sensemaking 0.10.0 → 0.11.0

package/dist/cjs/commands.js

@@ -419,7 +419,7 @@ function search(_0, _1, _2) {
                     fetch = scopeActive ? Math.max(k * 5, 50) : 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.
-                    wantsVectors = !opts.probe && effective.semantic && (0, _configts.anyPresetEmbeds)(cfg);
+                    wantsVectors = effective.semantic && (0, _configts.anyPresetEmbeds)(cfg);
                     if (wantsVectors && !(0, _embedts.modelPresent)(cfg)) {
                         throw new _errorsts.SenseError('EMBED_MODEL_MISSING', 'preset "'.concat(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'));
                     }
@@ -627,7 +627,8 @@ function presetCoverage(db, cfg) {
         return {
             name: name,
             files: files,
-            embedded: embedded
+            embedded: embedded,
+            semantic: (0, _configts.presetSemanticEnabled)(cfg, name)
         };
     });
 }
@@ -635,7 +636,8 @@ var INTERNAL_COLUMNS = new Set([
     'path',
     '_mtime',
     '_size',
-    '_rank'
+    '_rank',
+    '_parse_error'
 ]);
 // A result row is capped at SQLITE_MAX_COLUMN (2000, default); two aggregate expressions
 // per field keeps a chunk's row safely under that regardless of how many fields the tree has.
@@ -731,12 +733,13 @@ function resolveNote(paths, arg) {
 var PEEK_LIST_LIMIT = 20;
 function peek(db, cfg, pathArg) {
     var overrides = arguments.length > 3 && arguments[3] !== void 0 ? arguments[3] : {};
-    var _row__size;
+    var _row__parse_error, _row__size;
     var paths = db.prepare('SELECT "path" FROM frontmatter').all().map(function(r) {
         return r.path;
     });
     var path = resolveNote(paths, pathArg);
     var row = db.prepare('SELECT * FROM frontmatter WHERE "path" = ?').get(path);
+    var parseError = (_row__parse_error = row._parse_error) !== null && _row__parse_error !== void 0 ? _row__parse_error : null;
     var frontmatter = {};
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
@@ -786,6 +789,7 @@ function peek(db, cfg, pathArg) {
         path: path,
         tokens: Math.ceil(((_row__size = row._size) !== null && _row__size !== void 0 ? _row__size : 0) / 4),
         frontmatter: frontmatter,
+        parseError: parseError,
         sections: sections,
         outbound: outbound.slice(0, PEEK_LIST_LIMIT),
         backlinks: backlinks,
@@ -804,7 +808,7 @@ function peek(db, cfg, pathArg) {
 }
 function relatedNotes(db, cfg, pathArg, overrides, k) {
     return _async_to_generator(function() {
-        var paths, path, outbound, backlinks, exclude, allowed;
+        var paths, path, outbound, backlinks, exclude, effective, allowed;
         return _ts_generator(this, function(_state) {
             switch(_state.label){
                 case 0:
@@ -821,22 +825,38 @@ function relatedNotes(db, cfg, pathArg, overrides, k) {
                     exclude = new Set([
                         path
                     ].concat(_to_consumable_array(outbound), _to_consumable_array(backlinks)));
-                    allowed = scopedPaths(db, cfg, overrides);
-                    if (!scopeHasEmbeddings(db, cfg, allowed)) return [
-                        2,
-                        []
-                    ];
-                    // Vectors are the only signal, so [] would read as "nothing is related" rather than "no
-                    // model". Top up pending rows too, or a fresh index answers 0 until some search runs.
+                    // Vectors are the only signal `related` has, so every way of not having them is an error
+                    // naming the cause. An empty table then means one thing: nothing near in meaning that this
+                    // note does not already link to, which is a real answer.
+                    effective = (0, _configts.resolveSearch)(cfg, overrides);
+                    if (!(0, _configts.embedEnabled)(cfg)) {
+                        throw new _errorsts.SenseError('EMBED_DISABLED', 'related ranks notes by meaning, and this tree has no embedding model; add an "embed" block naming one to sense.config.json, then run `sense download` (search works without it, on words and links)');
+                    }
+                    // search gates on the same flag (see wantsVectors above); reading it here too keeps
+                    // `semantic: false` meaning one thing. Without this, an overlapping semantic-on preset's
+                    // vectors would answer for a scope that declined them.
+                    if (!effective.semantic) {
+                        throw new _errorsts.SenseError('PRESET_NOT_SEMANTIC', 'preset "'.concat(effective.presetName, '" sets "semantic": false, so this scope has no vectors and related has no other signal; search it instead (words and links), or set semantic back on for that preset'));
+                    }
                     if (!(0, _embedts.modelPresent)(cfg)) {
                         throw new _errorsts.SenseError('EMBED_MODEL_MISSING', 'related ranks notes by meaning, so it needs the embedding model, which is not downloaded; run `sense download` (search still works without it, on words and links)');
                     }
+                    allowed = scopedPaths(db, cfg, overrides);
+                    // Top up pending rows before the seed check, or a fresh index reports every note as
+                    // having no indexed text until some search has run.
                     return [
                         4,
                         (0, _embedts.embedPending)(db, cfg, cfg.baseDir)
                     ];
                 case 1:
                     _state.sent();
+                    if (!(0, _embedts.hasEmbedding)(db, path)) {
+                        throw new _errorsts.SenseError('NOTE_NOT_EMBEDDED', "".concat(path, " has no indexed text to compare -- a note that is frontmatter only, or empty, has nothing to rank by meaning"));
+                    }
+                    if (!scopeHasEmbeddings(db, cfg, allowed)) return [
+                        2,
+                        []
+                    ];
                     return [
                         2,
                         (0, _embedts.similarNotes)(db, cfg, path, {

package/dist/cjs/commands.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/commands.ts"],"sourcesContent":["import { readFileSync } from 'node:fs';\nimport { join, matchesGlob } from 'node:path';\nimport posix from 'node:path/posix';\nimport type { DatabaseSync } from 'node:sqlite';\nimport type { FeatureName, ResolvedConfig, SearchOverrides } from './config.ts';\nimport { anyPresetEmbeds, featureEnabled, featureStates, presetNames, resolveSearch } from './config.ts';\nimport { SenseError } from './errors.ts';\nimport { embedPending, modelPresent, semanticCandidates, similarNotes } from './features/embed.ts';\nimport { linkEdges } from './features/index.ts';\nimport { personalizedRank } from './graph.ts';\nimport type { Row } from './output.ts';\nimport { searchError } from './search-error.ts';\n\n// The three commands: mapTree (orient), search (locate), peek (structure).\n// Each returns data; cli.ts renders. All of them degrade when a feature is off.\n\nconst WEIGHTED_BM25 = 'bm25(content, 10.0, 5.0, 1.0)';\nconst RRF_K = 60;\n\n// snippet() re-tokenizes each candidate doc, superlinearly: ~10s for one 1MB doc\n// (BENCHMARKING.md). Past this bound, rows get the linear JS excerpt instead.\nconst SNIPPET_BOUND = 16_384;\nconst EXCERPT_WINDOW = 160;\n\n// Bare terms from an FTS5 query string: strips operators/quoting so the oversized-doc excerpt\n// scan matches the same words the query matched on, not FTS5 syntax.\nfunction extractBareTerms(query: string): string[] {\n  const cleaned = query\n    .replace(/\"/g, ' ')\n    .replace(/[()*]/g, ' ')\n    .replace(/\\b(AND|OR|NOT|NEAR)\\b(\\/\\d+)?/gi, ' ');\n  return cleaned\n    .split(/\\s+/)\n    .map((tok) => tok.replace(/^[A-Za-z_]\\w*:/, '')) // column filter, e.g. title:term\n    .map((tok) => tok.toLowerCase().trim())\n    .filter((tok) => tok.length > 0);\n}\n\nfunction findOccurrences(haystackLower: string, terms: string[]): Array<{ start: number; end: number; term: string }> {\n  const occ: Array<{ start: number; end: number; term: string }> = [];\n  for (const term of terms) {\n    let idx = 0;\n    for (;;) {\n      const found = haystackLower.indexOf(term, idx);\n      if (found === -1) break;\n      occ.push({ start: found, end: found + term.length, term });\n      idx = found + term.length;\n    }\n  }\n  // Longest span first at equal start, so \"tests\" beats its substring \"test\" and the\n  // whole word gets highlighted; the emit loop then absorbs the shorter overlap.\n  return occ.sort((a, b) => a.start - b.start || b.end - a.end);\n}\n\n// Slides a window over the sorted occurrences, same semantics as FTS5's own best-window\n// pick: most distinct terms, ties broken by most total hits.\nfunction bestWindowStart(occ: Array<{ start: number; end: number; term: string }>, windowSize: number): number {\n  let best = occ[0].start;\n  let bestDistinct = 0;\n  let bestCount = 0;\n  for (let i = 0; i < occ.length; i++) {\n    const winEnd = occ[i].start + windowSize;\n    const seen = new Set<string>();\n    let count = 0;\n    for (let j = i; j < occ.length && occ[j].start < winEnd; j++) {\n      seen.add(occ[j].term);\n      count++;\n    }\n    if (seen.size > bestDistinct || (seen.size === bestDistinct && count > bestCount)) {\n      best = occ[i].start;\n      bestDistinct = seen.size;\n      bestCount = count;\n    }\n  }\n  return best;\n}\n\n// snippet()-shaped excerpt: matched terms wrapped in «», … at cut edges. Linear in doc\n// length, only run for rows actually returned (<= k), unlike snippet()'s per-row cost.\nfunction computeExcerpt(text: string, terms: string[]): { excerpt: string; offset: number } {\n  const occ = findOccurrences(text.toLowerCase(), terms);\n  if (occ.length === 0) {\n    // This is a raw substring scan, not porter-stemmed: a doc matched only through a\n    // stemmed variant (query \"negotiate\" vs doc \"negotiating\") finds no occurrence here.\n    // Fall back to the doc's start, unmarked, rather than claim a match that isn't there.\n    const end = Math.min(text.length, EXCERPT_WINDOW);\n    return { excerpt: `${text.slice(0, end).replace(/\\s+/g, ' ').trim()}${end < text.length ? '…' : ''}`, offset: 0 };\n  }\n  const start = bestWindowStart(occ, EXCERPT_WINDOW);\n  const end = Math.min(text.length, start + EXCERPT_WINDOW);\n  let out = '';\n  let cursor = start;\n  for (const o of occ) {\n    if (o.start < start || o.end > end) continue;\n    // Occurrences of duplicate or substring-overlapping terms (\"test tests\") can overlap;\n    // emitting each would duplicate document text. Keep the first, absorb the rest.