@tekmidian/pai 0.5.6 → 0.6.0

package/dist/sync-BOsnEj2-.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"sync-BOsnEj2-.mjs","names":[],"sources":["../src/memory/indexer/sync.ts"],"sourcesContent":["/**\n * Synchronous (SQLite) indexer for the PAI federation memory engine.\n *\n * Scans project memory/ and Notes/ directories, chunks markdown files, and\n * inserts the resulting chunks into federation.db for BM25 search.\n *\n * Change detection: files whose SHA-256 hash has not changed since the last\n * index run are skipped, keeping incremental re-indexing fast.\n *\n * Uses raw better-sqlite3 Database directly for maximum SQLite performance\n * (synchronous transactions, no serialisation overhead).\n */\n\nimport { readFileSync, statSync, existsSync } from \"node:fs\";\nimport { join, relative, basename } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { chunkMarkdown } from \"../chunker.js\";\nimport {\n  sha256File,\n  chunkId,\n  detectTier,\n  walkMdFiles,\n  walkContentFiles,\n  isPathTooBroadForContentScan,\n  parseSessionTitleChunk,\n  yieldToEventLoop,\n  INDEX_YIELD_EVERY,\n} from \"./helpers.js\";\nimport type { IndexResult, EmbedResult } from \"./types.js\";\n\nexport type { IndexResult, EmbedResult };\n\n// Re-export detectTier for backward-compatibility (consumers import it from indexer.js)\nexport { detectTier };\n\n// ---------------------------------------------------------------------------\n// Single-file indexing\n// ---------------------------------------------------------------------------\n\n/**\n * Index a single file into the federation database.\n *\n * @returns true if the file was re-indexed (changed or new), false if skipped.\n */\nexport function indexFile(\n  db: Database,\n  projectId: number,\n  rootPath: string,\n  relativePath: string,\n  source: string,\n  tier: string,\n): boolean {\n  const absPath = join(rootPath, relativePath);\n\n  // Read file content\n  let content: string;\n  let stat: ReturnType<typeof statSync>;\n  try {\n    content = readFileSync(absPath, \"utf8\");\n    stat = statSync(absPath);\n  } catch {\n    // File unreadable or missing — skip silently\n    return false;\n  }\n\n  const hash = sha256File(content);\n  const mtime = Math.floor(stat.mtimeMs);\n  const size = stat.size;\n\n  // Check if the file has changed since last index\n  const existing = db\n    .prepare(\n      \"SELECT hash FROM memory_files WHERE project_id = ? AND path = ?\",\n    )\n    .get(projectId, relativePath) as { hash: string } | undefined;\n\n  if (existing?.hash === hash) {\n    // Unchanged — skip\n    return false;\n  }\n\n  // Delete old chunks for this file from both tables\n  const oldChunkIds = db\n    .prepare(\n      \"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\",\n    )\n    .all(projectId, relativePath) as Array<{ id: string }>;\n\n  const deleteFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n  const deleteChunk = db.prepare(\n    \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  db.transaction(() => {\n    for (const row of oldChunkIds) {\n      deleteFts.run(row.id);\n    }\n    deleteChunk.run(projectId, relativePath);\n  })();\n\n  // Chunk the new content\n  const chunks = chunkMarkdown(content);\n\n  // Insert new chunks into memory_chunks and memory_fts\n  const insertChunk = db.prepare(`\n    INSERT INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const insertFts = db.prepare(`\n    INSERT INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const upsertFile = db.prepare(`\n    INSERT INTO memory_files (project_id, path, source, tier, hash, mtime, size)\n    VALUES (?, ?, ?, ?, ?, ?, ?)