@tekmidian/pai 0.16.0 → 0.17.0

package/dist/zettelkasten-D0N_A_OE.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"zettelkasten-D0N_A_OE.mjs","names":["MAX_CHUNKS"],"sources":["../src/zettelkasten/explore.ts","../src/zettelkasten/surprise.ts","../src/zettelkasten/converse.ts","../src/zettelkasten/health.ts","../src/zettelkasten/suggest.ts","../src/zettelkasten/god-notes.ts","../src/zettelkasten/communities.ts"],"sourcesContent":["import type { StorageBackend } from \"../storage/interface.js\";\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\nasync function resolveStart(backend: StorageBackend, startNote: string): Promise<string | null> {\n  // Try direct lookup first\n  const files = await backend.getVaultFilesByPaths([startNote]);\n  if (files.length > 0) return files[0].vaultPath;\n\n  // Try alias lookup\n  const alias = await backend.getVaultAlias(startNote);\n  if (!alias) return null;\n\n  const canonical = await backend.getVaultFilesByPaths([alias.canonicalPath]);\n  return canonical.length > 0 ? canonical[0].vaultPath : null;\n}\n\nasync function getForwardNeighbors(backend: StorageBackend, path: string): Promise<string[]> {\n  const links = await backend.getLinksFromSource(path);\n  return links.filter(l => l.targetPath !== null).map(l => l.targetPath as string);\n}\n\nasync function getBackwardNeighbors(backend: StorageBackend, path: string): Promise<string[]> {\n  const links = await backend.getLinksToTarget(path);\n  return links.map(l => l.sourcePath);\n}\n\nasync function getFileInfo(\n  backend: StorageBackend,\n  path: string,\n): Promise<{ title: string | null; inbound: number; outbound: number }> {\n  const [files, health] = await Promise.all([\n    backend.getVaultFilesByPaths([path]),\n    backend.getVaultHealth(path),\n  ]);\n\n  return {\n    title: files[0]?.title ?? null,\n    inbound: health?.inboundCount ?? 0,\n    outbound: health?.outboundCount ?? 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 async function zettelExplore(backend: StorageBackend, opts: ExploreOptions): Promise<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 = await resolveStart(backend, 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 await getForwardNeighbors(backend, 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 await getBackwardNeighbors(backend, 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 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 = await getFileInfo(backend, 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 = await getFileInfo(backend, root);\n  if (rootInfo.outbound > 2) {\n    branchingPoints.unshift(root);\n  }\n\n  return { root, nodes, edges, branchingPoints, maxDepthReached };\n}\n","import type { StorageBackend } from \"../storage/interface.js\";\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 MAX_CHUNKS = 5000;\nconst BFS_HOP_CAP = 20;\n\nasync function getFileEmbeddings(\n  backend: StorageBackend,\n  projectId: number,\n): Promise<Map<string, { embedding: Float32Array; text: string }>> {\n  const rows = await backend.getChunksWithEmbeddings(projectId, MAX_CHUNKS);\n\n  const byPath = new Map<string, { sum: Float32Array; count: number; text: string }>();\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\nasync function getReferenceEmbedding(\n  backend: StorageBackend,\n  projectId: number,\n  path: string,\n): Promise<{ embedding: Float32Array; found: boolean }> {\n  const rows = await backend.getChunksForPath(projectId, path);\n\n  if (rows.length === 0) {\n    return { embedding: new Float32Array(0), found: false };\n  }\n\n  const embRows = rows.filter(r => r.embedding !== null) as Array<{ text: string; embedding: Buffer }>;\n  if (embRows.length === 0) {\n    return { embedding: new Float32Array(0), found: false };\n  }\n\n  const dim = deserializeEmbedding(embRows[0].embedding).length;\n  const sum = new Float32Array(dim);\n  for (const row of embRows) {\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] / embRows.length;\n  }\n  return { embedding: avg, found: true };\n}\n\nasync function bfsGraphDistance(backend: StorageBackend, source: string, target: string): Promise<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 [forwardLinks, backwardLinks] = await Promise.all([\n      backend.getLinksFromSource(path),\n      backend.getLinksToTarget(path),\n    ]);\n\n    const neighbors: string[] = [\n      ...forwardLinks.filter(l => l.targetPath !== null).map(l => l.targetPath as string),\n      ...backwardLinks.map(l => l.sourcePath),\n    ];\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  chunkRows: Array<{ text: string; embedding: Buffer | null }>,\n  refEmbedding: Float32Array,\n): string {\n  const rows = chunkRows.filter(r => r.embedding !== null) as Array<{ text: string; embedding: Buffer }>;\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  backend: StorageBackend,\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 } = await getReferenceEmbedding(\n    backend,\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 files = await backend.getVaultFilesByPaths([opts.referencePath]);\n    const text = files[0]?.title ?? opts.referencePath;\n    refEmbedding = await generateEmbedding(text, true);\n  }\n\n  const allFileEmbeddings = await getFileEmbeddings(backend, 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 = await bfsGraphDistance(backend, opts.referencePath, path);\n\n    const effectiveDistance = isFinite(graphDistance) ? graphDistance : BFS_HOP_CAP;\n    if (effectiveDistance < minGraphDistance) continue;\n\n    const files = await backend.getVaultFilesByPaths([path]);\n    const chunkRows = await backend.getChunksForPath(opts.vaultProjectId, path, 20);\n\n    const surpriseScore = sim * Math.log2(effectiveDistance + 1);\n    const sharedSnippet = getBestChunkText(chunkRows, refEmbedding);\n\n    results.push({\n      path,\n      title: files[0]?.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 { StorageBackend } from \"../storage/interface.js\";\nimport type { SearchResult } 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 */\nasync function expandNeighbors(backend: StorageBackend, paths: Set<string>): Promise<string[]> {\n  if (paths.size === 0) return [];\n  const pathList = Array.from(paths);\n\n  const [forwardLinks, backwardLinks] = await Promise.all([\n    backend.getVaultLinksFromPaths(pathList),\n    Promise.all(pathList.map(p => backend.getLinksToTarget(p))),\n  ]);\n\n  const neighbors: string[] = [];\n  for (const link of forwardLinks) {\n    if (link.targetPath) neighbors.push(link.targetPath);\n  }\n  for (const linkList of backwardLinks) {\n    for (const link of linkList) {\n      neighbors.push(link.sourcePath);\n    }\n  }\n  return neighbors;\n}\n\n/**\n * Hybrid search combining keyword + semantic results using the StorageBackend.\n */\nasync function hybridSearch(\n  backend: StorageBackend,\n  query: string,\n  queryEmbedding: Float32Array,\n  opts: { projectIds?: number[]; maxResults?: number },\n): Promise<SearchResult[]> {\n  const maxResults = opts.maxResults ?? 