@tekmidian/pai 0.5.7 → 0.6.0

package/dist/zettelkasten-e-a4rW_6.mjs.map

@@ -1 +0,0 @@
-{"version":3,"file":"zettelkasten-e-a4rW_6.mjs","names":["MAX_CHUNKS","MAX_CHUNKS"],"sources":["../src/zettelkasten/explore.ts","../src/zettelkasten/surprise.ts","../src/zettelkasten/converse.ts","../src/zettelkasten/themes.ts","../src/zettelkasten/health.ts","../src/zettelkasten/suggest.ts"],"sourcesContent":["import type { Database } from \"better-sqlite3\";\nimport { dirname } from \"node:path\";\n\nexport interface ExploreOptions {\n  startNote: string;\n  depth?: number;\n  direction?: \"forward\" | \"backward\" | \"both\";\n  mode?: \"sequential\" | \"associative\" | \"all\";\n}\n\nexport interface ExploreNode {\n  path: string;\n  title: string | null;\n  depth: number;\n  linkType: \"sequential\" | \"associative\";\n  inbound: number;\n  outbound: number;\n}\n\nexport interface ExploreResult {\n  root: string;\n  nodes: ExploreNode[];\n  edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }>;\n  branchingPoints: string[];\n  maxDepthReached: boolean;\n}\n\nfunction classifyEdge(source: string, target: string): \"sequential\" | \"associative\" {\n  return dirname(source) === dirname(target) ? \"sequential\" : \"associative\";\n}\n\nfunction resolveStart(db: Database, startNote: string): string | null {\n  const inFiles = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(startNote) as { vault_path: string } | undefined;\n  if (inFiles) return inFiles.vault_path;\n\n  const alias = db\n    .prepare(\"SELECT canonical_path FROM vault_aliases WHERE vault_path = ?\")\n    .get(startNote) as { canonical_path: string } | undefined;\n  if (!alias) return null;\n\n  const canonical = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(alias.canonical_path) as { vault_path: string } | undefined;\n  return canonical ? canonical.vault_path : null;\n}\n\nfunction getForwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT target_path FROM vault_links WHERE source_path = ? AND target_path IS NOT NULL\",\n      )\n      .all(path) as Array<{ target_path: string }>\n  ).map((r) => r.target_path);\n}\n\nfunction getBackwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT source_path FROM vault_links WHERE target_path = ?\",\n      )\n      .all(path) as Array<{ source_path: string }>\n  ).map((r) => r.source_path);\n}\n\nfunction getFileInfo(\n  db: Database,\n  path: string,\n): { title: string | null; inbound: number; outbound: number } {\n  const file = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n\n  const health = db\n    .prepare(\"SELECT inbound_count, outbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number; outbound_count: number } | undefined;\n\n  return {\n    title: file?.title ?? null,\n    inbound: health?.inbound_count ?? 0,\n    outbound: health?.outbound_count ?? 0,\n  };\n}\n\n/**\n * Traverse the Zettelkasten link graph using BFS, following chains of thought\n * from a starting note up to a configurable depth.\n */\nexport function zettelExplore(db: Database, opts: ExploreOptions): ExploreResult {\n  const depth = Math.min(Math.max(opts.depth ?? 3, 1), 10);\n  const direction = opts.direction ?? \"both\";\n  const mode = opts.mode ?? \"all\";\n\n  const root = resolveStart(db, opts.startNote);\n  if (!root) {\n    return {\n      root: opts.startNote,\n      nodes: [],\n      edges: [],\n      branchingPoints: [],\n      maxDepthReached: false,\n    };\n  }\n\n  const visited = new Set<string>([root]);\n  const nodes: ExploreNode[] = [];\n  const edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }> = [];\n  let maxDepthReached = false;\n\n  const queue: Array<{ path: string; depth: number }> = [{ path: root, depth: 0 }];\n\n  while (queue.length > 0) {\n    const current = queue.shift()!;\n\n    if (current.depth >= depth) {\n      maxDepthReached = true;\n      continue;\n    }\n\n    const neighbors: Array<{ neighbor: string; from: string; to: string }> = [];\n\n    if (direction === \"forward\" || direction === \"both\") {\n      for (const n of getForwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: current.path, to: n });\n      }\n    }\n\n    if (direction === \"backward\" || direction === \"both\") {\n      for (const n of getBackwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: n, to: current.path });\n      }\n    }\n\n    for (const { neighbor, from, to } of neighbors) {\n      const edgeType = classifyEdge(from, to);\n\n      if (mode !== \"all\" && edgeType !== mode) {\n        continue;\n      }\n\n      const edgeKey = `${from}|${to}`;\n      const alreadyHasEdge = edges.some((e) => e.from === from && e.to === to);\n      if (!alreadyHasEdge) {\n        edges.push({ from, to, type: edgeType });\n      }\n\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n\n        const info = getFileInfo(db, neighbor);\n        nodes.push({\n          path: neighbor,\n          title: info.title,\n          depth: current.depth + 1,\n          linkType: edgeType,\n          inbound: info.inbound,\n          outbound: info.outbound,\n        });\n\n        queue.push({ path: neighbor, depth: current.depth + 1 });\n      }\n    }\n  }\n\n  const branchingPoints = nodes\n    .filter((n) => n.outbound > 2)\n    .map((n) => n.path);\n\n  const rootInfo = getFileInfo(db, root);\n  if (rootInfo.outbound > 2) {\n    branchingPoints.unshift(root);\n  }\n\n  return { root, nodes, edges, branchingPoints, maxDepthReached };\n}\n","import type { Database } from \"better-sqlite3\";\nimport {\n  deserializeEmbedding,\n  generateEmbedding,\n  cosineSimilarity,\n} from \"../memory/embeddings.js\";\n\nexport interface SurpriseOptions {\n  referencePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  minSimilarity?: number;\n  minGraphDistance?: number;\n}\n\nexport interface SurpriseResult {\n  path: string;\n  title: string | null;\n  cosineSimilarity: number;\n  graphDistance: number;\n  surpriseScore: number;\n  sharedSnippet: string;\n}\n\nconst CHUNK_BATCH_SIZE = 500;\nconst MAX_CHUNKS = 5000;\nconst BFS_HOP_CAP = 20;\n\nfunction getFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, { embedding: Float32Array; text: string }> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding, text FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{\n    path: string;\n    embedding: Buffer;\n    text: string;\n  }>;\n\n  // Group chunks by path and accumulate embeddings for averaging\n  const byPath = new Map<string, { sum: Float32Array; count: number; text: string }>();\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1, text: row.text });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, { embedding: Float32Array; text: string }>();\n  for (const [path, { sum, count, text }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, { embedding: avg, text });\n  }\n  return result;\n}\n\nfunction getReferenceEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): { embedding: Float32Array; found: boolean } {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) {\n    return { embedding: new Float32Array(0), found: false };\n  }\n\n  const dim = deserializeEmbedding(rows[0].embedding).length;\n  const sum = new Float32Array(dim);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return { embedding: avg, found: true };\n}\n\nfunction bfsGraphDistance(db: Database, source: string, target: string): number {\n  if (source === target) return 0;\n\n  const visited = new Set<string>([source]);\n  const queue: Array<{ path: string; hops: number }> = [{ path: source, hops: 0 }];\n\n  while (queue.length > 0) {\n    const { path, hops } = queue.shift()!;\n    if (hops >= BFS_HOP_CAP) continue;\n\n    const neighbors = db\n      .prepare(\n        `SELECT target_path AS neighbor FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n         UNION\n         SELECT source_path AS neighbor FROM vault_links\n         WHERE target_path = ?`,\n      )\n      .all(path, path) as Array<{ neighbor: string }>;\n\n    for (const { neighbor } of neighbors) {\n      if (neighbor === target) return hops + 1;\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n        queue.push({ path: neighbor, hops: hops + 1 });\n      }\n    }\n  }\n\n  return Infinity;\n}\n\nfunction getBestChunkText(\n  db: Database,\n  projectId: number,\n  path: string,\n  refEmbedding: Float32Array,\n): string {\n  const rows = db\n    .prepare(\n      `SELECT text, embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL\n       LIMIT 20`,\n    )\n    .all(projectId, path) as Array<{ text: string; embedding: Buffer }>;\n\n  if (rows.length === 0) return \"\";\n\n  let bestText = rows[0].text;\n  let bestSim = -Infinity;\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const sim = cosineSimilarity(refEmbedding, vec);\n    if (sim > bestSim) {\n      bestSim = sim;\n      bestText = row.text;\n    }\n  }\n\n  return bestText.trim().slice(0, 200);\n}\n\n/**\n * Find notes that are semantically similar to a reference note but graph-distant —\n * revealing surprising conceptual connections across unrelated areas of the Zettelkasten.\n */\nexport async function zettelSurprise(\n  db: Database,\n  opts: SurpriseOptions,\n): Promise<SurpriseResult[]> {\n  const limit = opts.limit ?? 10;\n  const minSimilarity = opts.minSimilarity ?? 0.3;\n  const minGraphDistance = opts.minGraphDistance ?? 3;\n\n  let { embedding: refEmbedding, found } = getReferenceEmbedding(\n    db,\n    opts.vaultProjectId,\n    opts.referencePath,\n  );\n\n  // Fall back to generating an embedding from the file title if no chunks exist\n  if (!found) {\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(opts.referencePath) as { title: string | null } | undefined;\n    const text = file?.title ?? opts.referencePath;\n    refEmbedding = await generateEmbedding(text, true);\n  }\n\n  const allFileEmbeddings = getFileEmbeddings(db, opts.vaultProjectId);\n\n  // Remove the reference note itself from candidates\n  allFileEmbeddings.delete(opts.referencePath);\n\n  // First pass: filter by semantic similarity to avoid BFS on all nodes\n  const semanticCandidates: Array<{ path: string; sim: number }> = [];\n  for (const [path, { embedding }] of allFileEmbeddings) {\n    const sim = cosineSimilarity(refEmbedding, embedding);\n    if (sim >= minSimilarity) {\n      semanticCandidates.push({ path, sim });\n    }\n  }\n\n  // Compute graph distances for semantic candidates\n  const results: SurpriseResult[] = [];\n\n  for (const { path, sim } of semanticCandidates) {\n    const graphDistance = bfsGraphDistance(db, opts.referencePath, path);\n\n    const effectiveDistance = isFinite(graphDistance) ? graphDistance : BFS_HOP_CAP;\n    if (effectiveDistance < minGraphDistance) continue;\n\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(path) as { title: string | null } | undefined;\n\n    const surpriseScore = sim * Math.log2(effectiveDistance + 1);\n    const sharedSnippet = getBestChunkText(db, opts.vaultProjectId, path, refEmbedding);\n\n    results.push({\n      path,\n      title: file?.title ?? null,\n      cosineSimilarity: sim,\n      graphDistance: isFinite(graphDistance) ? graphDistance : Infinity,\n      surpriseScore,\n      sharedSnippet,\n    });\n  }\n\n  results.sort((a, b) => b.surpriseScore - a.surpriseScore);\n  return results.slice(0, limit);\n}\n","import type { Database } from \"better-sqlite3\";\nimport { searchMemoryHybrid } from \"../memory/search.js\";\nimport { generateEmbedding } from \"../memory/embeddings.js\";\n\nexport interface ConverseOptions {\n  /** The user's question or topic to explore. */\n  question: string;\n  /** project_id for vault chunks in memory_chunks. */\n  vaultProjectId: number;\n  /** Graph expansion