRoot, pathId);\n\n        try {\n          if (event === 'unlink') {\n            // Look up node by source path since pathId is a file path, not a stable ID\n            const existing = this.cache.getNodeByPath(filePath);\n            if (existing) {\n              this.cache.deleteNode(existing.id);\n              if (this.vectorIndex) {\n                try {\n                  await this.vectorIndex.delete(existing.id);\n                } catch (vectorErr) {\n                  console.warn(`Vector delete failed for ${pathId}:`, vectorErr);\n                }\n              }\n              processedIds.push(existing.id);\n            }\n          } else {\n            // add or change - use parseAndMaybeWriteId to ensure stable IDs\n            const mtime = await getFileMtime(filePath);\n            const { node, newMtime } = await this.parseAndMaybeWriteId(filePath, mtime);\n            // Use new mtime if ID was written back, otherwise original\n            const finalMtime = newMtime ?? mtime;\n\n            // Check if there's an existing node with a different ID for this path\n            // (can happen if file was modified externally and lost its ID)\n            const existingByPath = this.cache.getNodeByPath(filePath);\n            if (existingByPath && existingByPath.id !== node.id) {\n              // Delete the old node to avoid duplicates\n              this.cache.deleteNode(existingByPath.id);\n              if (this.vectorIndex) {\n                try {\n                  await this.vectorIndex.delete(existingByPath.id);\n                } catch {\n                  // Ignore vector delete failures for cleanup\n                }\n              }\n            }\n\n            this.cache.upsertNode(node, 'file', filePath, finalMtime);\n            processedIds.push(node.id);\n          }\n        } catch (err) {\n          console.warn(`Failed to process file change for ${pathId}:`, err);\n        }\n      }\n\n      // Resolve wiki-links and rebuild graph after processing all changes\n      if (processedIds.length > 0) {\n        this.resolveAllLinks();\n        await this.syncGraph();\n      }\n\n      // Call callback if provided\n      if (this.onChangeCallback && processedIds.length > 0) {\n        this.onChangeCallback(processedIds);\n      }\n    } finally {\n      // Resume watcher after batch processing\n      this.fileWatcher?.resume();\n    }\n  }\n\n  private resolveAllLinks(): void {\n    const nodes = this.cache.getAllNodes();\n\n    // Build title-based index for wikilink resolution\n    // buildFilenameIndex indexes by title (primary) and filename (fallback)\n    const filenameIndex = buildFilenameIndex(nodes);\n    const validNodeIds = new Set(nodes.map((n) => n.id));\n\n    // Build path-to-ID mapping for partial path resolution (e.g., [[folder/note]])\n    const pathToId = new Map<string, string>();\n    for (const node of nodes) {\n      if (node.sourceRef?.path) {\n        const relativePath = relative(this.sourceRoot, node.sourceRef.path);\n        const normalizedPath = normalizeId(relativePath);\n        pathToId.set(normalizedPath, node.id);\n      }\n    }\n\n    // Resolve links for each node\n    for (const node of nodes) {\n      const resolvedIds = resolveLinks(\n        node.outgoingLinks,\n        filenameIndex,\n        validNodeIds\n      );\n\n      // Second pass: resolve any remaining paths (like \"folder/target.md\") to stable IDs\n      const finalIds = resolvedIds.map((link) => {\n        // If already a valid stable ID, keep it\n        if (validNodeIds.has(link)) {\n          return link;\n        }\n        // Try path-based lookup for partial paths\n        const stableId = pathToId.get(link);\n        return stableId ?? link;\n      });\n\n      if (finalIds.some((r, i) => r !== node.outgoingLinks[i])) {\n        this.cache.updateOutgoingLinks(node.id, finalIds);\n      }\n    }\n  }\n\n  // ── Graph operations (override for path-based lookup) ─────\n\n  async getNeighbors(id: string, options: { direction: 'in' | 'out' | 'both'; limit?: number }): Promise<Node[]> {\n    // Resolve path to stable ID if needed\n    const node = await this.getNode(id);\n    if (!node) return [];\n    return super.getNeighbors(node.id, options);\n  }\n\n  async findPath(source: string, target: string): Promise<string[] | null> {\n    // Resolve paths to stable IDs\n    const sourceNode = await this.getNode(source);\n    const targetNode = await this.getNode(target);\n    if (!sourceNode || !targetNode) return null;\n    return super.findPath(sourceNode.id, targetNode.id);\n  }\n\n  async getHubs(metric: 'in_degree' | 'out_degree', limit: number): Promise<Array<[string, number]>> {\n    return super.getHubs(metric, limit);\n  }\n\n  // ── StoreProvider abstract method implementations ─────────\n\n  protected async loadAllNodes(): Promise<Node[]> {\n    return this.cache.getAllNodes();\n  }\n\n  protected async getNodesByIds(ids: string[]): Promise<Node[]> {\n    return this.cache.getNodes(ids);\n  }\n\n  protected onCentralityComputed(centrality: Map<string, CentralityMetrics>): void {\n    const now = Date.now();\n    for (const [id, metrics] of centrality) {\n      this.cache.storeCentrality(id, 0, metrics.inDegree, metrics.outDegree, now);\n    }\n  }\n\n  /**\n   * Parse a file and optionally write a generated ID back if missing.\n   * Returns the node (with stable ID) and whether a write occurred.\n   */\n  private async parseAndMaybeWriteId(\n    filePath: string,\n    originalMtime: number\n  ): Promise<{ node: Node; needsIdWrite: boolean; newMtime?: number }> {\n    const content = await readFileContent(filePath);\n    const relativePath = relative(this.sourceRoot, filePath);\n    const ext = extname(filePath).toLowerCase();\n    const actualMtime = new Date(originalMtime);\n\n    const context: FileContext = {\n      absolutePath: filePath,\n      relativePath,\n      extension: ext,\n      mtime: actualMtime,\n    };\n\n    const { node, needsIdWrite } = this.registry.parse(content, context);\n\n    if (!needsIdWrite) {\n      return { node, needsIdWrite: false };\n    }\n\n    // Generate and write ID back to file\n    const newId = generateId();\n    const writebackSuccess = await this.writeIdBack(filePath, newId, originalMtime, content);\n\n    if (!writebackSuccess) {\n      // File was modified during sync, skip caching this file\n      // Return the node but signal that caching should be skipped\n      console.warn(`File modified during sync, skipping ID writeback: ${filePath}`);\n      return { node, needsIdWrite: true };\n    }\n\n    // Update node with the new stable ID\n    const updatedNode: Node = {\n      ...node,\n      id: newId,\n    };\n\n    // Get new mtime after write\n    const newMtime = await getFileMtime(filePath);\n    return { node: updatedNode, needsIdWrite: true, newMtime };\n  }\n\n  /**\n   * Write a generated ID back to file's frontmatter.\n   * Returns false if file was modified since originalMtime (race condition).\n   */\n  private async writeIdBack(\n    filePath: string,\n    nodeId: string,\n    originalMtime: number,\n    originalContent: string\n  ): Promise<boolean> {\n    // Check if file was modified\n    const currentStat = await stat(filePath);\n    if (currentStat.mtimeMs !== originalMtime) {\n      return false;\n    }\n\n    // Parse and update frontmatter\n    const parsed = parseMarkdown(originalContent);\n    parsed.id = nodeId;\n    const newContent = serializeToMarkdown(parsed);\n    await writeFile(filePath, newContent, 'utf-8');\n    return true;\n  }\n}\n\nexport { Cache } from './cache.js';\nexport {\n  parseMarkdown,\n  extractWikiLinks,\n  normalizeId,\n  titleFromPath,\n  serializeToMarkdown,\n} from './parser.js';\nexport { FileWatcher, EXCLUDED_DIRS, type FileEventType } from './watcher.js';\nexport {\n  getFileMtime,\n  validatePathWithinSource,\n  collectFiles,\n  readFileContent,\n} from './file-operations.js';\nexport type { FormatReader, FileContext } from './types.js';\nexport { ReaderRegistry } from './reader-registry.js';\nexport { MarkdownReader } from './readers/index.js';\nexport { createDefaultRegistry };\n","import { DirectedGraph } from 'graphology';\nimport type { Node } from '../types/node.js';\n\n/**\n * Build a directed graph from an array of nodes.\n * Edges are derived from each node's outgoingLinks.\n * Links to non-existent nodes are ignored.\n */\nexport function buildGraph(nodes: Node[]): DirectedGraph {\n  const graph = new DirectedGraph();\n\n  // First pass: add all nodes\n  const nodeIds = new Set<string>();\n  for (const node of nodes) {\n    graph.addNode(node.id);\n    nodeIds.add(node.id);\n  }\n\n  // Second pass: add edges (only to existing nodes)\n  for (const node of nodes) {\n    const seen = new Set<string>();\n    for (const target of node.outgoingLinks) {\n      // Skip if target doesn't exist or we've already added this edge\n      if (!nodeIds.has(target) || seen.has(target)) {\n        continue;\n      }\n      seen.add(target);\n      graph.addDirectedEdge(node.id, target);\n    }\n  }\n\n  return graph;\n}\n","import type { DirectedGraph } from 'graphology';\nimport { bidirectional } from 'graphology-shortest-path';\nimport type { NeighborOptions, Metric } from '../types/provider.js';\nimport { MinHeap } from '../utils/heap.js';\n\n/**\n * Get neighbor IDs based on direction.\n * Returns empty array if node doesn't exist.\n * Uses iterator-based traversal for early termination when limit is specified.\n */\nexport function getNeighborIds(\n  graph: DirectedGraph,\n  id: string,\n  options: NeighborOptions\n): string[] {\n  if (!graph.hasNode(id)) {\n    return [];\n  }\n\n  const limit = options.limit;\n  if (limit !== undefined && limit <= 0) {\n    return [];\n  }\n\n  const maxCount = limit ?? Infinity;\n  const direction = options.direction;\n\n  // For 'both' direction, use graphology's neighborEntries which deduplicates\n  if (direction === 'both') {\n    const neighbors: string[] = [];\n    for (const entry of graph.neighborEntries(id)) {\n      if (neighbors.length >= maxCount) break;\n      neighbors.push(entry.neighbor);\n    }\n    return neighbors;\n  }\n\n  // For single direction, iterate directly\n  const neighbors: string[] = [];\n  const iterator =\n    direction === 'in'\n      ? graph.inNeighborEntries(id)\n      : graph.outNeighborEntries(id);\n\n  for (const entry of iterator) {\n    if (neighbors.length >= maxCount) break;\n    neighbors.push(entry.neighbor);\n  }\n\n  return neighbors;\n}\n\n/**\n * Find shortest path between two nodes.\n * Returns array of node IDs or null if no path exists.\n */\nexport function findPath(\n  graph: DirectedGraph,\n  source: string,\n  target: string\n): string[] | null {\n  if (!graph.hasNode(source) || !graph.hasNode(target)) {\n    return null;\n  }\n\n  if (source === target) {\n    return [source];\n  }\n\n  const path = bidirectional(graph, source, target);\n  return path;\n}\n\n/**\n * Get top nodes by centrality metric.\n * Returns array of [id, score] tuples sorted descending.\n * Uses min-heap for O(n log k) complexity instead of O(n log n).\n */\nexport function getHubs(\n  graph: DirectedGraph,\n  metric: Metric,\n  limit: number\n): Array<[string, number]> {\n  if (limit <= 0) {\n    return [];\n  }\n\n  const heap = new MinHeap<[string, number]>((a, b) => a[1] - b[1]);\n\n  graph.forEachNode((id) => {\n    const score = metric === 'in_degree' ? graph.inDegree(id) : graph.outDegree(id);\n\n    if (heap.size() < limit) {\n      heap.push([id, score]);\n    } else if (score > heap.peek()![1]) {\n      heap.pop();\n      heap.push([id, score]);\n    }\n  });\n\n  // Sort by score descending, then by node ID ascending for deterministic tie-breaking\n  return heap.toArray().sort((a, b) => {\n    const scoreDiff = b[1] - a[1];\n    if (scoreDiff !== 0) return scoreDiff;\n    return a[0].localeCompare(b[0]);\n  });\n}\n","import type { DirectedGraph } from 'graphology';\nimport type { CentralityMetrics } from '../types/provider.js';\n\n/**\n * Compute centrality metrics for all nodes.\n * For MVP, computes in_degree and out_degree only.\n */\nexport function computeCentrality(\n  graph: DirectedGraph\n): Map<string, CentralityMetrics> {\n  const result = new Map<string, CentralityMetrics>();\n\n  graph.forEachNode((id) => {\n    result.set(id, {\n      inDegree: graph.inDegree(id),\n      outDegree: graph.outDegree(id),\n    });\n  });\n\n  return result;\n}\n","import { DirectedGraph } from 'graphology';\nimport type { Node } from '../types/node.js';\nimport type { NeighborOptions, Metric, CentralityMetrics } from '../types/provider.js';\nimport { buildGraph } from './builder.js';\nimport { getNeighborIds, findPath, getHubs } from './traversal.js';\nimport { computeCentrality } from './analysis.js';\n\nexport class GraphNotReadyError extends Error {\n  constructor() {\n    super('Graph not built. Call build() before querying.');\n    this.name = 'GraphNotReadyError';\n  }\n}\n\nexport class GraphManager {\n  private graph: DirectedGraph | null = null;\n\n  /** Build graph and return centrality metrics. Caller stores as needed. */\n  build(nodes: Node[]): Map<string, CentralityMetrics> {\n    this.graph = buildGraph(nodes);\n    return computeCentrality(this.graph);\n  }\n\n  /** Throws GraphNotReadyError if not built. Returns graph for query use. */\n  assertReady(): DirectedGraph {\n    if (!this.graph) throw new GraphNotReadyError();\n    return this.graph;\n  }\n\n  isReady(): boolean {\n    return this.graph !