\n    ON CONFLICT(project_id, path) DO UPDATE SET\n      source = excluded.source,\n      tier   = excluded.tier,\n      hash   = excluded.hash,\n      mtime  = excluded.mtime,\n      size   = excluded.size\n  `);\n\n  const updatedAt = Date.now();\n\n  db.transaction(() => {\n    for (let i = 0; i < chunks.length; i++) {\n      const chunk = chunks[i]!;\n      const id = chunkId(projectId, relativePath, i, chunk.startLine, chunk.endLine);\n      insertChunk.run(\n        id,\n        projectId,\n        source,\n        tier,\n        relativePath,\n        chunk.startLine,\n        chunk.endLine,\n        chunk.hash,\n        chunk.text,\n        updatedAt,\n      );\n      insertFts.run(\n        chunk.text,\n        id,\n        projectId,\n        relativePath,\n        source,\n        tier,\n        chunk.startLine,\n        chunk.endLine,\n      );\n    }\n    upsertFile.run(projectId, relativePath, source, tier, hash, mtime, size);\n  })();\n\n  return true;\n}\n\n// ---------------------------------------------------------------------------\n// Project-level indexing\n// ---------------------------------------------------------------------------\n\n/**\n * Index all memory, Notes, and content files for a single registered project.\n *\n * Scans:\n *  - {rootPath}/MEMORY.md    → source='memory', tier='evergreen'\n *  - {rootPath}/memory/      → source='memory', tier from detectTier()\n *  - {rootPath}/Notes/       → source='notes',  tier='session'\n *  - {rootPath}/**\\/*.md    → source='content', tier='topic'  (all other .md files, recursive)\n *  - {claudeNotesDir}/       → source='notes',  tier='session'  (if set and different)\n */\nexport async function indexProject(\n  db: Database,\n  projectId: number,\n  rootPath: string,\n  claudeNotesDir?: string | null,\n): Promise<IndexResult> {\n  const result: IndexResult = {\n    filesProcessed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n  };\n\n  const filesToIndex: Array<{ absPath: string; rootBase: string; source: string; tier: string }> = [];\n\n  // Root-level MEMORY.md\n  const rootMemoryMd = join(rootPath, \"MEMORY.md\");\n  if (existsSync(rootMemoryMd)) {\n    filesToIndex.push({ absPath: rootMemoryMd, rootBase: rootPath, source: \"memory\", tier: \"evergreen\" });\n  }\n\n  // memory/ directory\n  const memoryDir = join(rootPath, \"memory\");\n  for (const absPath of walkMdFiles(memoryDir)) {\n    const relPath = relative(rootPath, absPath);\n    const tier = detectTier(relPath);\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"memory\", tier });\n  }\n\n  // {rootPath}/Notes/ directory\n  const notesDir = join(rootPath, \"Notes\");\n  for (const absPath of walkMdFiles(notesDir)) {\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"notes\", tier: \"session\" });\n  }\n\n  // Synthetic session-title chunks for Notes files with the standard filename format:\n  // \"NNNN - YYYY-MM-DD - Descriptive Title.md\"\n  {\n    const titleInsertChunk = db.prepare(`\n      INSERT OR IGNORE INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n    const titleInsertFts = db.prepare(`\n      INSERT OR IGNORE INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n    const updatedAt = Date.now();\n    for (const absPath of walkMdFiles(notesDir)) {\n      const fileName = basename(absPath);\n      const text = parseSessionTitleChunk(fileName);\n      if (!text) continue;\n      const relPath = relative(rootPath, absPath);\n      const syntheticPath = `${relPath}::title`;\n      const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n      const hash = sha256File(text);\n      db.transaction(() => {\n        titleInsertChunk.run(id, projectId, \"notes\", \"session\", syntheticPath, 0, 0, hash, text, updatedAt);\n        titleInsertFts.run(text, id, projectId, syntheticPath, \"notes\", \"session\", 0, 0);\n      })();\n    }\n  }\n\n  // {rootPath}/**/*.md — all other markdown content\n  if (!isPathTooBroadForContentScan(rootPath)) {\n    for (const absPath of walkContentFiles(rootPath)) {\n      filesToIndex.push({ absPath, rootBase: rootPath, source: \"content\", tier: \"topic\" });\n    }\n  }\n\n  // Claude Code session notes directory (~/.claude/projects/{encoded}/Notes/)\n  if (claudeNotesDir && claudeNotesDir !