depth. Default 2. */\n  depth?: number;\n  /** Maximum number of relevant notes to return. Default 15. */\n  limit?: number;\n}\n\nexport interface ConverseConnection {\n  fromPath: string;\n  toPath: string;\n  /** Top-level folder of fromPath. */\n  fromDomain: string;\n  /** Top-level folder of toPath. */\n  toDomain: string;\n  /** Link count between these two notes (can be > 1). */\n  strength: number;\n}\n\nexport interface ConverseResult {\n  relevantNotes: Array<{\n    path: string;\n    title: string | null;\n    snippet: string;\n    score: number;\n    domain: string;\n  }>;\n  /** Cross-domain connections found among the selected notes. */\n  connections: ConverseConnection[];\n  /** Unique domains involved across all selected notes. */\n  domains: string[];\n  /** AI-ready prompt combining notes + connections for insight generation. */\n  synthesisPrompt: string;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Extract the top-level folder from a vault path (first path segment). */\nfunction extractDomain(vaultPath: string): string {\n  const slash = vaultPath.indexOf(\"/\");\n  return slash === -1 ? vaultPath : vaultPath.slice(0, slash);\n}\n\n/**\n * Expand one level of graph neighbors for a set of paths.\n * Returns all outbound and inbound neighbor paths (excluding already-visited).\n */\nfunction expandNeighbors(db: Database, paths: Set<string>): string[] {\n  if (paths.size === 0) return [];\n\n  const placeholders = Array.from(paths).map(() => \"?\").join(\", \");\n  const pathList = Array.from(paths);\n\n  const forward = db\n    .prepare(\n      `SELECT DISTINCT target_path FROM vault_links WHERE source_path IN (${placeholders}) AND target_path IS NOT NULL`,\n    )\n    .all(...pathList) as Array<{ target_path: string }>;\n\n  const backward = db\n    .prepare(\n      `SELECT DISTINCT source_path FROM vault_links WHERE target_path IN (${placeholders})`,\n    )\n    .all(...pathList) as Array<{ source_path: string }>;\n\n  const neighbors: string[] = [];\n  for (const r of forward) neighbors.push(r.target_path);\n  for (const r of backward) neighbors.push(r.source_path);\n  return neighbors;\n}\n\n/**\n * Look up the title for a single vault path.\n * Returns null when the path is not found in vault_files.\n */\nfunction getTitle(db: Database, path: string): string | null {\n  const row = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n  return row?.title ?? null;\n}\n\n/**\n * Count inbound links for a path from vault_health.\n * Used as a tiebreaker when trimming neighbor-only notes.\n */\nfunction getInboundCount(db: Database, path: string): number {\n  const row = db\n    .prepare(\"SELECT inbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number } | undefined;\n  return row?.inbound_count ?? 0;\n}\n\n// ---------------------------------------------------------------------------\n// Main export\n// ---------------------------------------------------------------------------\n\n/**\n * Let the vault \"talk back\" — find notes relevant to a question, expand\n * through the link graph, identify cross-domain connections, and return a\n * structured result including a synthesis prompt for an AI to generate insights.\n */\nexport async function zettelConverse(\n  db: Database,\n  opts: ConverseOptions,\n): Promise<ConverseResult> {\n  const depth = Math.max(opts.depth ?? 2, 0);\n  const limit = Math.max(opts.limit ?? 15, 1);\n  const candidateLimit = 20;\n\n  // ------------------------------------------------------------------\n  // 1. Hybrid search: find top candidates via BM25 + semantic similarity\n  // ------------------------------------------------------------------\n  const queryEmbedding = await generateEmbedding(opts.question, true);\n\n  const searchResults = searchMemoryHybrid(\n    db,\n    opts.question,\n    queryEmbedding,\n    {\n      projectIds: [opts.vaultProjectId],\n      maxResults: candidateLimit,\n    },\n  );\n\n  // Map of path -> best score + snippet from search results\n  const searchHits = new Map<string, { score: number; snippet: string }>();\n  for (const r of searchResults) {\n    const existing = searchHits.get(r.path);\n    if (!existing || r.score > existing.score) {\n      searchHits.set(r.path, { score: r.score, snippet: r.snippet });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 2. Graph expansion: BFS from each search result up to `depth` levels\n  // ------------------------------------------------------------------\n  const allPaths = new Set<string>(searchHits.keys());\n  let frontier = new Set<string>(searchHits.keys());\n\n  for (let d = 0; d < depth; d++) {\n    const neighbors = expandNeighbors(db, frontier);\n    const newFrontier = new Set<string>();\n    for (const n of neighbors) {\n      if (!allPaths.has(n)) {\n        allPaths.add(n);\n        newFrontier.add(n);\n      }\n    }\n    if (newFrontier.size === 0) break;\n    frontier = newFrontier;\n  }\n\n  // ------------------------------------------------------------------\n  // 3. Deduplicate + trim to limit\n  //    Search results first (ranked by score), then neighbors by inbound count\n  // ------------------------------------------------------------------\n  const searchRanked = Array.from(searchHits.entries())\n    .sort((a, b) => b[1].score - a[1].score)\n    .map(([path, info]) => ({ path, ...info, isSearchResult: true }));\n\n  const neighborPaths = Array.from(allPaths).filter((p) => !searchHits.has(p));\n\n  // Sort neighbors by link popularity (inbound count) so that well-connected\n  // notes are preferred when we have budget for them.