== null;\n  }\n\n  getNeighborIds(id: string, options: NeighborOptions): string[] {\n    return getNeighborIds(this.assertReady(), id, options);\n  }\n\n  findPath(source: string, target: string): string[] | null {\n    return findPath(this.assertReady(), source, target);\n  }\n\n  getHubs(metric: Metric, limit: number): Array<[string, number]> {\n    return getHubs(this.assertReady(), metric, limit);\n  }\n}\n","import type { Node, NodeUpdates } from '../../types/node.js';\nimport type {\n  Metric,\n  CentralityMetrics,\n  VectorIndex,\n  VectorSearchResult,\n  TagMode,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../../types/provider.js';\nimport type { NeighborOptions } from '../../types/edge.js';\nimport { GraphManager } from '../../graph/manager.js';\nimport { resolveNames } from './resolve.js';\n\nexport interface StoreProviderOptions {\n  vectorIndex?: VectorIndex;\n}\n\nexport abstract class StoreProvider {\n  protected readonly graphManager = new GraphManager();\n  protected readonly vectorIndex: VectorIndex | null;\n\n  constructor(options?: StoreProviderOptions) {\n    this.vectorIndex = options?.vectorIndex ?? null;\n  }\n\n  // ── Abstract methods (subclasses MUST implement) ───────────\n\n  protected abstract loadAllNodes(): Promise<Node[]>;\n  protected abstract getNodesByIds(ids: string[]): Promise<Node[]>;\n  abstract createNode(node: Node): Promise<void>;\n  abstract updateNode(id: string, updates: NodeUpdates): Promise<void>;\n  abstract deleteNode(id: string): Promise<void>;\n  abstract getNode(id: string): Promise<Node | null>;\n  abstract getNodes(ids: string[]): Promise<Node[]>;\n  abstract close(): void;\n\n  // ── Graph operations (delegate to GraphManager) ────────────\n\n  async getNeighbors(id: string, options: NeighborOptions): Promise<Node[]> {\n    if (!this.graphManager.isReady()) return [];\n    const neighborIds = this.graphManager.getNeighborIds(id, options);\n    return this.getNodesByIds(neighborIds);\n  }\n\n  async findPath(source: string, target: string): Promise<string[] | null> {\n    if (!this.graphManager.isReady()) return null;\n    return this.graphManager.findPath(source, target);\n  }\n\n  async getHubs(metric: Metric, limit: number): Promise<Array<[string, number]>> {\n    if (!this.graphManager.isReady()) return [];\n    return this.graphManager.getHubs(metric, limit);\n  }\n\n  // ── Vector operations (delegate to VectorIndex) ────────────\n\n  async storeEmbedding(id: string, vector: number[], model: string): Promise<void> {\n    if (!this.vectorIndex) throw new Error('No VectorIndex configured');\n    return this.vectorIndex.store(id, vector, model);\n  }\n\n  async searchByVector(vector: number[], limit: number): Promise<VectorSearchResult[]> {\n    if (!this.vectorIndex) throw new Error('No VectorIndex configured');\n    return this.vectorIndex.search(vector, limit);\n  }\n\n  // ── Discovery ──────────────────────────────────────────────\n\n  async getRandomNode(tags?: string[]): Promise<Node | null> {\n    let candidates: Node[];\n    if (tags && tags.length > 0) {\n      candidates = await this.searchByTags(tags, 'any');\n    } else {\n      candidates = await this.loadAllNodes();\n    }\n    if (candidates.length === 0) return null;\n    return candidates[Math.floor(Math.random() * candidates.length)]!;\n  }\n\n  // ── Default implementations (overridable) ──────────────────\n\n  async searchByTags(tags: string[], mode: TagMode, limit?: number): Promise<Node[]> {\n    const allNodes = await this.loadAllNodes();\n    const lowerTags = tags.map(t => t.toLowerCase());\n    let results = allNodes.filter(node => {\n      const nodeTags = node.tags.map(t => t.toLowerCase());\n      return mode === 'any'\n        ? lowerTags.some(t => nodeTags.includes(t))\n        : lowerTags.every(t => nodeTags.includes(t));\n    });\n    if (limit !== undefined) results = results.slice(0, limit);\n    return results;\n  }\n\n  async listNodes(filter: ListFilter, options?: ListOptions): Promise<ListNodesResult> {\n    let nodes = await this.loadAllNodes();\n    if (filter.tag) {\n      const lower = filter.tag.toLowerCase();\n      nodes = nodes.filter(n => n.tags.some(t => t.toLowerCase() === lower));\n    }\n    if (filter.path) {\n      const lowerPath = filter.path.toLowerCase();\n      nodes = nodes.filter(n => n.id.startsWith(lowerPath));\n    }\n    const total = nodes.length;\n    const offset = options?.offset ?? 0;\n    const limit = Math.min(options?.limit ?? 100, 1000);\n    const sliced = nodes.slice(offset, offset + limit);\n    return {\n      nodes: sliced.map(n => ({ id: n.id, title: n.title })),\n      total,\n    };\n  }\n\n  async nodesExist(ids: string[]): Promise<Map<string, boolean>> {\n    if (ids.length === 0) return new Map();\n    const found = await this.getNodesByIds(ids);\n    const foundIds = new Set(found.map(n => n.id));\n    const result = new Map<string, boolean>();\n    for (const id of ids) {\n      result.set(id, foundIds.has(id));\n    }\n    return result;\n  }\n\n  async resolveTitles(ids: string[]): Promise<Map<string, string>> {\n    if (ids.length === 0) return new Map();\n    const nodes = await this.getNodesByIds(ids);\n    const result = new Map<string, string>();\n    for (const node of nodes) {\n      result.set(node.id, node.title);\n    }\n    return result;\n  }\n\n  async resolveNodes(names: string[], options?: ResolveOptions): Promise<ResolveResult[]> {\n    const strategy = options?.strategy ?? 'fuzzy';\n    if (strategy === 'semantic') {\n      return names.map(query => ({ query, match: null, score: 0 }));\n    }\n    const allNodes = await this.loadAllNodes();\n    let candidates = allNodes.map(n => ({ id: n.id, title: n.title }));\n    if (options?.tag) {\n      const lower = options.tag.toLowerCase();\n      const filtered = allNodes.filter(n => n.tags.some(t => t.toLowerCase() === lower));\n      candidates = filtered.map(n => ({ id: n.id, title: n.title }));\n    }\n    if (options?.path) {\n      const lowerPath = options.path.toLowerCase();\n      candidates = candidates.filter(c => c.id.startsWith(lowerPath));\n    }\n    return resolveNames(names, candidates, {\n      strategy,\n      threshold: options?.threshold ?? 0.7,\n    });\n  }\n\n  // ── Graph lifecycle ────────────────────────────────────────\n\n  protected async syncGraph(): Promise<void> {\n    const nodes = await this.loadAllNodes();\n    const centrality = this.graphManager.build(nodes);\n    this.onCentralityComputed(centrality);\n  }\n\n  protected onCentralityComputed(_centrality: Map<string, CentralityMetrics>): void {\n    // Default no-op. Subclasses override to persist centrality.\n  }\n}\n","import matter from 'gray-matter';\n\n/** Reserved frontmatter keys that are extracted to dedicated fields */\nexport const RESERVED_FRONTMATTER_KEYS = ['id', 'title', 'tags'] as const;\n\nexport interface ParsedMarkdown {\n  /** Stable frontmatter ID (12-char nanoid) */\n  id?: string;\n  title: string | undefined;\n  tags: string[];\n  properties: Record<string, unknown>;\n  content: string;\n  /** Raw wiki-link targets before normalization (e.g., [\"Other Note\", \"folder/file\"]) */\n  rawLinks: string[];\n}\n\n/** Set of reserved keys for O(1) lookup */\nconst RESERVED_KEYS_SET = new Set<string>(RESERVED_FRONTMATTER_KEYS);\n\n/**\n * Parse markdown with YAML frontmatter.\n * Handles missing/malformed frontmatter gracefully.\n */\nexport function parseMarkdown(raw: string): ParsedMarkdown {\n  let parsed: matter.GrayMatterFile<string>;\n  try {\n    parsed = matter(raw);\n  } catch {\n    // Malformed frontmatter - return content as-is\n    return {\n      title: undefined,\n      tags: [],\n      properties: {},\n      content: raw,\n      rawLinks: extractWikiLinks(raw),\n    };\n  }\n\n  const data = parsed.data as Record<string, unknown>;\n\n  // Extract id - must be a string\n  const id = typeof data['id'] === 'string' ? data['id'] : undefined;\n\n  // Extract title\n  const title = typeof data['title'] === 'string' ? data['title'] : undefined;\n\n  // Extract tags - must be an array of strings\n  let tags: string[] = [];\n  if (Array.isArray(data['tags'])) {\n    tags = data['tags'].filter((t): t is string => typeof t === 'string');\n  }\n\n  // Extract other properties (excluding all reserved keys)\n  const properties: Record<string, unknown> = {};\n  for (const [key, value] of Object.entries(data)) {\n    if (!RESERVED_KEYS_SET.has(key)) {\n      properties[key] = value;\n    }\n  }\n\n  const content = parsed.content.trim();\n\n  const result: ParsedMarkdown = {\n    title,\n    tags,\n    properties,\n    content,\n    rawLinks: extractWikiLinks(content),\n  };\n\n  // Only include id if it's a string (exactOptionalPropertyTypes)\n  if (id !== undefined) {\n    result.id = id;\n  }\n\n  return result;\n}\n\n/**\n * Extract wiki-link targets from markdown content.\n * Ignores links inside code blocks and inline code.\n * Deduplicates results.\n */\nexport function extractWikiLinks(content: string): string[] {\n  // Remove code blocks first\n  const withoutCodeBlocks = content.replace(/```[\\s\\S]*?```/g, '');\n\n  // Remove inline code\n  const withoutInlineCode = withoutCodeBlocks.replace(/`[^`]+`/g, '');\n\n  // Match wiki links: [[target]] or [[target|display]]\n  const linkRegex = /\\[\\[([^\\]|]+)(?:\\|[^\\]]+)?\\]\\]/g;\n  const seen = new Set<string>();\n  const links: string[] = [];\n\n  let match;\n  while ((match = linkRegex.exec(withoutInlineCode)) !== null) {\n    const target = match[1]?.trim();\n    if (target && !seen.has(target)) {\n      seen.add(target);\n      links.push(target);\n    }\n  }\n\n  return links;\n}\n\nimport { normalizePath } from './normalize.js';\n\n/**\n * Normalize a file path to a consistent ID format.\n * @deprecated Use normalizePath from './normalize.js' directly.\n */\nexport const normalizeId = normalizePath;\n\n/**\n * Derive a human-readable title from a file path.\n * - Removes directory prefix\n * - Removes extension\n * - Replaces hyphens/underscores with spaces\n * - Title-cases words\n */\nexport function titleFromPath(path: string): string {\n  // Get filename without directory\n  const parts = path.split(/[/\\\\]/);\n  // parts is always non-empty (even '' splits to [''])\n  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion\n  const filename = parts.at(-1)!;\n\n  // Remove extension\n  const withoutExt = filename.replace(/\\.[^.]+$/, '');\n\n  // Replace hyphens and underscores with spaces, collapse multiples\n  const spaced = withoutExt.replace(/[-_]+/g, ' ').toLowerCase();\n\n  // Title-case each word\n  return spaced\n    .split(' ')\n    .filter((w) => w.length > 0)\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\n    .join(' ');\n}\n\n/**\n * Serialize parsed markdown back to a string with YAML frontmatter.\n * Omits frontmatter if no metadata is present.\n * Places id FIRST in frontmatter for consistency.\n */\nexport function serializeToMarkdown(parsed: ParsedMarkdown): string {\n  const hasFrontmatter =\n    parsed.id !== undefined ||\n    parsed.title !== undefined ||\n    parsed.tags.length > 0 ||\n    Object.keys(parsed.properties).length > 0;\n\n  if (!hasFrontmatter) {\n    return parsed.content;\n  }\n\n  // Build frontmatter object with id FIRST\n  // Using insertion order which is preserved in modern JS\n  const frontmatter: Record<string, unknown> = {};\n\n  if (parsed.id !== undefined) {\n    frontmatter['id'] = parsed.id;\n  }\n\n  if (parsed.title !== undefined) {\n    frontmatter['title'] = parsed.title;\n  }\n\n  if (parsed.tags.length > 0) {\n    frontmatter['tags'] = parsed.tags;\n  }\n\n  // Add other properties\n  for (const [key, value] of Object.entries(parsed.properties)) {\n    frontmatter[key] = value;\n  }\n\n  // Use gray-matter to stringify\n  return matter.stringify(parsed.content, frontmatter);\n}\n","/**\n * Normalization utilities for file paths and wikilink targets.\n *\n * Single source of truth for path normalization in DocStore.\n */\n\n/**\n * Check if a path has a file extension.\n * Extension must be 1-4 chars and contain at least one letter\n * (excludes numeric-only like .2024, .123).\n */\nexport function hasFileExtension(path: string): boolean {\n  const match = path.match(/\\.([a-z0-9]{1,4})$/i);\n  if (!match?.[1]) return false;\n  return /[a-z]/i.test(match[1]);\n}\n\n/**\n * Normalize a file path: lowercase, forward slashes.\n * Use for file system paths and node IDs.\n */\nexport function normalizePath(path: string): string {\n  return path.toLowerCase().replace(/\\\\/g, '/');\n}\n\n/**\n * Normalize a wikilink target to a node ID.\n * Lowercases, converts backslashes, appends .md if no extension.\n * Use for resolving [[wikilinks]] to node IDs.\n */\nexport function normalizeLinkTarget(target: string): string {\n  let normalized = target.trim().toLowerCase().replace(/\\\\/g, '/');\n\n  if (!hasFileExtension(normalized)) {\n    normalized += '.md';\n  }\n\n  return normalized;\n}\n","/**\n * FileWatcher - Pure file system event emitter\n *\n * Responsibilities:\n * - Wraps chokidar\n * - Filters (.md only, excluded dirs)\n * - Coalesces events\n * - Debounces\n * - Emits batched events via callback\n */\n\nimport { watch, type FSWatcher } from 'chokidar';\nimport { relative, extname } from 'node:path';\nimport { EXCLUDED_DIRS } from './constants.js';\n\n// Re-export for backwards compatibility\nexport { EXCLUDED_DIRS } from './constants.js';\n\nexport type FileEventType = 'add' | 'change' | 'unlink';\n\nexport interface FileWatcherOptions {\n  root: string;\n  /** File extensions to watch (e.g., new Set(['.md', '.markdown'])). Required. */\n  extensions: ReadonlySet<string>;\n  debounceMs?: number;\n  /** Called after debounce with coalesced events. Exceptions (sync or async) are\n   *  logged and swallowed; watcher continues operating. */\n  onBatch: (events: Map<string, FileEventType>) => void | Promise<void>;\n}\n\nconst DEFAULT_DEBOUNCE_MS = 1000;\n\nexport class FileWatcher {\n  private readonly root: string;\n  private readonly extensions: ReadonlySet<string>;\n  private readonly debounceMs: number;\n  private readonly onBatch: (events: Map<string, FileEventType>) => void | Promise<void>;\n\n  private watcher: FSWatcher | null = null;\n  private debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  private pendingChanges: Map<string, FileEventType> = new Map();\n  private isPaused = false;\n\n  constructor(options: FileWatcherOptions) {\n    this.root = options.root;\n    this.extensions = options.extensions;\n    this.debounceMs = options.debounceMs ?? DEFAULT_DEBOUNCE_MS;\n    this.onBatch = options.onBatch;\n  }\n\n  start(): Promise<void> {\n    if (this.watcher) {\n      return Promise.reject(new Error('Already watching. Call stop() first.'));\n    }\n\n    return new Promise((resolve, reject) => {\n      let isReady = false;\n\n      this.watcher = watch(this.root, {\n        ignoreInitial: true,\n        ignored: [...EXCLUDED_DIRS].map((dir) => `**/${dir}/**`),\n        awaitWriteFinish: {\n          stabilityThreshold: 100,\n        },\n        followSymlinks: false,\n      });\n\n      this.watcher\n        .on('ready', () => {\n          isReady = true;\n          resolve();\n        })\n        .on('add', (path) => this.queueChange(path, 'add'))\n        .on('change', (path) => this.queueChange(path, 'change'))\n        .on('unlink', (path) => this.queueChange(path, 'unlink'))\n        .on('error', (err) => {\n          if ((err as NodeJS.ErrnoException).code === 'EMFILE') {\n            console.error(\n              'File watcher hit file descriptor limit. ' +\n                'Try: ulimit -n 65536 or reduce watched files.'