\n    if (o.start < cursor) continue;\n    out += `${text.slice(cursor, o.start)}«${text.slice(o.start, o.end)}»`;\n    cursor = o.end;\n  }\n  out += text.slice(cursor, end);\n  const prefix = start > 0 ? '…' : '';\n  const suffix = end < text.length ? '…' : '';\n  return { excerpt: `${prefix}${out.replace(/\\s+/g, ' ')}${suffix}`, offset: start };\n}\n\nfunction lineNumberAt(text: string, offset: number): number {\n  let line = 1;\n  for (let i = 0; i < offset; i++) if (text.charCodeAt(i) === 10) line++;\n  return line;\n}\n\nfunction lineRangeFor(db: DatabaseSync, path: string, line: number): string | null {\n  const row = db.prepare('SELECT start_line, end_line FROM sections WHERE \"path\" = ? AND start_line <= ? AND end_line >= ? ORDER BY start_line DESC LIMIT 1').get(path, line, line) as { start_line: number; end_line: number } | undefined;\n  return row ? `L${row.start_line}-${row.end_line}` : null;\n}\n\nexport interface SearchOptions {\n  k?: number;\n  where?: string; // SQL fragment against frontmatter alias `f`, e.g. \"f.status = 'active'\"\n  preset?: string; // named preset; unknown name throws listing declared presets, undefined -> \"default\"\n  include?: string[]; // ad hoc scope override (repeatable --include); independent of exclude\n  exclude?: string[]; // ad hoc scope override (repeatable --exclude); independent of include\n  noExclude?: boolean; // --no-exclude: drop the preset's exclude for this command\n  // Validation probe, no CLI flag: everything `check` validates lives in the lexical half, and\n  // a vector pass would embed the tree (or bill an api) to prove a saved search parses.\n  probe?: boolean;\n}\n\n// node:path's matchesGlob is experimental (stable behind an unstable-API flag) as of the\n// engines floor (Node >=22.20); scope filtering only ever needs single-pattern matching, so\n// it's used here in JS rather than running a directory walk in the query path.\nfunction inScope(path: string, include: string[], exclude?: string[]): boolean {\n  if (!include.some((g) => matchesGlob(path, g))) return false;\n  if (exclude?.some((g) => matchesGlob(path, g))) return false;\n  return true;\n}\n\nfunction scopeHasEmbeddings(db: DatabaseSync, cfg: ResolvedConfig, scopedPaths: Set<string>): boolean {\n  if (!anyPresetEmbeds(cfg)) return false; // the embeddings table doesn't exist at all in this case\n  const rows = db.prepare('SELECT DISTINCT \"path\" FROM embeddings').all() as Array<{ path: string }>;\n  return rows.some((r) => scopedPaths.has(r.path));\n}\n\n// BM25 + link expansion + vectors, fused by reciprocal rank; `via` names the signal per row.\n// `opts` arrives already resolved (config.ts:resolveSearch).\nexport async function search(db: DatabaseSync, cfg: ResolvedConfig, terms: string, opts: SearchOptions = {}): Promise<Row[]> {\n  const effective = resolveSearch(cfg, opts);\n  const { k, include, exclude } = effective;\n\n  const allPaths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  // A preset scope reads the coverage reconcile indexed; re-matching globs here could disagree\n  // with it. Only ad-hoc scope flags, which have no persisted coverage, pay the JS match.\n  const adHocScope = opts.include !== undefined || opts.exclude !== undefined || opts.noExclude === true;\n  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) as Array<{ path: string }>).map((r) => r.path));\n  // A scope narrower than the whole index needs a bigger candidate pool before filtering, or\n  // filtering can starve k even though enough in-scope matches exist further down the ranked\n  // list that a plain over-fetch wouldn't have reached.\n  const scopeActive = scopedPaths.size < allPaths.length;\n  const fetch = scopeActive ? Math.max(k * 5, 50) : Math.max(k * 3, 30);\n\n  // Asking for vectors without a model is a misconfiguration, not a mode: degrading would make\n  // the same search answer differently before and after a download. semantic:false never asks.\n  const wantsVectors = !opts.probe && effective.semantic && anyPresetEmbeds(cfg);\n  if (wantsVectors && !modelPresent(cfg)) {\n    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`);\n  }\n  const semanticEnabled = wantsVectors && scopeHasEmbeddings(db, cfg, scopedPaths);\n\n  // Terms pass verbatim to MATCH; invalid syntax errors rather than being rewritten. --where\n  // applies inside the candidate query (a post-filter would drop matches ranked past the pool)\n  // and again on the final select, for link-derived rows.\n  const scope = effective.where;\n  const whereJoin = scope ? `JOIN frontmatter f ON f.\"path\" = content.path` : '';\n  const whereCond = scope ? `AND (${scope})` : '';\n  // Docs past SNIPPET_BOUND skip snippet() entirely -- SQLite\n  // short-circuits the untaken CASE branch, so it's never invoked on them.\n  const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, -1, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;\n  let matchRows: Array<{ path: string; hit: string | null }>;\n  try {\n    matchRows = db.prepare(matchSql).all(terms) as Array<{ path: string; hit: string | null }>;\n  } catch (err) {\n    throw searchError(err as Error, terms, scope);\n  }\n  // Scope filtering happens in JS, on each candidate list, rather than in SQL: FTS5 match,\n  // link expansion, and vector search all run unscoped above (cheap to over-fetch), then get\n  // filtered here against the effective include/exclude before ranking is finalized.\n  matchRows = matchRows.filter((r) => scopedPaths.has(r.path));\n\n  const hits = new Map(matchRows.map((r) => [r.path, r.hit]));\n  // hit === null here means the bound suppressed snippet(), not \"no match\" -- distinguish\n  // from via='link' rows (never in matchRows, so absent from this set) below.\n  const oversized = new Set(matchRows.filter((r) => r.hit === null).map((r) => r.path));\n  const candidates = new Map<string, { score: number; via: string }>();\n  matchRows.forEach((r, i) => {\n    candidates.set(r.path, { score: 1 / (RRF_K + i), via: 'match' });\n  });\n\n  const edges = featureEnabled(cfg, 'links') && matchRows.length > 0 ? linkEdges(db) : [];\n  if (edges.length > 0) {\n    // Gates the label only, not the score: restart mass ranks every seed without an incident\n    // edge, but dropping it from the score reweights fusion (FEVER hit@10 0.997 -> 0.907).\n    const linked = new Set(edges.flat());\n    const seeds = new Map(matchRows.map((r, i) => [r.path, 1 / (i + 1)]));\n    const ranked = [...personalizedRank(allPaths, edges, seeds)]\n      .filter(([path, score]) => score > 1e-9 && scopedPaths.has(path))\n      .sort((a, b) => b[1] - a[1])\n      .slice(0, fetch);\n    ranked.forEach(([path], i) => {\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        if (linked.has(path)) existing.via = 'match+link';\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'link' });\n      }\n    });\n  }\n\n  // Vector expansion, invoked only: a third RRF list at the swept flat-region constants\n  // (weight 1, pool = fetch). Each row carries its best chunk's line range.\n  const chunkLines = new Map<string, string>();\n  const chunkSimilarity = new Map<string, number>();\n  if (semanticEnabled) {\n    const vec = (await semanticCandidates(db, cfg, terms, fetch)).filter((v) => scopedPaths.has(v.path));\n    vec.forEach(({ path, lines, similarity }, i) => {\n      chunkLines.set(path, lines);\n      chunkSimilarity.set(path, similarity);\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        existing.via = `${existing.via}+vector`;\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'vector' });\n      }\n    });\n  }\n\n  db.exec('DROP TABLE IF EXISTS _search');\n  db.exec('CREATE TEMP TABLE _search (\"path\" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');\n  const insert = db.prepare('INSERT INTO _search (\"path\", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');\n  for (const [path, c] of candidates) insert.run(path, c.score, c.via, hits.get(path) ?? null, chunkLines.get(path) ?? null, chunkSimilarity.get(path) ?? null);\n\n  // Already scope-filtered above; the final select reapplies --where only for link-derived\n  // rows, which never passed through whereCond.\n  const where = scope ? `WHERE (${scope})` : '';\n  // lines is always present now: semantic rows carry their chunk's range, oversized-doc\n  // lexical rows gain one below, everything else stays null. similarity stays semantic-only.\n  const similarityCol = semanticEnabled ? ', _search.similarity' : '';\n  const rows = db\n    .prepare(\n      `SELECT f.\"path\" AS path, content.title, content.summary, _search.hit, _search.via, round(_search.score, 4) AS score, _search.lines${similarityCol}\n       FROM _search JOIN frontmatter f ON f.\"path\" = _search.\"path\" JOIN content ON content.path = _search.\"path\"\n       ${where} ORDER BY _search.score DESC LIMIT ?`\n    )\n    .all(k) as Row[];\n\n  if (oversized.size > 0) {\n    const bareTerms = extractBareTerms(terms);\n    for (const row of rows) {\n      if (row.hit !== null || !oversized.has(row.path as string)) continue;\n      let text: string;\n      try {\n        text = readFileSync(join(cfg.baseDir, row.path as string), 'utf8');\n      } catch {\n        continue; // vanished since the match; leave hit/lines null rather than throw\n      }\n      const { excerpt, offset } = computeExcerpt(text, bareTerms);\n      row.hit = excerpt;\n      if (row.lines == null) row.lines = featureEnabled(cfg, 'sections') ? lineRangeFor(db, row.path as string, lineNumberAt(text, offset)) : null;\n    }\n  }\n\n  return rows;\n}\n\n// The scope resolver for non-search commands (path, peek, map): same coverage rule search()\n// applies (preset_files for a named preset, JS glob matching for an ad hoc include/exclude),\n// then narrowed by the resolved `where`.\nexport function scopedPaths(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides): Set<string> {\n  const effective = resolveSearch(cfg, overrides);\n  const { include, exclude, where } = effective;\n  const allPaths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const adHocScope = overrides.include !== undefined || overrides.exclude !== undefined || overrides.noExclude === true;\n  const paths = adHocScope ? new Set(allPaths.filter((p) => inScope(p, include, exclude))) : new Set((db.prepare('SELECT \"path\" FROM preset_files WHERE preset = ?').all(effective.presetName) as Array<{ path: string }>).map((r) => r.path));\n  if (!where) return paths;\n  const whereRows = db.prepare(`SELECT \"path\" FROM frontmatter f WHERE (${where})`).all() as Array<{ path: string }>;\n  const wherePaths = new Set(whereRows.map((r) => r.path));\n  return new Set([...paths].filter((p) => wherePaths.has(p)));\n}\n\nexport interface PresetCoverage {\n  name: string;\n  files: number;\n  embedded: number;\n}\n\n// Indexing derives from presets, so the derivation stays visible. Read from preset_files, not\n// recomputed from globs, so it reflects the cache rather than the config.