sensemaking 0.12.0 → 0.12.1

package/dist/cjs/features/embed.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/embed.ts"],"sourcesContent":["import { existsSync, mkdirSync, readFileSync, renameSync, writeFileSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { join } from 'node:path';\nimport type { DatabaseSync } from 'node:sqlite';\nimport type { Config, ResolvedConfig } from '../config.ts';\nimport { embedConfig } from '../config.ts';\nimport { SenseError } from '../errors.ts';\nimport { progress } from '../progress.ts';\nimport { parseFile } from '../scan.ts';\nimport type { Feature } from './types.ts';\n\n// Heading-based chunks, int8 vectors with a per-vector scale, NULL vector = not yet embedded.\n// Reconcile writes dirty rows; embedding tops up on the next search, so staleness costs recall.\n\n// Storage lever fixed by the bake-off (BENCHMARKING.md): int8 at 256 dims is\n// quality-free vs f32-512 when fused. Queries stay f32 at the same dims.\nconst STORE_DIMS = 256;\n// Seed chunks that participate in a `related` scan; see similarNotes for the measurement.\nconst TARGET_CHUNK_CAP = 16;\nconst BATCH = 64;\n\nexport interface EmbedProvider {\n  id: string; // model identity; participates in the cache key, change -> re-embed\n  dims: number;\n  embed(texts: string[]): Promise<Float32Array[]>;\n}\n\ninterface Chunk {\n  startLine: number;\n  endLine: number;\n  text: string;\n}\n\n// Deterministic, so embed time can re-derive text from stored line ranges. Heading-delimited,\n// preamble kept, whole body when no headings; the title/summary prefix mirrors bm25 weighting.\n//\n// Chunks the body, not the raw file, with `offset` shifting line numbers back onto the raw\n// file so a range stays a direct Read range (sections is 1-indexed over raw too). Chunking raw\n// put the frontmatter block in its own leading chunk on every note with a heading, which made\n// `lines` point at YAML and made frontmatter-only notes near-identical to each other. It also\n// disagreed with FTS, which indexes the body alone.\nfunction chunksOf(body: string, search?: { title: string; summary: string }, offset = 0): Chunk[] {\n  const lines = body.split('\\n');\n  const starts: number[] = [];\n  let inFence = false;\n  for (let i = 0; i < lines.length; i++) {\n    if (/^(```|~~~)/.test(lines[i])) {\n      inFence = !inFence;\n      continue;\n    }\n    if (!inFence && /^#{1,6} +/.test(lines[i])) starts.push(i + 1);\n  }\n  const bounds = starts.length === 0 ? [1] : starts[0] > 1 ? [1, ...starts] : starts;\n  const prefix = [search?.title, search?.summary].filter(Boolean).join('\\n');\n  const chunks: Chunk[] = [];\n  bounds.forEach((start, i) => {\n    const end = i + 1 < bounds.length ? bounds[i + 1] - 1 : lines.length;\n    const text = lines\n      .slice(start - 1, end)\n      .join('\\n')\n      .trim();\n    // A body with nothing in it yields no chunks at all, so a frontmatter-only note has no\n    // vectors rather than a vector of its own YAML.\n    if (text.length > 0) chunks.push({ startLine: start + offset, endLine: end + offset, text: prefix ? `${prefix}\\n${text}` : text });\n  });\n  return chunks;\n}\n\nexport const embed: Feature = {\n  name: 'embed',\n  schema(db) {\n    db.exec(`CREATE TABLE IF NOT EXISTS embeddings (\"path\" TEXT, chunk INTEGER, start_line INTEGER, end_line INTEGER, scale REAL, vector BLOB, PRIMARY KEY (\"path\", chunk))`);\n  },\n  extract(raw, body, search) {\n    // Lines the frontmatter occupies, so body line 1 maps back to its raw line number.\n    return chunksOf(body, search, raw.split('\\n').length - body.split('\\n').length);\n  },\n  remove(db, path) {\n    db.prepare('DELETE FROM embeddings WHERE \"path\" = ?').run(path);\n  },\n  // A tree with no embedding model never had extract() run for the doc (db.ts's per-file\n  // filter skips it), so extracted is undefined here -- store nothing, i.e. no rows.\n  store(db, path, extracted) {\n    if (!extracted) return;\n    const insert = db.prepare('INSERT INTO embeddings (\"path\", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)');\n    (extracted as Chunk[]).forEach((c, idx) => insert.run(path, idx, c.startLine, c.endLine));\n  },\n  enabledForFile(_cfg, file) {\n    return file.embed;\n  },\n};\n\n// --- static type: Model2Vec safetensors + pure-JS tokenizer, model cached in ~/.cache ---\n// Encode convention from model2vec/model.py: no special tokens, drop unk ids, mean-pool,\n// L2-normalize.\n\nconst MODEL_FILES = ['model.safetensors', 'tokenizer.json'];\n// The pair, for messages that name what a local model directory must contain.\nexport const MODEL_FILENAMES = MODEL_FILES.join(' and ');\n\n// A Hugging Face repo id: one slash, HF's charset. Anything else is a path, used as one rather\n// than flattened into a cache key Windows would reject.\nconst HF_MODEL_ID = /^[A-Za-z0-9][\\w.-]*\\/[A-Za-z0-9][\\w.-]*$/;\n\n// Downloadable iff it names a Hugging Face repo; a local path is the caller's to populate.\nexport function isDownloadable(model: string): boolean {\n  return HF_MODEL_ID.test(model);\n}\n\n// Machine-wide, not per-tree: `.sense/` is the index a rebuild throws away, while a 124 MB\n// model is shared by every tree on the machine. Honors XDG_CACHE_HOME where it is set;\n// elsewhere ~/.cache, which is also where Hugging Face's own libraries keep theirs.\nfunction cacheRoot(): string {\n  const xdg = process.env.XDG_CACHE_HOME;\n  return join(xdg && xdg.length > 0 ? xdg : join(homedir(), '.cache'), 'sensemaking', 'models');\n}\n\n// A model is either a local directory the caller pointed at, or the cache `sense download`\n// fills. Nothing here fetches: an absent model degrades search to its other signals rather\n// than pulling 124 MB out of a command that reads like a query.\nexport function modelDir(model: string): string {\n  if (!HF_MODEL_ID.test(model)) return model;\n  return join(cacheRoot(), model.replace(/\\//g, '--'));\n}\n\n// Both files, so an interrupted download reads as absent and the next one resumes it.\nexport function hasModelFiles(model: string): boolean {\n  const dir = modelDir(model);\n  return MODEL_FILES.every((file) => existsSync(join(dir, file)));\n}\n\n// api providers have nothing to download, so they are never \"missing\" here; an unreachable\n// endpoint surfaces as an EMBED_MODEL error at call time instead.\nexport function modelPresent(cfg: Config): boolean {\n  const e = embedConfig(cfg);\n  if (!e) return false;\n  return e.type === 'api' || hasModelFiles(e.model);\n}\n\nfunction fetchToFile(url: string, dest: string): Promise<void> {\n  return fetch(url).then(async (res) => {\n    if (!res.ok) throw new SenseError('EMBED_MODEL', `model download failed: ${url} -> HTTP ${res.status}`);\n    writeFileSync(`${dest}.part`, Buffer.from(await res.arrayBuffer()));\n    renameSync(`${dest}.part`, dest);\n  });\n}\n\n// The only code path that touches the network for weights. `sense download` calls it; no\n// query ever does. Idempotent: a file already on disk is left alone.