\n            );\n          }\n          if (isReady) {\n            // Error after ready - log and continue (graceful degradation)\n            console.error('FileWatcher error:', err);\n          } else {\n            // Error during startup - reject the promise\n            reject(err);\n          }\n        });\n    });\n  }\n\n  stop(): void {\n    if (this.debounceTimer) {\n      clearTimeout(this.debounceTimer);\n      this.debounceTimer = null;\n    }\n    this.pendingChanges.clear();\n\n    if (this.watcher) {\n      this.watcher.close();\n      this.watcher = null;\n    }\n  }\n\n  isWatching(): boolean {\n    return this.watcher !== null;\n  }\n\n  pause(): void {\n    this.isPaused = true;\n  }\n\n  resume(): void {\n    this.isPaused = false;\n  }\n\n  flush(): void {\n    if (this.debounceTimer) {\n      clearTimeout(this.debounceTimer);\n      this.debounceTimer = null;\n    }\n\n    if (this.pendingChanges.size === 0) {\n      return;\n    }\n\n    const batch = new Map(this.pendingChanges);\n    this.pendingChanges.clear();\n\n    try {\n      const result = this.onBatch(batch);\n      // Handle async onBatch (returns Promise)\n      if (result && typeof (result as Promise<void>).catch === 'function') {\n        (result as Promise<void>).catch((err) => {\n          console.error('FileWatcher onBatch callback threw an error:', err);\n        });\n      }\n    } catch (err) {\n      console.error('FileWatcher onBatch callback threw an error:', err);\n    }\n  }\n\n  private queueChange(filePath: string, event: FileEventType): void {\n    if (this.isPaused) return;\n\n    const relativePath = relative(this.root, filePath);\n\n    // Filter by extension using path.extname for correctness\n    const ext = extname(filePath).toLowerCase();\n    if (!ext || !this.extensions.has(ext)) {\n      return;\n    }\n\n    // Filter: excluded directories\n    const pathParts = relativePath.split('/');\n    for (const part of pathParts) {\n      if (EXCLUDED_DIRS.has(part)) {\n        return;\n      }\n    }\n\n    // Normalize ID (lowercase, forward slashes)\n    const id = relativePath.toLowerCase().replace(/\\\\/g, '/');\n\n    // Apply coalescing rules\n    const existing = this.pendingChanges.get(id);\n\n    if (existing) {\n      if (existing === 'add' && event === 'change') {\n        // add + change = add (keep as add)\n        return;\n      } else if (existing === 'add' && event === 'unlink') {\n        // add + unlink = remove from queue\n        this.pendingChanges.delete(id);\n        // If queue is now empty, clear timer and return early (no wasted flush)\n        if (this.pendingChanges.size === 0) {\n          if (this.debounceTimer) {\n            clearTimeout(this.debounceTimer);\n            this.debounceTimer = null;\n          }\n          return;\n        }\n      } else if (existing === 'change' && event === 'unlink') {\n        // change + unlink = unlink\n        this.pendingChanges.set(id, 'unlink');\n      } else if (existing === 'change' && event === 'add') {\n        // change + add = add (delete was missed, treat as new file)\n        this.pendingChanges.set(id, 'add');\n      } else if (existing === 'unlink' && event === 'add') {\n        // unlink + add = add (file deleted then re-created)\n        this.pendingChanges.set(id, 'add');\n      } else if (existing === 'unlink' && event === 'change') {\n        // unlink + change = unlink (spurious change ignored)\n        return;\n      }\n      // change + change = change (already set, no action needed)\n    } else {\n      this.pendingChanges.set(id, event);\n    }\n\n    // Reset debounce timer\n    if (this.debounceTimer) {\n      clearTimeout(this.debounceTimer);\n    }\n\n    this.debounceTimer = setTimeout(() => {\n      this.flush();\n    }, this.debounceMs);\n  }\n}\n","/**\n * Directories excluded from file scanning and watching.\n * Hidden directories (starting with .) and common non-content folders.\n */\nexport const EXCLUDED_DIRS: ReadonlySet<string> = new Set([\n  '.roux',\n  'node_modules',\n  '.git',\n  '.obsidian',\n]);\n","/**\n * Pure functions for wiki-link resolution.\n * Extracted from DocStore to reduce file size and improve testability.\n */\n\nimport {\n  hasFileExtension as hasFileExtensionImpl,\n  normalizeLinkTarget,\n} from './normalize.js';\n\n/**\n * Check if a path has a file extension.\n * @deprecated Use hasFileExtension from './normalize.js' directly.\n */\nexport const hasFileExtension = hasFileExtensionImpl;\n\n/**\n * Normalize a wiki-link target to an ID.\n * @deprecated Use normalizeLinkTarget from './normalize.js' directly.\n */\nexport const normalizeWikiLink = normalizeLinkTarget;\n\n/**\n * Node shape for building filename index.\n * Uses stable nanoid-based IDs with title and optional sourceRef.\n */\ninterface IndexableNode {\n  id: string;\n  title: string;\n  sourceRef?: { path?: string };\n}\n\n/**\n * Build an index mapping titles and filenames to node IDs.\n * Used for resolving wiki-links like [[My Note]] to their stable IDs.\n *\n * Resolution priority:\n * 1. Title (primary) - always indexed if non-empty\n * 2. Filename from sourceRef.path (fallback) - indexed if different from title\n */\nexport function buildFilenameIndex(\n  nodes: Iterable<IndexableNode>\n): Map<string, string[]> {\n  const index = new Map<string, string[]>();\n\n  for (const node of nodes) {\n    const path = node.sourceRef?.path ?? '';\n    const titleKey = node.title.toLowerCase();\n\n    // Warn if completely unindexable\n    if (!titleKey && !path) {\n      console.warn(\n        `Node ${node.id} has no title or path — link resolution will fail`\n      );\n    }\n\n    // Index by title (skip if empty)\n    if (titleKey) {\n      const existing = index.get(titleKey) ?? [];\n      existing.push(node.id);\n      index.set(titleKey, existing);\n    }\n\n    // Index by filename from path (if different from title)\n    if (path) {\n      const filename = path\n        .split('/')\n        .pop()\n        ?.replace(/\\.[^.]+$/, '')\n        .toLowerCase();\n      if (filename && filename !== titleKey) {\n        const existing = index.get(filename) ?? [];\n        existing.push(node.id);\n        index.set(filename, existing);\n      }\n    }\n  }\n\n  // Sort alphabetically for deterministic collision resolution\n  for (const ids of index.values()) {\n    ids.sort();\n  }\n\n  return index;\n}\n\n/**\n * Resolve an array of outgoing links to their full node IDs.\n * Pure function - returns resolved links without mutating anything.\n *\n * Resolution rules:\n * 1. If link already matches a valid node ID, keep it\n * 2. If link contains '/', keep it as-is (partial paths don't resolve)\n * 3. For bare filenames, look up in the filename index (after stripping .md)\n * 4. If no match found, try space/dash variant\n * 5. If still no match, keep original link\n */\nexport function resolveLinks(\n  outgoingLinks: string[],\n  filenameIndex: Map<string, string[]>,\n  validNodeIds: Set<string>\n): string[] {\n  return outgoingLinks.map((link) => {\n    // If link already exists as a valid node ID, keep it\n    if (validNodeIds.has(link)) {\n      return link;\n    }\n\n    // Only resolve bare filenames (no path separators)\n    // Partial paths like \"folder/target.md\" stay literal\n    if (link.includes('/')) {\n      return link;\n    }\n\n    // Strip .md extension for index lookup (titles are indexed without extension)\n    const lookupKey = link.replace(/\\.md$/i, '').toLowerCase();\n\n    // Try title/filename lookup\n    const matches = filenameIndex.get(lookupKey);\n    if (matches && matches.length > 0) {\n      return matches[0]!;\n    }\n\n    // Fallback: try space/dash variant\n    const variant = spaceDashVariant(lookupKey);\n    if (variant) {\n      const variantMatches = filenameIndex.get(variant);\n      if (variantMatches && variantMatches.length > 0) {\n        return variantMatches[0]!;\n      }\n    }\n\n    return link;\n  });\n}\n\n/**\n * Generate the space/dash variant of a filename.\n * Returns null if the filename has both or neither spaces and dashes.\n */\nexport function spaceDashVariant(filename: string): string | null {\n  const hasSpace = filename.includes(' ');\n  const hasDash = filename.includes('-');\n\n  if (hasSpace && !hasDash) {\n    return filename.replace(/ /g, '-');\n  }\n  if (hasDash && !hasSpace) {\n    return filename.replace(/-/g, ' ');\n  }\n  return null;\n}\n","/**\n * File operations for DocStore\n *\n * Generic file I/O utilities extracted from DocStore for reuse\n * by FormatReader implementations.\n */\n\nimport { readFile, stat, readdir } from 'node:fs/promises';\nimport { join, resolve, extname } from 'node:path';\nimport { EXCLUDED_DIRS } from './constants.js';\n\n/**\n * Get file modification time in milliseconds\n */\nexport async function getFileMtime(filePath: string): Promise<number> {\n  const stats = await stat(filePath);\n  return stats.mtimeMs;\n}\n\n/**\n * Validate that an ID resolves within the source root.\n * Throws if path traversal is detected.\n */\nexport function validatePathWithinSource(sourceRoot: string, id: string): void {\n  const resolvedPath = resolve(sourceRoot, id);\n  const resolvedRoot = resolve(sourceRoot);\n\n  if (!resolvedPath.startsWith(resolvedRoot + '/')) {\n    throw new Error(`Path traversal detected: ${id} resolves outside source root`);\n  }\n}\n\n/**\n * Recursively collect files matching given extensions.\n *\n * @param dir - Directory to search\n * @param extensions - Set of extensions to match (e.g., new Set(['.md', '.markdown']))\n * @returns Array of absolute file paths\n */\nexport async function collectFiles(\n  dir: string,\n  extensions: ReadonlySet<string>\n): Promise<string[]> {\n  // Empty extension set = no files to collect\n  if (extensions.size === 0) {\n    return [];\n  }\n\n  const results: string[] = [];\n\n  let entries;\n  try {\n    entries = await readdir(dir, { withFileTypes: true });\n  } catch {\n    // Directory doesn't exist\n    return results;\n  }\n\n  for (const entry of entries) {\n    const fullPath = join(dir, entry.name);\n\n    if (entry.isDirectory()) {\n      // Skip excluded directories\n      if (EXCLUDED_DIRS.has(entry.name)) {\n        continue;\n      }\n      const nested = await collectFiles(fullPath, extensions);\n      results.push(...nested);\n    } else if (entry.isFile()) {\n      const ext = extname(entry.name).toLowerCase();\n      // Skip files with no extension (README, .gitignore, etc.)\n      if (ext && extensions.has(ext)) {\n        results.push(fullPath);\n      }\n    }\n  }\n\n  return results;\n}\n\n/**\n * Read file content as UTF-8 string\n */\nexport async function readFileContent(filePath: string): Promise<string> {\n  return readFile(filePath, 'utf-8');\n}\n","import { nanoid } from 'nanoid';\n\n/** Pattern for valid nanoid: exactly 12 URL-safe characters */\nconst NANOID_PATTERN = /^[A-Za-z0-9_-]{12}$/;\n\n/**\n * Check if a string is a valid frontmatter ID (12-char nanoid).\n */\nexport const isValidId = (id: string): boolean => NANOID_PATTERN.test(id);\n\n/**\n * Generate a new frontmatter ID (12-char nanoid).\n */\nexport const generateId = (): string => nanoid(12);\n","/**\n * FormatReader plugin architecture\n *\n * Provides a registry for file format readers, enabling multi-format support\n * in DocStore while keeping format-specific logic isolated.\n */\n\nimport type { FormatReader, FileContext, ParseResult } from './types.js';\nimport { isValidId } from './id.js';\n\n/**\n * Registry for FormatReader implementations\n */\nexport class ReaderRegistry {\n  private readers: Map<string, FormatReader> = new Map();\n\n  /**\n   * Register a reader for its declared extensions.\n   * Throws if any extension is already registered (atomic - no partial registration).\n   */\n  register(reader: FormatReader): void {\n    // Check for conflicts first (atomic)\n    for (const ext of reader.extensions) {\n      const normalizedExt = ext.toLowerCase();\n      if (this.readers.has(normalizedExt)) {\n        throw new Error(`Extension already registered: ${ext}`);\n      }\n    }\n\n    // All clear - register all extensions\n    for (const ext of reader.extensions) {\n      const normalizedExt = ext.toLowerCase();\n      this.readers.set(normalizedExt, reader);\n    }\n  }\n\n  /**\n   * Get reader for an extension, or null if none registered.\n   * Case-insensitive.\n   */\n  getReader(extension: string): FormatReader | null {\n    return this.readers.get(extension.toLowerCase()) ?? null;\n  }\n\n  /**\n   * Get all registered extensions\n   */\n  getExtensions(): ReadonlySet<string> {\n    return new Set(this.readers.keys());\n  }\n\n  /**\n   * Check if an extension has a registered reader.\n   * Case-insensitive.\n   */\n  hasReader(extension: string): boolean {\n    return this.readers.has(extension.toLowerCase());\n  }\n\n  /**\n   * Parse content using the appropriate reader for the file's extension.