10;\n  const kw = 0.5;\n  const sw = 0.5;\n\n  const [keywordResults, semanticResults] = await Promise.all([\n    backend.searchKeyword(query, { ...opts, maxResults: 50 }),\n    backend.searchSemantic(queryEmbedding, { ...opts, maxResults: 50 }),\n  ]);\n\n  if (keywordResults.length === 0 && semanticResults.length === 0) return [];\n\n  const keyFor = (r: SearchResult) =>\n    `${r.projectId}:${r.path}:${r.startLine}:${r.endLine}`;\n\n  function minMaxNormalize(scores: number[]): number[] {\n    const min = Math.min(...scores);\n    const max = Math.max(...scores);\n    const range = max - min;\n    if (range === 0) return scores.map(() => 1.0);\n    return scores.map(s => (s - min) / range);\n  }\n\n  const kwNorm = minMaxNormalize(keywordResults.map(r => r.score));\n  const semNorm = minMaxNormalize(semanticResults.map(r => r.score));\n\n  const combined = new Map<string, SearchResult & { combinedScore: number }>();\n\n  for (let i = 0; i < keywordResults.length; i++) {\n    const r = keywordResults[i];\n    const k = keyFor(r);\n    combined.set(k, { ...r, combinedScore: kw * kwNorm[i] });\n  }\n\n  for (let i = 0; i < semanticResults.length; i++) {\n    const r = semanticResults[i];\n    const k = keyFor(r);\n    const existing = combined.get(k);\n    if (existing) {\n      existing.combinedScore += sw * semNorm[i];\n    } else {\n      combined.set(k, { ...r, combinedScore: sw * semNorm[i] });\n    }\n  }\n\n  const sorted = Array.from(combined.values())\n    .sort((a, b) => b.combinedScore - a.combinedScore)\n    .slice(0, maxResults);\n\n  return sorted.map(r => ({ ...r, score: r.combinedScore }));\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  backend: StorageBackend,\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 = await hybridSearch(\n    backend,\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 = await expandNeighbors(backend, 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  // ------------------------------------------------------------------\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  // Fetch health data for neighbor ranking\n  const neighborHealthRows = await Promise.all(\n    neighborPaths.map(p => backend.getVaultHealth(p))\n  );\n  const neighborRanked = neighborPaths\n    .map((path, idx) => ({\n      path,\n      score: 0,\n      snippet: \"\",\n      inbound: neighborHealthRows[idx]?.inboundCount ?? 0,\n      isSearchResult: false,\n    }))\n    .sort((a, b) => b.inbound - a.inbound);\n\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\n  // Fetch titles in bulk\n  const allSelectedPaths = Array.from(selectedPaths);\n  const fileRows = await backend.getVaultFilesByPaths(allSelectedPaths);\n  const titleMap = new Map<string, string | null>(fileRows.map(f => [f.vaultPath, f.title]));\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: titleMap.get(r.path) ?? null,\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: titleMap.get(r.path) ?? null,\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 pathSet = new Set(pathList);\n\n    // Get all outbound links from the selected paths\n    const linkRows = await backend.getVaultLinksFromPaths(pathList);\n\n    // Count links between selected paths\n    const edgeCounts = new Map<string, number>();\n    for (const link of linkRows) {\n      if (link.targetPath && pathSet.has(link.targetPath)) {\n        const key = `${link.sourcePath}|||${link.targetPath}`;\n        edgeCounts.set(key, (edgeCounts.get(key) ?? 0) + 1);\n      }\n    }\n\n    for (const [key, cnt] of edgeCounts) {\n      const [sourcePath, targetPath] = key.split(\"|||\");\n      connections.push({\n        fromPath: sourcePath,\n        toPath: targetPath,\n        fromDomain: extractDomain(sourcePath),\n        toDomain: extractDomain(targetPath),\n        strength: 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 { StorageBackend } from \"../storage/interface.js\";\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  /** Breakdown of links by confidence level (if confidence tagging is active). */\n  linkConfidence?: {\n    extracted: number;\n    inferred: number;\n    ambiguous: number;\n  };\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 */\nexport async function zettelHealth(backend: StorageBackend, opts?: HealthOptions): Promise<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 = await backend.countVaultFiles();\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalFiles = await backend.countVaultFilesWithPrefix(prefix);\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalFiles = await backend.countVaultFilesAfter(cutoff);\n  }\n\n  // --- totalLinks ---\n  let totalLinks = 0;\n  if (scope === \"full\") {\n    // Count total links via link graph length\n    const graph = await backend.getVaultLinkGraph();\n    totalLinks = graph.length;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalLinks = await backend.countVaultLinksWithPrefix(prefix);\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalLinks = await backend.countVaultLinksAfter(cutoff);\n  }\n\n  // --- deadLinks ---\n  let deadLinks: DeadLink[] = [];\n  if (include.includes(\"dead_links\")) {\n    if (scope === \"full\") {\n      deadLinks = await backend.getDeadLinksWithLineNumbers();\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      deadLinks = await backend.getDeadLinksWithPrefix(prefix);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      deadLinks = await backend.getDeadLinksAfter(cutoff);\n    }\n  }\n\n  // --- orphans ---\n  let orphans: string[] = [];\n  if (include.includes(\"orphans\")) {\n    if (scope === \"full\") {\n      const orphanRows = await backend.getOrphans();\n      orphans = orphanRows.map(r => r.vaultPath);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      orphans = await backend.getOrphansWithPrefix(prefix);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      orphans = await backend.getOrphansAfter(cutoff);\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, allEdges] = await Promise.all([\n        backend.getAllVaultFilePaths(),\n        backend.getVaultLinkEdges(),\n      ]);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      [allNodes, allEdges] = await Promise.all([\n        backend.getVaultFilePathsWithPrefix(prefix),\n        backend.getVaultLinkEdgesWithPrefix(prefix),\n      ]);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      [allNodes, allEdges] = await Promise.all([\n        backend.getVaultFilePathsAfter(cutoff),\n        backend.getVaultLinkEdgesAfter(cutoff),\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 = await backend.getLowConnectivity();\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      lowConnectivity = await backend.getLowConnectivityWithPrefix(prefix);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      lowConnectivity = await backend.getLowConnectivityAfter(cutoff);\n    }\n  }\n\n  // --- linkConfidence ---\n  // Count links by confidence level using a sampling of all vault file paths.\n  // We reuse the link graph data we already fetched for totalLinks when scope=full.