\nexport async function downloadModel(model: string, onFile?: (file: string, dir: string) => void): Promise<string> {\n  if (!isDownloadable(model)) {\n    throw new SenseError('EMBED_MODEL', `embed.model \"${model}\" is a local path, not a Hugging Face model id, so there is nothing to download; put model.safetensors and tokenizer.json in that directory, or name a model id like \"minishlab/potion-retrieval-32M\"`);\n  }\n  const dir = modelDir(model);\n  mkdirSync(dir, { recursive: true });\n  for (const file of MODEL_FILES) {\n    if (existsSync(join(dir, file))) continue;\n    onFile?.(file, dir);\n    await fetchToFile(`https://huggingface.co/${model}/resolve/main/${file}`, join(dir, file));\n  }\n  return dir;\n}\n\nasync function staticProvider(model: string): Promise<EmbedProvider> {\n  const dir = modelDir(model);\n  for (const file of MODEL_FILES) {\n    if (!existsSync(join(dir, file))) {\n      // A local path the caller controls gets told what is missing where; only a repo id can\n      // be fixed by downloading.\n      const fix = isDownloadable(model) ? 'run `sense download`' : `expected ${MODEL_FILENAMES} in that directory`;\n      throw new SenseError('EMBED_MODEL_MISSING', `embed model ${model} is not available (looked in ${dir}); ${fix}`);\n    }\n  }\n\n  const raw = readFileSync(join(dir, 'model.safetensors'));\n  const headerLen = Number(raw.readBigUInt64LE(0));\n  const header = JSON.parse(raw.subarray(8, 8 + headerLen).toString('utf8')) as Record<string, { dtype: string; shape: number[]; data_offsets: number[] }>;\n  const entry = Object.entries(header).find(([k]) => k !== '__metadata__');\n  if (!entry || entry[1].dtype !== 'F32') throw new SenseError('EMBED_MODEL', `${model}: expected an F32 safetensors matrix`);\n  const spec = entry[1];\n  const dims = spec.shape[1];\n  const dataStart = raw.byteOffset + 8 + headerLen + spec.data_offsets[0];\n  const matrix = dataStart % 4 === 0 ? new Float32Array(raw.buffer, dataStart, spec.shape[0] * dims) : new Float32Array(raw.buffer.slice(dataStart, dataStart + spec.shape[0] * dims * 4));\n\n  const tokenizerJson = JSON.parse(readFileSync(join(dir, 'tokenizer.json'), 'utf8'));\n  // Lazy import: the tokenizer loads only on the semantic path, never at CLI startup.\n  const { Tokenizer } = await import('@huggingface/tokenizers');\n  const tok = new Tokenizer(tokenizerJson, {});\n  const unkId = tokenizerJson.model?.vocab?.[tokenizerJson.model?.unk_token] ?? -1;\n\n  function one(text: string): Float32Array {\n    // The tokenizer yields undefined (not the unk id) for tokens outside the vocab; an\n    // undefined id would index the matrix at NaN and poison the whole mean-pool -- and the\n    // int8 conversion then stores the NaN vector as all zeros, silently. Keep integers only.\n    const ids = (tok.encode(text, { add_special_tokens: false }).ids as number[]).filter((id) => Number.isInteger(id) && id !== unkId);\n    const v = new Float32Array(dims);\n    if (ids.length === 0) return v;\n    for (const id of ids) {\n      const off = id * dims;\n      for (let d = 0; d < dims; d++) v[d] += matrix[off + d];\n    }\n    let norm = 0;\n    for (let d = 0; d < dims; d++) {\n      v[d] /= ids.length;\n      norm += v[d] * v[d];\n    }\n    norm = Math.sqrt(norm) + 1e-32;\n    for (let d = 0; d < dims; d++) v[d] /= norm;\n    return v;\n  }\n\n  return { id: `static:${model}`, dims, embed: async (texts) => texts.map(one) };\n}\n\n// --- api type: one POST against any OpenAI-compatible /embeddings endpoint ---\n\nasync function apiProvider(model: string, url: string | undefined, keyEnv: string | undefined): Promise<EmbedProvider> {\n  if (!url) throw new SenseError('EMBED_MODEL', 'features.embed.type \"api\" requires a url');\n  const base = url.replace(/\\/+$/, '');\n  const headers: Record<string, string> = { 'content-type': 'application/json' };\n  const key = keyEnv ? process.env[keyEnv] : undefined;\n  if (key) headers.authorization = `Bearer ${key}`;\n\n  async function post(texts: string[]): Promise<Float32Array[]> {\n    const res = await fetch(`${base}/embeddings`, { method: 'POST', headers, body: JSON.stringify({ model, input: texts }) });\n    if (!res.ok) throw new SenseError('EMBED_MODEL', `${base}/embeddings -> HTTP ${res.status}`);\n    const body = (await res.json()) as { data: Array<{ embedding: number[] }> };\n    return body.data.map((d) => Float32Array.from(d.embedding));\n  }\n\n  const dims = (await post(['dimension probe']))[0].length;\n  return { id: `api:${base}:${model}`, dims, embed: post };\n}\n\nconst providers = new Map<string, Promise<EmbedProvider>>();\n\nfunction getProvider(cfg: Config): Promise<EmbedProvider> {\n  const e = embedConfig(cfg);\n  if (!e) throw new SenseError('EMBED_DISABLED', 'this tree has no embedding model: add an \"embed\" block naming one to sense.config.json, then run `sense download`');\n  const sig = `${e.type}:${e.model}:${e.url ?? ''}`;\n  let p = providers.get(sig);\n  if (!p) {\n    p = e.type === 'api' ? apiProvider(e.model, e.url, e.key) : staticProvider(e.model);\n    providers.set(sig, p);\n  }\n  return p;\n}\n\n// Slice + re-normalize (Matryoshka); optionally round through int8 storage.\nfunction toStore(full: Float32Array, dims: number, int8: boolean): { v: Float32Array; scale: number } {\n  const v = new Float32Array(dims);\n  let norm = 0;\n  for (let d = 0; d < dims; d++) norm += full[d] * full[d];\n  norm = Math.sqrt(norm) + 1e-32;\n  for (let d = 0; d < dims; d++) v[d] = full[d] / norm;\n  if (!int8) return { v, scale: 1 };\n  let max = 0;\n  for (let d = 0; d < dims; d++) max = Math.max(max, Math.abs(v[d]));\n  return { v, scale: max / 127 || 1 };\n}\n\n// Embed rows whose vector is NULL, re-deriving chunk text from the files through the\n// same parse + chunker that stored the rows.\nexport async function embedPending(db: DatabaseSync, cfg: Config, baseDir: string): Promise<void> {\n  const provider = await getProvider(cfg); // throws EMBED_DISABLED before touching the table\n  const dirty = db.prepare('SELECT \"path\", chunk FROM embeddings WHERE vector IS NULL ORDER BY \"path\", chunk').all() as Array<{ path: string; chunk: number }>;\n  if (dirty.length === 0) return;\n  const storeDims = Math.min(STORE_DIMS, provider.dims);\n\n  const byPath = new Map<string, number[]>();\n  for (const row of dirty) {\n    const list = byPath.get(row.path) ?? [];\n    list.push(row.chunk);\n    byPath.set(row.path, list);\n  }\n\n  const jobs: Array<{ path: string; chunk: number; text: string }> = [];\n  for (const [path, chunkIdxs] of byPath) {\n    let chunks: Chunk[];\n    try {\n      // presets/embed are irrelevant here -- re-deriving chunk text for a doc that already\n      // has embeddings rows means the tree had an embedding model at reconcile time.