\n  const neighborRanked = neighborPaths\n    .map((path) => ({\n      path,\n      score: 0,\n      snippet: \"\",\n      inbound: getInboundCount(db, path),\n      isSearchResult: false,\n    }))\n    .sort((a, b) => b.inbound - a.inbound);\n\n  // Combine: search results fill the budget first, then neighbors\n  const budgetForNeighbors = Math.max(limit - searchRanked.length, 0);\n  const selectedNeighbors = neighborRanked.slice(0, budgetForNeighbors);\n\n  const selectedSearchPaths = searchRanked.slice(0, limit);\n  const selectedPaths = new Set<string>([\n    ...selectedSearchPaths.map((r) => r.path),\n    ...selectedNeighbors.map((r) => r.path),\n  ]);\n\n  // ------------------------------------------------------------------\n  // 4. Build relevantNotes with titles + domains\n  // ------------------------------------------------------------------\n  const relevantNotes: ConverseResult[\"relevantNotes\"] = [];\n\n  for (const r of selectedSearchPaths) {\n    if (!selectedPaths.has(r.path)) continue;\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: r.score,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  for (const r of selectedNeighbors) {\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: 0,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  // ------------------------------------------------------------------\n  // 5. Find connections between the selected notes\n  // ------------------------------------------------------------------\n  let connections: ConverseConnection[] = [];\n\n  if (selectedPaths.size > 0) {\n    const pathList = Array.from(selectedPaths);\n    const placeholders = pathList.map(() => \"?\").join(\", \");\n\n    const edgeRows = db\n      .prepare(\n        `SELECT source_path, target_path, COUNT(*) AS cnt\n         FROM vault_links\n         WHERE source_path IN (${placeholders})\n           AND target_path IN (${placeholders})\n         GROUP BY source_path, target_path`,\n      )\n      .all(...pathList, ...pathList) as Array<{\n        source_path: string;\n        target_path: string;\n        cnt: number;\n      }>;\n\n    for (const row of edgeRows) {\n      connections.push({\n        fromPath: row.source_path,\n        toPath: row.target_path,\n        fromDomain: extractDomain(row.source_path),\n        toDomain: extractDomain(row.target_path),\n        strength: row.cnt,\n      });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 6. Domains + cross-domain filter\n  // ------------------------------------------------------------------\n  const domainSet = new Set<string>(relevantNotes.map((n) => n.domain));\n  const domains = Array.from(domainSet).sort();\n\n  const crossDomainConnections = connections.filter(\n    (c) => c.fromDomain !== c.toDomain,\n  );\n\n  // ------------------------------------------------------------------\n  // 7. Build synthesis prompt\n  // ------------------------------------------------------------------\n  const notesSummary = relevantNotes\n    .map((n, i) => {\n      const title = n.title ? `\"${n.title}\"` : \"(untitled)\";\n      const domain = n.domain;\n      const scoreLabel = n.score > 0 ? ` [relevance: ${n.score.toFixed(3)}]` : \" [context]\";\n      const snippet = n.snippet.trim().slice(0, 300);\n      return `${i + 1}. [${domain}] ${title}${scoreLabel}\\n   Path: ${n.path}\\n   \"${snippet}\"`;\n    })\n    .join(\"\\n\\n\");\n\n  const connectionSummary =\n    crossDomainConnections.length > 0\n      ? crossDomainConnections\n          .map(\n            (c) =>\n              `- \"${c.fromPath}\" (${c.fromDomain}) → \"${c.toPath}\" (${c.toDomain}) [strength: ${c.strength}]`,\n          )\n          .join(\"\\n\")\n      : \"(no cross-domain connections found)\";\n\n  const domainList = domains.join(\", \");\n\n  const synthesisPrompt = `You are a Zettelkasten research assistant. The vault has surfaced the following notes in response to this question:\n\nQUESTION: ${opts.question}\n\n---\n\nRELEVANT NOTES (${relevantNotes.length} notes across ${domains.length} domain(s): ${domainList}):\n\n${notesSummary}\n\n---\n\nCROSS-DOMAIN CONNECTIONS (links bridging different knowledge areas):\n\n${connectionSummary}\n\n---\n\nSYNTHESIS TASK:\n\nBased on these notes and the connections between them, please:\n\n1. Identify the key insights that emerge in direct response to the question.\n2. Highlight any unexpected connections between notes from different domains (${domainList}).\n3. Point out tensions, contradictions, or open questions the vault raises but does not resolve.\n4. Suggest what is notably absent — what the vault does NOT yet contain that would strengthen the understanding of this topic.\n5. Propose 2-3 new notes that would meaningfully extend this knowledge cluster.\n\nThink like a scholar who has deeply internalized these ideas and is now synthesizing them for the first time.`;\n\n  return {\n    relevantNotes,\n    connections: crossDomainConnections,\n    domains,\n    synthesisPrompt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\n\nexport interface ThemeOptions {\n  vaultProjectId: number;\n  lookbackDays?: number;\n  minClusterSize?: number;\n  maxThemes?: number;\n  similarityThreshold?: number;\n}\n\nexport interface ThemeCluster {\n  id: number;\n  label: string;\n  notes: Array<{\n    path: string;\n    title: string | null;\n  }>;\n  size: number;\n  folderDiversity: number;\n  avgRecency: number;\n  linkedRatio: number;\n  suggestIndexNote: boolean;\n}\n\nexport interface ThemeResult {\n  themes: ThemeCluster[];\n  totalNotesAnalyzed: number;\n  timeWindow: { from: number; to: number };\n}\n\nconst MAX_CHUNKS = 5000;\n\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n  \"new\", \"note\", \"untitled\", \"page\", \"file\", \"doc\",\n]);\n\nfunction getTopFolder(vaultPath: string): string {\n  const parts = vaultPath.split(\"/\");\n  return parts.length > 1 ? parts[0] : \"\";\n}\n\nfunction generateLabel(titles: Array<string | null>): string {\n  const wordCounts = new Map<string, number>();\n  for (const title of titles) {\n    if (!title) continue;\n    const words = title\n      .toLowerCase()\n      .replace(/[^a-z0-9\\s]/g, \" \")\n      .split(/\\s+/)\n      .filter((w) => w.length > 2 && !STOP_WORDS.has(w));\n    for (const word of words) {\n      wordCounts.set(word, (wordCounts.get(word) ?? 