\n   * Validates frontmatter ID and signals if writeback is needed.\n   * Throws if no reader is registered for the extension.\n   *\n   * Note: Does NOT generate new IDs here - that happens in Phase 3's writeback.\n   * Files without valid frontmatter IDs keep their path-based ID for now,\n   * with needsIdWrite: true signaling that an ID should be generated and written.\n   */\n  parse(content: string, context: FileContext): ParseResult {\n    const reader = this.getReader(context.extension);\n    if (!reader) {\n      throw new Error(`No reader registered for extension: ${context.extension}`);\n    }\n    const node = reader.parse(content, context);\n\n    // Check if node has a valid stable frontmatter ID\n    const needsIdWrite = !isValidId(node.id);\n\n    return { node, needsIdWrite };\n  }\n}\n","/**\n * MarkdownReader - FormatReader implementation for Markdown files\n *\n * Handles .md and .markdown files, extracting:\n * - YAML frontmatter (title, tags, properties)\n * - Wiki-links from content\n * - Node ID from file path\n */\n\nimport type { Node } from '../../../types/node.js';\nimport type { FormatReader, FileContext } from '../types.js';\nimport {\n  parseMarkdown,\n  extractWikiLinks,\n  normalizeId,\n  titleFromPath,\n} from '../parser.js';\nimport { normalizeWikiLink } from '../links.js';\n\nexport class MarkdownReader implements FormatReader {\n  readonly extensions = ['.md', '.markdown'];\n\n  parse(content: string, context: FileContext): Node {\n    const parsed = parseMarkdown(content);\n\n    // Use frontmatter ID if present, otherwise derive from path\n    // (ReaderRegistry validates and generates if invalid)\n    const id = parsed.id ?? normalizeId(context.relativePath);\n\n    // Derive title from path if not in frontmatter\n    const title = parsed.title ?? titleFromPath(id);\n\n    // Extract and normalize wiki links\n    const rawLinks = extractWikiLinks(parsed.content);\n    const outgoingLinks = rawLinks.map((link) => normalizeWikiLink(link));\n\n    return {\n      id,\n      title,\n      content: parsed.content,\n      tags: parsed.tags,\n      outgoingLinks,\n      properties: parsed.properties,\n      sourceRef: {\n        type: 'file',\n        path: context.absolutePath,\n        lastModified: context.mtime,\n      },\n    };\n  }\n}\n","import { pipeline, type FeatureExtractionPipeline } from '@xenova/transformers';\nimport type { Embedding } from '../../types/provider.js';\n\nconst DEFAULT_MODEL = 'Xenova/all-MiniLM-L6-v2';\nconst DEFAULT_DIMENSIONS = 384;\n\nexport interface TransformersEmbeddingOptions {\n  model?: string;\n  dimensions?: number;\n  id?: string;\n}\n\nexport class TransformersEmbedding implements Embedding {\n  readonly id: string;\n  private model: string;\n  private dims: number;\n  private pipe: FeatureExtractionPipeline | null = null;\n\n  constructor(options: TransformersEmbeddingOptions = {}) {\n    const {\n      model = DEFAULT_MODEL,\n      dimensions = DEFAULT_DIMENSIONS,\n      id = 'transformers-embedding',\n    } = options;\n    this.id = id;\n    this.model = model;\n    this.dims = dimensions;\n  }\n\n  private async getPipeline(): Promise<FeatureExtractionPipeline> {\n    if (!this.pipe) {\n      this.pipe = await pipeline('feature-extraction', this.model);\n    }\n    return this.pipe;\n  }\n\n  async embed(text: string): Promise<number[]> {\n    const pipe = await this.getPipeline();\n    const output = await pipe(text, { pooling: 'mean', normalize: true });\n    return Array.from(output.data as Float32Array);\n  }\n\n  async embedBatch(texts: string[]): Promise<number[][]> {\n    if (texts.length === 0) {\n      return [];\n    }\n    return Promise.all(texts.map((t) => this.embed(t)));\n  }\n\n  dimensions(): number {\n    return this.dims;\n  }\n\n  modelId(): string {\n    return this.model;\n  }\n\n  // Lifecycle hooks\n\n  async onRegister(): Promise<void> {\n    // No-op: pipeline is lazy-loaded on first embed() call\n  }\n\n  async onUnregister(): Promise<void> {\n    // Release reference for GC\n    // NOTE: @xenova/transformers may not truly unload from GPU memory\n    this.pipe = null;\n  }\n}\n","import type { Node, NodeUpdates } from './node.js';\nimport type { Direction, NeighborOptions } from './edge.js';\n\nexport type Metric = 'in_degree' | 'out_degree';\n\n// Batch operation types\nexport interface ListFilter {\n  /** Filter by tag (case-insensitive) */\n  tag?: string;\n  /** Filter by path prefix (startsWith) */\n  path?: string;\n}\n\nexport interface ListOptions {\n  /** Default 100, max 1000 */\n  limit?: number;\n  /** Default 0 */\n  offset?: number;\n}\n\nexport interface NodeSummary {\n  id: string;\n  title: string;\n}\n\nexport interface ListNodesResult {\n  nodes: NodeSummary[];\n  /** Total matching nodes (before limit/offset applied) */\n  total: number;\n}\n\nexport type ResolveStrategy = 'exact' | 'fuzzy' | 'semantic';\n\nexport interface ResolveOptions {\n  /** Filter candidates by tag */\n  tag?: string;\n  /** Filter candidates by path prefix */\n  path?: string;\n  /** 0-1, default 0.7, ignored for 'exact' */\n  threshold?: number;\n  /** Default 'fuzzy' */\n  strategy?: ResolveStrategy;\n}\n\nexport interface ResolveResult {\n  /** Original input */\n  query: string;\n  /** Matched node ID or null */\n  match: string | null;\n  /** 0-1, 0 if no match */\n  score: number;\n}\n\nexport interface CentralityMetrics {\n  inDegree: number;\n  outDegree: number;\n}\n\nexport type TagMode = 'any' | 'all';\n\nexport interface VectorSearchResult {\n  id: string;\n  distance: number;\n}\n\n/** Link with resolved title for MCP responses. */\nexport interface LinkInfo {\n  id: string;\n  title: string;\n}\n\n// ============================================================================\n// Provider Base Types\n// ============================================================================\n\n/** Base fields all providers must implement. */\nexport interface ProviderBase {\n  /** Unique identifier for this provider instance. Must be non-empty. */\n  readonly id: string;\n}\n\n/**\n * Optional lifecycle hooks for providers.\n * - onRegister: Called after registration with GraphCore. Errors propagate to caller.\n * - onUnregister: Called before provider is replaced or GraphCore is destroyed. Best-effort, errors logged.\n */\nexport interface ProviderLifecycle {\n  onRegister?(): Promise<void>;\n  onUnregister?(): Promise<void>;\n}\n\n// ============================================================================\n// Provider Interfaces\n// ============================================================================\n\n/** Data persistence and graph operations. Required provider. */\nexport interface Store extends ProviderBase, ProviderLifecycle {\n  // CRUD\n  createNode(node: Node): Promise<void>;\n  updateNode(id: string, updates: NodeUpdates): Promise<void>;\n  deleteNode(id: string): Promise<void>;\n  getNode(id: string): Promise<Node | null>;\n  getNodes(ids: string[]): Promise<Node[]>;\n\n  // Graph operations\n  getNeighbors(id: string, options: NeighborOptions): Promise<Node[]>;\n  findPath(source: string, target: string): Promise<string[] | null>;\n  getHubs(metric: Metric, limit: number): Promise<Array<[string, number]>>;\n\n  // Vector storage\n  storeEmbedding(id: string, vector: number[], model: string): Promise<void>;\n  searchByVector(\n    vector: number[],\n    limit: number\n  ): Promise<VectorSearchResult[]>;\n\n  // Search\n  searchByTags(tags: string[], mode: TagMode, limit?: number): Promise<Node[]>;\n\n  // Discovery\n  getRandomNode(tags?: string[]): Promise<Node | null>;\n\n  // Link resolution (for MCP response formatting)\n  resolveTitles(ids: string[]): Promise<Map<string, string>>;\n\n  // Batch operations\n  listNodes(filter: ListFilter, options?: ListOptions): Promise<ListNodesResult>;\n  resolveNodes(names: string[], options?: ResolveOptions): Promise<ResolveResult[]>;\n  nodesExist(ids: string[]): Promise<Map<string, boolean>>;\n}\n\n/** Stateless vector generation. Storage handled by Store. */\nexport interface Embedding extends ProviderBase, ProviderLifecycle {\n  embed(text: string): Promise<number[]>;\n  embedBatch(texts: string[]): Promise<number[][]>;\n  /** For storage allocation */\n  dimensions(): number;\n  modelId(): string;\n}\n\n/** Pluggable vector storage and similarity search. */\nexport interface VectorIndex {\n  store(id: string, vector: number[], model: string): Promise<void>;\n  search(vector: number[], limit: number): Promise<VectorSearchResult[]>;\n  delete(id: string): Promise<void>;\n  getModel(id: string): Promise<string | null>;\n  hasEmbedding(id: string): boolean;\n}\n\nexport function isVectorIndex(value: unknown): value is VectorIndex {\n  if (value === null || typeof value !== 'object') {\n    return false;\n  }\n  const obj = value as Record<string, unknown>;\n  return (\n    typeof obj.store === 'function' &&\n    typeof obj.search === 'function' &&\n    typeof obj.delete === 'function' &&\n    typeof obj.getModel === 'function' &&\n    typeof obj.hasEmbedding === 'function'\n  );\n}\n\n/**\n * Runtime type guard for Store interface.\n * IMPORTANT: Update this function when Store interface changes.\n * Checks: id field (required, non-empty string) + 16 methods\n */\nexport function isStoreProvider(value: unknown): value is Store {\n  if (value === null || typeof value !== 'object') {\n    return false;\n  }\n  const obj = value as Record<string, unknown>;\n  return (\n    typeof obj.id === 'string' &&\n    obj.id.trim().length > 0 &&\n    typeof obj.createNode === 'function' &&\n    typeof obj.updateNode === 'function' &&\n    typeof obj.deleteNode === 'function' &&\n    typeof obj.getNode === 'function' &&\n    typeof obj.getNodes === 'function' &&\n    typeof obj.getNeighbors === 'function' &&\n    typeof obj.findPath === 'function' &&\n    typeof obj.getHubs === 'function' &&\n    typeof obj.storeEmbedding === 'function' &&\n    typeof obj.searchByVector === 'function' &&\n    typeof obj.searchByTags === 'function' &&\n    typeof obj.getRandomNode === 'function' &&\n    typeof obj.resolveTitles === 'function' &&\n    typeof obj.listNodes === 'function' &&\n    typeof obj.resolveNodes === 'function' &&\n    typeof obj.nodesExist === 'function'\n  );\n}\n\n/**\n * Runtime type guard for Embedding interface.\n * IMPORTANT: Update this function when Embedding interface changes.\n * Current method count: 4 + id field\n */\nexport function isEmbeddingProvider(value: unknown): value is Embedding {\n  if (value === null || typeof value !== 'object') {\n    return false;\n  }\n  const obj = value as Record<string, unknown>;\n  return (\n    typeof obj.id === 'string' &&\n    obj.id.trim().length > 0 &&\n    typeof obj.embed === 'function' &&\n    typeof obj.embedBatch === 'function' &&\n    typeof obj.dimensions === 'function' &&\n    typeof obj.modelId === 'function'\n  );\n}\n\n// Re-export for convenience\nexport type { Direction, NeighborOptions };\n","import type { Node, NodeUpdates, NodeWithContext } from '../types/node.js';\nimport type {\n  GraphCore,\n  SearchOptions,\n} from '../types/graphcore.js';\nimport type {\n  Store,\n  Embedding,\n  Metric,\n  TagMode,\n  NeighborOptions,\n  ListFilter,\n  ListOptions,\n  ListNodesResult,\n  ResolveOptions,\n  ResolveResult,\n} from '../types/provider.js';\nimport {\n  isStoreProvider,\n  isEmbeddingProvider,\n} from '../types/provider.js';\nimport type { RouxConfig } from '../types/config.js';\nimport { DocStore } from '../providers/docstore/index.js';\nimport { TransformersEmbedding } from '../providers/embedding/transformers.js';\nimport { cosineSimilarity } from '../utils/math.js';\n\nexport class GraphCoreImpl implements GraphCore {\n  private store: Store | null = null;\n  private embedding: Embedding | null = null;\n\n  async registerStore(provider: Store): Promise<void> {\n    if (!provider) {\n      throw new Error('Store provider is required');\n    }\n    if (!isStoreProvider(provider)) {\n      throw new Error('Invalid Store provider: missing required methods or id');\n    }\n\n    // Unregister previous provider if exists\n    if (this.store?.onUnregister) {\n      try {\n        await this.store.onUnregister();\n      } catch (err) {\n        console.warn('Error during store onUnregister:', err);\n      }\n    }\n\n    // Set new provider (before calling onRegister so it can use the store)\n    this.store = provider;\n\n    // Call lifecycle hook if exists\n    if (provider.onRegister) {\n      try {\n        await provider.onRegister();\n      } catch (err) {\n        // Rollback on failure\n        this.store = null;\n        throw err;\n      }\n    }\n  }\n\n  async registerEmbedding(provider: Embedding): Promise<void> {\n    if (!provider) {\n      throw new Error('Embedding provider is required');\n    }\n    if (!isEmbeddingProvider(provider)) {\n      throw new Error('Invalid Embedding provider: missing required methods or id');\n    }\n\n    // Unregister previous provider if exists\n    if (this.embedding?.onUnregister) {\n      try {\n        await this.embedding.onUnregister();\n      } catch (err) {\n        console.warn('Error during embedding onUnregister:', err);\n      }\n    }\n\n    // Set new provider\n    this.embedding = provider;\n\n    // Call lifecycle hook if exists\n    if (provider.onRegister) {\n      try {\n        await provider.onRegister();\n      } catch (err) {\n        // Rollback on failure\n        this.embedding = null;\n        throw err;\n      }\n    }\n  }\n\n  async destroy(): Promise<void> {\n    // Unregister in reverse order of typical registration\n    if (this.embedding?.onUnregister) {\n      try {\n        await this.embedding.onUnregister();\n      } catch (err) {\n        console.warn('Error during embedding onUnregister in destroy:', err);\n      }\n    }\n    if (this.store?.onUnregister) {\n      try {\n        await this.store.onUnregister();\n      } catch (err) {\n        console.warn('Error during store onUnregister in destroy:', err);\n      }\n    }\n\n    // Clear references\n    this.embedding = null;\n    this.store = null;\n  }\n\n  private requireStore(): Store {\n    if (!this.store) {\n      throw new Error('Store not registered');\n    }\n    return this.store;\n  }\n\n  private requireEmbedding(): Embedding {\n    if (!this.embedding) {\n      throw new Error('Embedding not registered');\n    }\n    return this.embedding;\n  }\n\n  async search(query: string, options?: SearchOptions): Promise<Node[]> {\n    const store = this.requireStore();\n    const embedding = this.requireEmbedding();\n\n    const limit = options?.limit ?? 