\n      chunks = parseFile({ relPath: path, absPath: join(baseDir, path), mtimeMs: 0, size: 0, presets: [], embed: true }, [embed]).doc.extracted.embed as Chunk[];\n    } catch {\n      continue; // vanished since reconcile; the next reconcile removes its rows\n    }\n    for (const idx of chunkIdxs) if (chunks[idx]) jobs.push({ path, chunk: idx, text: chunks[idx].text });\n  }\n\n  const update = db.prepare('UPDATE embeddings SET scale = ?, vector = ? WHERE \"path\" = ? AND chunk = ?');\n  // The lazy build is the one long silence a first search hits (measured 23s at\n  // 26k notes); progress makes it distinguishable from a hang.\n  const report = progress('embedding chunks', jobs.length);\n  for (let i = 0; i < jobs.length; i += BATCH) {\n    const batch = jobs.slice(i, i + BATCH);\n    const vectors = await provider.embed(batch.map((j) => j.text));\n    db.exec('BEGIN');\n    try {\n      batch.forEach((job, j) => {\n        const { v, scale } = toStore(vectors[j], storeDims, true);\n        const q = new Int8Array(storeDims);\n        for (let d = 0; d < storeDims; d++) q[d] = Math.round(v[d] / scale);\n        update.run(scale, Buffer.from(q.buffer), job.path, job.chunk);\n      });\n      db.exec('COMMIT');\n    } catch (err) {\n      db.exec('ROLLBACK');\n      throw err;\n    }\n    report.tick(Math.min(i + BATCH, jobs.length));\n  }\n  report.finish();\n}\n\n// Dequantised int8 dot products land a little either side of a true cosine, so an identical\n// pair prints 1.001 and undermines a column whose whole job is being a bounded number.\nfunction asCosine(score: number): number {\n  return Math.round(Math.min(1, Math.max(-1, score)) * 1000) / 1000;\n}\n\n// Best chunk per file by cosine, its line range riding along; FTS5 operators are stripped as\n// lexical syntax. Similarity comes back because the fused score cannot express match quality,\n// and nearest-neighbour search always returns a neighbour however far away.\nexport async function semanticCandidates(db: DatabaseSync, cfg: Config, terms: string, fetch: number): Promise<Array<{ path: string; lines: string; similarity: number }>> {\n  const baseDir = (cfg as Partial<ResolvedConfig>).baseDir;\n  if (!baseDir) throw new SenseError('EMBED_MODEL', 'semantic expansion needs a config with baseDir (use loadConfig/open)');\n  await embedPending(db, cfg, baseDir);\n\n  const provider = await getProvider(cfg);\n  const storeDims = Math.min(STORE_DIMS, provider.dims);\n  const text = (terms.match(/[\\p{L}\\p{N}]+/gu) ?? []).filter((t) => !['AND', 'OR', 'NOT', 'NEAR'].includes(t)).join(' ');\n  const { v: qv } = toStore((await provider.embed([text]))[0], storeDims, false);\n\n  const rows = db.prepare('SELECT \"path\", start_line, end_line, scale, vector FROM embeddings WHERE vector IS NOT NULL').all() as Array<{\n    path: string;\n    start_line: number;\n    end_line: number;\n    scale: number;\n    vector: Uint8Array;\n  }>;\n\n  const best = new Map<string, { score: number; lines: string }>();\n  for (const row of rows) {\n    const q = new Int8Array(row.vector.buffer, row.vector.byteOffset, Math.min(storeDims, row.vector.byteLength));\n    let dot = 0;\n    for (let d = 0; d < q.length; d++) dot += q[d] * qv[d];\n    const score = dot * row.scale;\n    const existing = best.get(row.path);\n    if (!existing || score > existing.score) best.set(row.path, { score, lines: `L${row.start_line}-${row.end_line}` });\n  }\n  return [...best.entries()]\n    .sort((a, b) => b[1].score - a[1].score)\n    .slice(0, fetch)\n    .map(([path, b]) => ({ path, lines: b.lines, similarity: asCosine(b.score) }));\n}\n\n// Whether a note has any chunk with a vector. Distinguishes \"nothing is near this note\" from\n// \"this note has no text\", which look the same in an empty result.\nexport function hasEmbedding(db: DatabaseSync, path: string): boolean {\n  const row = db.prepare('SELECT 1 AS ok FROM embeddings WHERE \"path\" = ? AND vector IS NOT NULL LIMIT 1').get(path) as { ok: number } | undefined;\n  return row !== undefined;\n}\n\n// Note-to-note similarity is the max cosine over (target chunk, other chunk) pairs, one linear\n// scan of stored vectors. Reads only what is stored, so it stays sync.\nexport function similarNotes(db: DatabaseSync, _cfg: Config, path: string, opts: { exclude: Set<string>; allowed?: Set<string>; k: number }): Array<{ path: string; similarity: number }> {\n  // Cost is target_chunks x stored_chunks, so a heading-dense seed multiplies a full-corpus\n  // scan (12.7s at 201 chunks/note). Sample evenly, so late sections still get a vote.\n  const targetRows = db.prepare('SELECT scale, vector FROM embeddings WHERE \"path\" = ? AND vector IS NOT NULL ORDER BY chunk').all(path) as Array<{ scale: number; vector: Uint8Array }>;\n  if (targetRows.length === 0) return [];\n  const step = Math.max(1, Math.ceil(targetRows.length / TARGET_CHUNK_CAP));\n  const target = targetRows.filter((_, i) => i % step === 0).map((row) => ({ v: new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength), scale: row.scale }));\n\n  const rows = db.prepare('SELECT \"path\", scale, vector FROM embeddings WHERE vector IS NOT NULL').all() as Array<{ path: string; scale: number; vector: Uint8Array }>;\n  const best = new Map<string, number>();\n  for (const row of rows) {\n    if (row.path === path || opts.exclude.has(row.path) || (opts.allowed && !opts.allowed.has(row.path))) continue;\n    const other = new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength);\n    for (const t of target) {\n      let dot = 0;\n      const len = Math.min(t.v.length, other.length);\n      for (let d = 0; d < len; d++) dot += t.v[d] * other[d];\n      const score = dot * t.scale * row.scale;\n      const existing = best.get(row.path);\n      if (existing === undefined || score > existing) best.set(row.path, score);\n    }\n  }\n\n  return [...best.entries()]\n    .sort((a, b) => b[1] - a[1])\n    .slice(0, opts.k)\n    .map(([p, score]) => ({ path: p, similarity: asCosine(score) 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Queries stay f32 at the same dims.\nconst STORE_DIMS = 256;\n// Seed chunks that participate in a `related` scan; see similarNotes for the measurement.\nconst TARGET_CHUNK_CAP = 16;\nconst BATCH = 64;\n\nexport interface EmbedProvider {\n  id: string; // model identity; participates in the cache key, change -> re-embed\n  dims: number;\n  embed(texts: string[]): Promise<Float32Array[]>;\n}\n\ninterface Chunk {\n  startLine: number;\n  endLine: number;\n  text: string;\n}\n\n// Deterministic, so embed time can re-derive text from stored line ranges. Heading-delimited,\n// preamble kept, whole body when no headings; the title/summary prefix mirrors bm25 weighting.\n//\n// Chunks the body, not the raw file, with `offset` shifting line numbers back onto the raw\n// file so a range stays a direct Read range (sections is 1-indexed over raw too). Chunking raw\n// put the frontmatter block in its own leading chunk on every note with a heading, which made\n// `lines` point at YAML and made frontmatter-only notes near-identical to each other. It also\n// disagreed with FTS, which indexes the body alone.