0) + 1);\n    }\n  }\n  const sorted = [...wordCounts.entries()].sort((a, b) => b[1] - a[1]);\n  return sorted\n    .slice(0, 3)\n    .map(([w]) => w)\n    .join(\" / \");\n}\n\nfunction computeLinkedRatio(db: Database, paths: string[]): number {\n  if (paths.length < 2) return 0;\n  const totalPairs = (paths.length * (paths.length - 1)) / 2;\n  const pathSet = new Set(paths);\n  let linkedPairs = 0;\n\n  for (const path of paths) {\n    const rows = db\n      .prepare(\n        `SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL`,\n      )\n      .all(path) as Array<{ target_path: string }>;\n    for (const { target_path } of rows) {\n      if (pathSet.has(target_path)) {\n        linkedPairs++;\n      }\n    }\n  }\n\n  // Each bidirectional pair might be counted once per direction; divide by 2 to normalize\n  const uniquePairs = linkedPairs / 2;\n  return Math.min(1, uniquePairs / totalPairs);\n}\n\ntype ClusterNode = {\n  paths: string[];\n  titles: Array<string | null>;\n  indexedAts: number[];\n  centroid: Float32Array;\n};\n\nfunction averageEmbeddings(embeddings: Float32Array[]): Float32Array {\n  if (embeddings.length === 0) return new Float32Array(0);\n  const dim = embeddings[0].length;\n  const sum = new Float32Array(dim);\n  for (const vec of embeddings) {\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / embeddings.length;\n  }\n  return avg;\n}\n\n/**\n * Detect emerging themes in recently-modified notes using agglomerative single-linkage\n * clustering of note-level embeddings.\n */\nexport async function zettelThemes(\n  db: Database,\n  opts: ThemeOptions,\n): Promise<ThemeResult> {\n  const lookbackDays = opts.lookbackDays ?? 30;\n  const minClusterSize = opts.minClusterSize ?? 3;\n  const maxThemes = opts.maxThemes ?? 10;\n  const similarityThreshold = opts.similarityThreshold ?? 0.65;\n\n  const now = Date.now();\n  const from = now - lookbackDays * 86400000;\n\n  // Step 1: get recent notes\n  const recentNotes = db\n    .prepare(\n      `SELECT vault_path, title, indexed_at FROM vault_files WHERE indexed_at > ?`,\n    )\n    .all(from) as Array<{ vault_path: string; title: string | null; indexed_at: number }>;\n\n  // Step 2: get file-level embeddings from memory_chunks\n  const chunkRows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(opts.vaultProjectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const embeddingsByPath = new Map<string, Float32Array[]>();\n  for (const row of chunkRows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const arr = embeddingsByPath.get(row.path);\n    if (!arr) {\n      embeddingsByPath.set(row.path, [vec]);\n    } else {\n      arr.push(vec);\n    }\n  }\n\n  const fileEmbeddings = new Map<string, Float32Array>();\n  for (const [path, vecs] of embeddingsByPath) {\n    fileEmbeddings.set(path, averageEmbeddings(vecs));\n  }\n\n  // Step 3: build initial clusters — only include notes that have embeddings\n  const clusters: ClusterNode[] = [];\n  for (const note of recentNotes) {\n    const embedding = fileEmbeddings.get(note.vault_path);\n    if (!embedding) continue;\n    clusters.push({\n      paths: [note.vault_path],\n      titles: [note.title],\n      indexedAts: [note.indexed_at],\n      centroid: embedding,\n    });\n  }\n\n  const totalNotesAnalyzed = clusters.length;\n\n  // Step 4: agglomerative single-linkage clustering\n  // Stop when no two clusters have similarity >= threshold\n  // Using centroid similarity as a proxy for single-linkage max similarity\n  let merged = true;\n  while (merged && clusters.length > 1) {\n    merged = false;\n    let bestSim = similarityThreshold;\n    let bestI = -1;\n    let bestJ = -1;\n\n    for (let i = 0; i < clusters.length; i++) {\n      for (let j = i + 1; j < clusters.length; j++) {\n        const sim = cosineSimilarity(clusters[i].centroid, clusters[j].centroid);\n        if (sim > bestSim) {\n          bestSim = sim;\n          bestI = i;\n          bestJ = j;\n        }\n      }\n    }\n\n    if (bestI === -1) break;\n\n    // Merge cluster j into cluster i\n    const ci = clusters[bestI];\n    const cj = clusters[bestJ];\n    const mergedPaths = [...ci.paths, ...cj.paths];\n    const mergedTitles = [...ci.titles, ...cj.titles];\n    const mergedIndexedAts = [...ci.indexedAts, ...cj.indexedAts];\n\n    // Recompute centroid from averaged embeddings of all member paths\n    const memberEmbeddings: Float32Array[] = [];\n    for (const p of mergedPaths) {\n      const emb = fileEmbeddings.get(p);\n      if (emb) memberEmbeddings.push(emb);\n    }\n\n    clusters[bestI] = {\n      paths: mergedPaths,\n      titles: mergedTitles,\n      indexedAts: mergedIndexedAts,\n      centroid: averageEmbeddings(memberEmbeddings),\n    };\n\n    clusters.splice(bestJ, 1);\n    merged = true;\n  }\n\n  // Step 5: filter and annotate clusters\n  const themes: ThemeCluster[] = [];\n  let clusterIndex = 0;\n\n  for (const cluster of clusters) {\n    if (cluster.paths.length < minClusterSize) continue;\n\n    const label = generateLabel(cluster.titles) || `Theme ${clusterIndex + 1}`;\n    const avgRecency =\n      cluster.indexedAts.reduce((sum, t) => sum + t, 0) / cluster.indexedAts.length;\n\n    const uniqueFolders = new Set(cluster.paths.map(getTopFolder));\n    const folderDiversity = uniqueFolders.size / cluster.paths.length;\n\n    const linkedRatio = computeLinkedRatio(db, cluster.paths);\n    const suggestIndexNote = linkedRatio < 0.3 && cluster.paths.length >= 5;\n\n    themes.push({\n      id: clusterIndex++,\n      label,\n      notes: cluster.paths.map((path, idx) => ({\n        path,\n        title: cluster.titles[idx],\n      })),\n      size: cluster.paths.length,\n      folderDiversity,\n      avgRecency,\n      linkedRatio,\n      suggestIndexNote,\n    });\n  }\n\n  // Step 6: rank by size * folderDiversity * recency_ratio\n  themes.sort(\n    (a, b) =>\n      b.size * b.folderDiversity * (b.avgRecency / now) -\n      a.size * a.folderDiversity * (a.avgRecency / now),\n  );\n\n  return {\n    themes: themes.slice(0, maxThemes),\n    totalNotesAnalyzed,\n    timeWindow: { from, to: now },\n  };\n}\n","import type { Database } from \"better-sqlite3\";\n\nexport interface HealthOptions {\n  scope?: \"full\" | \"recent\" | \"project\";\n  projectPath?: string;\n  recentDays?: number;\n  include?: Array<\"dead_links\" | \"orphans\" | \"disconnected\" | \"low_connectivity\">;\n}\n\nexport interface DeadLink {\n  sourcePath: string;\n  targetRaw: string;\n  lineNumber: number;\n}\n\nexport interface HealthResult {\n  totalFiles: number;\n  totalLinks: number;\n  deadLinks: DeadLink[];\n  orphans: string[];\n  disconnectedClusters: number;\n  lowConnectivity: string[];\n  healthScore: number;\n  computedAt: number;\n}\n\nfunction buildScopeFilter(\n  opts: HealthOptions,\n  tableAlias: string,\n  pathColumn: string,\n): { clause: string; params: unknown[] } {\n  const scope = opts.scope ?? \"full\";\n\n  if (scope === \"project\") {\n    const prefix = opts.projectPath ?? \"\";\n    return {\n      clause: `WHERE ${tableAlias}.${pathColumn} LIKE ? || '%'`,\n      params: [prefix],\n    };\n  }\n\n  if (scope === \"recent\") {\n    const days = opts.recentDays ?? 30;\n    const cutoff = Date.now() - days * 86400000;\n    return {\n      clause: `WHERE ${tableAlias}.indexed_at > ?`,\n      params: [cutoff],\n    };\n  }\n\n  return { clause: \"\", params: [] };\n}\n\nfunction countComponents(nodes: string[], edges: Array<{ source: string; target: string }>): number {\n  if (nodes.length === 0) return 0;\n\n  const parent = new Map<string, string>();\n  const rank = new Map<string, number>();\n\n  for (const n of nodes) {\n    parent.set(n, n);\n    rank.set(n, 0);\n  }\n\n  function find(x: string): string {\n    let root = x;\n    while (parent.get(root) !== root) {\n      root = parent.get(root)!;\n    }\n    let current = x;\n    while (current !== root) {\n      const next = parent.get(current)!;\n      parent.set(current, root);\n      current = next;\n    }\n    return root;\n  }\n\n  function union(a: string, b: string): void {\n    const ra = find(a);\n    const rb = find(b);\n    if (ra === rb) return;\n    const rankA = rank.get(ra) ?? 0;\n    const rankB = rank.get(rb) ?? 0;\n    if (rankA < rankB) {\n      parent.set(ra, rb);\n    } else if (rankA > rankB) {\n      parent.set(rb, ra);\n    } else {\n      parent.set(rb, ra);\n      rank.set(ra, rankA + 1);\n    }\n  }\n\n  for (const { source, target } of edges) {\n    if (parent.has(source) && parent.has(target)) {\n      union(source, target);\n    }\n  }\n\n  const roots = new Set<string>();\n  for (const n of nodes) {\n    roots.add(find(n));\n  }\n  return roots.size;\n}\n\n/**\n * Audit the structural health of the Zettelkasten vault using graph metrics.\n * Designed to complete in under 60ms for a full vault.\n */\nexport function zettelHealth(db: Database, opts?: HealthOptions): HealthResult {\n  const options = opts ?? {};\n  const scope = options.scope ?? \"full\";\n  const include = options.include ?? [\"dead_links\", \"orphans\", \"disconnected\", \"low_connectivity\"];\n\n  const computedAt = Date.now();\n\n  // --- totalFiles ---\n  let totalFiles = 0;\n  if (scope === \"full\") {\n    totalFiles = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_files\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE vault_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE indexed_at > ?\")\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- totalLinks ---\n  let totalLinks = 0;\n  if (scope === \"full\") {\n    totalLinks = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_links\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalLinks = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_links WHERE source_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalLinks = (\n      db\n        .prepare(\n          \"SELECT COUNT(*) AS n FROM vault_links WHERE source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n        )\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- deadLinks ---\n  let deadLinks: DeadLink[] = [];\n  if (include.includes(\"dead_links\")) {\n    if (scope === \"full\") {\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL\",\n          )\n          .all() as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    }\n  }\n\n  // --- orphans ---\n  let orphans: string[] = [];\n  if (include.includes(\"orphans\")) {\n    if (scope === \"full\") {\n      orphans = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_health WHERE is_orphan = 1\")\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE is_orphan = 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.is_orphan = 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- disconnectedClusters (union-find) ---\n  let disconnectedClusters = 1;\n  if (include.includes(\"disconnected\")) {\n    let allNodes: string[];\n    let allEdges: Array<{ source: string; target: string }>;\n\n    if (scope === \"full\") {\n      allNodes = (\n        db.prepare(\"SELECT vault_path FROM vault_files\").all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL\",\n          )\n          .all() as Array<{ source: string; target: string }>\n      );\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path LIKE ? || '%'\")\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source: string; target: string }>\n      );\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE indexed_at > ?