10;\n    const vector = await embedding.embed(query);\n    const results = await store.searchByVector(vector, limit);\n\n    // Results are already sorted by distance ascending\n    const ids = results.map((r) => r.id);\n    return store.getNodes(ids);\n  }\n\n  async getNode(id: string, depth?: number): Promise<NodeWithContext | null> {\n    const store = this.requireStore();\n    const node = await store.getNode(id);\n\n    if (!node) {\n      return null;\n    }\n\n    if (!depth || depth === 0) {\n      return node;\n    }\n\n    // Fetch neighbors for context\n    const [incomingNeighbors, outgoingNeighbors] = await Promise.all([\n      store.getNeighbors(id, { direction: 'in' }),\n      store.getNeighbors(id, { direction: 'out' }),\n    ]);\n\n    // Deduplicate neighbors (same node could be both incoming and outgoing)\n    const neighborMap = new Map<string, Node>();\n    for (const n of [...incomingNeighbors, ...outgoingNeighbors]) {\n      neighborMap.set(n.id, n);\n    }\n\n    const result: NodeWithContext = {\n      ...node,\n      neighbors: Array.from(neighborMap.values()),\n      incomingCount: incomingNeighbors.length,\n      outgoingCount: outgoingNeighbors.length,\n    };\n\n    return result;\n  }\n\n  async createNode(partial: Partial<Node>): Promise<Node> {\n    const store = this.requireStore();\n\n    if (!partial.id || partial.id.trim() === '') {\n      throw new Error('Node id is required and cannot be empty');\n    }\n    if (!partial.title) {\n      throw new Error('Node title is required');\n    }\n\n    const node: Node = {\n      id: partial.id,\n      title: partial.title,\n      content: partial.content ?? '',\n      tags: partial.tags ?? [],\n      outgoingLinks: partial.outgoingLinks ?? [],\n      properties: partial.properties ?? {},\n      ...(partial.sourceRef && { sourceRef: partial.sourceRef }),\n    };\n\n    await store.createNode(node);\n    return (await store.getNode(node.id)) ?? node;\n  }\n\n  async updateNode(id: string, updates: NodeUpdates): Promise<Node> {\n    const store = this.requireStore();\n    await store.updateNode(id, updates);\n    const updated = await store.getNode(id);\n    if (!updated) {\n      throw new Error(`Node not found after update: ${id}`);\n    }\n    return updated;\n  }\n\n  async deleteNode(id: string): Promise<boolean> {\n    const store = this.requireStore();\n    try {\n      await store.deleteNode(id);\n      return true;\n    } catch (err) {\n      // Only swallow \"not found\" errors - propagate everything else\n      if (err instanceof Error && /not found/i.test(err.message)) {\n        return false;\n      }\n      throw err;\n    }\n  }\n\n  async getNeighbors(id: string, options: NeighborOptions): Promise<Node[]> {\n    const store = this.requireStore();\n    return store.getNeighbors(id, options);\n  }\n\n  async findPath(source: string, target: string): Promise<string[] | null> {\n    const store = this.requireStore();\n    return store.findPath(source, target);\n  }\n\n  async getHubs(\n    metric: Metric,\n    limit: number\n  ): Promise<Array<[string, number]>> {\n    const store = this.requireStore();\n    return store.getHubs(metric, limit);\n  }\n\n  async searchByTags(\n    tags: string[],\n    mode: TagMode,\n    limit?: number\n  ): Promise<Node[]> {\n    const store = this.requireStore();\n    return store.searchByTags(tags, mode, limit);\n  }\n\n  async getRandomNode(tags?: string[]): Promise<Node | null> {\n    const store = this.requireStore();\n    return store.getRandomNode(tags);\n  }\n\n  async listNodes(\n    filter: ListFilter,\n    options?: ListOptions\n  ): Promise<ListNodesResult> {\n    return this.requireStore().listNodes(filter, options);\n  }\n\n  async resolveNodes(\n    names: string[],\n    options?: ResolveOptions\n  ): Promise<ResolveResult[]> {\n    const store = this.requireStore();\n    const strategy = options?.strategy ?? 'fuzzy';\n\n    // Semantic strategy requires embedding provider\n    if (strategy === 'semantic') {\n      if (!this.embedding) {\n        throw new Error('Semantic resolution requires Embedding');\n      }\n\n      // Build filter without undefined values\n      const filter: ListFilter = {};\n      if (options?.tag) filter.tag = options.tag;\n      if (options?.path) filter.path = options.path;\n\n      // Get candidates from store with filters\n      const { nodes: candidates } = await store.listNodes(filter, { limit: 1000 });\n\n      if (candidates.length === 0 || names.length === 0) {\n        return names.map((query) => ({ query, match: null, score: 0 }));\n      }\n\n      const threshold = options?.threshold ?? 0.7;\n\n      // Embed all queries in batch\n      const queryVectors = await this.embedding.embedBatch(names);\n\n      // Embed all candidate titles in batch\n      const candidateTitles = candidates.map((c) => c.title);\n      const candidateVectors = await this.embedding.embedBatch(candidateTitles);\n\n      // Validate dimensions match\n      if (queryVectors.length > 0 && candidateVectors.length > 0) {\n        const queryDim = queryVectors[0]!.length;\n        const candidateDim = candidateVectors[0]!.length;\n        if (queryDim !== candidateDim) {\n          throw new Error(\n            `Embedding dimension mismatch: query=${queryDim}, candidate=${candidateDim}`\n          );\n        }\n      }\n\n      // For each query, find best matching candidate by cosine similarity\n      return names.map((query, qIdx): ResolveResult => {\n        const queryVector = queryVectors[qIdx]!;\n        let bestScore = 0;\n        let bestMatch: string | null = null;\n\n        for (let cIdx = 0; cIdx < candidates.length; cIdx++) {\n          const similarity = cosineSimilarity(queryVector, candidateVectors[cIdx]!);\n          if (similarity > bestScore) {\n            bestScore = similarity;\n            bestMatch = candidates[cIdx]!.id;\n          }\n        }\n\n        if (bestScore >= threshold) {\n          return { query, match: bestMatch, score: bestScore };\n        }\n        return { query, match: null, score: 0 };\n      });\n    }\n\n    // Exact and fuzzy delegate to store\n    return store.resolveNodes(names, options);\n  }\n\n  static async fromConfig(config: RouxConfig): Promise<GraphCoreImpl> {\n    if (!config.providers?.store) {\n      throw new Error('Store configuration is required');\n    }\n\n    const core = new GraphCoreImpl();\n\n    try {\n      // Create store based on config\n      if (config.providers.store.type === 'docstore') {\n        const sourcePath = config.source?.path ?? '.';\n        const cachePath = config.cache?.path ?? '.roux';\n        const store = new DocStore({ sourceRoot: sourcePath, cacheDir: cachePath });\n        await core.registerStore(store);\n      } else {\n        throw new Error(\n          `Unsupported store provider type: ${config.providers.store.type}. Supported: docstore`\n        );\n      }\n\n      // Create embedding provider (defaults to local transformers)\n      const embeddingConfig = config.providers.embedding;\n      if (!embeddingConfig || embeddingConfig.type === 'local') {\n        const model = embeddingConfig?.model;\n        const embedding = new TransformersEmbedding(model ? { model } : {});\n        await core.registerEmbedding(embedding);\n      } else {\n        throw new Error(\n          `Unsupported embedding provider type: ${embeddingConfig.type}. Supported: local`\n        );\n      }\n\n      return core;\n    } catch (err) {\n      // Clean up any registered providers on failure\n      await core.destroy();\n      throw err;\n    }\n  }\n}\n","import { Server } from '@modelcontextprotocol/sdk/server/index.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport {\n  CallToolRequestSchema,\n  ListToolsRequestSchema,\n  type CallToolResult,\n} from '@modelcontextprotocol/sdk/types.js';\n\nimport type { GraphCore } from '../types/graphcore.js';\nimport type { Store } from '../types/provider.js';\nimport { DEFAULT_NAMING, type NamingConventions } from '../types/config.js';\nimport { VERSION } from '../index.js';\nimport { McpError } from './types.js';\nimport { dispatchTool, getToolDefinitions, type HandlerContext } from './handlers/index.js';\n\nexport interface McpServerOptions {\n  /** GraphCore instance for operations */\n  core: GraphCore;\n  /** Store for link resolution and direct store access */\n  store: Store;\n  /** Whether embedding provider is available (enables search tool) */\n  hasEmbedding: boolean;\n  /** Naming conventions for file creation */\n  naming?: NamingConventions;\n}\n\n/** MCP Transport interface for server connection. */\nexport interface McpTransport {\n  start?(): Promise<void>;\n  close?(): Promise<void>;\n}\n\n/** Factory function to create a transport. Defaults to StdioServerTransport. */\nexport type TransportFactory = () => McpTransport;\n\n/** Response format for MCP tool calls. Extends SDK's CallToolResult. */\nexport type McpToolResponse = CallToolResult;\n\n/**\n * Format a successful tool result for MCP response.\n */\nexport function formatToolResponse(result: unknown): McpToolResponse {\n  return {\n    content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],\n  };\n}\n\n/**\n * Format an error for MCP response.\n * Handles McpError, generic Error, and non-Error thrown values.\n */\nexport function formatErrorResponse(error: unknown): McpToolResponse {\n  if (error instanceof McpError) {\n    return {\n      content: [{ type: 'text', text: JSON.stringify(error.toResponse()) }],\n      isError: true,\n    };\n  }\n  const mcpError = new McpError(\n    'PROVIDER_ERROR',\n    error instanceof Error ? error.message : 'Unknown error'\n  );\n  return {\n    content: [{ type: 'text', text: JSON.stringify(mcpError.toResponse()) }],\n    isError: true,\n  };\n}\n\n/**\n * Execute a tool call and return formatted MCP response.\n * Handles dispatching to the appropriate handler and error formatting.\n */\nexport async function executeToolCall(\n  ctx: HandlerContext,\n  name: string,\n  args: Record<string, unknown>\n): Promise<McpToolResponse> {\n  try {\n    const result = await dispatchTool(ctx, name, args);\n    return formatToolResponse(result);\n  } catch (error) {\n    return formatErrorResponse(error);\n  }\n}\n\nexport class McpServer {\n  private server: Server;\n  private ctx: HandlerContext;\n\n  constructor(options: McpServerOptions) {\n    this.ctx = {\n      core: options.core,\n      store: options.store,\n      hasEmbedding: options.hasEmbedding,\n      naming: options.naming ?? DEFAULT_NAMING,\n    };\n\n    this.server = new Server(\n      { name: 'roux', version: VERSION },\n      { capabilities: { tools: {} } }\n    );\n\n    this.setupHandlers();\n  }\n\n  private setupHandlers(): void {\n    this.server.setRequestHandler(ListToolsRequestSchema, async () => ({\n      tools: getToolDefinitions(this.ctx.hasEmbedding),\n    }));\n\n    this.server.setRequestHandler(CallToolRequestSchema, async (request) => {\n      const { name, arguments: args } = request.params;\n      return executeToolCall(this.ctx, name, args ?? {});\n    });\n  }\n\n  /**\n   * Start the server with optional transport factory.\n   * @param transportFactory Factory to create transport. Defaults to StdioServerTransport.\n   */\n  async start(transportFactory?: TransportFactory): Promise<void> {\n    const transport = transportFactory\n      ? transportFactory()\n      : new StdioServerTransport();\n    await this.server.connect(transport as Parameters<typeof this.server.connect>[0]);\n  }\n\n  async close(): Promise<void> {\n    await this.server.close();\n  }\n}\n\n/**\n * Create and start an MCP server.