\n  let linkConfidence: HealthResult[\"linkConfidence\"] | undefined;\n  if (scope === \"full\") {\n    try {\n      // Get all file paths to iterate their outbound links with confidence\n      const samplePaths = await backend.getAllVaultFilePaths();\n      const sampleSize = Math.min(samplePaths.length, 200); // limit for performance\n      const sampled = samplePaths.slice(0, sampleSize);\n      let extracted = 0;\n      let inferred = 0;\n      let ambiguous = 0;\n      for (const path of sampled) {\n        const links = await backend.getLinksFromSource(path);\n        for (const link of links) {\n          const c = link.confidence ?? \"EXTRACTED\";\n          if (c === \"EXTRACTED\") extracted++;\n          else if (c === \"INFERRED\") inferred++;\n          else ambiguous++;\n        }\n      }\n      // Extrapolate if we sampled\n      const factor = samplePaths.length > 0 ? samplePaths.length / sampleSize : 1;\n      linkConfidence = {\n        extracted: Math.round(extracted * factor),\n        inferred: Math.round(inferred * factor),\n        ambiguous: Math.round(ambiguous * factor),\n      };\n    } catch {\n      // Backend may not support confidence field yet — ignore\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    linkConfidence,\n  };\n}\n","import type { StorageBackend } from \"../storage/interface.js\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\nimport { basename } from \"node:path\";\nimport { STOP_WORDS } from \"../utils/stop-words.js\";\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 imported from utils/stop-words.ts\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 jaccardSimilarity(a: Set<string>, b: Set<string>): number {\n  if (a.size === 0 && b.size === 0) return 0;\n  let intersection = 0;\n  for (const tag of a) {\n    if (b.has(tag)) intersection++;\n  }\n  const union = a.size + b.size - intersection;\n  return union === 0 ? 0 : intersection / union;\n}\n\nfunction buildReason(\n  semanticScore: number,\n  tagScore: number,\n  neighborScore: number,\n  neighborCount: number,\n): string {\n  const signals: Array<{ label: string; value: number }> = [\n    { label: `Semantically similar (${semanticScore.toFixed(2)})`, value: semanticScore * SEMANTIC_WEIGHT },\n    { label: `Shared tags (${tagScore.toFixed(2)} Jaccard)`, value: tagScore * TAG_WEIGHT },\n    { label: `Linked by ${neighborCount} mutual connection${neighborCount !== 1 ? \"s\" : \"\"}`, value: neighborScore * NEIGHBOR_WEIGHT },\n  ];\n  signals.sort((a, b) => b.value - a.value);\n  return signals[0].label;\n}\n\nfunction suggestedWikilink(vaultPath: string): string {\n  const base = basename(vaultPath);\n  const name = base.endsWith(\".md\") ? base.slice(0, -3) : base;\n  return `[[${name}]]`;\n}\n\n/**\n * Proactively find notes worth linking to a given note, combining semantic similarity,\n * shared tags, and graph-neighborhood signals into a ranked list of suggestions.\n */\nexport async function zettelSuggest(\n  backend: StorageBackend,\n  opts: SuggestOptions,\n): Promise<Suggestion[]> {\n  const limit = opts.limit ?? 5;\n  const excludeLinked = opts.excludeLinked ?? true;\n\n  // Step 1: get current outbound links\n  const outboundLinks = await backend.getLinksFromSource(opts.notePath);\n  const linkedPaths = new Set(outboundLinks.filter(l => l.targetPath !== null).map(l => l.targetPath as string));\n\n  // Step 2a: get all file-level embeddings for semantic scoring\n  const chunkRows = await backend.getChunksWithEmbeddings(opts.vaultProjectId, MAX_CHUNKS);\n\n  const byPath = new Map<string, { sum: Float32Array; count: number }>();\n  for (const row of chunkRows) {\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 allEmbeddings = 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    allEmbeddings.set(path, avg);\n  }\n  allEmbeddings.delete(opts.notePath);\n\n  // Step 2b: get source embedding\n  const sourceEmbedding = allEmbeddings.get(opts.notePath) ?? null;\n\n  // Step 2c: get source tags\n  const sourceChunkTexts = await backend.getChunksForPath(opts.vaultProjectId, opts.notePath, 5);\n  const sourceTags = extractTagsFromChunkTexts(sourceChunkTexts.map(r => r.text));\n\n  // Step 2d: compute graph neighborhood (friends-of-friends)\n  const directLinks = await backend.getLinksFromSource(opts.notePath);\n  const directTargets = directLinks.filter(l => l.targetPath !== null).map(l => l.targetPath as string);\n\n  const friendLinkCounts = new Map<string, number>();\n  for (const target of directTargets) {\n    const friendLinks = await backend.getLinksFromSource(target);\n    for (const link of friendLinks) {\n      if (link.targetPath && link.targetPath !== opts.notePath) {\n        friendLinkCounts.set(link.targetPath, (friendLinkCounts.get(link.targetPath) ?? 0) + 1);\n      }\n    }\n  }\n  const maxFriendLinks = Math.max(1, ...friendLinkCounts.values());\n\n  // Get all vault files to enumerate candidates\n  const allFiles = await backend.getAllVaultFiles();\n\n  const suggestions: Suggestion[] = [];\n\n  for (const fileRow of allFiles) {\n    const vault_path = fileRow.vaultPath;\n    const title = fileRow.title;\n\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) {\n      const candidateEmbedding = allEmbeddings.get(vault_path);\n      if (candidateEmbedding) {\n        semanticScore = Math.max(0, cosineSimilarity(sourceEmbedding, candidateEmbedding));\n      }\n    }\n\n    // Tag score (only compute if candidate might have chunks)\n    let tagScore = 0;\n    if (allEmbeddings.has(vault_path)) {\n      const candidateChunkTexts = await backend.getChunksForPath(opts.vaultProjectId, vault_path, 5);\n      const candidateTags = extractTagsFromChunkTexts(candidateChunkTexts.map(r => r.text));\n      tagScore = jaccardSimilarity(sourceTags, candidateTags);\n    }\n\n    // Neighbor score\n    const friendCount = friendLinkCounts.get(vault_path) ?? 0;\n    const neighborScore = friendCount / maxFriendLinks;\n\n    const score =\n      SEMANTIC_WEIGHT * semanticScore +\n      TAG_WEIGHT * tagScore +\n      NEIGHBOR_WEIGHT * neighborScore;\n\n    // Only include if there is at least some signal\n    if (score <= 0) continue;\n\n    const reason = buildReason(semanticScore, tagScore, neighborScore, friendCount);\n\n    suggestions.push({\n      path: vault_path,\n      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, limit);\n}\n","/**\n * God-note detection — find hub notes via degree centrality on the vault link graph.\n *\n * Hub notes (or \"god notes\") are notes with unusually high inbound link counts.\n * They represent core concepts that the rest of the vault frequently references.\n * Structural pages (index, MOC, master notes, tag pages) are filtered out.\n */\n\nimport type { StorageBackend } from \"../storage/interface.js\";\n\nexport interface GodNoteOptions {\n  /** Maximum number of hub notes to return. Default: 20. */\n  limit?: number;\n  /** Minimum inbound link count to qualify as a hub. Default: 3. */\n  minInbound?: number;\n  /** Include outbound counts in the result. Default: true. */\n  includeOutbound?: boolean;\n}\n\nexport interface GodNote {\n  path: string;\n  title: string | null;\n  inboundCount: number;\n  outboundCount: number;\n  /** Ratio of inbound to total degree — higher means more \"sink\"-like. */\n  inboundRatio: number;\n}\n\nexport interface GodNoteResult {\n  godNotes: GodNote[];\n  totalVaultFiles: number;\n  /** Median inbound count across all vault files (for context). */\n  medianInbound: number;\n}\n\n/** Patterns that identify structural/meta pages rather than concept notes. */\nconst STRUCTURAL_PATTERNS = [\n  /\\bindex\\b/i,\n  /\\bMOC\\b/,\n  /\\bmaster\\b/i,\n  /\\btag\\s*page/i,\n  /\\bhome\\b/i,\n  /\\bdashboard\\b/i,\n  /\\btemplate/i,\n  /^_/,\n];\n\nfunction isStructuralNote(title: string | null, path: string): boolean {\n  const text = title ?? path;\n  return STRUCTURAL_PATTERNS.some((pattern) => pattern.test(text));\n}\n\n/**\n * Find hub/\"god\" notes in the vault — notes with the highest inbound link counts,\n * excluding structural pages.