\nfunction chunksOf(body: string, search?: { title: string; summary: string }, offset = 0): Chunk[] {\n  const lines = body.split('\\n');\n  const starts: number[] = [];\n  let inFence = false;\n  for (let i = 0; i < lines.length; i++) {\n    if (/^(```|~~~)/.test(lines[i])) {\n      inFence = !inFence;\n      continue;\n    }\n    if (!inFence && /^#{1,6} +/.test(lines[i])) starts.push(i + 1);\n  }\n  const bounds = starts.length === 0 ? [1] : starts[0] > 1 ? [1, ...starts] : starts;\n  const prefix = [search?.title, search?.summary].filter(Boolean).join('\\n');\n  const chunks: Chunk[] = [];\n  bounds.forEach((start, i) => {\n    const end = i + 1 < bounds.length ? bounds[i + 1] - 1 : lines.length;\n    const text = lines\n      .slice(start - 1, end)\n      .join('\\n')\n      .trim();\n    // A body with nothing in it yields no chunks at all, so a frontmatter-only note has no\n    // vectors rather than a vector of its own YAML.\n    if (text.length > 0) chunks.push({ startLine: start + offset, endLine: end + offset, text: prefix ? `${prefix}\\n${text}` : text });\n  });\n  return chunks;\n}\n\nexport const embed: Feature = {\n  name: 'embed',\n  schema(db) {\n    db.exec(`CREATE TABLE IF NOT EXISTS embeddings (\"path\" TEXT, chunk INTEGER, start_line INTEGER, end_line INTEGER, scale REAL, vector BLOB, PRIMARY KEY (\"path\", chunk))`);\n  },\n  extract(raw, body, search) {\n    // Lines the frontmatter occupies, so body line 1 maps back to its raw line number.\n    return chunksOf(body, search, raw.split('\\n').length - body.split('\\n').length);\n  },\n  remove(db, path) {\n    db.prepare('DELETE FROM embeddings WHERE \"path\" = ?').run(path);\n  },\n  // A tree with no embedding model never had extract() run for the doc (db.ts's per-file\n  // filter skips it), so extracted is undefined here -- store nothing, i.e. no rows.\n  store(db, path, extracted) {\n    if (!extracted) return;\n    const insert = db.prepare('INSERT INTO embeddings (\"path\", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)');\n    (extracted as Chunk[]).forEach((c, idx) => insert.run(path, idx, c.startLine, c.endLine));\n  },\n  enabledForFile(_cfg, file) {\n    return file.embed;\n  },\n};\n\n// --- static type: Model2Vec safetensors + pure-JS tokenizer, model cached in ~/.cache ---\n// Encode convention from model2vec/model.py: no special tokens, drop unk ids, mean-pool,\n// L2-normalize.\n\nconst MODEL_FILES = ['model.safetensors', 'tokenizer.json'];\n// The pair, for messages that name what a local model directory must contain.\nexport const MODEL_FILENAMES = MODEL_FILES.join(' and ');\n\n// A Hugging Face repo id: one slash, HF's charset. Anything else is a path, used as one rather\n// than flattened into a cache key Windows would reject.\nconst HF_MODEL_ID = /^[A-Za-z0-9][\\w.-]*\\/[A-Za-z0-9][\\w.-]*$/;\n\n// Downloadable iff it names a Hugging Face repo; a local path is the caller's to populate.\nexport function isDownloadable(model: string): boolean {\n  return HF_MODEL_ID.test(model);\n}\n\n// Machine-wide, not per-tree: `.sense/` is the index a rebuild throws away, while a 124 MB\n// model is shared by every tree on the machine. Honors XDG_CACHE_HOME where it is set;\n// elsewhere ~/.cache, which is also where Hugging Face's own libraries keep theirs.\nfunction cacheRoot(): string {\n  const xdg = process.env.XDG_CACHE_HOME;\n  return join(xdg && xdg.length > 0 ? xdg : join(homedir(), '.cache'), 'sensemaking', 'models');\n}\n\n// A model is either a local directory the caller pointed at, or the cache `sense download`\n// fills. Nothing here fetches: an absent model degrades search to its other signals rather\n// than pulling 124 MB out of a command that reads like a query.\nexport function modelDir(model: string): string {\n  if (!HF_MODEL_ID.test(model)) return model;\n  return join(cacheRoot(), model.replace(/\\//g, '--'));\n}\n\n// Both files, so an interrupted download reads as absent and the next one resumes it.\nexport function hasModelFiles(model: string): boolean {\n  const dir = modelDir(model);\n  return MODEL_FILES.every((file) => existsSync(join(dir, file)));\n}\n\n// api providers have nothing to download, so they are never \"missing\" here; an unreachable\n// endpoint surfaces as an EMBED_MODEL error at call time instead.\nexport function modelPresent(cfg: Config): boolean {\n  const e = embedConfig(cfg);\n  if (!e) return false;\n  return e.type === 'api' || hasModelFiles(e.model);\n}\n\nfunction fetchToFile(url: string, dest: string): Promise<void> {\n  return fetch(url).then(async (res) => {\n    if (!res.ok) throw new SenseError('EMBED_MODEL', `model download failed: ${url} -> HTTP ${res.status}`);\n    writeFileSync(`${dest}.part`, Buffer.from(await res.arrayBuffer()));\n    renameSync(`${dest}.part`, dest);\n  });\n}\n\n// The only code path that touches the network for weights. `sense download` calls it; no\n// query ever does. Idempotent: a file already on disk is left alone.\nexport async function downloadModel(model: string, onFile?: (file: string, dir: string) => void): Promise<string> {\n  if (!isDownloadable(model)) {\n    throw new SenseError('EMBED_MODEL', `embed.model \"${model}\" is a local path, not a Hugging Face model id, so there is nothing to download; put model.safetensors and tokenizer.json in that directory, or name a model id like \"minishlab/potion-retrieval-32M\"`);\n  }\n  const dir = modelDir(model);\n  mkdirSync(dir, { recursive: true });\n  for (const file of MODEL_FILES) {\n    if (existsSync(join(dir, file))) continue;\n    onFile?.(file, dir);\n    await fetchToFile(`https://huggingface.co/${model}/resolve/main/${file}`, join(dir, file));\n  }\n  return dir;\n}\n\nasync function staticProvider(model: string): Promise<EmbedProvider> {\n  const dir = modelDir(model);\n  for (const file of MODEL_FILES) {\n    if (!existsSync(join(dir, file))) {\n      // A local path the caller controls gets told what is missing where; only a repo id can\n      // be fixed by downloading.\n      const fix = isDownloadable(model) ? 'run `sense download`' : `expected ${MODEL_FILENAMES} in that directory`;\n      throw new SenseError('EMBED_MODEL_MISSING', `embed model ${model} is not available (looked in ${dir}); ${fix}`);\n    }\n  }\n\n  const raw = readFileSync(join(dir, 'model.safetensors'));\n  const headerLen = Number(raw.readBigUInt64LE(0));\n  const header = JSON.parse(raw.subarray(8, 8 + headerLen).toString('utf8')) as Record<string, { dtype: string; shape: number[]; data_offsets: number[] }>;\n  const entry = Object.entries(header).find(([k]) => k !== '__metadata__');\n  if (!entry || entry[1].dtype !