\n * @param options Server configuration\n * @param transportFactory Optional transport factory for testing\n */\nexport async function createMcpServer(\n  options: McpServerOptions,\n  transportFactory?: TransportFactory\n): Promise<McpServer> {\n  const server = new McpServer(options);\n  await server.start(transportFactory);\n  return server;\n}\n","export interface SourceConfig {\n  /** Relative to config file */\n  path: string;\n  include: string[];\n  /** .roux/ always excluded (hardcoded) */\n  exclude: string[];\n}\n\nexport interface CacheConfig {\n  /** SQLite directory */\n  path: string;\n}\n\nexport type ModelChangeBehavior = 'lazy' | 'eager';\n\nexport interface SystemConfig {\n  onModelChange: ModelChangeBehavior;\n}\n\nexport type FilenameSeparator = 'space' | 'dash';\nexport type TitleCasing = 'title' | 'sentence' | 'as-is';\n\nexport interface NamingConventions {\n  filename: FilenameSeparator;\n  title: TitleCasing;\n}\n\nexport const DEFAULT_NAMING: NamingConventions = {\n  filename: 'space',\n  title: 'title',\n};\n\nexport interface DocStoreConfig {\n  type: 'docstore';\n}\n\nexport interface LocalEmbeddingConfig {\n  type: 'local';\n  /** Default: Xenova/all-MiniLM-L6-v2 */\n  model?: string;\n}\n\nexport interface OllamaEmbeddingConfig {\n  type: 'ollama';\n  model: string;\n  endpoint?: string;\n  timeout?: number;\n}\n\nexport interface OpenAIEmbeddingConfig {\n  type: 'openai';\n  model: string;\n  timeout?: number;\n}\n\nexport type EmbeddingConfig =\n  | LocalEmbeddingConfig\n  | OllamaEmbeddingConfig\n  | OpenAIEmbeddingConfig;\n\nexport interface OllamaLLMConfig {\n  type: 'ollama';\n  model: string;\n  endpoint?: string;\n  timeout?: number;\n}\n\nexport interface OpenAILLMConfig {\n  type: 'openai';\n  model: string;\n  timeout?: number;\n}\n\nexport type LLMConfig = OllamaLLMConfig | OpenAILLMConfig;\n\nexport type StoreConfig = DocStoreConfig;\n\nexport interface ProvidersConfig {\n  store: StoreConfig;\n  embedding?: EmbeddingConfig;\n  llm?: LLMConfig;\n}\n\nexport interface RouxConfig {\n  source?: SourceConfig;\n  cache?: CacheConfig;\n  system?: SystemConfig;\n  naming?: NamingConventions;\n  providers: ProvidersConfig;\n}\n\nexport const DEFAULT_CONFIG: Required<\n  Pick<RouxConfig, 'source' | 'cache' | 'system'>\n> & { providers: { store: DocStoreConfig } } = {\n  source: {\n    path: '.',\n    include: ['*.md'],\n    exclude: [],\n  },\n  cache: {\n    path: '.roux/',\n  },\n  system: {\n    onModelChange: 'lazy',\n  },\n  providers: {\n    store: {\n      type: 'docstore',\n    },\n  },\n};\n","// Roux - Graph Programming Interface\n\nexport const VERSION = '0.1.3';\n\n// Re-export all types\nexport * from './types/index.js';\n\n// Core\nexport { GraphCoreImpl } from './core/graphcore.js';\n\n// Providers\nexport { StoreProvider, type StoreProviderOptions } from './providers/store/index.js';\nexport { DocStore } from './providers/docstore/index.js';\nexport { TransformersEmbedding } from './providers/embedding/index.js';\nexport { SqliteVectorIndex } from './providers/vector/index.js';\n","import type { LinkInfo } from '../types/provider.js';\n\n/** Metadata-only response for browsing operations (search, get_neighbors). */\nexport interface NodeMetadataResponse {\n  id: string;\n  title: string;\n  tags: string[];\n  links: LinkInfo[];\n  properties: Record<string, unknown>;\n}\n\n/** Full response including content (for get_node, create, update, etc.). */\nexport interface NodeResponse extends NodeMetadataResponse {\n  content: string;\n}\n\n/** Extended response for get_node with depth > 0. */\nexport interface NodeWithContextResponse extends NodeResponse {\n  incomingNeighbors: NodeResponse[];\n  outgoingNeighbors: NodeResponse[];\n  incomingCount: number;\n  outgoingCount: number;\n}\n\n/** Search results include similarity score. Content optional based on include_content param. */\nexport interface SearchResultResponse extends NodeMetadataResponse {\n  score: number;\n  content?: string;\n}\n\n/** Hub results pair ID with metric value. */\nexport interface HubResponse {\n  id: string;\n  title: string;\n  score: number;\n}\n\n/** Path results are ordered node IDs. */\nexport interface PathResponse {\n  path: string[];\n  length: number;\n}\n\n/** Delete operation result. */\nexport interface DeleteResponse {\n  deleted: boolean;\n}\n\n/** Standard error response shape. */\nexport interface ErrorResponse {\n  error: {\n    code: ErrorCode;\n    message: string;\n  };\n}\n\n/** Known error codes. */\nexport type ErrorCode =\n  | 'INVALID_PARAMS'\n  | 'NODE_EXISTS'\n  | 'NODE_NOT_FOUND'\n  | 'LINK_INTEGRITY'\n  | 'PROVIDER_ERROR';\n\n/** Custom error class for MCP operations. */\nexport class McpError extends Error {\n  constructor(\n    public readonly code: ErrorCode,\n    message: string\n  ) {\n    super(message);\n    this.name = 'McpError';\n  }\n\n  toResponse(): ErrorResponse {\n    return {\n      error: {\n        code: this.code,\n        message: this.message,\n      },\n    };\n  }\n}\n","import type { HandlerContext } from './types.js';\nimport type { SearchResultResponse } from '../types.js';\nimport { McpError } from '../types.js';\nimport { coerceLimit } from '../validation.js';\nimport { nodesToSearchResults } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    query: {\n      type: 'string',\n      description: 'Natural language search query',\n    },\n    limit: {\n      type: 'integer',\n      minimum: 1,\n      maximum: 50,\n      default: 10,\n      description: 'Maximum results to return',\n    },\n    include_content: {\n      type: 'boolean',\n      default: false,\n      description:\n        'Include node content in results. Default false returns metadata only (id, title, tags, properties, links). Set true to include truncated content.',\n    },\n  },\n  required: ['query'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<SearchResultResponse[]> {\n  if (!ctx.hasEmbedding) {\n    throw new McpError('PROVIDER_ERROR', 'Search requires embedding provider');\n  }\n\n  const query = args.query;\n  const limit = coerceLimit(args.limit, 10);\n  const includeContent = args.include_content === true;\n\n  if (typeof query !== 'string' || query.trim() === '') {\n    throw new McpError('INVALID_PARAMS', 'query is required and must be a non-empty string');\n  }\n\n  const nodes = await ctx.core.search(query, { limit });\n\n  const scores = new Map<string, number>();\n  nodes.forEach((node, index) => {\n    scores.set(node.id, Math.max(0, 1 - index * 0.05));\n  });\n\n  return nodesToSearchResults(nodes, scores, ctx.store, includeContent);\n}\n","import { McpError } from './types.js';\n\nexport function coerceInt(\n  value: unknown,\n  defaultValue: number,\n  minValue: number,\n  fieldName: string\n): number {\n  if (value === undefined || value === null) {\n    return defaultValue;\n  }\n  const num = Number(value);\n  if (Number.isNaN(num)) {\n    return defaultValue;\n  }\n  const floored = Math.floor(num);\n  if (floored < minValue) {\n    throw new McpError('INVALID_PARAMS', `${fieldName} must be at least ${minValue}`);\n  }\n  return floored;\n}\n\nexport function coerceLimit(value: unknown, defaultValue: number): number {\n  return coerceInt(value, defaultValue, 1, 'limit');\n}\n\nexport function coerceOffset(value: unknown, defaultValue: number): number {\n  return coerceInt(value, defaultValue, 0, 'offset');\n}\n\nexport function coerceDepth(value: unknown): number {\n  if (value === undefined || value === null) {\n    return 0;\n  }\n  const num = Number(value);\n  if (Number.isNaN(num)) {\n    return 0;\n  }\n  return num >= 1 ? 1 : 0;\n}\n\n/**\n * Validate that value is an array of strings.\n * Allows empty arrays — callers should check length if non-empty is required.\n */\nexport function validateStringArray(\n  value: unknown,\n  fieldName: string\n): string[] {\n  if (!Array.isArray(value)) {\n    throw new McpError('INVALID_PARAMS', `${fieldName} is required and must be an array`);\n  }\n  if (!value.every((item) => typeof item === 'string')) {\n    throw new McpError('INVALID_PARAMS', `${fieldName} must contain only strings`);\n  }\n  return value;\n}\n\nexport function validateRequiredString(\n  value: unknown,\n  fieldName: string\n): string {\n  if (value === undefined || value === null || typeof value !== 'string') {\n    throw new McpError('INVALID_PARAMS', `${fieldName} is required and must be a string`);\n  }\n  return value;\n}\n\nexport function validateEnum<T extends string>(\n  value: unknown,\n  validValues: readonly T[],\n  fieldName: string,\n  defaultValue: T\n): T {\n  if (value === undefined || value === null) {\n    return defaultValue;\n  }\n  if (!validValues.includes(value as T)) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      `${fieldName} must be one of: ${validValues.join(', ')}`\n    );\n  }\n  return value as T;\n}\n\n/**\n * Validate optional tags array.\n * Returns undefined if not provided, validated array otherwise.\n */\nexport function validateOptionalTags(value: unknown): string[] | undefined {\n  if (value === undefined) {\n    return undefined;\n  }\n  if (!Array.isArray(value)) {\n    throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n  }\n  if (!value.every((t) => typeof t === 'string')) {\n    throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n  }\n  return value;\n}\n\n/**\n * Validate required non-empty tags array.\n */\nexport function validateRequiredTags(value: unknown): string[] {\n  if (!Array.isArray(value) || value.length === 0) {\n    throw new McpError('INVALID_PARAMS', 'tags is required and must be a non-empty array');\n  }\n  if (!value.every((t) => typeof t === 'string')) {\n    throw new McpError('INVALID_PARAMS', 'tags must contain only strings');\n  }\n  return value;\n}\n","/** Content truncation limits by context. */\nexport const TRUNCATION_LIMITS = {\n  /** Primary node (get_node, single result) */\n  primary: 10_000,\n  /** List results (search, neighbors) */\n  list: 500,\n  /** Neighbor nodes in context */\n  neighbor: 200,\n} as const;\n\nexport type TruncationContext = keyof typeof TRUNCATION_LIMITS;\n\nconst TRUNCATION_SUFFIX = '... [truncated]';\n\n/**\n * Truncate content to limit, appending suffix if truncated.\n * Returns original content if within limit.\n * Ensures valid UTF-16 output by not splitting surrogate pairs.\n */\nexport function truncateContent(\n  content: string,\n  context: TruncationContext\n): string {\n  const limit = TRUNCATION_LIMITS[context];\n\n  if (content.length <= limit) {\n    return content;\n  }\n\n  // Account for suffix length when truncating, guard against negative\n  let truncatedLength = Math.max(0, limit - TRUNCATION_SUFFIX.length);\n\n  // Don't split surrogate pairs - if we'd end on a high surrogate, back up one\n  if (truncatedLength > 0) {\n    const lastCharCode = content.charCodeAt(truncatedLength - 1);\n    // High surrogate range: 0xD800-0xDBFF\n    if (lastCharCode >= 0xd800 && lastCharCode <= 0xdbff) {\n      truncatedLength--;\n    }\n  }\n\n  return content.slice(0, truncatedLength) + TRUNCATION_SUFFIX;\n}\n\n/**\n * Check if content was truncated (ends with truncation suffix).\n */\nexport function isTruncated(content: string): boolean {\n  return content.endsWith(TRUNCATION_SUFFIX);\n}\n","import type { Node } from '../types/node.js';\nimport type { LinkInfo, Store } from '../types/provider.js';\nimport type {\n  NodeResponse,\n  NodeMetadataResponse,\n  NodeWithContextResponse,\n  SearchResultResponse,\n  HubResponse,\n  PathResponse,\n} from './types.js';\nimport { truncateContent, type TruncationContext } from './truncate.js';\n\n/** Maximum neighbors to include in NodeWithContextResponse. */\nexport const MAX_NEIGHBORS = 20;\n\n/** Maximum links to resolve titles for (prevents OOM on nodes with massive link counts). */\nexport const MAX_LINKS_TO_RESOLVE = 100;\n\n/**\n * Transform a Node to NodeResponse, resolving link titles.\n */\nexport async function nodeToResponse(\n  node: Node,\n  store: Store,\n  truncation: TruncationContext\n): Promise<NodeResponse> {\n  // Limit links to prevent OOM on nodes with massive outgoing link counts\n  const linksToResolve = node.outgoingLinks.slice(0, MAX_LINKS_TO_RESOLVE);\n  const titles = await store.resolveTitles(linksToResolve);\n\n  const links: LinkInfo[] = linksToResolve.map((id) => ({\n    id,\n    title: titles.get(id) ?? id,\n  }));\n\n  return {\n    id: node.id,\n    title: node.title,\n    content: truncateContent(node.content, truncation),\n    tags: node.tags,\n    links,\n    properties: node.properties,\n  };\n}\n\n/**\n * Transform multiple nodes to responses, resolving all link titles in batch.\n * When includeContent is false, returns NodeMetadataResponse[] (no content field).\n * When includeContent is true, returns NodeResponse[] (with truncated content).\n */\nexport async function nodesToResponses(\n  nodes: Node[],\n  store: Store,\n  truncation: TruncationContext,\n  includeContent: boolean\n): Promise<NodeResponse[] | NodeMetadataResponse[]> {\n  // Collect unique link IDs, limiting per-node to prevent OOM\n  const allLinkIds = new Set<string>();\n  const nodeLinkLimits = new Map<string, string[]>();\n\n  for (const node of nodes) {\n    const limitedLinks = node.outgoingLinks.slice(0, MAX_LINKS_TO_RESOLVE);\n    nodeLinkLimits.set(node.id, limitedLinks);\n    for (const linkId of limitedLinks) {\n      allLinkIds.add(linkId);\n    }\n  }\n\n  // Batch resolve titles\n  const titles = await store.resolveTitles(Array.from(allLinkIds));\n\n  // Transform nodes using limited links\n  return nodes.map((node) => {\n    // Invariant: all node IDs are populated in the loop above\n    const limitedLinks = nodeLinkLimits.get(node.id)!;\n    const base: NodeMetadataResponse = {\n      id: node.id,\n      title: node.title,\n      tags: node.tags,\n      links: limitedLinks.map((id) => ({\n        id,\n        title: titles.get(id) ?? id,\n      })),\n      properties: node.properties,\n    };\n\n    if (includeContent) {\n      return {\n        ...base,\n        content: truncateContent(node.content, truncation),\n      } as NodeResponse;\n    }\n\n    return base;\n  });\n}\n\n/**\n * Transform a Node with neighbor context to NodeWithContextResponse.\n */\nexport async function nodeToContextResponse(\n  node: Node,\n  incomingNeighbors: Node[],\n  outgoingNeighbors: Node[],\n  store: Store\n): Promise<NodeWithContextResponse> {\n  // Get primary node response\n  const primary = await nodeToResponse(node, store, 'primary');\n\n  // Limit neighbors\n  const limitedIncoming = incomingNeighbors.slice(0, MAX_NEIGHBORS);\n  const limitedOutgoing = outgoingNeighbors.slice(0, MAX_NEIGHBORS);\n\n  // Transform neighbors with neighbor truncation\n  // Context responses always include content (truncated for neighbors)\n  const [incomingResponses, outgoingResponses] = await Promise.all([\n    nodesToResponses(limitedIncoming, store, 'neighbor', true) as Promise<NodeResponse[]>,\n    nodesToResponses(limitedOutgoing, store, 'neighbor', true) as Promise<NodeResponse[]>,\n  ]);\n\n  return {\n    ...primary,\n    incomingNeighbors: incomingResponses,\n    outgoingNeighbors: outgoingResponses,\n    incomingCount: incomingNeighbors.length,\n    outgoingCount: outgoingNeighbors.length,\n  };\n}\n\n/**\n * Transform search results with scores.\n * When includeContent is false, content field is omitted.\n * When includeContent is true, content is truncated and included.\n */\nexport async function nodesToSearchResults(\n  nodes: Node[],\n  scores: Map<string, number>,\n  store: Store,\n  includeContent: boolean\n): Promise<SearchResultResponse[]> {\n  const responses = await nodesToResponses(nodes, store, 'list', includeContent);\n\n  return responses.map((response) => ({\n    ...response,\n    score: scores.get(response.id) ?? 