\nexport function presetCoverage(db: DatabaseSync, cfg: ResolvedConfig): PresetCoverage[] {\n  const embedActive = anyPresetEmbeds(cfg);\n  return presetNames(cfg).map((name) => {\n    const files = (db.prepare('SELECT COUNT(*) AS n FROM preset_files WHERE preset = ?').get(name) as { n: number }).n;\n    const embedded = embedActive ? (db.prepare('SELECT COUNT(*) AS n FROM preset_files pf WHERE pf.preset = ? AND EXISTS (SELECT 1 FROM embeddings e WHERE e.\"path\" = pf.\"path\" AND e.vector IS NOT NULL)').get(name) as { n: number }).n : 0;\n    return { name, files, embedded };\n  });\n}\n\nexport interface TreeMap {\n  docs: { count: number; bytes: number };\n  fields: Row[]; // top 20 by coverage; fieldsTotal carries the real count\n  fieldsTotal: number;\n  features: { on: FeatureName[]; off: FeatureName[] };\n  presets: PresetCoverage[];\n  hubs: Row[];\n  recent: Row[];\n}\n\nconst INTERNAL_COLUMNS = new Set(['path', '_mtime', '_size', '_rank']);\n\n// A result row is capped at SQLITE_MAX_COLUMN (2000, default); two aggregate expressions\n// per field keeps a chunk's row safely under that regardless of how many fields the tree has.\nconst MAP_COLUMN_CHUNK = 300;\n\nfunction chunk<T>(items: T[], size: number): T[][] {\n  const out: T[][] = [];\n  for (let i = 0; i < items.length; i += size) out.push(items.slice(i, i + size));\n  return out;\n}\n\n// Materializes the resolved scope into a temp table (same shape as traverse.ts's\n// allowed_nodes) so every mapTree query can join/filter against it cheaply.\nfunction setupMapScope(db: DatabaseSync, paths: Set<string>): void {\n  db.exec('DROP TABLE IF EXISTS _map_scope');\n  db.exec('CREATE TEMP TABLE _map_scope (\"path\" TEXT PRIMARY KEY)');\n  db.prepare('INSERT INTO _map_scope SELECT DISTINCT value FROM json_each(?1)').run(JSON.stringify([...paths]));\n}\n\n// What is this scope: fixed-size output regardless of tree size. Coverage and features stay\n// global -- they describe the tree, not the current question.\nexport function mapTree(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides = {}): TreeMap {\n  setupMapScope(db, scopedPaths(db, cfg, overrides));\n  const scopeWhere = 'WHERE \"path\" IN (SELECT \"path\" FROM _map_scope)';\n  const scopeAnd = 'AND f.\"path\" IN (SELECT \"path\" FROM _map_scope)';\n\n  const docs = db.prepare(`SELECT COUNT(*) AS count, COALESCE(SUM(\"_size\"), 0) AS bytes FROM frontmatter ${scopeWhere}`).get() as { count: number; bytes: number };\n\n  const columns = (db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>).map((r) => r.name).filter((name) => !INTERNAL_COLUMNS.has(name));\n  // Observed types, not declared: SQLite types per value, so a field can be text in most notes\n  // and numeric in a few. One aggregate scan per chunk of columns; FILTER matches COUNT's nulls.\n  const allFields: Row[] = [];\n  for (const group of chunk(columns, MAP_COLUMN_CHUNK)) {\n    const exprs = group.map((name, i) => {\n      const quoted = `\"${name.split('\"').join('\"\"')}\"`;\n      return `COUNT(${quoted}) AS n${i}, GROUP_CONCAT(DISTINCT typeof(${quoted})) FILTER (WHERE ${quoted} IS NOT NULL) AS t${i}`;\n    });\n    const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter ${scopeWhere}`).get() as Record<string, number | string | null>;\n    group.forEach((name, i) => allFields.push({ field: name, coverage: result[`n${i}`] as number, type: (result[`t${i}`] as string) ?? '' }));\n  }\n  allFields.sort((a, b) => (b.coverage as number) - (a.coverage as number));\n  const fields = allFields.slice(0, 20);\n\n  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() as Row[]) : [];\n\n  const recent = db.prepare(`SELECT \"path\", datetime(\"_mtime\" / 1000, 'unixepoch') AS modified FROM frontmatter ${scopeWhere} ORDER BY \"_mtime\" DESC LIMIT 5`).all() as Row[];\n\n  return { docs, fields, fieldsTotal: allFields.length, features: featureStates(cfg), presets: presetCoverage(db, cfg), hubs, recent };\n}\n\n// Note resolution shared by peek and path: an exact path, or a unique basename (case\n// insensitive, .md stripped).\nexport function resolveNote(paths: string[], arg: string): string {\n  const exact = paths.find((p) => p === arg);\n  if (exact) return exact;\n  const base = posix.basename(arg).replace(/\\.md$/i, '').toLowerCase();\n  const matches = paths.filter((p) => posix.basename(p).replace(/\\.md$/i, '').toLowerCase() === base);\n  if (matches.length === 1) return matches[0];\n  if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `\"${arg}\" is ambiguous: ${matches.join(', ')}`);\n  throw new SenseError('NOTE_NOT_FOUND', `no note matches \"${arg}\"`);\n}\n\nexport interface Peek {\n  path: string;\n  tokens: number;\n  frontmatter: Row;\n  sections: Row[];\n  outbound: string[];\n  backlinks: string[];\n  unresolved: string[];\n  // Totals before truncation: a hub can have thousands of backlinks (or a note thousands of\n  // headings), and peek's whole point is bounded output. Query the sections/links tables\n  // directly for the full list.\n  sectionsTotal: number;\n  outboundTotal: number;\n  backlinksTotal: number;\n  unresolvedTotal: number;\n  // Bounded k-hop expansion beyond the immediate ring already shown by outbound/backlinks\n  // (depth starts at 2).\n  off: FeatureName[]; // disabled features whose blocks are omitted (not empty)\n}\n\nconst PEEK_LIST_LIMIT = 20;\n\n// peek: everything about one note except its prose -- frontmatter, outline with line\n// ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.\nexport function peek(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string, overrides: SearchOverrides = {}): Peek {\n  const paths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const path = resolveNote(paths, pathArg);\n\n  const row = db.prepare('SELECT * FROM frontmatter WHERE \"path\" = ?').get(path) as Row;\n  const frontmatter: Row = {};\n  for (const [key, value] of Object.entries(row)) {\n    if (!INTERNAL_COLUMNS.has(key) && value !== null) frontmatter[key] = value;\n  }\n\n  const sectionsTotal = featureEnabled(cfg, 'sections') ? 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All of them degrade when a feature is off.\n\nconst WEIGHTED_BM25 = 'bm25(content, 10.0, 5.0, 1.0)';\nconst RRF_K = 60;\n\n// snippet() re-tokenizes each candidate doc, superlinearly: ~10s for one 1MB doc\n// (BENCHMARKING.md). 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Linear in doc\n// length, only run for rows actually returned (<= k), unlike snippet()'s per-row cost.\nfunction computeExcerpt(text: string, terms: string[]): { excerpt: string; offset: number } {\n  const occ = findOccurrences(text.toLowerCase(), terms);\n  if (occ.length === 0) {\n    // This is a raw substring scan, not porter-stemmed: a doc matched only through a\n    // stemmed variant (query \"negotiate\" vs doc \"negotiating\") finds no occurrence here.\n    // Fall back to the doc's start, unmarked, rather than claim a match that isn't there.\n    const end = Math.min(text.length, EXCERPT_WINDOW);\n    return { excerpt: `${text.slice(0, end).replace(/\\s+/g, ' ').trim()}${end < text.length ? '…' : ''}`, offset: 0 };\n  }\n  const start = bestWindowStart(occ, EXCERPT_WINDOW);\n  const end = Math.min(text.length, start + EXCERPT_WINDOW);\n  let out = '';\n  let cursor = start;\n  for (const o of occ) {\n    if (o.start < start || o.end > end) continue;\n    // Occurrences of duplicate or substring-overlapping terms (\"test tests\") can overlap;\n    // emitting each would duplicate document text. Keep the first, absorb the rest.\n    if (o.start < cursor) continue;\n    out += `${text.slice(cursor, o.start)}«${text.slice(o.start, o.end)}»`;\n    cursor = o.end;\n  }\n  out += text.slice(cursor, end);\n  const prefix = start > 0 ? '…' : '';\n  const suffix = end < text.length ? '…' : '';\n  return { excerpt: `${prefix}${out.replace(/\\s+/g, ' ')}${suffix}`, offset: start };\n}\n\nfunction lineNumberAt(text: string, offset: number): number {\n  let line = 1;\n  for (let i = 0; i < offset; i++) if (text.charCodeAt(i) === 10) line++;\n  return line;\n}\n\nfunction lineRangeFor(db: DatabaseSync, path: string, line: number): string | null {\n  const row = db.prepare('SELECT start_line, end_line FROM sections WHERE \"path\" = ? AND start_line <= ? AND end_line >= ? ORDER BY start_line DESC LIMIT 1').get(path, line, line) as { start_line: number; end_line: number } | undefined;\n  return row ? `L${row.start_line}-${row.end_line}` : null;\n}\n\nexport interface SearchOptions {\n  k?: number;\n  where?: string; // SQL fragment against frontmatter alias `f`, e.g. \"f.status = 'active'\"\n  preset?: string; // named preset; unknown name throws listing declared presets, undefined -> \"default\"\n  include?: string[]; // ad hoc scope override (repeatable --include); independent of exclude\n  exclude?: string[]; // ad hoc scope override (repeatable --exclude); independent of include\n  noExclude?: boolean; // --no-exclude: drop the preset's exclude for this command\n}\n\n// node:path's matchesGlob is experimental (stable behind an unstable-API flag) as of the\n// engines floor (Node >=22.20); scope filtering only ever needs single-pattern matching, so\n// it's used here in JS rather than running a directory walk in the query path.\nfunction inScope(path: string, include: string[], exclude?: string[]): boolean {\n  if (!include.some((g) => matchesGlob(path, g))) return false;\n  if (exclude?.some((g) => matchesGlob(path, g))) return false;\n  return true;\n}\n\nfunction scopeHasEmbeddings(db: DatabaseSync, cfg: ResolvedConfig, scopedPaths: Set<string>): boolean {\n  if (!anyPresetEmbeds(cfg)) return false; // the embeddings table doesn't exist at all in this case\n  const rows = db.prepare('SELECT DISTINCT \"path\" FROM embeddings').all() as Array<{ path: string }>;\n  return rows.some((r) => scopedPaths.has(r.path));\n}\n\n// BM25 + link expansion + vectors, fused by reciprocal rank; `via` names the signal per row.\n// `opts` arrives already resolved (config.ts:resolveSearch).\nexport async function search(db: DatabaseSync, cfg: ResolvedConfig, terms: string, opts: SearchOptions = {}): Promise<Row[]> {\n  const effective = resolveSearch(cfg, opts);\n  const { k, include, exclude } = effective;\n\n  const allPaths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  // A preset scope reads the coverage reconcile indexed; re-matching globs here could disagree\n  // with it. Only ad-hoc scope flags, which have no persisted coverage, pay the JS match.\n  const adHocScope = opts.include !== undefined || opts.exclude !