== notesDir) {\n    for (const absPath of walkMdFiles(claudeNotesDir)) {\n      filesToIndex.push({ absPath, rootBase: claudeNotesDir, source: \"notes\", tier: \"session\" });\n    }\n\n    // Synthetic title chunks for claude notes dir\n    {\n      const updatedAt = Date.now();\n      const titleInsertChunk2 = db.prepare(`\n        INSERT OR IGNORE INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n      `);\n      const titleInsertFts2 = db.prepare(`\n        INSERT OR IGNORE INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n      `);\n      for (const absPath of walkMdFiles(claudeNotesDir)) {\n        const fileName = basename(absPath);\n        const text = parseSessionTitleChunk(fileName);\n        if (!text) continue;\n        const relPath = relative(claudeNotesDir, absPath);\n        const syntheticPath = `${relPath}::title`;\n        const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n        const hash = sha256File(text);\n        db.transaction(() => {\n          titleInsertChunk2.run(id, projectId, \"notes\", \"session\", syntheticPath, 0, 0, hash, text, updatedAt);\n          titleInsertFts2.run(text, id, projectId, syntheticPath, \"notes\", \"session\", 0, 0);\n        })();\n      }\n    }\n\n    // Derive the sibling memory/ directory: .../Notes/ → .../memory/\n    if (claudeNotesDir.endsWith(\"/Notes\")) {\n      const claudeProjectDir = claudeNotesDir.slice(0, -\"/Notes\".length);\n      const claudeMemoryDir = join(claudeProjectDir, \"memory\");\n\n      const claudeMemoryMd = join(claudeProjectDir, \"MEMORY.md\");\n      if (existsSync(claudeMemoryMd)) {\n        filesToIndex.push({\n          absPath: claudeMemoryMd,\n          rootBase: claudeProjectDir,\n          source: \"memory\",\n          tier: \"evergreen\",\n        });\n      }\n\n      for (const absPath of walkMdFiles(claudeMemoryDir)) {\n        const relPath = relative(claudeProjectDir, absPath);\n        const tier = detectTier(relPath);\n        filesToIndex.push({ absPath, rootBase: claudeProjectDir, source: \"memory\", tier });\n      }\n    }\n  }\n\n  // Yield after collection phase before processing\n  await yieldToEventLoop();\n\n  let filesSinceYield = 0;\n\n  for (const { absPath, rootBase, source, tier } of filesToIndex) {\n    if (filesSinceYield >= INDEX_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const relPath = relative(rootBase, absPath);\n    const changed = indexFile(db, projectId, rootBase, relPath, source, tier);\n\n    if (changed) {\n      const count = db\n        .prepare(\n          \"SELECT COUNT(*) as n FROM memory_chunks WHERE project_id = ? AND path = ?\",\n        )\n        .get(projectId, relPath) as { n: number };\n\n      result.filesProcessed++;\n      result.chunksCreated += count.n;\n    } else {\n      result.filesSkipped++;\n    }\n  }\n\n  // Prune stale paths: remove DB entries for files that no longer exist on disk.\n  const livePaths = new Set<string>();\n  for (const { absPath, rootBase } of filesToIndex) {\n    livePaths.add(relative(rootBase, absPath));\n  }\n\n  const dbChunkPaths = db\n    .prepare(\"SELECT DISTINCT path FROM memory_chunks WHERE project_id = ?\")\n    .all(projectId) as Array<{ path: string }>;\n\n  const stalePaths: string[] = [];\n  for (const row of dbChunkPaths) {\n    const basePath = row.path.endsWith(\"::title\")\n      ? row.path.slice(0, -\"::title\".length)\n      : row.path;\n    if (!livePaths.has(basePath)) {\n      stalePaths.push(row.path);\n    }\n  }\n\n  if (stalePaths.length > 0) {\n    const deleteChunksFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n    const deleteChunks = db.prepare(\n      \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n    );\n    const deleteFile = db.prepare(\n      \"DELETE FROM memory_files WHERE project_id = ? AND path = ?