\")\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source: string; target: string }>\n      );\n    }\n\n    disconnectedClusters = countComponents(allNodes, allEdges);\n  }\n\n  // --- lowConnectivity ---\n  let lowConnectivity: string[] = [];\n  if (include.includes(\"low_connectivity\")) {\n    if (scope === \"full\") {\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1\",\n          )\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.inbound_count + vh.outbound_count <= 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- healthScore ---\n  const deadRatio = totalLinks > 0 ? deadLinks.length / totalLinks : 0;\n  const orphanRatio = totalFiles > 0 ? orphans.length / totalFiles : 0;\n  const lowConnRatio = totalFiles > 0 ? lowConnectivity.length / totalFiles : 0;\n  const healthScore = Math.round(\n    100 * (1 - deadRatio) * (1 - orphanRatio * 0.5) * (1 - lowConnRatio * 0.3),\n  );\n\n  return {\n    totalFiles,\n    totalLinks,\n    deadLinks,\n    orphans,\n    disconnectedClusters,\n    lowConnectivity,\n    healthScore,\n    computedAt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\nimport { basename } from \"node:path\";\n\nexport interface SuggestOptions {\n  notePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  excludeLinked?: boolean;\n}\n\nexport interface Suggestion {\n  path: string;\n  title: string | null;\n  score: number;\n  semanticScore: number;\n  tagScore: number;\n  neighborScore: number;\n  reason: string;\n  suggestedWikilink: string;\n}\n\nconst MAX_CHUNKS = 5000;\nconst SEMANTIC_WEIGHT = 0.5;\nconst TAG_WEIGHT = 0.2;\nconst NEIGHBOR_WEIGHT = 0.3;\n\n// Stop words to ignore when generating tag/label strings\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n]);\n\nfunction extractTagsFromChunkTexts(texts: string[]): Set<string> {\n  const tags = new Set<string>();\n  for (const text of texts) {\n    // Match YAML frontmatter tags block: \"tags:\\n  - tag1\\n  - tag2\"\n    const match = text.match(/^tags:\\s*\\n((?:[ \\t]*-[ \\t]*.+\\n?)*)/m);\n    if (!match) continue;\n    const block = match[1];\n    const lines = block.split(\"\\n\");\n    for (const line of lines) {\n      const tagMatch = line.match(/^[ \\t]*-[ \\t]*(.+)/);\n      if (tagMatch) {\n        const tag = tagMatch[1].trim().toLowerCase();\n        if (tag) tags.add(tag);\n      }\n    }\n  }\n  return tags;\n}\n\nfunction getFileAvgEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): Float32Array | null {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) return null;\n\n  const first = deserializeEmbedding(rows[0].embedding);\n  const sum = new Float32Array(first.length);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < vec.length; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(sum.length);\n  for (let i = 0; i < sum.length; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return avg;\n}\n\nfunction getAllFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, Float32Array> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const byPath = new Map<string, { sum: Float32Array; count: number }>();\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1 });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, Float32Array>();\n  for (const [path, { sum, count }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, avg);\n  }\n  return result;\n}\n\nfunction getFileTags(db: Database, projectId: number, path: string): Set<string> {\n  const rows = db\n    .prepare(\n      `SELECT text FROM memory_chunks\n       WHERE project_id = ? 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AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ target_path: string }>;\n  const linkedPaths = new Set(outboundRows.map((r) => r.target_path));\n\n  // Step 2: get source embedding\n  const sourceEmbedding = getFileAvgEmbedding(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3a: get all file-level embeddings for semantic scoring\n  const allEmbeddings = getAllFileEmbeddings(db, opts.vaultProjectId);\n  allEmbeddings.delete(opts.notePath);\n\n  // Step 3b: get source tags\n  const sourceTags = getFileTags(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3c: compute graph neighborhood (friends-of-friends)\n  const friendTargetRows = db\n    .prepare(\n      `SELECT DISTINCT target_path AS path FROM vault_links\n       WHERE source_path IN (\n         SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n       ) AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ path: string }>;\n\n  // For each friend-of-friend, count how many of source's direct friends link to them\n  const friendLinkCounts = new Map<string, number>();\n  for (const { path } of friendTargetRows) {\n    if (path === opts.notePath) continue;\n    friendLinkCounts.set(path, (friendLinkCounts.get(path) ?? 0) + 1);\n  }\n  const maxFriendLinks = Math.max(1, ...friendLinkCounts.values());\n\n  // Get all vault files to enumerate candidates\n  const allFiles = db\n    .prepare(\"SELECT vault_path, title FROM vault_files\")\n    .all() as Array<{ vault_path: string; title: string | null }>;\n\n  const suggestions: Suggestion[] = [];\n\n  for (const { vault_path, title } of allFiles) {\n    if (vault_path === opts.notePath) continue;\n    if (excludeLinked && linkedPaths.has(vault_path)) continue;\n\n    // Semantic score\n    let semanticScore = 0;\n    if (sourceEmbedding) 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 title,\n      score,\n      semanticScore,\n      tagScore,\n      neighborScore,\n      reason,\n      suggestedWikilink: suggestedWikilink(vault_path),\n    });\n  }\n\n  suggestions.sort((a, b) => b.score - a.score);\n  return suggestions.slice(0, 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package/templates/README.md

@@ -1,181 +0,0 @@
-# PAI Configuration Templates
-
-This directory contains example configuration files for personalizing your PAI Knowledge OS setup.