== undefined || opts.noExclude === true;\n  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) as Array<{ path: string }>).map((r) => r.path));\n  // A scope narrower than the whole index needs a bigger candidate pool before filtering, or\n  // filtering can starve k even though enough in-scope matches exist further down the ranked\n  // list that a plain over-fetch wouldn't have reached.\n  const scopeActive = scopedPaths.size < allPaths.length;\n  const fetch = scopeActive ? Math.max(k * 5, 50) : Math.max(k * 3, 30);\n\n  // Asking for vectors without a model is a misconfiguration, not a mode: degrading would make\n  // the same search answer differently before and after a download. semantic:false never asks.\n  const wantsVectors = effective.semantic && anyPresetEmbeds(cfg);\n  if (wantsVectors && !modelPresent(cfg)) {\n    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`);\n  }\n  const semanticEnabled = wantsVectors && scopeHasEmbeddings(db, cfg, scopedPaths);\n\n  // Terms pass verbatim to MATCH; invalid syntax errors rather than being rewritten. --where\n  // applies inside the candidate query (a post-filter would drop matches ranked past the pool)\n  // and again on the final select, for link-derived rows.\n  const scope = effective.where;\n  const whereJoin = scope ? `JOIN frontmatter f ON f.\"path\" = content.path` : '';\n  const whereCond = scope ? `AND (${scope})` : '';\n  // Docs past SNIPPET_BOUND skip snippet() entirely -- SQLite\n  // short-circuits the untaken CASE branch, so it's never invoked on them.\n  const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, -1, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;\n  let matchRows: Array<{ path: string; hit: string | null }>;\n  try {\n    matchRows = db.prepare(matchSql).all(terms) as Array<{ path: string; hit: string | null }>;\n  } catch (err) {\n    throw searchError(err as Error, terms, scope);\n  }\n  // Scope filtering happens in JS, on each candidate list, rather than in SQL: FTS5 match,\n  // link expansion, and vector search all run unscoped above (cheap to over-fetch), then get\n  // filtered here against the effective include/exclude before ranking is finalized.\n  matchRows = matchRows.filter((r) => scopedPaths.has(r.path));\n\n  const hits = new Map(matchRows.map((r) => [r.path, r.hit]));\n  // hit === null here means the bound suppressed snippet(), not \"no match\" -- distinguish\n  // from via='link' rows (never in matchRows, so absent from this set) below.\n  const oversized = new Set(matchRows.filter((r) => r.hit === null).map((r) => r.path));\n  const candidates = new Map<string, { score: number; via: string }>();\n  matchRows.forEach((r, i) => {\n    candidates.set(r.path, { score: 1 / (RRF_K + i), via: 'match' });\n  });\n\n  const edges = featureEnabled(cfg, 'links') && matchRows.length > 0 ? linkEdges(db) : [];\n  if (edges.length > 0) {\n    // Gates the label only, not the score: restart mass ranks every seed without an incident\n    // edge, but dropping it from the score reweights fusion (FEVER hit@10 0.997 -> 0.907).\n    const linked = new Set(edges.flat());\n    const seeds = new Map(matchRows.map((r, i) => [r.path, 1 / (i + 1)]));\n    const ranked = [...personalizedRank(allPaths, edges, seeds)]\n      .filter(([path, score]) => score > 1e-9 && scopedPaths.has(path))\n      .sort((a, b) => b[1] - a[1])\n      .slice(0, fetch);\n    ranked.forEach(([path], i) => {\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        if (linked.has(path)) existing.via = 'match+link';\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'link' });\n      }\n    });\n  }\n\n  // Vector expansion, invoked only: a third RRF list at the swept flat-region constants\n  // (weight 1, pool = fetch). Each row carries its best chunk's line range.\n  const chunkLines = new Map<string, string>();\n  const chunkSimilarity = new Map<string, number>();\n  if (semanticEnabled) {\n    const vec = (await semanticCandidates(db, cfg, terms, fetch)).filter((v) => scopedPaths.has(v.path));\n    vec.forEach(({ path, lines, similarity }, i) => {\n      chunkLines.set(path, lines);\n      chunkSimilarity.set(path, similarity);\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        existing.via = `${existing.via}+vector`;\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'vector' });\n      }\n    });\n  }\n\n  db.exec('DROP TABLE IF EXISTS _search');\n  db.exec('CREATE TEMP TABLE _search (\"path\" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');\n  const insert = db.prepare('INSERT INTO _search (\"path\", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');\n  for (const [path, c] of candidates) insert.run(path, c.score, c.via, hits.get(path) ?? null, chunkLines.get(path) ?? null, chunkSimilarity.get(path) ?? null);\n\n  // Already scope-filtered above; the final select reapplies --where only for link-derived\n  // rows, which never passed through whereCond.\n  const where = scope ? `WHERE (${scope})` : '';\n  // lines is always present now: semantic rows carry their chunk's range, oversized-doc\n  // lexical rows gain one below, everything else stays null. similarity stays semantic-only.\n  const similarityCol = semanticEnabled ? ', _search.similarity' : '';\n  const rows = db\n    .prepare(\n      `SELECT f.\"path\" AS path, content.title, content.summary, _search.hit, _search.via, round(_search.score, 4) AS score, _search.lines${similarityCol}\n       FROM _search JOIN frontmatter f ON f.\"path\" = _search.\"path\" JOIN content ON content.path = _search.\"path\"\n       ${where} ORDER BY _search.score DESC LIMIT ?`\n    )\n    .all(k) as Row[];\n\n  if (oversized.size > 0) {\n    const bareTerms = extractBareTerms(terms);\n    for (const row of rows) {\n      if (row.hit !== null || !oversized.has(row.path as string)) continue;\n      let text: string;\n      try {\n        text = readFileSync(join(cfg.baseDir, row.path as string), 'utf8');\n      } catch {\n        continue; // vanished since the match; leave hit/lines null rather than throw\n      }\n      const { excerpt, offset } = computeExcerpt(text, bareTerms);\n      row.hit = excerpt;\n      if (row.lines == null) row.lines = featureEnabled(cfg, 'sections') ? lineRangeFor(db, row.path as string, lineNumberAt(text, offset)) : null;\n    }\n  }\n\n  return rows;\n}\n\n// The scope resolver for non-search commands (path, peek, map): same coverage rule search()\n// applies (preset_files for a named preset, JS glob matching for an ad hoc include/exclude),\n// then narrowed by the resolved `where`.\nexport function scopedPaths(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides): Set<string> {\n  const effective = resolveSearch(cfg, overrides);\n  const { include, exclude, where } = effective;\n  const allPaths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const adHocScope = overrides.include !== undefined || overrides.exclude !== undefined || overrides.noExclude === true;\n  const paths = adHocScope ? new Set(allPaths.filter((p) => inScope(p, include, exclude))) : new Set((db.prepare('SELECT \"path\" FROM preset_files WHERE preset = ?').all(effective.presetName) as Array<{ path: string }>).map((r) => r.path));\n  if (!where) return paths;\n  const whereRows = db.prepare(`SELECT \"path\" FROM frontmatter f WHERE (${where})`).all() as Array<{ path: string }>;\n  const wherePaths = new Set(whereRows.map((r) => r.path));\n  return new Set([...paths].filter((p) => wherePaths.has(p)));\n}\n\nexport interface PresetCoverage {\n  name: string;\n  files: number;\n  embedded: number;\n  // Reported so 0 embedded reads as \"this scope declined vectors\" rather than \"not yet built\".\n  semantic: boolean;\n}\n\n// Indexing derives from presets, so the derivation stays visible. Read from preset_files, not\n// recomputed from globs, so it reflects the cache rather than the config.\nexport function presetCoverage(db: DatabaseSync, cfg: ResolvedConfig): PresetCoverage[] {\n  const embedActive = anyPresetEmbeds(cfg);\n  return presetNames(cfg).map((name) => {\n    const files = (db.prepare('SELECT COUNT(*) AS n FROM preset_files WHERE preset = ?').get(name) as { n: number }).n;\n    const embedded = embedActive ? (db.prepare('SELECT COUNT(*) AS n FROM preset_files pf WHERE pf.preset = ? AND EXISTS (SELECT 1 FROM embeddings e WHERE e.\"path\" = pf.\"path\" AND e.vector IS NOT NULL)').get(name) as { n: number }).n : 0;\n    return { name, files, embedded, semantic: presetSemanticEnabled(cfg, name) };\n  });\n}\n\nexport interface TreeMap {\n  docs: { count: number; bytes: number };\n  fields: Row[]; // top 20 by coverage; fieldsTotal carries the real count\n  fieldsTotal: number;\n  features: { on: FeatureName[]; off: FeatureName[] };\n  presets: PresetCoverage[];\n  hubs: Row[];\n  recent: Row[];\n}\n\nconst INTERNAL_COLUMNS = new Set(['path', '_mtime', '_size', '_rank', '_parse_error']);\n\n// A result row is capped at SQLITE_MAX_COLUMN (2000, default); two aggregate expressions\n// per field keeps a chunk's row safely under that regardless of how many fields the tree has.\nconst MAP_COLUMN_CHUNK = 300;\n\nfunction chunk<T>(items: T[], size: number): T[][] {\n  const out: T[][] = [];\n  for (let i = 0; i < items.length; i += size) out.push(items.slice(i, i + size));\n  return out;\n}\n\n// Materializes the resolved scope into a temp table (same shape as traverse.ts's\n// allowed_nodes) so every mapTree query can join/filter against it cheaply.\nfunction setupMapScope(db: DatabaseSync, paths: Set<string>): void {\n  db.exec('DROP TABLE IF EXISTS _map_scope');\n  db.exec('CREATE TEMP TABLE _map_scope (\"path\" TEXT PRIMARY KEY)');\n  db.prepare('INSERT INTO _map_scope SELECT DISTINCT value FROM json_each(?1)').run(JSON.stringify([...paths]));\n}\n\n// What is this scope: fixed-size output regardless of tree size. Coverage and features stay\n// global -- they describe the tree, not the current question.\nexport function mapTree(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides = {}): TreeMap {\n  setupMapScope(db, scopedPaths(db, cfg, overrides));\n  const scopeWhere = 'WHERE \"path\" IN (SELECT \"path\" FROM _map_scope)';\n  const scopeAnd = 'AND f.\"path\" IN (SELECT \"path\" FROM _map_scope)';\n\n  const docs = db.prepare(`SELECT COUNT(*) AS count, COALESCE(SUM(\"_size\"), 0) AS bytes FROM frontmatter ${scopeWhere}`).get() as { count: number; bytes: number };\n\n  const columns = (db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>).map((r) => r.name).filter((name) => !INTERNAL_COLUMNS.has(name));\n  // Observed types, not declared: SQLite types per value, so a field can be text in most notes\n  // and numeric in a few. One aggregate scan per chunk of columns; FILTER matches COUNT's nulls.