== 'F32') throw new SenseError('EMBED_MODEL', `${model}: expected an F32 safetensors matrix`);\n  const spec = entry[1];\n  const dims = spec.shape[1];\n  const dataStart = raw.byteOffset + 8 + headerLen + spec.data_offsets[0];\n  const matrix = dataStart % 4 === 0 ? new Float32Array(raw.buffer, dataStart, spec.shape[0] * dims) : new Float32Array(raw.buffer.slice(dataStart, dataStart + spec.shape[0] * dims * 4));\n\n  const tokenizerJson = JSON.parse(readFileSync(join(dir, 'tokenizer.json'), 'utf8'));\n  // Lazy import: the tokenizer loads only on the semantic path, never at CLI startup.\n  const { Tokenizer } = await import('@huggingface/tokenizers');\n  const tok = new Tokenizer(tokenizerJson, {});\n  const unkId = tokenizerJson.model?.vocab?.[tokenizerJson.model?.unk_token] ?? -1;\n\n  function one(text: string): Float32Array {\n    // The tokenizer yields undefined (not the unk id) for tokens outside the vocab; an\n    // undefined id would index the matrix at NaN and poison the whole mean-pool -- and the\n    // int8 conversion then stores the NaN vector as all zeros, silently. Keep integers only.\n    const ids = (tok.encode(text, { add_special_tokens: false }).ids as number[]).filter((id) => Number.isInteger(id) && id !== unkId);\n    const v = new Float32Array(dims);\n    if (ids.length === 0) return v;\n    for (const id of ids) {\n      const off = id * dims;\n      for (let d = 0; d < dims; d++) v[d] += matrix[off + d];\n    }\n    let norm = 0;\n    for (let d = 0; d < dims; d++) {\n      v[d] /= ids.length;\n      norm += v[d] * v[d];\n    }\n    norm = Math.sqrt(norm) + 1e-32;\n    for (let d = 0; d < dims; d++) v[d] /= norm;\n    return v;\n  }\n\n  return { id: `static:${model}`, dims, embed: async (texts) => texts.map(one) };\n}\n\n// --- api type: one POST against any OpenAI-compatible /embeddings endpoint ---\n\nasync function apiProvider(model: string, url: string | undefined, keyEnv: string | undefined): Promise<EmbedProvider> {\n  if (!url) throw new SenseError('EMBED_MODEL', 'features.embed.type \"api\" requires a url');\n  const base = url.replace(/\\/+$/, '');\n  const headers: Record<string, string> = { 'content-type': 'application/json' };\n  const key = keyEnv ? process.env[keyEnv] : undefined;\n  if (key) headers.authorization = `Bearer ${key}`;\n\n  async function post(texts: string[]): Promise<Float32Array[]> {\n    const res = await fetch(`${base}/embeddings`, { method: 'POST', headers, body: JSON.stringify({ model, input: texts }) });\n    if (!res.ok) throw new SenseError('EMBED_MODEL', `${base}/embeddings -> HTTP ${res.status}`);\n    const body = (await res.json()) as { data: Array<{ embedding: number[] }> };\n    return body.data.map((d) => Float32Array.from(d.embedding));\n  }\n\n  const dims = (await post(['dimension probe']))[0].length;\n  return { id: `api:${base}:${model}`, dims, embed: post };\n}\n\nconst providers = new Map<string, Promise<EmbedProvider>>();\n\nfunction getProvider(cfg: Config): Promise<EmbedProvider> {\n  const e = embedConfig(cfg);\n  if (!e) throw new SenseError('EMBED_DISABLED', 'this tree has no embedding model: add an \"embed\" block naming one to sense.config.json, then run `sense download`');\n  const sig = `${e.type}:${e.model}:${e.url ?? ''}`;\n  let p = providers.get(sig);\n  if (!p) {\n    p = e.type === 'api' ? apiProvider(e.model, e.url, e.key) : staticProvider(e.model);\n    providers.set(sig, p);\n  }\n  return p;\n}\n\n// Slice + re-normalize (Matryoshka); optionally round through int8 storage.\nfunction toStore(full: Float32Array, dims: number, int8: boolean): { v: Float32Array; scale: number } {\n  const v = new Float32Array(dims);\n  let norm = 0;\n  for (let d = 0; d < dims; d++) norm += full[d] * full[d];\n  norm = Math.sqrt(norm) + 1e-32;\n  for (let d = 0; d < dims; d++) v[d] = full[d] / norm;\n  if (!int8) return { v, scale: 1 };\n  let max = 0;\n  for (let d = 0; d < dims; d++) max = Math.max(max, Math.abs(v[d]));\n  return { v, scale: max / 127 || 1 };\n}\n\n// Embed rows whose vector is NULL, re-deriving chunk text from the files through the\n// same parse + chunker that stored the rows.\nexport async function embedPending(db: DatabaseSync, cfg: Config, baseDir: string): Promise<void> {\n  const provider = await getProvider(cfg); // throws EMBED_DISABLED before touching the table\n  const dirty = db.prepare('SELECT \"path\", chunk FROM embeddings WHERE vector IS NULL ORDER BY \"path\", chunk').all() as Array<{ path: string; chunk: number }>;\n  if (dirty.length === 0) return;\n  const storeDims = Math.min(STORE_DIMS, provider.dims);\n\n  const byPath = new Map<string, number[]>();\n  for (const row of dirty) {\n    const list = byPath.get(row.path) ?? [];\n    list.push(row.chunk);\n    byPath.set(row.path, list);\n  }\n\n  const jobs: Array<{ path: string; chunk: number; text: string }> = [];\n  for (const [path, chunkIdxs] of byPath) {\n    let chunks: Chunk[];\n    try {\n      // presets/embed are irrelevant here -- re-deriving chunk text for a doc that already\n      // has embeddings rows means the tree had an embedding model at reconcile time.\n      chunks = parseFile({ relPath: path, absPath: join(baseDir, path), mtimeMs: 0, size: 0, presets: [], embed: true }, [embed]).doc.extracted.embed as Chunk[];\n    } catch {\n      continue; // vanished since reconcile; the next reconcile removes its rows\n    }\n    for (const idx of chunkIdxs) if (chunks[idx]) jobs.push({ path, chunk: idx, text: chunks[idx].text });\n  }\n\n  const update = db.prepare('UPDATE embeddings SET scale = ?, vector = ? WHERE \"path\" = ? AND chunk = ?');\n  // The lazy build is the one long silence a first search hits (measured 23s at\n  // 26k notes); progress makes it distinguishable from a hang.\n  const report = progress('embedding chunks', jobs.length);\n  for (let i = 0; i < jobs.length; i += BATCH) {\n    const batch = jobs.slice(i, i + BATCH);\n    const vectors = await provider.embed(batch.map((j) => j.text));\n    db.exec('BEGIN');\n    try {\n      batch.forEach((job, j) => {\n        const { v, scale } = toStore(vectors[j], storeDims, true);\n        const q = new Int8Array(storeDims);\n        for (let d = 0; d < storeDims; d++) q[d] = Math.round(v[d] / scale);\n        update.run(scale, Buffer.from(q.buffer), job.path, job.chunk);\n      });\n      db.exec('COMMIT');\n    } catch (err) {\n      db.exec('ROLLBACK');\n      throw err;\n    }\n    report.tick(Math.min(i + BATCH, jobs.length));\n  }\n  report.finish();\n}\n\n// Dequantised int8 dot products land a little either side of a true cosine, so an identical\n// pair prints 1.001 and undermines a column whose whole job is being a bounded number.\nfunction asCosine(score: number): number {\n  return Math.round(Math.min(1, Math.max(-1, score)) * 1000) / 1000;\n}\n\n// Best chunk per file by cosine, its line range riding along; FTS5 operators are stripped as\n// lexical syntax. 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package/dist/cjs/index.d.cts

