sensemaking 0.12.2 → 0.13.0

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, allowed?: Set<string>): 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    if (allowed && !allowed.has(row.path)) continue;\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, ctimeMs: 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, allowed?: Set<string>): 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) ?? 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package/dist/cjs/features/index.d.cts

@@ -1,4 +1,4 @@
-import type { Config } from '../config.js';
+import type { Config } from '../config/index.js';
 import type { Feature } from './types.js';
 export declare const FEATURES: Feature[];
 export declare function activeFeatures(cfg: Config): Feature[];

package/dist/cjs/features/index.d.ts

@@ -1,4 +1,4 @@
-import type { Config } from '../config.js';
+import type { Config } from '../config/index.js';
 import type { Feature } from './types.js';
 export declare const FEATURES: Feature[];
 export declare function activeFeatures(cfg: Config): Feature[];

package/dist/cjs/features/index.js

@@ -19,20 +19,22 @@ _export(exports, {
         return _linksts.linkEdges;
     }
 });
-var _configts = require("../config.js");
+var _indexts = require("../config/index.js");
 var _embedts = require("./embed.js");
 var _linksts = require("./links.js");
 var _rankts = require("./rank.js");
 var _sectionsts = require("./sections.js");
+var _tagsts = require("./tags.js");
 var FEATURES = [
     _linksts.links,
     _sectionsts.sections,
+    _tagsts.tags,
     _rankts.rank,
     _embedts.embed
 ];
 function activeFeatures(cfg) {
     return FEATURES.filter(function(feature) {
-        return (0, _configts.featureEnabled)(cfg, feature.name);
+        return (0, _indexts.featureEnabled)(cfg, feature.name);
     });
 }
 /* CJS INTEROP */ if (exports.__esModule && exports.default) { try { Object.defineProperty(exports.default, '__esModule', { value: true }); for (var key in exports) { exports.default[key] = exports[key]; } } catch (_) {}; module.exports = exports.default; }

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/index.ts"],"sourcesContent":["import type { Config } from '../config.ts';\nimport { featureEnabled } from '../config.ts';\nimport { embed } from './embed.ts';\nimport { links } from './links.ts';\nimport { rank } from './rank.ts';\nimport { sections } from './sections.ts';\nimport type { Feature } from './types.ts';\n\n// Registry order matters: rank reads the links table in afterReconcile.\nexport const FEATURES: Feature[] = [links, sections, rank, embed];\n\nexport function activeFeatures(cfg: Config): Feature[] {\n  return FEATURES.filter((feature) => featureEnabled(cfg, feature.name));\n}\n\nexport { linkEdges } from './links.ts';\nexport type { Section } from './sections.ts';\nexport type { Feature } from './types.ts';\n"],"names":["FEATURES","activeFeatures","linkEdges","links","sections","rank","embed","cfg","filter","feature","featureEnabled","name"],"mappings":";;;;;;;;;;;QASaA;eAAAA;;QAEGC;eAAAA;;QAIPC;eAAAA,kBAAS;;;wBAda;uBACT;uBACA;sBACD;0BACI;AAIlB,IAAMF,WAAsB;IAACG,cAAK;IAAEC,oBAAQ;IAAEC,YAAI;IAAEC,cAAK;CAAC;AAE1D,SAASL,eAAeM,GAAW;IACxC,OAAOP,SAASQ,MAAM,CAAC,SAACC;eAAYC,IAAAA,wBAAc,EAACH,KAAKE,QAAQE,IAAI;;AACtE"}
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/index.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { featureEnabled } from '../config/index.ts';\nimport { embed } from './embed.ts';\nimport { links } from './links.ts';\nimport { rank } from './rank.ts';\nimport { sections } from './sections.ts';\nimport { tags } from './tags.ts';\nimport type { Feature } from './types.ts';\n\n// Registry order matters: rank reads the links table in afterReconcile.\nexport const FEATURES: Feature[] = [links, sections, tags, rank, embed];\n\nexport function activeFeatures(cfg: Config): Feature[] {\n  return FEATURES.filter((feature) => featureEnabled(cfg, feature.name));\n}\n\nexport { linkEdges } from './links.ts';\nexport type { Section } from './sections.ts';\nexport type { Feature } from './types.ts';\n"],"names":["FEATURES","activeFeatures","linkEdges","links","sections","tags","rank","embed","cfg","filter","feature","featureEnabled","name"],"mappings":";;;;;;;;;;;QAUaA;eAAAA;;QAEGC;eAAAA;;QAIPC;eAAAA,kBAAS;;;uBAfa;uBACT;uBACA;sBACD;0BACI;sBACJ;AAId,IAAMF,WAAsB;IAACG,cAAK;IAAEC,oBAAQ;IAAEC,YAAI;IAAEC,YAAI;IAAEC,cAAK;CAAC;AAEhE,SAASN,eAAeO,GAAW;IACxC,OAAOR,SAASS,MAAM,CAAC,SAACC;eAAYC,IAAAA,uBAAc,EAACH,KAAKE,QAAQE,IAAI;;AACtE"}