\",\n    );\n\n    db.transaction(() => {\n      for (const stalePath of stalePaths) {\n        const chunkIds = db\n          .prepare(\"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\")\n          .all(projectId, stalePath) as Array<{ id: string }>;\n        for (const { id } of chunkIds) {\n          deleteChunksFts.run(id);\n        }\n        deleteChunks.run(projectId, stalePath);\n        deleteFile.run(projectId, stalePath);\n      }\n    })();\n  }\n\n  return result;\n}\n\n// ---------------------------------------------------------------------------\n// Global indexing (all registered projects)\n// ---------------------------------------------------------------------------\n\n/**\n * Index all active projects registered in the registry DB.\n *\n * Async: yields to the event loop between each project so that the daemon's\n * Unix socket server can process IPC requests (e.g. status) while indexing.\n */\nexport async function indexAll(\n  db: Database,\n  registryDb: Database,\n): Promise<{ projects: number; result: IndexResult }> {\n  const projects = registryDb\n    .prepare(\"SELECT id, root_path, claude_notes_dir FROM projects WHERE status = 'active'\")\n    .all() as Array<{ id: number; root_path: string; claude_notes_dir: string | null }>;\n\n  const totals: IndexResult = {\n    filesProcessed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n  };\n\n  for (const project of projects) {\n    await yieldToEventLoop();\n    const r = await indexProject(db, project.id, project.root_path, project.claude_notes_dir);\n    totals.filesProcessed += r.filesProcessed;\n    totals.chunksCreated += r.chunksCreated;\n    totals.filesSkipped += r.filesSkipped;\n  }\n\n  return { projects: projects.length, result: totals };\n}\n\n// ---------------------------------------------------------------------------\n// Embedding generation\n// ---------------------------------------------------------------------------\n\n/**\n * Generate and store embeddings for chunks that do not yet have one.\n *\n * Because better-sqlite3 is synchronous but the embedding pipeline is async,\n * we fetch all unembedded chunk texts first, generate embeddings in batches,\n * and then write them back in a transaction.\n *\n * @param db         Open federation database.\n * @param projectId  Optional — restrict to a specific project.\n * @param batchSize  Number of chunks to embed per round. Default 50.\n * @param onProgress Optional callback called after each batch with running totals.\n */\nexport async function embedChunks(\n  db: Database,\n  projectId?: number,\n  batchSize = 50,\n  onProgress?: (embedded: number, total: number) => void,\n): Promise<EmbedResult> {\n  // Dynamic import — keeps the heavy ML runtime out of the module load path\n  const { generateEmbedding, serializeEmbedding } = await import(\"../embeddings.js\");\n\n  const conditions = [\"embedding IS NULL\"];\n  const params: (string | number)[] = [];\n\n  if (projectId !== undefined) {\n    conditions.push(\"project_id = ?\");\n    params.push(projectId);\n  }\n\n  const where = \"WHERE \" + conditions.join(\" AND \");\n\n  const rows = db\n    .prepare(`SELECT id, text FROM memory_chunks ${where} ORDER BY id`)\n    .all(...params) as Array<{ id: string; text: string }>;\n\n  if (rows.length === 0) {\n    return { chunksEmbedded: 0, chunksSkipped: 0 };\n  }\n\n  const updateStmt = db.prepare(\n    \"UPDATE memory_chunks SET embedding = ? WHERE id = ?