\n  const allFields: Row[] = [];\n  for (const group of chunk(columns, MAP_COLUMN_CHUNK)) {\n    const exprs = group.map((name, i) => {\n      const quoted = `\"${name.split('\"').join('\"\"')}\"`;\n      return `COUNT(${quoted}) AS n${i}, GROUP_CONCAT(DISTINCT typeof(${quoted})) FILTER (WHERE ${quoted} IS NOT NULL) AS t${i}`;\n    });\n    const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter ${scopeWhere}`).get() as Record<string, number | string | null>;\n    group.forEach((name, i) => allFields.push({ field: name, coverage: result[`n${i}`] as number, type: (result[`t${i}`] as string) ?? '' }));\n  }\n  allFields.sort((a, b) => (b.coverage as number) - (a.coverage as number));\n  const fields = allFields.slice(0, 20);\n\n  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() as Row[]) : [];\n\n  const recent = db.prepare(`SELECT \"path\", datetime(\"_mtime\" / 1000, 'unixepoch') AS modified FROM frontmatter ${scopeWhere} ORDER BY \"_mtime\" DESC LIMIT 5`).all() as Row[];\n\n  return { docs, fields, fieldsTotal: allFields.length, features: featureStates(cfg), presets: presetCoverage(db, cfg), hubs, recent };\n}\n\n// Note resolution shared by peek and path: an exact path, or a unique basename (case\n// insensitive, .md stripped).\nexport function resolveNote(paths: string[], arg: string): string {\n  const exact = paths.find((p) => p === arg);\n  if (exact) return exact;\n  const base = posix.basename(arg).replace(/\\.md$/i, '').toLowerCase();\n  const matches = paths.filter((p) => posix.basename(p).replace(/\\.md$/i, '').toLowerCase() === base);\n  if (matches.length === 1) return matches[0];\n  if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `\"${arg}\" is ambiguous: ${matches.join(', ')}`);\n  throw new SenseError('NOTE_NOT_FOUND', `no note matches \"${arg}\"`);\n}\n\nexport interface Peek {\n  path: string;\n  tokens: number;\n  frontmatter: Row;\n  // Set when the note's frontmatter was refused, so an empty frontmatter block reads as \"did\n  // not parse\" rather than \"has none\". Same reason `_parse_error` sits in the row.\n  parseError: string | null;\n  sections: Row[];\n  outbound: string[];\n  backlinks: string[];\n  unresolved: string[];\n  // Totals before truncation: a hub can have thousands of backlinks (or a note thousands of\n  // headings), and peek's whole point is bounded output. Query the sections/links tables\n  // directly for the full list.\n  sectionsTotal: number;\n  outboundTotal: number;\n  backlinksTotal: number;\n  unresolvedTotal: number;\n  // Bounded k-hop expansion beyond the immediate ring already shown by outbound/backlinks\n  // (depth starts at 2).\n  off: FeatureName[]; // disabled features whose blocks are omitted (not empty)\n}\n\nconst PEEK_LIST_LIMIT = 20;\n\n// peek: everything about one note except its prose -- frontmatter, outline with line\n// ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.\nexport function peek(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string, overrides: SearchOverrides = {}): Peek {\n  const paths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const path = resolveNote(paths, pathArg);\n\n  const row = db.prepare('SELECT * FROM frontmatter WHERE \"path\" = ?').get(path) as Row;\n  const parseError = (row._parse_error as string | null) ?? null;\n  const frontmatter: Row = {};\n  for (const [key, value] of Object.entries(row)) {\n    if (!INTERNAL_COLUMNS.has(key) && value !== null) frontmatter[key] = value;\n  }\n\n  const sectionsTotal = featureEnabled(cfg, 'sections') ? (db.prepare('SELECT COUNT(*) AS n FROM sections WHERE \"path\" = ?').get(path) as { n: number }).n : 0;\n  const sections = featureEnabled(cfg, 'sections') ? (db.prepare('SELECT level, heading, start_line, end_line, tokens FROM sections WHERE \"path\" = ? ORDER BY idx LIMIT ?').all(path, PEEK_LIST_LIMIT) as Row[]) : [];\n\n  let outbound: string[] = [];\n  let backlinks: string[] = [];\n  let unresolved: string[] = [];\n  let backlinksTotal = 0;\n  const _allowed = scopedPaths(db, cfg, overrides);\n  if (featureEnabled(cfg, 'links')) {\n    const out = db.prepare('SELECT target, dst FROM links WHERE src = ? ORDER BY target').all(path) as Array<{ target: string; dst: string | null }>;\n    outbound = [...new Set(out.filter((l) => l.dst !== null).map((l) => l.dst as string))];\n    unresolved = out.filter((l) => l.dst === null).map((l) => l.target);\n    backlinksTotal = (db.prepare('SELECT COUNT(DISTINCT src) AS n FROM links WHERE dst = ?').get(path) as { n: number }).n;\n    backlinks = (db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? ORDER BY src LIMIT ?').all(path, PEEK_LIST_LIMIT) as Array<{ src: string }>).map((r) => r.src);\n  }\n\n  return {\n    path,\n    tokens: Math.ceil(((row._size as number) ?? 0) / 4),\n    frontmatter,\n    parseError,\n    sections,\n    outbound: outbound.slice(0, PEEK_LIST_LIMIT),\n    backlinks,\n    unresolved: unresolved.slice(0, PEEK_LIST_LIMIT),\n    sectionsTotal,\n    outboundTotal: outbound.length,\n    backlinksTotal,\n    unresolvedTotal: unresolved.length,\n    off: (['sections', 'links'] as FeatureName[]).filter((name) => !featureEnabled(cfg, name)),\n  };\n}\n\n// Notes most similar by cosine, excluding self and everything already linked either way.\n// Its own command, not a peek section: a full embeddings scan is ~480ms at 26k notes.\nexport async function relatedNotes(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string, overrides: SearchOverrides, k: number): Promise<Array<{ path: string; similarity: number }>> {\n  const paths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const path = resolveNote(paths, pathArg);\n\n  const outbound = (db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL').all(path) as Array<{ dst: string }>).map((r) => r.dst);\n  const backlinks = (db.prepare('SELECT DISTINCT src FROM links WHERE dst = ?').all(path) as Array<{ src: string }>).map((r) => r.src);\n  const exclude = new Set([path, ...outbound, ...backlinks]);\n\n  // Vectors are the only signal `related` has, so every way of not having them is an error\n  // naming the cause. An empty table then means one thing: nothing near in meaning that this\n  // note does not already link to, which is a real answer.\n  const effective = resolveSearch(cfg, overrides);\n  if (!embedEnabled(cfg)) {\n    throw new SenseError('EMBED_DISABLED', 'related ranks notes by meaning, and this tree has no embedding model; add an \"embed\" block naming one to sense.config.json, then run `sense download` (search works without it, on words and links)');\n  }\n  // search gates on the same flag (see wantsVectors above); reading it here too keeps\n  // `semantic: false` meaning one thing. Without this, an overlapping semantic-on preset's\n  // vectors would answer for a scope that declined them.\n  if (!effective.semantic) {\n    throw new SenseError('PRESET_NOT_SEMANTIC', `preset \"${effective.presetName}\" sets \"semantic\": false, so this scope has no vectors and related has no other signal; search it instead (words and links), or set semantic back on for that preset`);\n  }\n  if (!modelPresent(cfg)) {\n    throw new SenseError('EMBED_MODEL_MISSING', 'related ranks notes by meaning, so it needs the embedding model, which is not downloaded; run `sense download` (search still works without it, on words and links)');\n  }\n  const allowed = scopedPaths(db, cfg, overrides);\n  // Top up pending rows before the seed check, or a fresh index reports every note as\n  // having no indexed text until some search has run.\n  await embedPending(db, cfg, cfg.baseDir);\n  if (!hasEmbedding(db, path)) {\n    throw new SenseError('NOTE_NOT_EMBEDDED', `${path} has no indexed text to compare -- a note that is frontmatter only, or empty, has nothing to rank by meaning`);\n  }\n  if (!scopeHasEmbeddings(db, cfg, allowed)) return [];\n  return similarNotes(db, cfg, path, { exclude, allowed, k 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package/dist/cjs/db.d.cts

@@ -1,7 +1,7 @@
 import { DatabaseSync } from 'node:sqlite';
 import type { Config, ResolvedConfig } from './config.js';
 export declare const DB_FILENAME = "cache.db";
-export declare const SCHEMA_VERSION = "8";
+export declare const SCHEMA_VERSION = "9";
 export interface OpenResult {
     db: DatabaseSync;
     cfg: ResolvedConfig;
@@ -17,4 +17,4 @@ export declare function reconcile(db: DatabaseSync, cfg: Config, baseDir: string
     warnings: string[];
 };
 export declare function open(cfg: ResolvedConfig): OpenResult;
-export declare function rebuild(cfg: ResolvedConfig): OpenResult;
+export declare function clearCache(cfg: ResolvedConfig): void;

package/dist/cjs/db.d.ts

@@ -1,7 +1,7 @@
 import { DatabaseSync } from 'node:sqlite';
 import type { Config, ResolvedConfig } from './config.js';
 export declare const DB_FILENAME = "cache.db";
-export declare const SCHEMA_VERSION = "8";
+export declare const SCHEMA_VERSION = "9";
 export interface OpenResult {
     db: DatabaseSync;
     cfg: ResolvedConfig;
@@ -17,4 +17,4 @@ export declare function reconcile(db: DatabaseSync, cfg: Config, baseDir: string
     warnings: string[];
 };
 export declare function open(cfg: ResolvedConfig): OpenResult;
-export declare function rebuild(cfg: ResolvedConfig): OpenResult;
+export declare function clearCache(cfg: ResolvedConfig): void;

package/dist/cjs/db.js

@@ -17,6 +17,9 @@ _export(exports, {
     get SCHEMA_VERSION () {
         return SCHEMA_VERSION;
     },
+    get clearCache () {
+        return clearCache;
+    },
     get docCount () {
         return docCount;
     },
@@ -26,9 +29,6 @@ _export(exports, {
     get open () {
         return open;
     },
-    get rebuild () {
-        return rebuild;
-    },
     get reconcile () {
         return reconcile;
     },
@@ -107,10 +107,11 @@ function _unsupported_iterable_to_array(o, minLen) {
 var CORE_FRONTMATTER_COLUMNS = new Set([
     'path',
     '_mtime',
-    '_size'
+    '_size',
+    '_parse_error'
 ]);
 var DB_FILENAME = 'cache.db';
-var SCHEMA_VERSION = '8';
+var SCHEMA_VERSION = '9';
 // SQLite's compile-time SQLITE_MAX_COLUMN, default 2000 (https://www.sqlite.org/limits.html).
 var MAX_FRONTMATTER_COLUMNS = 2000;
 function quoteIdent(name) {
@@ -149,7 +150,7 @@ function getColumns(db) {
 // Content is a separate table (not a column on frontmatter) so `SELECT * FROM frontmatter`
 // can't dump file text into context. Features add their own tables after the core ones.
 function ensureSchema(db, cfg) {
-    db.exec('CREATE TABLE IF NOT EXISTS frontmatter ("path" TEXT PRIMARY KEY, "_mtime" REAL, "_size" INTEGER)');
+    db.exec('CREATE TABLE IF NOT EXISTS frontmatter ("path" TEXT PRIMARY KEY, "_mtime" REAL, "_size" INTEGER, "_parse_error" TEXT)');
     db.exec("CREATE VIRTUAL TABLE IF NOT EXISTS content USING fts5(title, summary, text, path UNINDEXED, tokenize = 'porter unicode61')");
     // Coverage, not ownership: a path can appear under several presets. path leads the PK so the
     // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.