\n */\nexport async function zettelGodNotes(\n  backend: StorageBackend,\n  opts?: GodNoteOptions,\n): Promise<GodNoteResult> {\n  const limit = opts?.limit ?? 20;\n  const minInbound = opts?.minInbound ?? 3;\n\n  // Get the full link graph\n  const linkGraph = await backend.getVaultLinkGraph();\n\n  // Count inbound and outbound per path\n  const inboundCounts = new Map<string, number>();\n  const outboundCounts = new Map<string, number>();\n\n  for (const { source_path, target_path } of linkGraph) {\n    inboundCounts.set(target_path, (inboundCounts.get(target_path) ?? 0) + 1);\n    outboundCounts.set(source_path, (outboundCounts.get(source_path) ?? 0) + 1);\n  }\n\n  // Get all vault files for title lookup and total count\n  const allFiles = await backend.getAllVaultFiles();\n  const titleMap = new Map<string, string | null>();\n  for (const f of allFiles) {\n    titleMap.set(f.vaultPath, f.title);\n  }\n\n  const totalVaultFiles = allFiles.length;\n\n  // Compute median inbound for context\n  const allInbounds = allFiles.map((f) => inboundCounts.get(f.vaultPath) ?? 0);\n  allInbounds.sort((a, b) => a - b);\n  const medianInbound =\n    allInbounds.length > 0\n      ? allInbounds[Math.floor(allInbounds.length / 2)]\n      : 0;\n\n  // Build candidate list: all paths with inbound >= minInbound, excluding structural\n  const candidates: GodNote[] = [];\n\n  for (const [path, inbound] of inboundCounts) {\n    if (inbound < minInbound) continue;\n\n    const title = titleMap.get(path) ?? null;\n    if (isStructuralNote(title, path)) continue;\n\n    const outbound = outboundCounts.get(path) ?? 0;\n    const totalDegree = inbound + outbound;\n    const inboundRatio = totalDegree > 0 ? inbound / totalDegree : 0;\n\n    candidates.push({\n      path,\n      title,\n      inboundCount: inbound,\n      outboundCount: outbound,\n      inboundRatio: Math.round(inboundRatio * 1000) / 1000,\n    });\n  }\n\n  // Sort by inbound count descending\n  candidates.sort((a, b) => b.inboundCount - a.inboundCount);\n\n  return {\n    godNotes: candidates.slice(0, limit),\n    totalVaultFiles,\n    medianInbound,\n  };\n}\n","/**\n * Community detection for the Zettelkasten vault link graph.\n *\n * Implements the Louvain algorithm in pure TypeScript for discovering\n * densely connected clusters of notes. This reveals emergent knowledge\n * communities that may not be obvious from folder structure alone.\n *\n * The Louvain method optimizes modularity in two phases:\n *  1. Local: each node greedily moves to the community that maximizes modularity gain.\n *  2. Aggregation: communities are collapsed into super-nodes, forming a new graph.\n * Repeat until no further improvement.\n */\n\nimport type { StorageBackend } from \"../storage/interface.js\";\n\nexport interface CommunityOptions {\n  /** Minimum community size to include in results. Default: 3. */\n  minSize?: number;\n  /** Maximum number of communities to return. Default: 20. */\n  maxCommunities?: number;\n  /** Resolution parameter for Louvain (higher = more communities). Default: 1.0. */\n  resolution?: number;\n}\n\nexport interface CommunityNode {\n  path: string;\n  title: string | null;\n  /** Degree (inbound + outbound) within the community. */\n  internalDegree: number;\n}\n\nexport interface Community {\n  id: number;\n  /** Label derived from most common words in note titles. */\n  label: string;\n  nodes: CommunityNode[];\n  size: number;\n  /** Cohesion: ratio of internal edges to total possible internal edges. */\n  cohesion: number;\n  /** Top folders represented in this community. */\n  topFolders: string[];\n}\n\nexport interface CommunityResult {\n  communities: Community[];\n  totalNodes: number;\n  totalEdges: number;\n  /** Global modularity score of the partition. */\n  modularity: number;\n}\n\n// ---------------------------------------------------------------------------\n// Louvain algorithm implementation\n// ---------------------------------------------------------------------------\n\ninterface Graph {\n  /** All node IDs */\n  nodes: string[];\n  /** Adjacency list: node -> Map<neighbor, weight> */\n  adj: Map<string, Map<string, number>>;\n  /** Total edge weight (sum of all edge weights, counting undirected edges once) */\n  totalWeight: number;\n  /** Weighted degree per node */\n  degree: Map<string, number>;\n}\n\nfunction buildUndirectedGraph(\n  edges: Array<{ source_path: string; target_path: string }>\n): Graph {\n  const adj = new Map<string, Map<string, number>>();\n  const nodeSet = new Set<string>();\n\n  function getOrCreate(node: string): Map<string, number> {\n    let m = adj.get(node);\n    if (!m) {\n      m = new Map();\n      adj.set(node, m);\n    }\n    nodeSet.add(node);\n    return m;\n  }\n\n  let totalWeight = 0;\n\n  for (const { source_path, target_path } of edges) {\n    if (source_path === target_path) continue; // skip self-loops\n\n    const aMap = getOrCreate(source_path);\n    const bMap = getOrCreate(target_path);\n\n    // Undirected: add weight in both directions\n    aMap.set(target_path, (aMap.get(target_path) ?? 0) + 1);\n    bMap.set(source_path, (bMap.get(source_path) ?? 0) + 1);\n    totalWeight += 1; // each undirected edge counted once\n  }\n\n  // Compute weighted degree\n  const degree = new Map<string, number>();\n  for (const [node, neighbors] of adj) {\n    let d = 0;\n    for (const w of neighbors.values()) d += w;\n    degree.set(node, d);\n  }\n\n  return {\n    nodes: Array.from(nodeSet),\n    adj,\n    totalWeight,\n    degree,\n  };\n}\n\n/**\n * Run one pass of Phase 1: local node movement.\n * Returns true if any node changed community.\n */\nfunction louvainPhase1(\n  graph: Graph,\n  community: Map<string, number>,\n  resolution: number,\n): boolean {\n  const m2 = 2 * graph.totalWeight;\n  if (m2 === 0) return false;\n\n  // Community -> sum of degrees of nodes in community\n  const communityDegreeSum = new Map<number, number>();\n  // Community -> sum of internal edge weights\n  const communityInternalWeight = new Map<number, number>();\n\n  for (const node of graph.nodes) {\n    const c = community.get(node)!;\n    communityDegreeSum.set(c, (communityDegreeSum.get(c) ?? 0) + (graph.degree.get(node) ?? 0));\n  }\n\n  // Compute internal weights\n  for (const [node, neighbors] of graph.adj) {\n    const nc = community.get(node)!;\n    for (const [neighbor, weight] of neighbors) {\n      if (community.get(neighbor) === nc) {\n        communityInternalWeight.set(nc, (communityInternalWeight.get(nc) ?? 0) + weight);\n      }\n    }\n  }\n  // Each internal edge is counted twice (both endpoints), so divide\n  for (const [c, w] of communityInternalWeight) {\n    communityInternalWeight.set(c, w / 2);\n  }\n\n  let improved = false;\n  // Shuffle node order for better convergence\n  const shuffled = [...graph.nodes];\n  for (let i = shuffled.length - 1; i > 0; i--) {\n    const j = Math.floor(Math.random() * (i + 1));\n    [shuffled[i], shuffled[j]] = [shuffled[j], shuffled[i]];\n  }\n\n  for (const node of shuffled) {\n    const currentComm = community.get(node)!;\n    const ki = graph.degree.get(node) ?? 