@@ -6,7 +6,7 @@ export type { OpenResult } from './db.js';
 export { clearCache, open } from './db.js';
 export type { SenseErrorCode } from './errors.js';
 export { SenseError } from './errors.js';
-export type { Row } from './output.js';
+export type { Format, Row, RowFormat } from './output.js';
 export { printRows } from './output.js';
 export type { WatchEvent, WatchOptions } from './watch.js';
 export { runWatch } from './watch.js';

package/dist/cjs/index.d.ts

@@ -6,7 +6,7 @@ export type { OpenResult } from './db.js';
 export { clearCache, open } from './db.js';
 export type { SenseErrorCode } from './errors.js';
 export { SenseError } from './errors.js';
-export type { Row } from './output.js';
+export type { Format, Row, RowFormat } from './output.js';
 export { printRows } from './output.js';
 export type { WatchEvent, WatchOptions } from './watch.js';
 export { runWatch } from './watch.js';

package/dist/cjs/index.js.map

@@ -1 +1 @@
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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/index.ts"],"sourcesContent":["// Public library API. Deliberately small: every export is a stability promise;\n// internals (feature registry, graph, scan, meta) stay module-private.\n\nexport type { Peek, PresetCoverage, SearchOptions, TreeMap } from './commands.ts';\nexport { mapTree, peek, presetCoverage, search } from './commands.ts';\nexport type { Config, EmbedConfig, FeatureName, Preset, ResolvedConfig, SavedQuery, SavedSearch, SearchOverrides } from './config.ts';\nexport { CONFIG_FILENAME, initConfig, loadConfig, migrateConfig, STATE_DIR, SUPPORTED_CONFIG_VERSION } from './config.ts';\nexport type { OpenResult } from './db.ts';\nexport { clearCache, open } from './db.ts';\nexport type { SenseErrorCode } from './errors.ts';\nexport { SenseError } from './errors.ts';\nexport type { Format, Row, RowFormat } from './output.ts';\nexport { printRows } from './output.ts';\n\nexport type { WatchEvent, WatchOptions } from './watch.ts';\nexport { runWatch } from './watch.ts';\n"],"names":["CONFIG_FILENAME","STATE_DIR","SUPPORTED_CONFIG_VERSION","SenseError","clearCache","initConfig","loadConfig","mapTree","migrateConfig","open","peek","presetCoverage","printRows","runWatch","search"],"mappings":"AAAA,+EAA+E;AAC/E,uEAAuE;;;;;;;;;;;;QAK9DA;eAAAA,yBAAe;;QAAyCC;eAAAA,mBAAS;;QAAEC;eAAAA,kCAAwB;;QAI3FC;eAAAA,oBAAU;;QAFVC;eAAAA,gBAAU;;QAFOC;eAAAA,oBAAU;;QAAEC;eAAAA,oBAAU;;QAFvCC;eAAAA,mBAAO;;QAEkCC;eAAAA,uBAAa;;QAE1CC;eAAAA,UAAI;;QAJPC;eAAAA,gBAAI;;QAAEC;eAAAA,0BAAc;;QAQ7BC;eAAAA,mBAAS;;QAGTC;eAAAA,iBAAQ;;QAXuBC;eAAAA,kBAAM;;;0BAAQ;wBAEsD;oBAE3E;wBAEN;wBAED;uBAGD"}

package/dist/cjs/output.d.cts

@@ -33,6 +33,7 @@ export declare function renderMap(result: {
     }>;
     hubs: Row[];
     recent: Row[];
+    recentCaveat: string | null;
 }): string;
 export declare function renderPeek(result: {
     path: string;

package/dist/cjs/output.d.ts

@@ -33,6 +33,7 @@ export declare function renderMap(result: {
     }>;
     hubs: Row[];
     recent: Row[];
+    recentCaveat: string | null;
 }): string;
 export declare function renderPeek(result: {
     path: string;

package/dist/cjs/output.js

@@ -334,7 +334,9 @@ function renderMap(result) {
     if (result.fieldsTotal > result.fields.length) parts.push("(+".concat(result.fieldsTotal - result.fields.length, " more fields)"));
     if (result.hubs.length > 0) parts.push('\nhubs (by link rank):', renderRows(result.hubs, 'table'));
     else if (result.features.off.includes('rank')) parts.push("\nhubs: off (".concat(featureOffHint('rank'), ")"));
-    parts.push('\nrecent:', renderRows(result.recent, 'table'));
+    parts.push('\nrecent:');
+    if (result.recentCaveat) parts.push(result.recentCaveat);
+    parts.push(renderRows(result.recent, 'table'));
     return parts.join('\n');
 }
 function renderPeek(result) {

