@gettymade/roux 0.1.0

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../node_modules/string-similarity/src/index.js","../src/types/node.ts","../src/types/provider.ts","../src/types/config.ts","../src/providers/docstore/index.ts","../src/providers/docstore/cache.ts","../src/providers/vector/sqlite.ts","../src/providers/docstore/parser.ts","../src/graph/builder.ts","../src/graph/operations.ts","../src/providers/embedding/transformers.ts","../src/core/graphcore.ts","../src/index.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","export interface SourceRef {\n  type: 'file' | 'api' | 'manual';\n  path?: string;\n  lastModified?: Date;\n}\n\n/** The canonical data model. All modules speak Node. */\nexport interface Node {\n  /** Store-specific format */\n  id: string;\n  title: string;\n  content: string;\n  tags: string[];\n  /** By id */\n  outgoingLinks: string[];\n  properties: Record<string, unknown>;\n  sourceRef?: SourceRef;\n}\n\nexport interface NodeWithContext extends Node {\n  /** Populated when depth > 0 */\n  neighbors?: Node[];\n  incomingCount?: number;\n  outgoingCount?: number;\n}\n\nexport function isNode(value: unknown): value is Node {\n  if (typeof value !== 'object' || value === null) {\n    return false;\n  }\n  const obj = value as Record<string, unknown>;\n  return (\n    typeof obj['id'] === 'string' &&\n    typeof obj['title'] === 'string' &&\n    typeof obj['content'] === 'string' &&\n    Array.isArray(obj['tags']) &&\n    obj['tags'].every((t) => typeof t === 'string') &&\n    Array.isArray(obj['outgoingLinks']) &&\n    obj['outgoingLinks'].every((l) => typeof l === 'string') &&\n    typeof obj['properties'] === 'object' &&\n    obj['properties'] !== null\n  );\n}\n\nexport function isSourceRef(value: unknown): value is SourceRef {\n  if (typeof value !== 'object' || value === null) {\n    return false;\n  }\n  const obj = value as Record<string, unknown>;\n  const validTypes = ['file', 'api', 'manual'];\n  return (\n    typeof obj['type'] === 'string' &&\n    validTypes.includes(obj['type']) &&\n    (obj['path'] === undefined || typeof obj['path'] === 'string') &&\n    (obj['lastModified'] === undefined || obj['lastModified'] instanceof Date)\n  );\n}\n","import type { Node } from './node.js';\nimport type { Direction, NeighborOptions } from './edge.js';\n\nexport type Metric = 'pagerank' | '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/** Data persistence and graph operations. Required provider. */\nexport interface StoreProvider {\n  // CRUD\n  createNode(node: Node): Promise<void>;\n  updateNode(id: string, updates: Partial<Node>): 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): 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 StoreProvider. */\nexport interface EmbeddingProvider {\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 VectorProvider {\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 isVectorProvider(value: unknown): value is VectorProvider {\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// Re-export for convenience\nexport type { Direction, NeighborOptions };\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  /** Embedding regeneration strategy */\n  onModelChange: ModelChangeBehavior;\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  /** Defaults to local */\n  embedding?: EmbeddingConfig;\n  llm?: LLMConfig;\n}\n\nexport interface RouxConfig {\n  source?: SourceConfig;\n  cache?: CacheConfig;\n  system?: SystemConfig;\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","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 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 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","// Roux - Graph Programming Interface\n\nexport const VERSION = '0.1.0';\n\n// Re-export all types\nexport * from './types/index.js';\n\n// Core\nexport { GraphCoreImpl } from './core/graphcore.js';\n\n// Providers\nexport { DocStore } from './providers/docstore/index.js';\nexport { TransformersEmbeddingProvider } from './providers/embedding/index.js';\nexport { SqliteVectorProvider } from 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package/package.json

@@ -0,0 +1,67 @@
+{
+  "name": "@gettymade/roux",
+  "version": "0.1.0",
+  "description": "Graph Programming Interface for knowledge bases",
+  "type": "module",
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "bin": {
+    "roux": "./dist/cli/index.js"
+  },
+  "files": [
+    "dist"
+  ],
+  "scripts": {
+    "build": "tsup",
+    "dev": "tsup --watch",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "lint": "eslint src tests",
+    "lint:fix": "eslint src tests --fix",
+    "format": "prettier --write .",
+    "format:check": "prettier --check .",
+    "typecheck": "tsc --noEmit"
+  },
+  "keywords": [
+    "graph",
+    "knowledge-base",
+    "mcp",
+    "obsidian",
+    "semantic-search"
+  ],
+  "author": "",
+  "license": "MIT",
+  "engines": {
+    "node": ">=20"
+  },
+  "devDependencies": {
+    "@types/better-sqlite3": "^7.6.13",
+    "@types/chokidar": "^1.7.5",
+    "@types/node": "^20.17.0",
+    "@types/string-similarity": "^4.0.2",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
+    "@vitest/coverage-v8": "^2.0.0",
+    "eslint": "^9.0.0",
+    "eslint-config-prettier": "^9.0.0",
+    "prettier": "^3.0.0",
+    "string-similarity": "^4.0.4",
+    "tsup": "^8.0.0",
+    "typescript": "^5.6.0",
+    "vitest": "^2.0.0"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.25.3",
+    "@xenova/transformers": "^2.17.2",
+    "better-sqlite3": "^12.6.2",
+    "chokidar": "^5.0.0",
+    "commander": "^14.0.2",
+    "graphology": "^0.26.0",
+    "graphology-shortest-path": "^2.1.0",
+    "graphology-types": "^0.24.8",
+    "gray-matter": "^4.0.3",
+    "roux": "github:alexgetty/roux",
+    "yaml": "^2.8.2"
+  }
+}