@@ -407,6 +408,8 @@ function reconcile(db, cfg, baseDir) {
                         if (col === 'path') return doc.relPath;
                         if (col === '_mtime') return doc.mtimeMs;
                         if (col === '_size') return doc.size;
+                        // Written per parse, unlike _rank, which a feature pass owns and the upsert skips.
+                        if (col === '_parse_error') return doc.parseError;
                         return (_doc_data_col = doc.data[col]) !== null && _doc_data_col !== void 0 ? _doc_data_col : null;
                     });
                     (_insert = insert).run.apply(_insert, _to_consumable_array(values));
@@ -626,10 +629,7 @@ function open(cfg) {
             console.error("sense: config change (".concat(changed, ") rebuilds the index"));
         }
         db.close();
-        (0, _nodefs.rmSync)(stateDir, {
-            recursive: true,
-            force: true
-        });
+        clearCache(cfg);
         return open(cfg);
     }
     ensureSchema(db, cfg);
@@ -646,11 +646,10 @@ function open(cfg) {
         warnings: warnings
     };
 }
-function rebuild(cfg) {
+function clearCache(cfg) {
     (0, _nodefs.rmSync)((0, _nodepath.join)(cfg.baseDir, _configts.STATE_DIR), {
         recursive: true,
         force: true
     });
-    return open(cfg);
 }
 /* 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/db.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/db.ts"],"sourcesContent":["// The Node floor (>=22.20) is explained here and nowhere else: 22.20 is the first release with\n// both FTS5 and row-returning INSERT ... RETURNING. Raise it only for a load-bearing capability.\nimport { mkdirSync, rmSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { DatabaseSync } from 'node:sqlite';\nimport type { Config, ResolvedConfig } from './config.ts';\nimport { featureSignature, STATE_DIR } from './config.ts';\nimport { SenseError } from './errors.ts';\nimport { activeFeatures } from './features/index.ts';\nimport type { ReconcileDelta } from './features/types.ts';\nimport { progress } from './progress.ts';\nimport type { ParsedDoc } from './scan.ts';\nimport { listFiles, parseFile, RESERVED_COLUMNS } from './scan.ts';\n\n// Feature-owned columns (`_rank`) must stay out of the upsert: a reparse would null the last\n// computed value on every touch, not just the reconciles that recompute it.\nconst CORE_FRONTMATTER_COLUMNS = new Set(['path', '_mtime', '_size']);\n\n// Rows -> SQLite: core schema, reconcile loop, has(). Parsing lives in scan.ts;\n// everything beyond frontmatter + content lives in src/features/.\n\nexport const DB_FILENAME = 'cache.db';\n// Cache shape version, independent of the config's own `version`. Bumping it rebuilds\n// existing trees on first query.\nexport const SCHEMA_VERSION = '8';\n\n// SQLite's compile-time SQLITE_MAX_COLUMN, default 2000 (https://www.sqlite.org/limits.html).\nconst MAX_FRONTMATTER_COLUMNS = 2000;\n\nexport interface OpenResult {\n  db: DatabaseSync;\n  cfg: ResolvedConfig;\n  dbPath: string;\n  parsed: number;\n  warnings: string[];\n}\n\nfunction quoteIdent(name: string): string {\n  return `\"${name.split('\"').join('\"\"')}\"`;\n}\n\n// has(field, value): JSON-array field -> membership, string field -> substring, NULL -> false.\nfunction registerFunctions(db: DatabaseSync): void {\n  db.function('has', { deterministic: true, varargs: false }, (field: unknown, value: unknown): number => {\n    if (field === null || field === undefined) return 0;\n\n    const needle = String(value);\n\n    if (typeof field === 'string') {\n      if (field.startsWith('[')) {\n        try {\n          const parsed = JSON.parse(field);\n          if (Array.isArray(parsed)) {\n            return parsed.some((item) => String(item) === needle) ? 1 : 0;\n          }\n        } catch {}\n      }\n      return field.includes(needle) ? 1 : 0;\n    }\n\n    return String(field).includes(needle) ? 1 : 0;\n  });\n}\n\nfunction getColumns(db: DatabaseSync): Set<string> {\n  const rows = db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>;\n  return new Set(rows.map((r) => r.name));\n}\n\n// Content is a separate table (not a column on frontmatter) so `SELECT * FROM frontmatter`\n// can't dump file text into context. Features add their own tables after the core ones.\nfunction ensureSchema(db: DatabaseSync, cfg: Config): void {\n  db.exec(`CREATE TABLE IF NOT EXISTS frontmatter (\"path\" TEXT PRIMARY KEY, \"_mtime\" REAL, \"_size\" INTEGER)`);\n  db.exec(`CREATE VIRTUAL TABLE IF NOT EXISTS content USING fts5(title, summary, text, path UNINDEXED, tokenize = 'porter unicode61')`);\n  // Coverage, not ownership: a path can appear under several presets. path leads the PK so the\n  // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.\n  db.exec(`CREATE TABLE IF NOT EXISTS preset_files (\"path\" TEXT, preset TEXT, PRIMARY KEY (\"path\", preset))`);\n  db.exec('CREATE INDEX IF NOT EXISTS preset_files_preset ON preset_files(preset)');\n  for (const feature of activeFeatures(cfg)) feature.schema(db);\n  if (getMeta(db, 'schema_version') === null) setMeta(db, 'schema_version', SCHEMA_VERSION);\n  if (getMeta(db, 'features') === null) setMeta(db, 'features', featureSignature(cfg));\n}\n\nexport function getMeta(db: DatabaseSync, key: string): string | null {\n  const row = db.prepare('SELECT value FROM meta WHERE key = ?').get(key) as { value: string } | undefined;\n  return row ? row.value : null;\n}\n\nexport function setMeta(db: DatabaseSync, key: string, value: string | null): void {\n  if (value === null) {\n    db.prepare('DELETE FROM meta WHERE key = ?').run(key);\n    return;\n  }\n  db.prepare('INSERT INTO meta (key, value) VALUES (?, ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value').run(key, value);\n}\n\nexport function docCount(db: DatabaseSync): number {\n  const row = db.prepare('SELECT COUNT(*) AS n FROM frontmatter').get() as { n: number };\n  return row.n;\n}\n\nexport function reconcile(db: DatabaseSync, cfg: Config, baseDir: string): { parsed: number; warnings: string[] } {\n  const files = listFiles(cfg, baseDir);\n  const currentSet = new Set(files.map((f) => f.relPath));\n\n  const existingRows = db.prepare(`SELECT \"path\", \"_mtime\", \"_size\" FROM frontmatter`).all() as Array<{\n    path: string;\n    _mtime: number;\n    _size: number;\n  }>;\n  const existing = new Map(existingRows.map((r) => [r.path, r]));\n  const vanished = existingRows.filter((r) => !currentSet.has(r.path)).map((r) => r.path);\n\n  const toReparse = files.filter((f) => {\n    const row = existing.get(f.relPath);\n    return !row || row._mtime !== f.mtimeMs || row._size !== f.size;\n  });\n\n  if (vanished.length === 0 && toReparse.length === 0) return { parsed: 0, warnings: [] };\n\n  const features = activeFeatures(cfg);\n  const seenColumns = getColumns(db);\n  const newColumns: string[] = [];\n  const parsedDocs: ParsedDoc[] = [];\n  const warnings: string[] = [];\n\n  // Bulk reparses (a sync, a cold build) are the long silences a query can hit; short\n  // reconciles stay silent (progress() has a threshold).\n  const report = progress('reparsing files', toReparse.length);\n  let parsedCount = 0;\n  for (const file of toReparse) {\n    // A doc only gets extract/store from features that apply to it (currently: embed, via\n    // FileStat.embed -- true iff the config names an embedding model).\n    const fileFeatures = features.filter((feature) => !feature.enabledForFile || feature.enabledForFile(cfg, file));\n    const { doc, warnings: fileWarnings } = parseFile(file, fileFeatures);\n    report.tick(++parsedCount);\n    warnings.push(...fileWarnings);\n    for (const key of Object.keys(doc.data)) {\n      if (!seenColumns.has(key)) {\n        seenColumns.add(key);\n        newColumns.push(key);\n      }\n    }\n    parsedDocs.push(doc);\n  }\n  report.finish();\n\n  const allColumns = [...seenColumns];\n  // Fence before ALTERing: SQLite's own failure past this point is a raw\n  // \"too many columns on sqlite_altertab_frontmatter\" with no indication of the boundary or the levers.\n  if (allColumns.length > MAX_FRONTMATTER_COLUMNS) {\n    throw new SenseError(\n      'COLUMN_LIMIT',\n      `frontmatter would need ${allColumns.length} columns, crossing SQLite's compile-time SQLITE_MAX_COLUMN limit (default ${MAX_FRONTMATTER_COLUMNS}; see https://www.sqlite.org/limits.html). Narrow the presets' include globs so fewer/other files are indexed, or fix whatever is generating unbounded frontmatter keys.`\n    );\n  }\n  // Columns the frontmatter upsert actually writes: core + parsed frontmatter keys, never a\n  // feature-owned reserved column (see CORE_FRONTMATTER_COLUMNS above).\n  const writableColumns = allColumns.filter((c) => CORE_FRONTMATTER_COLUMNS.has(c) || !RESERVED_COLUMNS.has(c));\n  // ON CONFLICT UPDATE (not OR REPLACE) keeps the row's rowid stable across reparses --\n  // content rows are coupled to that rowid below.\n  const insertSql = `INSERT INTO frontmatter (${writableColumns.map(quoteIdent).join(', ')}) VALUES (${writableColumns.map(() => '?').join(', ')}) ON CONFLICT(\"path\") DO UPDATE SET ${writableColumns\n    .filter((c) => c !== 'path')\n    .map((c) => `${quoteIdent(c)} = excluded.${quoteIdent(c)}`)\n    .join(', ')}`;\n\n  const added = toReparse.filter((f) => !existing.has(f.relPath)).map((f) => f.relPath);\n  const delta: ReconcileDelta = { files, reparsed: parsedDocs.map((d) => d.relPath), added, vanished };\n\n  const txStart = Date.now();\n  db.exec('BEGIN');\n  try {\n    for (const col of newColumns) db.exec(`ALTER TABLE frontmatter ADD COLUMN ${quoteIdent(col)}`);\n    // FTS5 has no upsert, so delete-before-insert into `content`; coupled to the\n    // frontmatter rowid (indexed via its PRIMARY KEY) instead of the UNINDEXED `path`\n    // column, which a per-row DELETE would otherwise scan the whole table to find.\n    const delBody = db.prepare(`DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE \"path\" = ?)`);\n    const delPresetFiles = db.prepare(`DELETE FROM preset_files WHERE \"path\" = ?`);\n    const insertPresetFile = db.prepare(`INSERT INTO preset_files (\"path\", preset) VALUES (?, ?)`);\n    if (vanished.length > 0) {\n      const del = db.prepare(`DELETE FROM frontmatter WHERE \"path\" = ?