package/dist/cjs/output.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/output.ts"],"sourcesContent":["// rows -> table (default) | json | csv\n\nexport type Row = Record<string, unknown>;\n\n// map/peek/status/path render structures rather than a row set, so csv has nothing to mean\n// there; the commands that emit rows take RowFormat.\nexport type Format = 'table' | 'json';\nexport type RowFormat = Format | 'csv';\n\n// Warned about on stderr (keeps --format json stdout machine-readable), never truncated.\nconst OVERSIZE_BYTES = 50_000;\n\n// Flatten embedded newlines so they can't break table column alignment; JSON output is left alone.\nfunction cell(value: unknown): string {\n  return String(value ?? '').replace(/\\s*\\n\\s*/g, ' ');\n}\n\n// RFC 4180, and deliberately not cell(): csv is the format for redirecting a result to a\n// file, so it keeps every character, embedded newlines included. What it cannot carry is\n// NULL vs empty string, or a value's type -- that is what json is for.\nfunction csvField(value: unknown): string {\n  const text = value === null || value === undefined ? 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Object.keys(rows[0]) : [...new Set(columns ?? [])];\n    if (names.length === 0) return;\n    const rendered = [csvLine(names), ...rows.map((row) => csvLine(names.map((name) => row[name])))].join('\\n');\n    console.log(rendered);\n    // Bytes, not code units -- CJK is 3 bytes per character.\n    warnOversize(Buffer.byteLength(rendered), rows.length);\n    return;\n  }\n  const rendered = renderRows(rows, format);\n  console.log(rendered);\n  warnOversize(Buffer.byteLength(rendered), rows.length);\n}\n\n// Streaming counterpart for the one unbounded caller, `sense sql`: rows arrive from an\n// iterator, so a large result is never held here as rows and again as a rendered string.\n// Table buffers by necessity (a column is as wide as its widest cell, which the last row can\n// change); json and csv write row by row. 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package/dist/esm/commands.d.ts

@@ -32,6 +32,7 @@ export interface TreeMap {
     presets: PresetCoverage[];
     hubs: Row[];
     recent: Row[];
+    recentCaveat: string | null;
 }
 export declare function mapTree(db: DatabaseSync, cfg: ResolvedConfig, overrides?: SearchOverrides): TreeMap;
 export declare function resolveNote(paths: string[], arg: string): string;