package/dist/cjs/features/links.js

@@ -47,18 +47,30 @@ function _unsupported_iterable_to_array(o, minLen) {
     if (n === "Map" || n === "Set") return Array.from(n);
     if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _array_like_to_array(o, minLen);
 }
-// links(src, target, target_base, dst): target as written, target_base its baseKey
+// links(src, target, target_base, dst, embed): target as written, target_base its baseKey
 // (indexed, for the incremental resolve below), dst the resolved path or NULL (a
-// queryable dead link).
+// queryable dead link), embed whether it's `![[x]]`/`![](x.md)` rather than `[[x]]`/`[](x.md)`
+// -- Obsidian's grain: a target both linked and embedded in the same note is two rows.
 // Wikilinks ([[target]], [[target#anchor|alias]], embeds) plus relative markdown links to .md files.
 function extract(_raw, body) {
-    var targets = new Set();
+    var seen = new Set();
+    var results = [];
+    var add = function add(target, embed) {
+        var key = "".concat(target, "\0").concat(embed ? '1' : '0');
+        if (seen.has(key)) return;
+        seen.add(key);
+        results.push({
+            target: target,
+            embed: embed
+        });
+    };
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
         for(var _iterator = body.matchAll(/\[\[([^\]|#]+)(?:#[^\]|]*)?(?:\|[^\]]*)?\]\]/g)[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
             var m = _step.value;
+            var _m_index;
             var target = m[1].trim();
-            if (target) targets.add(target);
+            if (target) add(target, body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!');
         }
     } catch (err) {
         _didIteratorError = true;
@@ -76,10 +88,10 @@ function extract(_raw, body) {
     }
     var _iteratorNormalCompletion1 = true, _didIteratorError1 = false, _iteratorError1 = undefined;
     try {
-        for(var _iterator1 = body.matchAll(/\]\(([^)]+\.md)(?:#[^)]*)?\)/g)[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
+        for(var _iterator1 = body.matchAll(/(!)?\[[^\]]*\]\(([^)]+\.md)(?:#[^)]*)?\)/g)[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
             var m1 = _step1.value;
-            var target1 = m1[1].trim();
-            if (target1 && !/^[a-z]+:\/\//i.test(target1)) targets.add(target1);
+            var target1 = m1[2].trim();
+            if (target1 && !/^[a-z]+:\/\//i.test(target1)) add(target1, m1[1] === '!');
         }
     } catch (err) {
         _didIteratorError1 = true;
@@ -95,7 +107,7 @@ function extract(_raw, body) {
             }
         }
     }
-    return _to_consumable_array(targets);
+    return results;
 }
 function cleanTarget(target) {
     return target.replace(/\\/g, '/').replace(/^\.\//, '');
@@ -152,7 +164,9 @@ function buildByBase(files) {
     }
     return byBase;
 }
-// Applies resolveTarget to `rows`, writing only rows whose dst actually changes.
+// Applies resolveTarget to `rows`, writing only rows whose dst actually changes. The UPDATE
+// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's
+// mismatch rewrites both.
 function resolveRows(db, rows, pathSet, byBase) {
     var update = db.prepare('UPDATE links SET dst = ? WHERE src = ? AND target = ?');
     var changed = false;
@@ -189,7 +203,7 @@ function resolveAll(db, files) {
         return f.relPath;
     }));
     var byBase = buildByBase(files);
-    var rows = db.prepare('SELECT src, target, dst FROM links').all();
+    var rows = db.prepare('SELECT src, target, dst, embed FROM links').all();
     return resolveRows(db, rows, pathSet, byBase);
 }
 // Re-resolve only what this reconcile could have touched: re-stored sources, links whose
@@ -248,7 +262,7 @@ function resolveIncremental(db, delta) {
         try {
             for(var _iterator = rows[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
                 var row = _step.value;
-                candidates.set("".concat(row.src, "\0").concat(row.target), row);
+                candidates.set("".concat(row.src, "\0").concat(row.target, "\0").concat(row.embed), row);
             }
         } catch (err) {
             _didIteratorError = true;
@@ -274,7 +288,7 @@ function resolveIncremental(db, delta) {
             var placeholders = chunk.map(function() {
                 return '?';
             }).join(', ');