0,\n  }));\n}\n\n/**\n * Transform hub results (id, score pairs) to HubResponse[].\n */\nexport async function hubsToResponses(\n  hubs: Array<[string, number]>,\n  store: Store\n): Promise<HubResponse[]> {\n  const ids = hubs.map(([id]) => id);\n  const titles = await store.resolveTitles(ids);\n\n  return hubs.map(([id, score]) => ({\n    id,\n    title: titles.get(id) ?? id,\n    score,\n  }));\n}\n\n/**\n * Transform a path (array of node IDs) to PathResponse.\n */\nexport function pathToResponse(path: string[]): PathResponse {\n  return {\n    path,\n    length: path.length - 1,\n  };\n}\n","import type { HandlerContext } from './types.js';\nimport type { NodeResponse, NodeWithContextResponse } from '../types.js';\nimport { coerceDepth, validateRequiredString } from '../validation.js';\nimport { nodeToResponse, nodeToContextResponse } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    id: {\n      type: 'string',\n      description:\n        'Node ID (file path for DocStore). ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n    depth: {\n      type: 'integer',\n      minimum: 0,\n      maximum: 1,\n      default: 0,\n      description: '0 = node only, 1 = include neighbors',\n    },\n  },\n  required: ['id'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse | NodeWithContextResponse | null> {\n  const id = validateRequiredString(args.id, 'id');\n  const depth = coerceDepth(args.depth);\n\n  const node = await ctx.core.getNode(id, depth);\n  if (!node) {\n    return null;\n  }\n\n  if (depth === 0) {\n    return nodeToResponse(node, ctx.store, 'primary');\n  }\n\n  const [incomingNeighbors, outgoingNeighbors] = await Promise.all([\n    ctx.core.getNeighbors(id, { direction: 'in' }),\n    ctx.core.getNeighbors(id, { direction: 'out' }),\n  ]);\n\n  return nodeToContextResponse(node, incomingNeighbors, outgoingNeighbors, ctx.store);\n}\n","import type { HandlerContext } from './types.js';\nimport type { NodeResponse, NodeMetadataResponse } from '../types.js';\nimport { coerceLimit, validateEnum, validateRequiredString } from '../validation.js';\nimport { nodesToResponses } from '../transforms.js';\n\nconst VALID_DIRECTIONS = ['in', 'out', 'both'] as const;\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    id: {\n      type: 'string',\n      description:\n        'Source node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n    direction: {\n      type: 'string',\n      enum: ['in', 'out', 'both'],\n      default: 'both',\n      description: 'in = nodes linking here, out = nodes linked to, both = all',\n    },\n    limit: {\n      type: 'integer',\n      minimum: 1,\n      maximum: 50,\n      default: 20,\n      description: 'Maximum neighbors to return',\n    },\n    include_content: {\n      type: 'boolean',\n      default: false,\n      description:\n        'Include node content in results. Default false returns metadata only (id, title, tags, properties, links). Set true to include truncated content.',\n    },\n  },\n  required: ['id'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse[] | NodeMetadataResponse[]> {\n  const id = validateRequiredString(args.id, 'id');\n  const limit = coerceLimit(args.limit, 20);\n  const includeContent = args.include_content === true;\n\n  const direction = validateEnum(args.direction, VALID_DIRECTIONS, 'direction', 'both');\n\n  const neighbors = await ctx.core.getNeighbors(id, { direction, limit });\n  return nodesToResponses(neighbors, ctx.store, 'list', includeContent);\n}\n","import type { HandlerContext } from './types.js';\nimport type { PathResponse } from '../types.js';\nimport { validateRequiredString } from '../validation.js';\nimport { pathToResponse } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    source: {\n      type: 'string',\n      description:\n        'Start node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n    target: {\n      type: 'string',\n      description:\n        'End node ID. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n  },\n  required: ['source', 'target'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<PathResponse | null> {\n  const source = validateRequiredString(args.source, 'source');\n  const target = validateRequiredString(args.target, 'target');\n\n  const path = await ctx.core.findPath(source, target);\n  if (!path) {\n    return null;\n  }\n\n  return pathToResponse(path);\n}\n","import type { HandlerContext } from './types.js';\nimport type { Metric } from '../../types/provider.js';\nimport type { HubResponse } from '../types.js';\nimport { coerceLimit, validateEnum } from '../validation.js';\nimport { hubsToResponses } from '../transforms.js';\n\nconst VALID_METRICS = ['in_degree', 'out_degree'] as const;\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    metric: {\n      type: 'string',\n      enum: ['in_degree', 'out_degree'],\n      default: 'in_degree',\n      description: 'Centrality metric',\n    },\n    limit: {\n      type: 'integer',\n      minimum: 1,\n      maximum: 50,\n      default: 10,\n      description: 'Maximum results',\n    },\n  },\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<HubResponse[]> {\n  const limit = coerceLimit(args.limit, 10);\n  const metric = validateEnum(args.metric, VALID_METRICS, 'metric', 'in_degree');\n\n  const hubs = await ctx.core.getHubs(metric as Metric, limit);\n  return hubsToResponses(hubs, ctx.store);\n}\n","import type { HandlerContext } from './types.js';\nimport type { TagMode } from '../../types/provider.js';\nimport type { NodeResponse, NodeMetadataResponse } from '../types.js';\nimport { coerceLimit, validateEnum, validateRequiredTags } from '../validation.js';\nimport { nodesToResponses } from '../transforms.js';\n\nconst VALID_TAG_MODES = ['any', 'all'] as const;\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    tags: {\n      type: 'array',\n      items: { type: 'string' },\n      minItems: 1,\n      description: 'Tags to match',\n    },\n    mode: {\n      type: 'string',\n      enum: ['any', 'all'],\n      default: 'any',\n      description: 'any = OR matching, all = AND matching',\n    },\n    limit: {\n      type: 'integer',\n      minimum: 1,\n      maximum: 100,\n      default: 20,\n      description: 'Maximum results',\n    },\n    include_content: {\n      type: 'boolean',\n      default: false,\n      description:\n        'Include node content in results. Default false returns metadata only.',\n    },\n  },\n  required: ['tags'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse[] | NodeMetadataResponse[]> {\n  const tags = validateRequiredTags(args.tags);\n  const limit = coerceLimit(args.limit, 20);\n  const includeContent = args.include_content === true;\n\n  const mode = validateEnum(args.mode, VALID_TAG_MODES, 'mode', 'any');\n\n  const nodes = await ctx.core.searchByTags(tags, mode as TagMode, limit);\n  return nodesToResponses(nodes, ctx.store, 'list', includeContent);\n}\n","import type { HandlerContext } from './types.js';\nimport type { NodeResponse } from '../types.js';\nimport { validateOptionalTags } from '../validation.js';\nimport { nodeToResponse } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    tags: {\n      type: 'array',\n      items: { type: 'string' },\n      description: 'Optional: limit to nodes with these tags (any match)',\n    },\n  },\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse | null> {\n  const tags = validateOptionalTags(args.tags);\n\n  const node = await ctx.core.getRandomNode(tags);\n  if (!node) {\n    return null;\n  }\n\n  return nodeToResponse(node, ctx.store, 'primary');\n}\n","import type { HandlerContext } from './types.js';\nimport type { NodeResponse } from '../types.js';\nimport { McpError } from '../types.js';\nimport { validateRequiredString, validateOptionalTags } from '../validation.js';\nimport { DEFAULT_NAMING, type NamingConventions } from '../../types/config.js';\nimport { nodeToResponse } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    id: {\n      type: 'string',\n      description:\n        'Full path for new node (must end in .md). Will be lowercased (spaces and special characters preserved). Example: \"notes/My Note.md\" creates \"notes/my note.md\"',\n    },\n    title: {\n      type: 'string',\n      description:\n        'Optional display title. Defaults to filename without .md extension.',\n    },\n    content: {\n      type: 'string',\n      description: 'Full text content (markdown)',\n    },\n    tags: {\n      type: 'array',\n      items: { type: 'string' },\n      default: [],\n      description: 'Classification tags',\n    },\n  },\n  required: ['id', 'content'],\n} as const;\n\n/**\n * Normalize a raw ID for node creation.\n * Applies filename separator convention (space↔dash), then lowercases.\n */\nexport function normalizeCreateId(\n  rawId: string,\n  naming: NamingConventions = DEFAULT_NAMING\n): string {\n  let normalized = rawId.replace(/\\\\/g, '/').toLowerCase();\n\n  if (naming.filename === 'space') {\n    normalized = normalized.replace(/-/g, ' ');\n  } else {\n    normalized = normalized.replace(/ /g, '-');\n  }\n\n  return normalized;\n}\n\n/**\n * Derive display title from node ID.\n * Extracts filename without extension, applies naming conventions.\n * Returns 'Untitled' for empty or all-special-char filenames.\n */\nexport function deriveTitle(id: string, naming?: NamingConventions): string {\n  const basename = id.split('/').pop() || '';\n  const rawTitle = basename.replace(/\\.md$/i, '');\n\n  if (!rawTitle || !/[a-zA-Z0-9]/.test(rawTitle)) {\n    return 'Untitled';\n  }\n\n  if (!naming) {\n    return rawTitle;\n  }\n\n  const spaced = naming.filename === 'dash'\n    ? rawTitle.replace(/-/g, ' ')\n    : rawTitle;\n\n  switch (naming.title) {\n    case 'title':\n      return spaced.replace(/\\b\\w/g, (c) => c.toUpperCase());\n    case 'sentence':\n      return spaced.charAt(0).toUpperCase() + spaced.slice(1);\n    case 'as-is':\n      return rawTitle;\n  }\n}\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse> {\n  const idRaw = validateRequiredString(args.id, 'id');\n\n  if (!idRaw.toLowerCase().endsWith('.md')) {\n    throw new McpError('INVALID_PARAMS', 'id must end with .md extension');\n  }\n\n  const content = validateRequiredString(args.content, 'content');\n  const titleRaw = args.title as string | undefined;\n  const tags = validateOptionalTags(args.tags) ?? [];\n\n  const id = normalizeCreateId(idRaw, ctx.naming);\n  const title = titleRaw ?? deriveTitle(id, ctx.naming);\n\n  const existing = await ctx.core.getNode(id);\n  if (existing) {\n    throw new McpError('NODE_EXISTS', `Node already exists: ${id}`);\n  }\n\n  const node = await ctx.core.createNode({\n    id,\n    title,\n    content,\n    tags,\n  });\n\n  return nodeToResponse(node, ctx.store, 'primary');\n}\n","import type { HandlerContext } from './types.js';\nimport type { NodeUpdates } from '../../types/node.js';\nimport type { NodeResponse } from '../types.js';\nimport { McpError } from '../types.js';\nimport { validateRequiredString, validateOptionalTags } from '../validation.js';\nimport { nodeToResponse } from '../transforms.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    id: {\n      type: 'string',\n      description:\n        'Node ID to update. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n    title: {\n      type: 'string',\n      description: 'New title (renames file for DocStore)',\n    },\n    content: {\n      type: 'string',\n      description: 'New content (replaces entirely)',\n    },\n    tags: {\n      type: 'array',\n      items: { type: 'string' },\n      description: 'New tags (replaces existing)',\n    },\n  },\n  required: ['id'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodeResponse> {\n  const id = validateRequiredString(args.id, 'id');\n  const title = args.title as string | undefined;\n  const content = args.content as string | undefined;\n  const tags = validateOptionalTags(args.tags);\n\n  if (title === undefined && content === undefined && tags === undefined) {\n    throw new McpError(\n      'INVALID_PARAMS',\n      'At least one of title, content, or tags must be provided'\n    );\n  }\n\n  const existing = await ctx.core.getNode(id);\n  if (!existing) {\n    throw new McpError('NODE_NOT_FOUND', `Node not found: ${id}`);\n  }\n\n  if (title !== undefined && title !== existing.title) {\n    const incomingNeighbors = await ctx.core.getNeighbors(id, { direction: 'in' });\n    if (incomingNeighbors.length > 0) {\n      throw new McpError(\n        'LINK_INTEGRITY',\n        `Cannot rename node with ${incomingNeighbors.length} incoming links`\n      );\n    }\n  }\n\n  const updates: NodeUpdates = {};\n  if (title !== undefined) updates.title = title;\n  if (content !== undefined) updates.content = content;\n  if (tags !