-
-## Files
-
-### `agent-prefs.example.md`
-
-**Template for**: `~/.config/pai/agent-prefs.md`
-
-Contains your personal preferences for PAI agents:
-- Identity and role information
-- Directory search restrictions
-- Project-code directory mappings
-- Notification preferences (WhatsApp, ntfy.sh)
-- Voice configuration for TTS
-- Git commit rules
-- Code quality standards
-- Language and framework preferences
-- Workflow customization options
-
-**Size**: 362 lines, comprehensive with examples
-
-**Setup**:
-```bash
-cp agent-prefs.example.md ~/.config/pai/agent-prefs.md
-# Then customize with your settings
-```
-
-### `voices.example.json`
-
-**Template for**: `~/.config/pai/voices.json`
-
-Configures voice output for different agents and channels:
-- TTS system selection (Kokoro local or ElevenLabs cloud)
-- Voice assignments per agent type
-- WhatsApp voice note configuration
-- Local speaker output settings
-- Named personas for easy reference
-- Multiple profiles (professional, casual, focus)
-- Complete examples for different setups
-- Troubleshooting guide
-
-**Size**: 251 lines, valid JSON with comments
-
-**Setup**:
-```bash
-cp voices.example.json ~/.config/pai/voices.json
-# Then customize voice selections
-```
-
-## Quick Start
-
-```bash
-# Create config directory if needed
-mkdir -p ~/.config/pai
-
-# Copy templates
-cp agent-prefs.example.md ~/.config/pai/agent-prefs.md
-cp voices.example.json ~/.config/pai/voices.json
-
-# Edit with your preferences
-nano ~/.config/pai/agent-prefs.md
-nano ~/.config/pai/voices.json
-```
-
-## Key Features
-
-### Agent Preferences
-
-- **Directory Restrictions**: Prevent expensive searches in large directories
-- **Project Mappings**: Automate end-session commits to the right directories
-- **Workflow Customization**: Tailor agent behavior to your development style
-- **Voice and Notifications**: Configure how agents communicate with you
-
-### Voice Configuration
-
-- **Kokoro TTS**: Free, local, no API key required (~160MB download once)
-- **ElevenLabs**: Premium quality voices, requires API key
-- **Agent-Specific Voices**: Different voices for different agent types
-- **Profiles**: Switch between professional/casual/focus modes
-
-## Privacy and Version Control
-
-These files contain personal preferences and should **NOT** be committed:
-
-```bash
-# Add to your .gitignore
-echo "~/.config/pai/" >> ~/.gitignore
-```
-
-Keep these files private:
-```bash
-chmod 600 ~/.config/pai/agent-prefs.md
-chmod 600 ~/.config/pai/voices.json
-```
-
-## Integration with PAI
-
-The PAI daemon automatically:
-- Reads `~/.config/pai/agent-prefs.md` on startup
-- Loads voice configuration from `~/.config/pai/voices.json`
-- Uses these settings for all agent operations
-- Falls back to sensible defaults if files are missing
-
-**No restart needed**: Changes to these files take effect immediately on next operation.
-
-## Customization Examples
-
-### Minimal Setup (Just Defaults)
-
-```bash
-# Copy templates
-cp agent-prefs.example.md ~/.config/pai/agent-prefs.md
-cp voices.example.json ~/.config/pai/voices.json
-
-# Use defaults as-is, customize later as needed
-```
-
-### Engineer-Heavy Workflow
-
-Focus on technical tools and code quality:
-- Set default language to TypeScript
-- Configure strict testing requirements
-- Map multiple code directories
-- Use technical-sounding voices
-
-### Research-Heavy Workflow
-
-Focus on information gathering:
-- Configure ntfy.sh notifications for task completion
-- Set longer timeouts for research agents
-- Map knowledge base directories
-- Use calm, analytical voices
-
-## Environment Variables
-
-Some settings can also be configured via environment variables:
-
-```bash
-export ELEVENLABS_API_KEY="sk-..."        # ElevenLabs API key
-export NTFY_TOPIC="my-private-topic"      # ntfy.sh topic
-export PAI_CONFIG_DIR="~/.config/pai"     # Custom config directory
-```
-
-## Troubleshooting
-
-**Q: My preferences aren't being used**
-- Check file exists: `ls ~/.config/pai/agent-prefs.md`
-- Check JSON is valid: `python3 -m json.tool ~/.config/pai/voices.json`
-- Check permissions: `ls -l ~/.config/pai/`
-
-**Q: Voice not working**
-- Verify ElevenLabs API key if using ElevenLabs
-- Check internet connection if using cloud TTS
-- Try local Kokoro TTS as fallback
-- See troubleshooting section in `voices.example.json`
-
-**Q: Configuration not loading**
-- Daemon reads from `~/.config/pai/` (not `~/.claude/`)
-- Create directory if missing: `mkdir -p ~/.config/pai`
-- Copy templates to this location
-
-## Further Customization
-
-Once you've customized the basic templates, you can:
-
-1. **Create project-specific overrides** in project `.claude.json` files
-2. **Add team standards** to agent-prefs.md under "Team Standards"
-3. **Define CI/CD rules** in git commit section
-4. **Experiment with voice profiles** for different working modes
-
-## Related Documentation
-
-- PAI Knowledge OS: `~/projects/PAI/README.md`
-- Configuration reference: `~/.claude.json` (Claude Code configuration)
-- PAI daemon docs: `~/projects/PAI/src/daemon/`
-
----
-
-**Template Version**: 1.0