`);\n      for (const path of vanished) {\n        // content delete must run first: it looks up the frontmatter rowid by path, which\n        // the frontmatter delete below would otherwise have already removed.\n        delBody.run(path);\n        del.run(path);\n        delPresetFiles.run(path);\n        for (const feature of features) feature.remove?.(db, path, delta);\n      }\n    }\n    if (parsedDocs.length > 0) {\n      const insert = db.prepare(insertSql);\n      const insertBody = db.prepare(`INSERT INTO content (rowid, title, summary, text, \"path\") VALUES ((SELECT rowid FROM frontmatter WHERE \"path\" = ?), ?, ?, ?, ?)`);\n      for (const doc of parsedDocs) {\n        const values = writableColumns.map((col) => {\n          if (col === 'path') return doc.relPath;\n          if (col === '_mtime') return doc.mtimeMs;\n          if (col === '_size') return doc.size;\n          return doc.data[col] ?? null;\n        });\n        // Frontmatter upsert first: content's rowid lookup below depends on this row existing.\n        insert.run(...values);\n        // Only for docs that have rows: an unconditional delete made cold crawls quadratic.\n        if (existing.has(doc.relPath)) {\n          delBody.run(doc.relPath);\n          for (const feature of features) feature.remove?.(db, doc.relPath, delta);\n        }\n        insertBody.run(doc.relPath, doc.search.title, doc.search.summary, doc.search.text, doc.relPath);\n        // A preset edit forces a full rebuild, so an unchanged doc's coverage is already\n        // correct; new docs have nothing to clear, which keeps cold builds linear.\n        if (existing.has(doc.relPath)) delPresetFiles.run(doc.relPath);\n        for (const presetName of doc.presets) insertPresetFile.run(doc.relPath, presetName);\n        for (const feature of features) feature.store?.(db, doc.relPath, doc.extracted[feature.name], delta);\n      }\n    }\n    for (const feature of features) feature.afterReconcile?.(db, delta);\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n\n  // Reconcile's own write-transaction duration, for open()'s derived busy_timeout (F):\n  // keep the observed max so a big watcher reconcile's lock hold is what the next open bounds its wait against.\n  const durationMs = Date.now() - txStart;\n  const prevRaw = getMeta(db, 'reconcile_max_ms');\n  // -1, not 0, so a genuinely 0ms first reconcile (sub-millisecond, common on a tiny tree)\n  // still gets recorded instead of losing to the \"nothing recorded yet\" default.\n  const prevMax = prevRaw === null ? -1 : Number(prevRaw);\n  if (durationMs > prevMax) setMeta(db, 'reconcile_max_ms', String(durationMs));\n\n  return { parsed: parsedDocs.length, warnings };\n}\n\n// Names what moved between two feature signatures (see config.featureSignature's format:\n// global features, embed provider, then one segment per preset) for the rebuild notice.\nfunction signatureDiff(before: string, after: string): string {\n  // Segment keys: `features`, `embed`, `preset:<name>` (config.featureSignature's format).\n  const keyOf = (part: string) => (part.startsWith('preset:') ? part.split(':').slice(0, 2).join(':') : part.split(':')[0]);\n  const parse = (sig: string) => new Map(sig.split('|').map((part) => [keyOf(part), part]));\n  const a = parse(before);\n  const b = parse(after);\n  const changed = new Set<string>();\n  for (const [key, val] of b) if (a.get(key) !== val) changed.add(key);\n  for (const key of a.keys()) if (!b.has(key)) changed.add(key);\n  const label = (key: string) => (key === 'embed' ? 'embed settings' : key.startsWith('preset:') ? `preset \"${key.slice(7)}\"` : 'features');\n  return changed.size === 0 ? 'features' : [...changed].map(label).join(', ');\n}\n\nexport function open(cfg: ResolvedConfig): OpenResult {\n  const stateDir = join(cfg.baseDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, DB_FILENAME);\n\n  const db = new DatabaseSync(dbPath);\n  db.exec('PRAGMA journal_mode = WAL');\n  // Covers a concurrent watcher's bulk reconcile (~5s for 500 files at 26k notes). A query\n  // that outwaits it still fails loudly.\n  db.exec('PRAGMA busy_timeout = 30000');\n  registerFunctions(db);\n\n  db.exec('CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT)');\n\n  // Schema-version or feature-set mismatch: reconcile only reparses changed files, so an\n  // old cache can't be patched incrementally -- rebuild instead (cheap: nothing expensive lives here).\n  const version = getMeta(db, 'schema_version');\n  const features = getMeta(db, 'features');\n  const wantFeatures = featureSignature(cfg);\n  if ((version !== null && version !== SCHEMA_VERSION) || (features !== null && features !== wantFeatures)) {\n    // Indexing derives from presets, so a config edit rebuilding the cache must say so and\n    // name what changed -- silent rebuilds make derived indexing look like a hang or a bug.\n    if (version !== null && version !== SCHEMA_VERSION) {\n      console.error('sense: cache format changed (new sensemaking version); rebuilding the index');\n    } else {\n      const changed = signatureDiff(features ?? 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Raise it only for a load-bearing capability.\nimport { mkdirSync, rmSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { DatabaseSync } from 'node:sqlite';\nimport type { Config, ResolvedConfig } from './config.ts';\nimport { featureSignature, STATE_DIR } from './config.ts';\nimport { SenseError } from './errors.ts';\nimport { activeFeatures } from './features/index.ts';\nimport type { ReconcileDelta } from './features/types.ts';\nimport { progress } from './progress.ts';\nimport type { ParsedDoc } from './scan.ts';\nimport { listFiles, parseFile, RESERVED_COLUMNS } from './scan.ts';\n\n// Feature-owned columns (`_rank`) must stay out of the upsert: a reparse would null the last\n// computed value on every touch, not just the reconciles that recompute it.\nconst CORE_FRONTMATTER_COLUMNS = new Set(['path', '_mtime', '_size', '_parse_error']);\n\n// Rows -> SQLite: core schema, reconcile loop, has(). Parsing lives in scan.ts;\n// everything beyond frontmatter + content lives in src/features/.\n\nexport const DB_FILENAME = 'cache.db';\n// Cache shape version, independent of the config's own `version`. Bumping it rebuilds\n// existing trees on first query.\nexport const SCHEMA_VERSION = '9';\n\n// SQLite's compile-time SQLITE_MAX_COLUMN, default 2000 (https://www.sqlite.org/limits.html).\nconst MAX_FRONTMATTER_COLUMNS = 2000;\n\nexport interface OpenResult {\n  db: DatabaseSync;\n  cfg: ResolvedConfig;\n  dbPath: string;\n  parsed: number;\n  warnings: string[];\n}\n\nfunction quoteIdent(name: string): string {\n  return `\"${name.split('\"').join('\"\"')}\"`;\n}\n\n// has(field, value): JSON-array field -> membership, string field -> substring, NULL -> false.\nfunction registerFunctions(db: DatabaseSync): void {\n  db.function('has', { deterministic: true, varargs: false }, (field: unknown, value: unknown): number => {\n    if (field === null || field === undefined) return 0;\n\n    const needle = String(value);\n\n    if (typeof field === 'string') {\n      if (field.startsWith('[')) {\n        try {\n          const parsed = JSON.parse(field);\n          if (Array.isArray(parsed)) {\n            return parsed.some((item) => String(item) === needle) ? 1 : 0;\n          }\n        } catch {}\n      }\n      return field.includes(needle) ? 1 : 0;\n    }\n\n    return String(field).includes(needle) ? 1 : 0;\n  });\n}\n\nfunction getColumns(db: DatabaseSync): Set<string> {\n  const rows = db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>;\n  return new Set(rows.map((r) => r.name));\n}\n\n// Content is a separate table (not a column on frontmatter) so `SELECT * FROM frontmatter`\n// can't dump file text into context. Features add their own tables after the core ones.\nfunction ensureSchema(db: DatabaseSync, cfg: Config): void {\n  db.exec(`CREATE TABLE IF NOT EXISTS frontmatter (\"path\" TEXT PRIMARY KEY, \"_mtime\" REAL, \"_size\" INTEGER, \"_parse_error\" TEXT)`);\n  db.exec(`CREATE VIRTUAL TABLE IF NOT EXISTS content USING fts5(title, summary, text, path UNINDEXED, tokenize = 'porter unicode61')`);\n  // Coverage, not ownership: a path can appear under several presets. path leads the PK so the\n  // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.\n  db.exec(`CREATE TABLE IF NOT EXISTS preset_files (\"path\" TEXT, preset TEXT, PRIMARY KEY (\"path\", preset))`);\n  db.exec('CREATE INDEX IF NOT EXISTS preset_files_preset ON preset_files(preset)');\n  for (const feature of activeFeatures(cfg)) feature.schema(db);\n  if (getMeta(db, 'schema_version') === null) setMeta(db, 'schema_version', SCHEMA_VERSION);\n  if (getMeta(db, 'features') === null) setMeta(db, 'features', featureSignature(cfg));\n}\n\nexport function getMeta(db: DatabaseSync, key: string): string | null {\n  const row = db.prepare('SELECT value FROM meta WHERE key = ?').get(key) as { value: string } | undefined;\n  return row ? row.value : null;\n}\n\nexport function setMeta(db: DatabaseSync, key: string, value: string | null): void {\n  if (value === null) {\n    db.prepare('DELETE FROM meta WHERE key = ?').run(key);\n    return;\n  }\n  db.prepare('INSERT INTO meta (key, value) VALUES (?, ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value').run(key, value);\n}\n\nexport function docCount(db: DatabaseSync): number {\n  const row = db.prepare('SELECT COUNT(*) AS n FROM frontmatter').get() as { n: number };\n  return row.n;\n}\n\nexport function reconcile(db: DatabaseSync, cfg: Config, baseDir: string): { parsed: number; warnings: string[] } {\n  const files = listFiles(cfg, baseDir);\n  const currentSet = new Set(files.map((f) => f.relPath));\n\n  const existingRows = db.prepare(`SELECT \"path\", \"_mtime\", \"_size\" FROM frontmatter`).all() as Array<{\n    path: string;\n    _mtime: number;\n    _size: number;\n  }>;\n  const existing = new Map(existingRows.map((r) => [r.path, r]));\n  const vanished = existingRows.filter((r) => !currentSet.has(r.path)).map((r) => r.path);\n\n  const toReparse = files.filter((f) => {\n    const row = existing.get(f.relPath);\n    return !row || row._mtime !== f.mtimeMs || row._size !