== undefined) updates.tags = tags;\n\n  const updated = await ctx.core.updateNode(id, updates);\n  return nodeToResponse(updated, ctx.store, 'primary');\n}\n","import type { HandlerContext } from './types.js';\nimport type { DeleteResponse } from '../types.js';\nimport { validateRequiredString } from '../validation.js';\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    id: {\n      type: 'string',\n      description:\n        'Node ID to delete. ID is normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n  },\n  required: ['id'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<DeleteResponse> {\n  const id = validateRequiredString(args.id, 'id');\n\n  const deleted = await ctx.core.deleteNode(id);\n  return { deleted };\n}\n","import type { HandlerContext } from './types.js';\nimport type { ListFilter, NodeSummary } from '../../types/provider.js';\nimport { coerceLimit, coerceOffset } from '../validation.js';\n\nexport interface ListNodesResponse {\n  nodes: NodeSummary[];\n  total: number;\n}\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    tag: {\n      type: 'string',\n      description:\n        'Filter by tag from the \"tags\" frontmatter array (case-insensitive). Does NOT search other frontmatter fields like \"type\" or \"category\".',\n    },\n    path: {\n      type: 'string',\n      description: 'Filter by path prefix (startsWith, case-insensitive)',\n    },\n    limit: {\n      type: 'integer',\n      minimum: 1,\n      maximum: 1000,\n      default: 100,\n      description: 'Maximum results to return',\n    },\n    offset: {\n      type: 'integer',\n      minimum: 0,\n      default: 0,\n      description: 'Skip this many results (for pagination)',\n    },\n  },\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<ListNodesResponse> {\n  const tag = args.tag as string | undefined;\n  const path = args.path as string | undefined;\n  const limit = coerceLimit(args.limit, 100);\n  const offset = coerceOffset(args.offset, 0);\n\n  const filter: ListFilter = {};\n  if (tag) filter.tag = tag;\n  if (path) filter.path = path;\n\n  return ctx.core.listNodes(filter, { limit, offset });\n}\n","import type { HandlerContext } from './types.js';\nimport type { ResolveOptions, ResolveStrategy, ResolveResult } from '../../types/provider.js';\nimport { McpError } from '../types.js';\nimport { validateEnum, validateStringArray } from '../validation.js';\n\nconst VALID_STRATEGIES = ['exact', 'fuzzy', 'semantic'] as const;\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    names: {\n      type: 'array',\n      items: { type: 'string' },\n      description: 'Names to resolve to existing nodes',\n    },\n    strategy: {\n      type: 'string',\n      enum: ['exact', 'fuzzy', 'semantic'],\n      default: 'fuzzy',\n      description:\n        'How to match names to nodes. \"exact\": case-insensitive title equality. \"fuzzy\": string similarity (Dice coefficient) — use for typos, misspellings, partial matches. \"semantic\": embedding cosine similarity — use for synonyms or related concepts (NOT typos). Misspellings embed poorly because they produce unrelated vectors.',\n    },\n    threshold: {\n      type: 'number',\n      minimum: 0,\n      maximum: 1,\n      default: 0.7,\n      description:\n        'Minimum similarity score (0-1). Lower values match more loosely. For typo tolerance, use fuzzy with threshold 0.5-0.6. Ignored for exact strategy.',\n    },\n    tag: {\n      type: 'string',\n      description:\n        'Filter candidates by tag from \"tags\" frontmatter array (case-insensitive)',\n    },\n    path: {\n      type: 'string',\n      description: 'Filter candidates by path prefix (case-insensitive)',\n    },\n  },\n  required: ['names'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<ResolveResult[]> {\n  const names = validateStringArray(args.names, 'names');\n  const threshold = args.threshold as number | undefined;\n  const tag = args.tag as string | undefined;\n  const path = args.path as string | undefined;\n\n  const strategy = validateEnum(\n    args.strategy,\n    VALID_STRATEGIES,\n    'strategy',\n    'fuzzy'\n  ) as ResolveStrategy;\n\n  if (strategy === 'semantic' && !ctx.hasEmbedding) {\n    throw new McpError('PROVIDER_ERROR', 'Semantic resolution requires embedding provider');\n  }\n\n  const options: ResolveOptions = { strategy };\n  if (threshold !== undefined) options.threshold = threshold;\n  if (tag) options.tag = tag;\n  if (path) options.path = path;\n\n  return ctx.core.resolveNodes(names, options);\n}\n","import type { HandlerContext } from './types.js';\nimport { validateStringArray } from '../validation.js';\n\nexport interface NodesExistResponse {\n  [id: string]: boolean;\n}\n\nexport const schema = {\n  type: 'object',\n  properties: {\n    ids: {\n      type: 'array',\n      items: { type: 'string' },\n      description:\n        'Node IDs to check existence. IDs are normalized to lowercase (e.g., \"Recipes/Bulgogi.md\" becomes \"recipes/bulgogi.md\").',\n    },\n  },\n  required: ['ids'],\n} as const;\n\nexport async function handler(\n  ctx: HandlerContext,\n  args: Record<string, unknown>\n): Promise<NodesExistResponse> {\n  const ids = validateStringArray(args.ids, 'ids');\n\n  const result = await ctx.store.nodesExist(ids);\n\n  const response: NodesExistResponse = {};\n  for (const [id, exists] of result) {\n    response[id] = exists;\n  }\n  return response;\n}\n","import type { Tool } from '@modelcontextprotocol/sdk/types.js';\nimport type { HandlerContext } from './types.js';\nimport type { ResolveResult } from '../../types/provider.js';\nimport type {\n  NodeResponse,\n  NodeWithContextResponse,\n  SearchResultResponse,\n  HubResponse,\n  PathResponse,\n  DeleteResponse,\n} from '../types.js';\nimport { McpError } from '../types.js';\nimport type { ListNodesResponse } from './list_nodes.js';\nimport type { NodesExistResponse } from './nodes_exist.js';\n\nimport * as search from './search.js';\nimport * as getNode from './get_node.js';\nimport * as getNeighbors from './get_neighbors.js';\nimport * as findPath from './find_path.js';\nimport * as getHubs from './get_hubs.js';\nimport * as searchByTags from './search_by_tags.js';\nimport * as randomNode from './random_node.js';\nimport * as createNode from './create_node.js';\nimport * as updateNode from './update_node.js';\nimport * as deleteNode from './delete_node.js';\nimport * as listNodes from './list_nodes.js';\nimport * as resolveNodes from './resolve_nodes.js';\nimport * as nodesExist from './nodes_exist.js';\n\nexport type { HandlerContext } from './types.js';\nexport { normalizeCreateId, deriveTitle } from './create_node.js';\nexport { coerceInt } from '../validation.js';\nexport type { ListNodesResponse } from './list_nodes.js';\nexport type { NodesExistResponse } from './nodes_exist.js';\n\ntype Handler = {\n  schema: object;\n  handler: (ctx: HandlerContext, args: Record<string, unknown>) => Promise<unknown>;\n};\n\nconst handlers: Record<string, Handler> = {\n  search,\n  get_node: getNode,\n  get_neighbors: getNeighbors,\n  find_path: findPath,\n  get_hubs: getHubs,\n  search_by_tags: searchByTags,\n  random_node: randomNode,\n  create_node: createNode,\n  update_node: updateNode,\n  delete_node: deleteNode,\n  list_nodes: listNodes,\n  resolve_nodes: resolveNodes,\n  nodes_exist: nodesExist,\n};\n\nconst TOOL_DESCRIPTIONS: Record<string, string> = {\n  search: 'Semantic similarity search across all nodes',\n  get_node: 'Retrieve a single node by ID with optional neighbor context',\n  get_neighbors: 'Get nodes linked to or from a specific node',\n  find_path: 'Find the shortest path between two nodes',\n  get_hubs: 'Get the most central nodes by graph metric',\n  search_by_tags: 'Filter nodes by tags (AND or OR matching)',\n  random_node: 'Get a random node for discovery, optionally filtered by tags',\n  create_node: 'Create a new node (writes file for DocStore)',\n  update_node: 'Update an existing node. Title changes rejected if incoming links exist.',\n  delete_node: 'Delete a node by ID',\n  list_nodes: 'List nodes with optional filters and pagination. Tag filter searches the \"tags\" frontmatter array only. All IDs returned are lowercase.',\n  resolve_nodes: 'Batch resolve names to existing node IDs. Strategy selection: \"exact\" for known titles, \"fuzzy\" for typos/misspellings (e.g., \"chikken\" -> \"chicken\"), \"semantic\" for synonyms/concepts (e.g., \"poultry leg meat\" -> \"chicken thigh\"). Semantic does NOT handle typos — misspellings produce garbage embeddings.',\n  nodes_exist: 'Batch check if node IDs exist. IDs are normalized to lowercase before checking.',\n};\n\n/** Cast schema to Tool inputSchema type (readonly arrays → mutable) */\ntype InputSchema = Tool['inputSchema'];\nconst asSchema = (s: unknown): InputSchema => s as InputSchema;\n\nexport function getToolDefinitions(hasEmbedding: boolean): Tool[] {\n  // Tool order: read operations first (get/find/search), then mutations (create/update/delete),\n  // then batch utilities. Search is prepended only when embedding provider is available.\n  const toolOrder = [\n    'get_node',\n    'get_neighbors',\n    'find_path',\n    'get_hubs',\n    'search_by_tags',\n    'random_node',\n    'create_node',\n    'update_node',\n    'delete_node',\n    'list_nodes',\n    'resolve_nodes',\n    'nodes_exist',\n  ];\n\n  const tools: Tool[] = toolOrder.map((name) => ({\n    name,\n    description: TOOL_DESCRIPTIONS[name]!,\n    inputSchema: asSchema(handlers[name]!.schema),\n  }));\n\n  if (hasEmbedding) {\n    tools.unshift({\n      name: 'search',\n      description: TOOL_DESCRIPTIONS.search!,\n      inputSchema: asSchema(handlers.search!.schema),\n    });\n  }\n\n  return tools;\n}\n\nexport type ToolResult =\n  | NodeResponse\n  | NodeWithContextResponse\n  | SearchResultResponse[]\n  | NodeResponse[]\n  | HubResponse[]\n  | PathResponse\n  | DeleteResponse\n  | ListNodesResponse\n  | ResolveResult[]\n  | NodesExistResponse\n  | null;\n\nexport async function dispatchTool(\n  ctx: HandlerContext,\n  name: string,\n  args: Record<string, unknown>\n): Promise<ToolResult> {\n  const h = handlers[name];\n  if (!h) {\n    throw new McpError('INVALID_PARAMS', `Unknown tool: ${name}`);\n  }\n  return h.handler(ctx, args) as Promise<ToolResult>;\n}\n","import { access, writeFile, mkdir } from 'node:fs/promises';\nimport { join, dirname } from 'node:path';\nimport { Cache } from '../../providers/docstore/cache.js';\n\nexport interface VizOptions {\n  output?: string | undefined;\n  open?: boolean | undefined;\n}\n\nexport interface VizResult {\n  outputPath: string;\n  nodeCount: number;\n  edgeCount: number;\n  shouldOpen: boolean;\n}\n\ninterface GraphNode {\n  id: string;\n  title: string;\n  inDegree: number;\n}\n\ninterface GraphEdge {\n  source: string;\n  target: string;\n}\n\nexport async function vizCommand(\n  directory: string,\n  options: VizOptions = {}\n): Promise<VizResult> {\n  const configPath = join(directory, 'roux.yaml');\n\n  // Check if initialized\n  try {\n    await access(configPath);\n  } catch {\n    throw new Error(`Directory not initialized. Run 'roux init' first.`);\n  }\n\n  const cacheDir = join(directory, '.roux');\n  const outputPath = options.output ?? join(cacheDir, 'graph.html');\n\n  const cache = new Cache(cacheDir);\n\n  try {\n    const nodes = cache.getAllNodes();\n    const graphNodes: GraphNode[] = [];\n    const graphEdges: GraphEdge[] = [];\n\n    // Build set of existing node IDs for edge filtering\n    const existingNodeIds = new Set(nodes.map((n) => n.id));\n\n    // Build node list with degree info\n    for (const node of nodes) {\n      const centrality = cache.getCentrality(node.id);\n      graphNodes.push({\n        id: node.id,\n        title: node.title,\n        inDegree: centrality?.inDegree ?? 0,\n      });\n\n      // Build edges from outgoing links, filtering to existing targets only\n      for (const target of node.outgoingLinks) {\n        if (existingNodeIds.has(target)) {\n          graphEdges.push({\n            source: node.id,\n            target,\n          });\n        }\n      }\n    }\n\n    // Generate HTML\n    const html = generateHtml(graphNodes, graphEdges);\n\n    // Ensure output directory exists\n    await mkdir(dirname(outputPath), { recursive: true });\n    await writeFile(outputPath, html, 'utf-8');\n\n    return {\n      outputPath,\n      nodeCount: graphNodes.length,\n      edgeCount: graphEdges.length,\n      shouldOpen: options.open ?? false,\n    };\n  } finally {\n    cache.close();\n  }\n}\n\nfunction generateHtml(nodes: GraphNode[], edges: GraphEdge[]): string {\n  const nodesJson = JSON.stringify(nodes);\n  const edgesJson = JSON.stringify(edges);\n\n  return `<!DOCTYPE html>\n<html lang=\"en\">\n<head>\n  <meta charset=\"UTF-8\">\n  <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">\n  <title>Roux Graph Visualization</title>\n  <script src=\"https://d3js.org/d3.v7.min.js\"></script>\n  <style>\n    * { margin: 0; padding: 0; box-sizing: border-box; }\n    body { font-family: system-ui, sans-serif; background: #1a1a2e; overflow: hidden; }\n    svg { display: block; width: 100vw; height: 100vh; }\n    .node circle { cursor: pointer; }\n    .node text { fill: #e0e0e0; font-size: 10px; pointer-events: none; }\n    .link { stroke: #4a4a6a; stroke-opacity: 0.6; fill: none; }\n    .tooltip {\n      position: absolute;\n      background: #16213e;\n      color: #e0e0e0;\n      padding: 8px 12px;\n      border-radius: 4px;\n      font-size: 12px;\n      pointer-events: none;\n      opacity: 0;\n      transition: opacity 0.2s;\n      border: 1px solid #4a4a6a;\n    }\n  </style>\n</head>\n<body>\n  <div class=\"tooltip\" id=\"tooltip\"></div>\n  <svg></svg>\n  <script>\n    const nodes = ${nodesJson};\n    const links = ${edgesJson};\n\n    const width = window.innerWidth;\n    const height = window.innerHeight;\n\n    const svg = d3.select(\"svg\")\n      .attr(\"viewBox\", [0, 0, width, height]);\n\n    const g = svg.append(\"g\");\n\n    // Zoom behavior\n    svg.call(d3.zoom()\n      .scaleExtent([0.1, 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.replace(/</g, '&lt;')\n        .replace(/>/g, '&gt;')\n        .replace(/\"/g, '&quot;')\n        .replace(/'/g, '&#039;');\n    }\n\n    // Tooltip\n    const tooltip = d3.select(\"#tooltip\");\n    node\n      .on(\"mouseover\", (event, d) => {\n        tooltip\n          .style(\"opacity\", 1)\n          .html(\\`<strong>\\${escapeHtml(d.title)}</strong><br>ID: \\${escapeHtml(d.id)}<br>Incoming links: \\${d.inDegree}\\`);\n      })\n      .on(\"mousemove\", (event) => {\n        tooltip\n          .style(\"left\", (event.pageX + 10) + \"px\")\n          .style(\"top\", (event.pageY - 10) + \"px\");\n      })\n      .on(\"mouseout\", () => tooltip.style(\"opacity\", 0));\n\n    // Simulation tick\n    simulation.on(\"tick\", () => {\n      link\n        .attr(\"x1\", d => d.source.x)\n        .attr(\"y1\", d => d.source.y)\n        .attr(\"x2\", d => d.target.x)\n        .attr(\"y2\", d => d.target.y);\n\n      node.attr(\"transform\", d => \\`translate(\\${d.x},\\${d.y})\\`);\n    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