\",\n  );\n\n  let embedded = 0;\n  const total = rows.length;\n\n  for (let i = 0; i < rows.length; i += batchSize) {\n    const batch = rows.slice(i, i + batchSize);\n\n    // Generate embeddings for the batch (async — must happen OUTSIDE transaction)\n    const embeddings: Array<{ id: string; blob: Buffer }> = [];\n    for (const row of batch) {\n      const vec = await generateEmbedding(row.text);\n      const blob = serializeEmbedding(vec);\n      embeddings.push({ id: row.id, blob });\n    }\n\n    // Write the batch in a single transaction\n    db.transaction(() => {\n      for (const { id, blob } of embeddings) {\n        updateStmt.run(blob, id);\n      }\n    })();\n\n    embedded += embeddings.length;\n    onProgress?.(embedded, total);\n  }\n\n  return { chunksEmbedded: embedded, chunksSkipped: 0 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package/dist/themes-BvYF0W8T.mjs

@@ -0,0 +1,148 @@
+import { n as cosineSimilarity, r as deserializeEmbedding } from "./embeddings-DGRAPAYb.mjs";
+import { t as STOP_WORDS } from "./stop-words-BaMEGVeY.mjs";
+
+//#region src/zettelkasten/themes.ts
+const MAX_CHUNKS = 5e3;
+function getTopFolder(vaultPath) {
+	const parts = vaultPath.split("/");
+	return parts.length > 1 ? parts[0] : "";
+}
+function generateLabel(titles) {
+	const wordCounts = /* @__PURE__ */ new Map();
+	for (const title of titles) {
+		if (!title) continue;
+		const words = title.toLowerCase().replace(/[^a-z0-9\s]/g, " ").split(/\s+/).filter((w) => w.length > 2 && !STOP_WORDS.has(w));
+		for (const word of words) wordCounts.set(word, (wordCounts.get(word) ?? 0) + 1);
+	}
+	return [...wordCounts.entries()].sort((a, b) => b[1] - a[1]).slice(0, 3).map(([w]) => w).join(" / ");
+}
+async function computeLinkedRatio(backend, paths) {
+	if (paths.length < 2) return 0;
+	const totalPairs = paths.length * (paths.length - 1) / 2;
+	const pathSet = new Set(paths);
+	let linkedPairs = 0;
+	for (const path of paths) {
+		const links = await backend.getLinksFromSource(path);
+		for (const link of links) if (link.targetPath && pathSet.has(link.targetPath)) linkedPairs++;
+	}
+	const uniquePairs = linkedPairs / 2;
+	return Math.min(1, uniquePairs / totalPairs);
+}
+function averageEmbeddings(embeddings) {
+	if (embeddings.length === 0) return new Float32Array(0);
+	const dim = embeddings[0].length;
+	const sum = new Float32Array(dim);
+	for (const vec of embeddings) for (let i = 0; i < dim; i++) sum[i] += vec[i];
+	const avg = new Float32Array(dim);
+	for (let i = 0; i < dim; i++) avg[i] = sum[i] / embeddings.length;
+	return avg;
+}
+/**
+* Detect emerging themes in recently-modified notes using agglomerative single-linkage
+* clustering of note-level embeddings.
+*/
+async function zettelThemes(backend, opts) {
+	const lookbackDays = opts.lookbackDays ?? 30;
+	const minClusterSize = opts.minClusterSize ?? 3;
+	const maxThemes = opts.maxThemes ?? 10;
+	const similarityThreshold = opts.similarityThreshold ?? .65;
+	const now = Date.now();
+	const from = now - lookbackDays * 864e5;
+	const recentNotes = (await backend.getRecentVaultFiles(from)).map((f) => ({
+		vault_path: f.vaultPath,
+		title: f.title,
+		indexed_at: f.indexedAt
+	}));
+	const chunkRows = await backend.getChunksWithEmbeddings(opts.vaultProjectId, MAX_CHUNKS);
+	const embeddingsByPath = /* @__PURE__ */ new Map();
+	for (const row of chunkRows) {
+		const vec = deserializeEmbedding(row.embedding);
+		const arr = embeddingsByPath.get(row.path);
+		if (!arr) embeddingsByPath.set(row.path, [vec]);
+		else arr.push(vec);
+	}
+	const fileEmbeddings = /* @__PURE__ */ new Map();
+	for (const [path, vecs] of embeddingsByPath) fileEmbeddings.set(path, averageEmbeddings(vecs));
+	const clusters = [];
+	for (const note of recentNotes) {
+		const embedding = fileEmbeddings.get(note.vault_path);
+		if (!embedding) continue;
+		clusters.push({
+			paths: [note.vault_path],
+			titles: [note.title],