0;\n    const neighbors = graph.adj.get(node) ?? new Map();\n\n    // Compute weight to each neighboring community\n    const weightToComm = new Map<number, number>();\n    for (const [neighbor, weight] of neighbors) {\n      const nc = community.get(neighbor)!;\n      weightToComm.set(nc, (weightToComm.get(nc) ?? 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0) + ki);\n    const weightToBest = weightToComm.get(bestComm) ?? 0;\n    communityInternalWeight.set(\n      bestComm,\n      (communityInternalWeight.get(bestComm) ?? 0) + weightToBest,\n    );\n\n    if (bestComm !== currentComm) {\n      improved = true;\n    }\n  }\n\n  return improved;\n}\n\n/**\n * Compute modularity for a given partition.\n */\nfunction computeModularity(\n  graph: Graph,\n  community: Map<string, number>,\n  resolution: number,\n): number {\n  const m2 = 2 * graph.totalWeight;\n  if (m2 === 0) return 0;\n\n  let q = 0;\n  for (const [node, neighbors] of graph.adj) {\n    const ci = community.get(node)!;\n    const ki = graph.degree.get(node) ?? 0;\n\n    for (const [neighbor, weight] of neighbors) {\n      if (community.get(neighbor) === ci) {\n        q += weight - resolution * (ki * (graph.degree.get(neighbor) ?? 0)) / m2;\n      }\n    }\n  }\n  return q / m2;\n}\n\n/**\n * Run Louvain community detection on the vault link graph.\n */\nfunction runLouvain(\n  graph: Graph,\n  resolution: number,\n): Map<string, number> {\n  // Initialize: each node in its own community\n  const community = new Map<string, number>();\n  let nextComm = 0;\n  for (const node of graph.nodes) {\n    community.set(node, nextComm++);\n  }\n\n  // Phase 1: iteratively move nodes until no improvement\n  const MAX_ITERATIONS = 20;\n  for (let iter = 0; iter < MAX_ITERATIONS; iter++) {\n    const improved = louvainPhase1(graph, community, resolution);\n    if (!improved) break;\n  }\n\n  // Compact community IDs\n  const commRemap = new Map<number, number>();\n  let remapIdx = 0;\n  for (const [, c] of community) {\n    if (!commRemap.has(c)) {\n      commRemap.set(c, remapIdx++);\n    }\n  }\n  for (const [node, c] of community) {\n    community.set(node, commRemap.get(c)!);\n  }\n\n  return community;\n}\n\n// ---------------------------------------------------------------------------\n// Label generation\n// ---------------------------------------------------------------------------\n\nconst STOP_WORDS = new Set([\n  \"the\", \"and\", \"for\", \"are\", \"but\", \"not\", \"you\", \"all\", \"can\", \"her\",\n  \"was\", \"one\", \"our\", \"out\", \"has\", \"had\", \"how\", \"its\", \"may\", \"new\",\n  \"now\", \"old\", \"see\", \"way\", \"who\", \"did\", \"get\", \"let\", \"say\", \"she\",\n  \"too\", \"use\", \"from\", \"with\", \"this\", \"that\", \"will\", \"been\", \"have\",\n  \"each\", \"make\", \"like\", \"long\", \"look\", \"many\", \"them\", \"then\", \"what\",\n  \"when\", \"some\", \"time\", \"very\", \"your\", \"about\", \"could\", \"into\", \"just\",\n  \"more\", \"note\", \"notes\", \"than\", \"over\",\n]);\n\nfunction generateCommunityLabel(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(\" / \") || \"unnamed\";\n}\n\nfunction getTopFolder(path: string): string {\n  const slash = path.indexOf(\"/\");\n  return slash === -1 ? path : path.slice(0, slash);\n}\n\n// ---------------------------------------------------------------------------\n// Main export\n// ---------------------------------------------------------------------------\n\n/**\n * Detect communities in the vault link graph using the Louvain algorithm.\n * Returns clusters of densely connected notes with labels and cohesion scores.\n */\nexport async function zettelCommunities(\n  backend: StorageBackend,\n  opts?: CommunityOptions,\n): Promise<CommunityResult> {\n  const minSize = opts?.minSize ?? 3;\n  const maxCommunities = opts?.maxCommunities ?? 20;\n  const resolution = opts?.resolution ?? 1.0;\n\n  // Get the full link graph\n  const linkGraph = await backend.getVaultLinkGraph();\n  const graph = buildUndirectedGraph(linkGraph);\n\n  if (graph.nodes.length === 0) {\n    return {\n      communities: [],\n      totalNodes: 0,\n      totalEdges: 0,\n      modularity: 0,\n    };\n  }\n\n  // Run Louvain\n  const communityMap = runLouvain(graph, resolution);\n\n  // Compute modularity\n  const modularity = computeModularity(graph, communityMap, resolution);\n\n  // Group nodes by community\n  const groups = new Map<number, string[]>();\n  for (const [node, comm] of communityMap) {\n    const arr = groups.get(comm);\n    if (arr) arr.push(node);\n    else groups.set(comm, [node]);\n  }\n\n  // Get all vault files for title lookup\n  const allFiles = await backend.getAllVaultFiles();\n  const titleMap = new Map<string, string | null>();\n  for (const f of allFiles) {\n    titleMap.set(f.vaultPath, f.title);\n  }\n\n  // Build community results\n  const communities: Community[] = [];\n  let commId = 0;\n\n  for (const [, members] of groups) {\n    if (members.length < minSize) continue;\n\n    const memberSet = new Set(members);\n    const titles = members.map((p) => titleMap.get(p) ?? null);\n    const label = generateCommunityLabel(titles);\n\n    // Compute internal degree per node\n    const nodes: CommunityNode[] = members.map((path) => {\n      const neighbors = graph.adj.get(path) ?? new Map();\n      let internalDeg = 0;\n      for (const [neighbor, weight] of neighbors) {\n        if (memberSet.has(neighbor)) internalDeg += weight;\n      }\n      return {\n        path,\n        title: titleMap.get(path) ?? null,\n        internalDegree: internalDeg,\n      };\n    });\n\n    // Sort nodes by internal degree descending\n    nodes.sort((a, b) => b.internalDegree - a.internalDegree);\n\n    // Compute cohesion: ratio of actual internal edges to possible\n    let internalEdges = 0;\n    for (const node of nodes) {\n      internalEdges += node.internalDegree;\n    }\n    internalEdges /= 2; // each edge counted twice\n    const possibleEdges = (members.length * (members.length - 1)) / 2;\n    const cohesion = possibleEdges > 0 ? Math.round((internalEdges / possibleEdges) * 1000) / 1000 : 0;\n\n    // Top folders\n    const folderCounts = new Map<string, number>();\n    for (const path of members) {\n      const folder = getTopFolder(path);\n      folderCounts.set(folder, (folderCounts.get(folder) ?? 0) + 1);\n    }\n    const topFolders = [...folderCounts.entries()]\n      .sort((a, b) => b[1] - a[1])\n      .slice(0, 5)\n      .map(([f]) => f);\n\n    communities.push({\n      id: commId++,\n      label,\n      nodes,\n      size: members.length,\n      cohesion,\n      topFolders,\n    });\n  }\n\n  // Sort by size descending\n  communities.sort((a, b) => b.size - a.size);\n\n  return {\n    communities: communities.slice(0, maxCommunities),\n    totalNodes: graph.nodes.length,\n    totalEdges: graph.totalWeight,\n    modularity: Math.round(modularity * 10000) / 10000,\n  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package/docs/commands/README.md