== f.size;\n  });\n\n  if (vanished.length === 0 && toReparse.length === 0) return { parsed: 0, warnings: [] };\n\n  const features = activeFeatures(cfg);\n  const seenColumns = getColumns(db);\n  const newColumns: string[] = [];\n  const parsedDocs: ParsedDoc[] = [];\n  const warnings: string[] = [];\n\n  // Bulk reparses (a sync, a cold build) are the long silences a query can hit; short\n  // reconciles stay silent (progress() has a threshold).\n  const report = progress('reparsing files', toReparse.length);\n  let parsedCount = 0;\n  for (const file of toReparse) {\n    // A doc only gets extract/store from features that apply to it (currently: embed, via\n    // FileStat.embed -- true iff the config names an embedding model).\n    const fileFeatures = features.filter((feature) => !feature.enabledForFile || feature.enabledForFile(cfg, file));\n    const { doc, warnings: fileWarnings } = parseFile(file, fileFeatures);\n    report.tick(++parsedCount);\n    warnings.push(...fileWarnings);\n    for (const key of Object.keys(doc.data)) {\n      if (!seenColumns.has(key)) {\n        seenColumns.add(key);\n        newColumns.push(key);\n      }\n    }\n    parsedDocs.push(doc);\n  }\n  report.finish();\n\n  const allColumns = [...seenColumns];\n  // Fence before ALTERing: SQLite's own failure past this point is a raw\n  // \"too many columns on sqlite_altertab_frontmatter\" with no indication of the boundary or the levers.\n  if (allColumns.length > MAX_FRONTMATTER_COLUMNS) {\n    throw new SenseError(\n      'COLUMN_LIMIT',\n      `frontmatter would need ${allColumns.length} columns, crossing SQLite's compile-time SQLITE_MAX_COLUMN limit (default ${MAX_FRONTMATTER_COLUMNS}; see https://www.sqlite.org/limits.html). Narrow the presets' include globs so fewer/other files are indexed, or fix whatever is generating unbounded frontmatter keys.`\n    );\n  }\n  // Columns the frontmatter upsert actually writes: core + parsed frontmatter keys, never a\n  // feature-owned reserved column (see CORE_FRONTMATTER_COLUMNS above).\n  const writableColumns = allColumns.filter((c) => CORE_FRONTMATTER_COLUMNS.has(c) || !RESERVED_COLUMNS.has(c));\n  // ON CONFLICT UPDATE (not OR REPLACE) keeps the row's rowid stable across reparses --\n  // content rows are coupled to that rowid below.\n  const insertSql = `INSERT INTO frontmatter (${writableColumns.map(quoteIdent).join(', ')}) VALUES (${writableColumns.map(() => '?').join(', ')}) ON CONFLICT(\"path\") DO UPDATE SET ${writableColumns\n    .filter((c) => c !== 'path')\n    .map((c) => `${quoteIdent(c)} = excluded.${quoteIdent(c)}`)\n    .join(', ')}`;\n\n  const added = toReparse.filter((f) => !existing.has(f.relPath)).map((f) => f.relPath);\n  const delta: ReconcileDelta = { files, reparsed: parsedDocs.map((d) => d.relPath), added, vanished };\n\n  const txStart = Date.now();\n  db.exec('BEGIN');\n  try {\n    for (const col of newColumns) db.exec(`ALTER TABLE frontmatter ADD COLUMN ${quoteIdent(col)}`);\n    // FTS5 has no upsert, so delete-before-insert into `content`; coupled to the\n    // frontmatter rowid (indexed via its PRIMARY KEY) instead of the UNINDEXED `path`\n    // column, which a per-row DELETE would otherwise scan the whole table to find.\n    const delBody = db.prepare(`DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE \"path\" = ?)`);\n    const delPresetFiles = db.prepare(`DELETE FROM preset_files WHERE \"path\" = ?`);\n    const insertPresetFile = db.prepare(`INSERT INTO preset_files (\"path\", preset) VALUES (?, ?)`);\n    if (vanished.length > 0) {\n      const del = db.prepare(`DELETE FROM frontmatter WHERE \"path\" = ?`);\n      for (const path of vanished) {\n        // content delete must run first: it looks up the frontmatter rowid by path, which\n        // the frontmatter delete below would otherwise have already removed.\n        delBody.run(path);\n        del.run(path);\n        delPresetFiles.run(path);\n        for (const feature of features) feature.remove?.(db, path, delta);\n      }\n    }\n    if (parsedDocs.length > 0) {\n      const insert = db.prepare(insertSql);\n      const insertBody = db.prepare(`INSERT INTO content (rowid, title, summary, text, \"path\") VALUES ((SELECT rowid FROM frontmatter WHERE \"path\" = ?), ?, ?, ?, ?)`);\n      for (const doc of parsedDocs) {\n        const values = writableColumns.map((col) => {\n          if (col === 'path') return doc.relPath;\n          if (col === '_mtime') return doc.mtimeMs;\n          if (col === '_size') return doc.size;\n          // Written per parse, unlike _rank, which a feature pass owns and the upsert skips.\n          if (col === '_parse_error') return doc.parseError;\n          return doc.data[col] ?? null;\n        });\n        // Frontmatter upsert first: content's rowid lookup below depends on this row existing.\n        insert.run(...values);\n        // Only for docs that have rows: an unconditional delete made cold crawls quadratic.\n        if (existing.has(doc.relPath)) {\n          delBody.run(doc.relPath);\n          for (const feature of features) feature.remove?.(db, doc.relPath, delta);\n        }\n        insertBody.run(doc.relPath, doc.search.title, doc.search.summary, doc.search.text, doc.relPath);\n        // A preset edit forces a full rebuild, so an unchanged doc's coverage is already\n        // correct; new docs have nothing to clear, which keeps cold builds linear.\n        if (existing.has(doc.relPath)) delPresetFiles.run(doc.relPath);\n        for (const presetName of doc.presets) insertPresetFile.run(doc.relPath, presetName);\n        for (const feature of features) feature.store?.(db, doc.relPath, doc.extracted[feature.name], delta);\n      }\n    }\n    for (const feature of features) feature.afterReconcile?.(db, delta);\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n\n  // Reconcile's own write-transaction duration, for open()'s derived busy_timeout (F):\n  // keep the observed max so a big watcher reconcile's lock hold is what the next open bounds its wait against.\n  const durationMs = Date.now() - txStart;\n  const prevRaw = getMeta(db, 'reconcile_max_ms');\n  // -1, not 0, so a genuinely 0ms first reconcile (sub-millisecond, common on a tiny tree)\n  // still gets recorded instead of losing to the \"nothing recorded yet\" default.\n  const prevMax = prevRaw === null ? -1 : Number(prevRaw);\n  if (durationMs > prevMax) setMeta(db, 'reconcile_max_ms', String(durationMs));\n\n  return { parsed: parsedDocs.length, warnings };\n}\n\n// Names what moved between two feature signatures (see config.featureSignature's format:\n// global features, embed provider, then one segment per preset) for the rebuild notice.\nfunction signatureDiff(before: string, after: string): string {\n  // Segment keys: `features`, `embed`, `preset:<name>` (config.featureSignature's format).\n  const keyOf = (part: string) => (part.startsWith('preset:') ? part.split(':').slice(0, 2).join(':') : part.split(':')[0]);\n  const parse = (sig: string) => new Map(sig.split('|').map((part) => [keyOf(part), part]));\n  const a = parse(before);\n  const b = parse(after);\n  const changed = new Set<string>();\n  for (const [key, val] of b) if (a.get(key) !== val) changed.add(key);\n  for (const key of a.keys()) if (!b.has(key)) changed.add(key);\n  const label = (key: string) => (key === 'embed' ? 'embed settings' : key.startsWith('preset:') ? `preset \"${key.slice(7)}\"` : 'features');\n  return changed.size === 0 ? 'features' : [...changed].map(label).join(', ');\n}\n\nexport function open(cfg: ResolvedConfig): OpenResult {\n  const stateDir = join(cfg.baseDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, DB_FILENAME);\n\n  const db = new DatabaseSync(dbPath);\n  db.exec('PRAGMA journal_mode = WAL');\n  // Covers a concurrent watcher's bulk reconcile (~5s for 500 files at 26k notes). A query\n  // that outwaits it still fails loudly.\n  db.exec('PRAGMA busy_timeout = 30000');\n  registerFunctions(db);\n\n  db.exec('CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT)');\n\n  // Schema-version or feature-set mismatch: reconcile only reparses changed files, so an\n  // old cache can't be patched incrementally -- rebuild instead (cheap: nothing expensive lives here).\n  const version = getMeta(db, 'schema_version');\n  const features = getMeta(db, 'features');\n  const wantFeatures = featureSignature(cfg);\n  if ((version !== null && version !== SCHEMA_VERSION) || (features !== null && features !== wantFeatures)) {\n    // Indexing derives from presets, so a config edit rebuilding the cache must say so and\n    // name what changed -- silent rebuilds make derived indexing look like a hang or a bug.\n    if (version !== null && version !== SCHEMA_VERSION) {\n      console.error('sense: cache format changed (new sensemaking version); rebuilding the index');\n    } else {\n      const changed = signatureDiff(features ?? 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package/dist/cjs/errors.d.cts

@@ -1,4 +1,4 @@
-export type SenseErrorCode = 'CONFIG_NOT_FOUND' | 'CONFIG_EXISTS' | 'CONFIG_INVALID' | 'CONFIG_VERSION_UNSUPPORTED' | 'WATCH_ACTIVE' | 'NOTE_NOT_FOUND' | 'NOTE_AMBIGUOUS' | 'EMBED_DISABLED' | 'EMBED_MODEL' | 'EMBED_MODEL_MISSING' | 'SEARCH_SYNTAX' | 'COLUMN_LIMIT' | 'PRESET_UNKNOWN';
+export type SenseErrorCode = 'CONFIG_NOT_FOUND' | 'CONFIG_EXISTS' | 'CONFIG_INVALID' | 'CONFIG_VERSION_UNSUPPORTED' | 'WATCH_ACTIVE' | 'NOTE_NOT_FOUND' | 'NOTE_AMBIGUOUS' | 'EMBED_DISABLED' | 'EMBED_MODEL' | 'EMBED_MODEL_MISSING' | 'SEARCH_SYNTAX' | 'COLUMN_LIMIT' | 'PRESET_UNKNOWN' | 'PRESET_NOT_SEMANTIC' | 'NOTE_NOT_EMBEDDED';
 export declare class SenseError extends Error {
     code: SenseErrorCode;
     constructor(code: SenseErrorCode, message: string);

package/dist/cjs/errors.d.ts

@@ -1,4 +1,4 @@
-export type SenseErrorCode = 'CONFIG_NOT_FOUND' | 'CONFIG_EXISTS' | 'CONFIG_INVALID' | 'CONFIG_VERSION_UNSUPPORTED' | 'WATCH_ACTIVE' | 'NOTE_NOT_FOUND' | 'NOTE_AMBIGUOUS' | 'EMBED_DISABLED' | 'EMBED_MODEL' | 'EMBED_MODEL_MISSING' | 'SEARCH_SYNTAX' | 'COLUMN_LIMIT' | 'PRESET_UNKNOWN';
+export type SenseErrorCode = 'CONFIG_NOT_FOUND' | 'CONFIG_EXISTS' | 'CONFIG_INVALID' | 'CONFIG_VERSION_UNSUPPORTED' | 'WATCH_ACTIVE' | 'NOTE_NOT_FOUND' | 'NOTE_AMBIGUOUS' | 'EMBED_DISABLED' | 'EMBED_MODEL' | 'EMBED_MODEL_MISSING' | 'SEARCH_SYNTAX' | 'COLUMN_LIMIT' | 'PRESET_UNKNOWN' | 'PRESET_NOT_SEMANTIC' | 'NOTE_NOT_EMBEDDED';
 export declare class SenseError extends Error {
     code: SenseErrorCode;
     constructor(code: SenseErrorCode, message: string);