+			indexedAts: [note.indexed_at],
+			centroid: embedding
+		});
+	}
+	const totalNotesAnalyzed = clusters.length;
+	let merged = true;
+	while (merged && clusters.length > 1) {
+		merged = false;
+		let bestSim = similarityThreshold;
+		let bestI = -1;
+		let bestJ = -1;
+		for (let i = 0; i < clusters.length; i++) for (let j = i + 1; j < clusters.length; j++) {
+			const sim = cosineSimilarity(clusters[i].centroid, clusters[j].centroid);
+			if (sim > bestSim) {
+				bestSim = sim;
+				bestI = i;
+				bestJ = j;
+			}
+		}
+		if (bestI === -1) break;
+		const ci = clusters[bestI];
+		const cj = clusters[bestJ];
+		const mergedPaths = [...ci.paths, ...cj.paths];
+		const mergedTitles = [...ci.titles, ...cj.titles];
+		const mergedIndexedAts = [...ci.indexedAts, ...cj.indexedAts];
+		const memberEmbeddings = [];
+		for (const p of mergedPaths) {
+			const emb = fileEmbeddings.get(p);
+			if (emb) memberEmbeddings.push(emb);
+		}
+		clusters[bestI] = {
+			paths: mergedPaths,
+			titles: mergedTitles,
+			indexedAts: mergedIndexedAts,
+			centroid: averageEmbeddings(memberEmbeddings)
+		};
+		clusters.splice(bestJ, 1);
+		merged = true;
+	}
+	const themes = [];
+	let clusterIndex = 0;
+	for (const cluster of clusters) {
+		if (cluster.paths.length < minClusterSize) continue;
+		const label = generateLabel(cluster.titles) || `Theme ${clusterIndex + 1}`;
+		const avgRecency = cluster.indexedAts.reduce((sum, t) => sum + t, 0) / cluster.indexedAts.length;
+		const folderDiversity = new Set(cluster.paths.map(getTopFolder)).size / cluster.paths.length;
+		const linkedRatio = await computeLinkedRatio(backend, cluster.paths);
+		const suggestIndexNote = linkedRatio < .3 && cluster.paths.length >= 5;
+		themes.push({
+			id: clusterIndex++,
+			label,
+			notes: cluster.paths.map((path, idx) => ({
+				path,
+				title: cluster.titles[idx]
+			})),
+			size: cluster.paths.length,
+			folderDiversity,
+			avgRecency,
+			linkedRatio,
+			suggestIndexNote
+		});
+	}
+	themes.sort((a, b) => b.size * b.folderDiversity * (b.avgRecency / now) - a.size * a.folderDiversity * (a.avgRecency / now));
+	return {
+		themes: themes.slice(0, maxThemes),
+		totalNotesAnalyzed,
+		timeWindow: {
+			from,
+			to: now
+		}
+	};
+}
+
+//#endregion
+export { zettelThemes as t };
+//# sourceMappingURL=themes-BvYF0W8T.mjs.map

package/dist/themes-BvYF0W8T.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"themes-BvYF0W8T.mjs","names":[],"sources":["../src/zettelkasten/themes.ts"],"sourcesContent":["import type { StorageBackend } from \"../storage/interface.js\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\nimport { STOP_WORDS } from \"../utils/stop-words.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\n// STOP_WORDS imported from utils/stop-words.ts\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\nasync function computeLinkedRatio(backend: StorageBackend, paths: string[]): Promise<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 links = await backend.getLinksFromSource(path);\n    for (const link of links) {\n      if (link.targetPath && pathSet.has(link.targetPath)) {\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  backend: StorageBackend,\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 recentFiles = await backend.getRecentVaultFiles(from);\n  const recentNotes = recentFiles.map(f => ({ vault_path: f.vaultPath, title: f.title, indexed_at: f.indexedAt }));\n\n  // Step 2: get file-level embeddings from memory_chunks\n  const chunkRows = await backend.getChunksWithEmbeddings(opts.vaultProjectId, MAX_CHUNKS);\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  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 = await computeLinkedRatio(backend, 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  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