@@ -139,10 +139,11 @@ Generated man pages for every `pai` command area. Read any page in the terminal
 | `pai session` | Session management: list, info, checkpoint, handover, cleanup, slug, tag, route. |
 | `pai session active` | Show currently active Claude Code sessions. |
 | `pai session auto-route` | Auto-detect which project this session belongs to. |
+| `pai session autosave` | Refresh the ## Continue checkpoint from the transcript and working tree. |
 | `pai session checkpoint <message>` | Append a timestamped checkpoint to the active session note. |
 | `pai session cleanup [project-slug]` | Clean up session notes: delete empties, auto-name unnamed, move into YYYY/MM/ hierarchy, renumber |
 | `pai session goto <name-or-id>` | Go to a session: resume if a resumable snapshot exists, start fresh otherwise. |
-| `pai session handover [project-slug] [session-id]` | Write a ## Continue section to the project's TODO.md. |
+| `pai session handover [project-slug] [number-or-latest]` | Write a ## Continue section to the project's TODO.md. |
 | `pai session info <project-slug> <number>` | Show full details for a specific session |
 | `pai session list` | Resumable sessions catalog — named sessions with resume status. |
 | `pai session pause` | Write a ## Continue checkpoint to the project's TODO.md. |

package/docs/commands/pause.md

@@ -28,7 +28,7 @@ pai pause [target] [options]
 | `--session-id <uuid>` | Claude Code session UUID — recorded as the `claude --resume` handle |  |
 | `--no-body` | Deliberately write a metadata-only checkpoint (no content) |  |
 | `--exit` | (pause all only) Also send /exit to each session after pausing |  |
-| `--wait <ms>` | (pause all only) Milliseconds to wait before /exit (default: 5000) | `5000` |
+| `--wait <ms>` | (pause all only) Max milliseconds to wait for a session to finish its checkpoint before /exit. Not a fixed delay — sessions are exited as soon as they return to the prompt, and any still busy at the deadline are left open rather than killed mid-write. (default: 180000) | `180000` |
 