package/dist/esm/commands.js

@@ -127,24 +127,27 @@ function scopeHasEmbeddings(db, cfg, scopedPaths) {
 export async function search(db, cfg, terms, opts = {}) {
     var _hits_get, _chunkLines_get, _chunkSimilarity_get;
     const effective = resolveSearch(cfg, opts);
-    const { k, include, exclude } = effective;
+    const { k } = effective;
     const allPaths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
-    // A preset scope reads the coverage reconcile indexed; re-matching globs here could disagree
-    // with it. Only ad-hoc scope flags, which have no persisted coverage, pay the JS match.
-    const adHocScope = opts.include !== undefined || opts.exclude !== undefined || opts.noExclude === true;
-    const scopedPaths = adHocScope ? new Set(allPaths.filter((p)=>inScope(p, include, exclude))) : new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
-    // A scope narrower than the whole index needs a bigger candidate pool before filtering, or
-    // filtering can starve k even though enough in-scope matches exist further down the ranked
-    // list that a plain over-fetch wouldn't have reached.
-    const scopeActive = scopedPaths.size < allPaths.length;
-    const fetch = scopeActive ? Math.max(k * 5, 50) : Math.max(k * 3, 30);
+    const scopePaths = rawScope(db, cfg, opts, allPaths);
+    const scopeActive = scopePaths.size < allPaths.length;
+    // The set every candidate pool must be filtered to before truncation: scope narrowed by
+    // --where, the same composition scopedPaths() gives the other commands. Runs the same where
+    // fragment matchSql does, so a bad column gets the same attributed error either way.
+    let allowedPaths;
+    try {
+        allowedPaths = narrowByWhere(db, scopePaths, effective.where);
+    } catch (err) {
+        throw searchError(err, terms, effective.where);
+    }
+    const fetch = Math.max(k * 3, 30);
     // Asking for vectors without a model is a misconfiguration, not a mode: degrading would make
     // the same search answer differently before and after a download. semantic:false never asks.
     const wantsVectors = effective.semantic && anyPresetEmbeds(cfg);
     if (wantsVectors && !modelPresent(cfg)) {
         throw new SenseError('EMBED_MODEL_MISSING', `preset "${effective.presetName}" searches with vectors, but the embedding model is not available; run \`sense download\`, or set "semantic": false on that preset to search on words and links`);
     }
-    const semanticEnabled = wantsVectors && scopeHasEmbeddings(db, cfg, scopedPaths);
+    const semanticEnabled = wantsVectors && scopeHasEmbeddings(db, cfg, allowedPaths);
     // Terms pass to MATCH as written, with one transform: a run of text whose language marks no
     // word boundaries becomes a quoted grapheme phrase (and a title:/summary:/text: qualifier
     // ahead of it retargets its _seg column), matching how it was indexed. Text that already
@@ -158,12 +161,18 @@ export async function search(db, cfg, terms, opts = {}) {
     const scope = effective.where;
     const whereJoin = scope ? `JOIN frontmatter f ON f."path" = content.path` : '';
     const whereCond = scope ? `AND (${scope})` : '';
+    // A scope narrower than the whole index must filter the candidate pool before LIMIT, not
+    // after -- otherwise scoped notes ranking below the global top-`fetch` never reach the
+    // filter. A join against a temp table, not a bound parameter list: real scopes run to
+    // thousands of paths, past SQLITE_MAX_VARIABLE_NUMBER on older builds.
+    if (scopeActive) materializeScope(db, '_search_scope', scopePaths);
+    const scopeCond = scopeActive ? `AND content.path IN (SELECT "path" FROM _search_scope)` : '';
     // Docs past SNIPPET_BOUND skip snippet() entirely -- SQLite
     // short-circuits the untaken CASE branch, so it's never invoked on them.
     // Column 2 (text), not -1 (best column): -1 could surface a _seg sidecar as the excerpt,
     // which is machine-spaced and not what the author wrote. A row that matches only in a
     // sidecar gets an unhighlighted text excerpt below instead -- a stated cost.
-    const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, 2, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;
+    const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, 2, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ${scopeCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;
     const query = contentTokenize(cfg) === undefined ? segmentMatch(terms) : terms;
     let matchRows;
     try {
@@ -171,10 +180,6 @@ export async function search(db, cfg, terms, opts = {}) {
     } catch (err) {
         throw searchError(err, terms, scope);
     }
-    // Scope filtering happens in JS, on each candidate list, rather than in SQL: FTS5 match,
-    // link expansion, and vector search all run unscoped above (cheap to over-fetch), then get
-    // filtered here against the effective include/exclude before ranking is finalized.
-    matchRows = matchRows.filter((r)=>scopedPaths.has(r.path));
     const hits = new Map(matchRows.map((r)=>[
             r.path,
             r.hit
@@ -200,7 +205,7 @@ export async function search(db, cfg, terms, opts = {}) {
             ]));
         const ranked = [
             ...personalizedRank(allPaths, edges, seeds)
-        ].filter(([path, score])=>score > 1e-9 && scopedPaths.has(path)).sort((a, b)=>b[1] - a[1]).slice(0, fetch);
+        ].filter(([path, score])=>score > 1e-9 && allowedPaths.has(path)).sort((a, b)=>b[1] - a[1]).slice(0, fetch);
         ranked.forEach(([path], i)=>{
             const existing = candidates.get(path);
             if (existing) {
@@ -219,7 +224,7 @@ export async function search(db, cfg, terms, opts = {}) {
     const chunkLines = new Map();
     const chunkSimilarity = new Map();
     if (semanticEnabled) {
-        const vec = (await semanticCandidates(db, cfg, terms, fetch)).filter((v)=>scopedPaths.has(v.path));
+        const vec = await semanticCandidates(db, cfg, terms, fetch, allowedPaths);
         vec.forEach(({ path, lines, similarity }, i)=>{
             chunkLines.set(path, lines);
             chunkSimilarity.set(path, similarity);
@@ -239,8 +244,9 @@ export async function search(db, cfg, terms, opts = {}) {
     db.exec('CREATE TEMP TABLE _search ("path" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');
     const insert = db.prepare('INSERT INTO _search ("path", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');
     for (const [path, c] of candidates)insert.run(path, c.score, c.via, (_hits_get = hits.get(path)) !== null && _hits_get !== void 0 ? _hits_get : null, (_chunkLines_get = chunkLines.get(path)) !== null && _chunkLines_get !== void 0 ? _chunkLines_get : null, (_chunkSimilarity_get = chunkSimilarity.get(path)) !== null && _chunkSimilarity_get !== void 0 ? _chunkSimilarity_get : null);
-    // Already scope-filtered above; the final select reapplies --where only for link-derived
-    // rows, which never passed through whereCond.
+    // All three candidate paths (match, link, vector) already filtered to scope+where before
+    // reaching _search; this reapplies --where anyway since the join to frontmatter is already
+    // needed for the path column.
     const where = scope ? `WHERE (${scope})` : '';
     // lines is always present now: semantic rows carry their chunk's range, oversized-doc
     // lexical rows gain one below, everything else stays null. similarity stays semantic-only.
@@ -265,15 +271,18 @@ export async function search(db, cfg, terms, opts = {}) {
     }
     return rows;
 }
-// The scope resolver for non-search commands (path, peek, map): same coverage rule search()
-// applies (preset_files for a named preset, JS glob matching for an ad hoc include/exclude),
-// then narrowed by the resolved `where`.
-export function scopedPaths(db, cfg, overrides) {
+// Scope only (no --where): preset_files for a named preset, JS glob matching for an ad hoc
+// include/exclude override. Shared by scopedPaths() and search(), which also needs the
+// pre-where set to size the candidate-pool filter.
+function rawScope(db, cfg, overrides, allPaths) {
     const effective = resolveSearch(cfg, overrides);
-    const { include, exclude, where } = effective;
-    const allPaths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
+    const { include, exclude } = effective;
     const adHocScope = overrides.include !== undefined || overrides.exclude !== undefined || overrides.noExclude === true;
-    const paths = adHocScope ? new Set(allPaths.filter((p)=>inScope(p, include, exclude))) : new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
+    if (!adHocScope) return new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
+    const paths = allPaths !== null && allPaths !== void 0 ? allPaths : db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
+    return new Set(paths.filter((p)=>inScope(p, include, exclude)));
+}
+function narrowByWhere(db, paths, where) {
     if (!where) return paths;
     const whereRows = db.prepare(`SELECT "path" FROM frontmatter f WHERE (${where})`).all();
     const wherePaths = new Set(whereRows.map((r)=>r.path));
@@ -281,6 +290,12 @@ export function scopedPaths(db, cfg, overrides) {
         ...paths
     ].filter((p)=>wherePaths.has(p)));
 }
+// The scope resolver for non-search commands (path, peek, map): same coverage rule search()
+// applies, then narrowed by the resolved `where`.
+export function scopedPaths(db, cfg, overrides) {
+    const effective = resolveSearch(cfg, overrides);
+    return narrowByWhere(db, rawScope(db, cfg, overrides), effective.where);
+}
 // Indexing derives from presets, so the derivation stays visible. Read from preset_files, not
 // recomputed from globs, so it reflects the cache rather than the config.
 export function presetCoverage(db, cfg) {
@@ -311,15 +326,18 @@ function chunk(items, size) {
     for(let i = 0; i < items.length; i += size)out.push(items.slice(i, i + size));
     return out;
 }
-// Materializes the resolved scope into a temp table (same shape as traverse.ts's
-// allowed_nodes) so every mapTree query can join/filter against it cheaply.
-function setupMapScope(db, paths) {
-    db.exec('DROP TABLE IF EXISTS _map_scope');
-    db.exec('CREATE TEMP TABLE _map_scope ("path" TEXT PRIMARY KEY)');
-    db.prepare('INSERT INTO _map_scope SELECT DISTINCT value FROM json_each(?1)').run(JSON.stringify([
+// Materializes a path set into a named temp table (same shape as traverse.ts's allowed_nodes)
+// so a query can join/filter against it cheaply instead of binding a parameter per path.
+function materializeScope(db, table, paths) {
+    db.exec(`DROP TABLE IF EXISTS ${table}`);
+    db.exec(`CREATE TEMP TABLE ${table} ("path" TEXT PRIMARY KEY)`);
+    db.prepare(`INSERT INTO ${table} SELECT DISTINCT value FROM json_each(?1)`).run(JSON.stringify([
         ...paths
     ]));
 }
+function setupMapScope(db, paths) {
+    materializeScope(db, '_map_scope', paths);
+}
 // What is this scope: fixed-size output regardless of tree size. Coverage and features stay
 // global -- they describe the tree, not the current question.
 export function mapTree(db, cfg, overrides = {}) {
@@ -350,6 +368,10 @@ export function mapTree(db, cfg, overrides = {}) {
     const fields = allFields.slice(0, 20);
     const hubs = featureEnabled(cfg, 'rank') ? db.prepare(`SELECT f."path" AS path, round(f."_rank" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f."path" WHERE f."_rank" IS NOT NULL ${scopeAnd} ORDER BY f."_rank" DESC LIMIT 8`).all() : [];
     const recent = db.prepare(`SELECT "path", datetime("_mtime" / 1000, 'unixepoch') AS modified FROM frontmatter ${scopeWhere} ORDER BY "_mtime" DESC LIMIT 5`).all();
+    // A fresh clone/copy stamps files with checkout time, not edit history; second granularity
+    // matches the `recent` table above and is coarse enough to catch that without an exact-ms match.
+    const topSecond = db.prepare(`SELECT COUNT(*) AS n FROM frontmatter ${scopeWhere} GROUP BY CAST("_mtime" / 1000 AS INTEGER) ORDER BY n DESC LIMIT 1`).get();
+    const recentCaveat = topSecond && docs.count > 1 && topSecond.n > docs.count / 2 ? `${topSecond.n} of ${docs.count} files share one modified second, so recency likely reflects a checkout or copy, not edit history` : null;
     return {
         docs,
         fields,
@@ -357,7 +379,8 @@ export function mapTree(db, cfg, overrides = {}) {
         features: featureStates(cfg),
         presets: presetCoverage(db, cfg),
         hubs,
-        recent
+        recent,
+        recentCaveat
     };
 }
 // Note resolution shared by peek and path: an exact path, or a unique basename (case