-            collect((_db_prepare = db.prepare("SELECT src, target, dst FROM links WHERE ".concat(column, " IN (").concat(placeholders, ")"))).all.apply(_db_prepare, _to_consumable_array(chunk)));
+            collect((_db_prepare = db.prepare("SELECT src, target, dst, embed FROM links WHERE ".concat(column, " IN (").concat(placeholders, ")"))).all.apply(_db_prepare, _to_consumable_array(chunk)));
         }
     };
     collectIn('src', delta.reparsed);
@@ -283,7 +297,7 @@ function resolveIncremental(db, delta) {
     return resolveRows(db, _to_consumable_array(candidates.values()), pathSet, byBase);
 }
 function linkEdges(db) {
-    return db.prepare('SELECT src, dst FROM links WHERE dst IS NOT NULL').all().map(function(r) {
+    return db.prepare('SELECT DISTINCT src, dst FROM links WHERE dst IS NOT NULL').all().map(function(r) {
         return [
             r.src,
             r.dst
@@ -314,7 +328,7 @@ function vanishedSet(delta) {
 var links = {
     name: 'links',
     schema: function schema(db) {
-        db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, PRIMARY KEY (src, target))');
+        db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');
         db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');
         db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');
     },
@@ -329,7 +343,8 @@ var links = {
     },
     store: function store(db, path, extracted, delta) {
         var targets = extracted;
-        // Stale rows (targets the new parse no longer contains) are real edge removals.
+        // Stale rows (target/embed pairs the new parse no longer contains) are real edge removals.
+        // \0 can't appear in a target, so the composite key never collides.
         var stale;
         if (targets.length === 0) {
             stale = db.prepare('DELETE FROM links WHERE src = ?').run(path);
@@ -338,19 +353,22 @@ var links = {
             var placeholders = targets.map(function() {
                 return '?';
             }).join(', ');
-            stale = (_db_prepare = db.prepare("DELETE FROM links WHERE src = ? AND target NOT IN (".concat(placeholders, ")"))).run.apply(_db_prepare, [
+            var keys = targets.map(function(t) {
+                return "".concat(t.target, "\0").concat(t.embed ? '1' : '0');
+            });
+            stale = (_db_prepare = db.prepare("DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (".concat(placeholders, ")"))).run.apply(_db_prepare, [
                 path
-            ].concat(_to_consumable_array(targets)));
+            ].concat(_to_consumable_array(keys)));
         }
         if (Number(stale.changes) > 0) recordRemoved(delta, path);
         // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same
         // value and reports no change; only genuinely new rows start at NULL.
-        var insert = db.prepare('INSERT INTO links (src, target, target_base, dst) VALUES (?, ?, ?, NULL) ON CONFLICT(src, target) DO UPDATE SET target_base = excluded.target_base');
+        var insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base');
         var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
         try {
             for(var _iterator = targets[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
-                var target = _step.value;
-                insert.run(path, target, baseKey(cleanTarget(target)));
+                var _step_value = _step.value, target = _step_value.target, embed = _step_value.embed;
+                insert.run(path, target, baseKey(cleanTarget(target)), embed ? 1 : 0);
             }
         } catch (err) {
             _didIteratorError = true;

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

@@ -1 +1 @@
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The UPDATE\n// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's\n// mismatch rewrites both.\nfunction resolveRows(db: DatabaseSync, rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): boolean {\n  const update = db.prepare('UPDATE links SET dst = ? WHERE src = ? 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package/dist/cjs/features/tags.d.cts

@@ -0,0 +1,2 @@
+import type { Feature } from './types.js';
+export declare const tags: Feature;

package/dist/cjs/features/tags.d.ts

@@ -0,0 +1,2 @@
+import type { Feature } from './types.js';
+export declare const tags: Feature;