 ## See also
 

package/docs/commands/session.md

@@ -22,8 +22,9 @@ pai session <subcommand> [options]
 | [`pai session slug <project-slug> <number>`](#pai-session-slug-project-slug-number) | Generate a descriptive slug from the session JSONL transcript |
 | [`pai session tag <project-slug> <number> [tags...]`](#pai-session-tag-project-slug-number-tags) | Set or show tags on a session. Tags can be space-separated or comma-separated. |
 | [`pai session route <project-slug> <number> <target-project>`](#pai-session-route-project-slug-number-target-project) | Create a cross-reference link from a session to a target project |
-| [`pai session handover [project-slug] [session-id]`](#pai-session-handover-project-slug-session-id) | Write a ## Continue section to the project's TODO.md. |
+| [`pai session handover [project-slug] [number-or-latest]`](#pai-session-handover-project-slug-number-or-latest) | Write a ## Continue section to the project's TODO.md. |
 | [`pai session checkpoint <message>`](#pai-session-checkpoint-message) | Append a timestamped checkpoint to the active session note. |
+| [`pai session autosave`](#pai-session-autosave) | Refresh the ## Continue checkpoint from the transcript and working tree. |
 | [`pai session active`](#pai-session-active) | Show currently active Claude Code sessions. |
 | [`pai session recent`](#pai-session-recent) | [Deprecated] Use `pai session list` or `pai sessions` instead. |
 | [`pai session goto <name-or-id>`](#pai-session-goto-name-or-id) | Go to a session: resume if a resumable snapshot exists, start fresh otherwise. |
@@ -123,7 +124,7 @@ Create a cross-reference link from a session to a target project
 | `--type <type>` | Link type: related \| follow-up \| reference | `related` |
 
 
-### pai session handover [project-slug] [session-id]
+### pai session handover [project-slug] [number-or-latest]
 
 Write a ## Continue section to the project's TODO.md.
 
@@ -136,7 +137,13 @@ so the next session can resume from the correct context.
 | Argument | Kind |
 |----------|------|
 | `[project-slug]` | optional |
-| `[session-id]` | optional |
+| `[number-or-latest]` | optional |
+
+**Options**
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--session-id <uuid>` | Claude session UUID. Used to decide whether an existing authored checkpoint belongs to this session and must be preserved. Without it the comparison falls back to the session note filename, which the stop hook itself renames — so pass it whenever it is known. |  |
 
 
 ### pai session checkpoint <message>
@@ -159,6 +166,23 @@ Rate-limited: skips silently if last checkpoint was < --min-gap seconds ago.
 | `--min-gap <seconds>` | Minimum seconds between checkpoints (default: 300 = 5 minutes) | `300` |
 
 
+### pai session autosave
+
+Refresh the ## Continue checkpoint from the transcript and working tree.
+
+Runs unattended from live hooks so an interrupted session still leaves
+a usable handover. Writes in auto mode, so a model-authored checkpoint
+for the same session is preserved untouched. Silent; always exits 0.
+
+**Options**
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--session-id <uuid>` | Claude session UUID — the key that decides whether an existing authored checkpoint belongs to this session and must be left alone. |  |
+| `--min-gap <seconds>` | Minimum seconds between autosaves, shared across all triggers (default: 240) | `240` |
+| `--dry-run` | Print the block that would be written and exit |  |
+
+
 ### pai session active
 
 Show currently active Claude Code sessions.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tekmidian/pai",
-  "version": "0.16.0",
+  "version": "0.17.0",
   "description": "PAI Knowledge OS — Personal AI Infrastructure with federated memory and project management",
   "type": "module",
   "main": "dist/index.mjs",

package/plugins/context-preservation/hooks/hooks.json

@@ -1,7 +1,18 @@
 {
   "module": "context-preservation",
-  "description": "Context compression and relay across compaction cycles",
+  "description": "Context preservation across compaction cycles, restarts, and interrupted sessions",
   "hooks": [
+    {
+      "event": "UserPromptSubmit",
+      "command": "${PAI_DIR}/Hooks/pai-session-autosave.sh",
+      "description": "Refresh the rolling ## Continue checkpoint from the transcript and working tree (rate-limited). Never overwrites a model-authored checkpoint for the same session."
+    },
+    {
+      "event": "PostToolUse",
+      "matcher": "*",
+      "command": "${PAI_DIR}/Hooks/pai-session-autosave.sh",
+      "description": "Same rolling checkpoint, so a long working turn interrupted by Ctrl+C still leaves recoverable state"
+    },
     {
       "event": "PreCompact",
       "command": "${PAI_DIR}/Hooks/context-compression-hook.mjs",

package/scripts/build-hooks.mjs

@@ -170,6 +170,7 @@ if (doSync) {
   const shellHooks = [
     ["src/hooks/pre-compact.sh", "pai-pre-compact.sh"],
     ["src/hooks/session-stop.sh", "pai-session-stop.sh"],
+    ["src/hooks/session-autosave.sh", "pai-session-autosave.sh"],
   ];
   for (const [src, destName] of shellHooks) {
     if (existsSync(src)) {

package/src/hooks/session-autosave.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+# PAI Knowledge OS — rolling session autosave
+#
+# Fires from live hooks (UserPromptSubmit, PostToolUse) so that a session which
+# never gets a model-authored checkpoint still leaves a usable ## Continue
+# behind. Ctrl+C kills the process without running any stop hook, and /exit does
+# not invoke the model — so an exit-time-only guarantee is no guarantee at all.
+# The state has to be written while the session is still running.
+#
+# Writes in "auto" mode, so a model-authored checkpoint for the same session is
+# preserved untouched. This is the floor, never a replacement for the ceiling.
+#
+# NEVER exits non-zero, NEVER prints — this must not interrupt Claude Code.
+
+PAI_OS="pai"
+command -v "$PAI_OS" &>/dev/null || exit 0
+
+# ---------------------------------------------------------------------------
+# Shell-side rate limit
+# ---------------------------------------------------------------------------
+# PostToolUse fires after every single tool call. The CLI rate-limits too, but
+# reaching it costs a Node start-up each time — hundreds of milliseconds, paid
+# on every tool call in the session. Checking a sentinel's mtime here costs a
+# stat, so the expensive path is only taken when it will actually do work.
+
+MIN_GAP_SECONDS="${PAI_AUTOSAVE_MIN_GAP:-240}"
+
+SENTINEL_KEY=$(printf '%s' "$PWD" | tr -c 'a-zA-Z0-9' '-' | tail -c 80)
+SENTINEL="${TMPDIR:-/tmp}/pai-autosave-hook-${SENTINEL_KEY}"
+
+if [ -f "$SENTINEL" ]; then
+  NOW=$(date +%s)
+  # stat is not portable: BSD/macOS uses -f %m, GNU/Linux uses -c %Y.
+  LAST=$(stat -f %m "$SENTINEL" 2>/dev/null || stat -c %Y "$SENTINEL" 2>/dev/null || echo 0)
+  if [ $((NOW - LAST)) -lt "$MIN_GAP_SECONDS" ]; then
+    exit 0
+  fi
+fi
+
+# ---------------------------------------------------------------------------
+# Session UUID from the hook payload
+# ---------------------------------------------------------------------------
+# The UUID decides whether an existing authored checkpoint belongs to this
+# session and must be left alone. Without it the comparison falls back to the
+# session note filename, which other stop-hook steps rename underneath us.
+
+CLAUDE_SESSION_UUID=""
+if [ ! -t 0 ]; then
+  HOOK_INPUT=$(timeout 2 cat 2>/dev/null || true)
+  if [ -n "$HOOK_INPUT" ]; then
+    if command -v jq &>/dev/null; then
+      CLAUDE_SESSION_UUID=$(printf '%s' "$HOOK_INPUT" | jq -r '.session_id // empty' 2>/dev/null || true)
+    else
+      CLAUDE_SESSION_UUID=$(printf '%s' "$HOOK_INPUT" | python3 -c \
+        "import sys,json; print(json.load(sys.stdin).get('session_id',''))" 2>/dev/null || true)
+    fi
+  fi
+fi
+
+touch "$SENTINEL" 2>/dev/null || true
+
+if [ -n "$CLAUDE_SESSION_UUID" ]; then
+  "$PAI_OS" session autosave --session-id "$CLAUDE_SESSION_UUID" \
+    --min-gap "$MIN_GAP_SECONDS" &>/dev/null || true
+else
+  "$PAI_OS" session autosave --min-gap "$MIN_GAP_SECONDS" &>/dev/null || true
+fi
+
+exit 0

package/src/hooks/session-stop.sh

@@ -12,6 +12,32 @@ PAI_OS="pai"
 command -v "$PAI_OS" &>/dev/null || exit 0
 command -v sqlite3 &>/dev/null || exit 0
 
+# ---------------------------------------------------------------------------
+# Read the Claude session UUID from the hook payload
+# ---------------------------------------------------------------------------
+# Claude Code delivers the Stop event as JSON on stdin, carrying `session_id`.
+# That UUID is the only stable handle on this session: the steps below rename
+# (`session slug --apply`) and renumber (`session cleanup --execute`) the
+# session note, so anything derived from its filename has already changed by
+# the time the handover runs. Passing the UUID through is what lets the
+# handover recognise a checkpoint `pai pause` wrote minutes earlier instead of
+# mistaking it for a stale one and overwriting it.
+#
+# Read non-blocking: when no payload is piped in, carry on without it.
+
+CLAUDE_SESSION_UUID=""
+if [ ! -t 0 ]; then
+  HOOK_INPUT=$(timeout 2 cat 2>/dev/null || true)
+  if [ -n "$HOOK_INPUT" ]; then
+    if command -v jq &>/dev/null; then
+      CLAUDE_SESSION_UUID=$(printf '%s' "$HOOK_INPUT" | jq -r '.session_id // empty' 2>/dev/null || true)
+    else
+      CLAUDE_SESSION_UUID=$(printf '%s' "$HOOK_INPUT" | python3 -c \
+        "import sys,json; print(json.load(sys.stdin).get('session_id',''))" 2>/dev/null || true)
+    fi
+  fi
+fi
+
 REGISTRY_DB="$HOME/.pai/registry.db"
 [ -f "$REGISTRY_DB" ] || exit 0
 
@@ -88,7 +114,12 @@ fi
 # a handover section. If the command doesn't exist yet, fail gracefully.
 #
 
-"$PAI_OS" session handover "$PROJECT_SLUG" latest 2>/dev/null || true
+if [ -n "$CLAUDE_SESSION_UUID" ]; then
+  "$PAI_OS" session handover "$PROJECT_SLUG" latest \
+    --session-id "$CLAUDE_SESSION_UUID" 2>/dev/null || true
+else
+  "$PAI_OS" session handover "$PROJECT_SLUG" latest 2>/dev/null || true
+fi
 
 # Set tab color to completed state when session ends
 TAB_COLOR="${PAI_DIR:-$HOME/.claude}/tab-color-command.sh"

package/src/hooks/ts/session-start/load-project-context.ts

@@ -21,6 +21,7 @@ import { join, basename, dirname, resolve } from 'path';
 import { homedir } from 'os';
 import { execSync } from 'child_process';
 import { buildWakeupContext } from '../../../memory/wakeup.js';
+import { readContinueCheckpoint } from '../../../session/checkpoint-block.js';
 import {
   PAI_DIR,
   findNotesDir,
@@ -489,6 +490,49 @@ Session Commands:
   // Output to stdout for Claude to receive
   console.log(reminder);
 
+  // 8.5. INJECT THE PAUSE CHECKPOINT
+  //
+  // `pai pause` writes the handover to TODO.md under `## Continue`. Until now
+  // nothing read it back: the session-commands hook only told the model to look
+  // there *if the user typed "go"*, so a resumed session started blind unless
+  // the user knew the magic word. Writing a handover nobody delivers is not a
+  // handover. Inject it, and say plainly that it is the previous session's
+  // state rather than an instruction to act on.
+  if (existsSync(todoPath)) {
+    try {
+      const checkpoint = readContinueCheckpoint(readFileSync(todoPath, 'utf-8'));
+      if (checkpoint) {
+        const from = checkpoint.meta?.session
+          ? `\nFrom session: ${checkpoint.meta.session}`
+          : '';
+        const when = checkpoint.meta?.ts ? `\nPaused at: ${checkpoint.meta.ts}` : '';
+        const resume = checkpoint.meta?.sessionId
+          ? `\nResume that session with: claude --resume ${checkpoint.meta.sessionId}`
+          : '';
+
+        console.log(`
+<system-reminder>
+HANDOVER FROM THE PREVIOUS SESSION
+
+Source: ${todoPath} (## Continue)${from}${when}${resume}
+
+${checkpoint.body}
+
+---
+This is recorded state, not a new instruction. Do not start acting on it
+unprompted. If the user says "go", "continue", or "weiter", resume from here.
+</system-reminder>
+`);
+        console.error(`Injected pause checkpoint (${checkpoint.body.length} chars)`);
+      } else {
+        console.error('No pause checkpoint body in TODO.md — nothing to hand over');
+      }
+    } catch (error) {
+      // Non-fatal — a malformed TODO.md must never block session start.
+      console.error('Checkpoint injection failed:', error);
+    }
+  }
+
   // 9. INJECT CLAUDE.md contents as system-reminders
   // This ensures Claude actually reads and processes the instructions
   for (const { path, content } of claudeMdContents) {