sensemaking 0.9.4 → 0.10.0

package/dist/esm/commands.js

@@ -3,7 +3,7 @@ import { join, matchesGlob } from 'node:path';
 import posix from 'node:path/posix';
 import { anyPresetEmbeds, featureEnabled, featureStates, presetNames, resolveSearch } from './config.js';
 import { SenseError } from './errors.js';
-import { semanticCandidates } from './features/embed.js';
+import { embedPending, modelPresent, semanticCandidates, similarNotes } from './features/embed.js';
 import { linkEdges } from './features/index.js';
 import { personalizedRank } from './graph.js';
 import { searchError } from './search-error.js';
@@ -11,11 +11,8 @@ import { searchError } from './search-error.js';
 // Each returns data; cli.ts renders. All of them degrade when a feature is off.
 const WEIGHTED_BM25 = 'bm25(content, 10.0, 5.0, 1.0)';
 const RRF_K = 60;
-// FTS5 snippet() re-tokenizes the whole doc per candidate row, superlinearly: measured
-// 2ms at 4KB docs but 189ms at 64KB for one query's pool, and ~10s for a single 1MB doc
-// (plans/performance-findings.md finding A). 16KB keeps the whole pool's snippet cost in
-// the low-ms range; bigger docs get the JS-computed excerpt, linear and only for the rows
-// actually returned.
+// snippet() re-tokenizes each candidate doc, superlinearly: ~10s for one 1MB doc
+// (BENCHMARKING.md). Past this bound, rows get the linear JS excerpt instead.
 const SNIPPET_BOUND = 16384;
 const EXCERPT_WINDOW = 160;
 // Bare terms from an FTS5 query string: strips operators/quoting so the oversized-doc excerpt
@@ -110,8 +107,8 @@ function lineRangeFor(db, path, line) {
     return row ? `L${row.start_line}-${row.end_line}` : null;
 }
 // node:path's matchesGlob is experimental (stable behind an unstable-API flag) as of the
-// engines floor (Node >=22.16); scope filtering only ever needs single-pattern matching, so
-// it's used here in JS rather than pulling fast-glob's directory walk into the query path.
+// engines floor (Node >=22.20); scope filtering only ever needs single-pattern matching, so
+// it's used here in JS rather than running a directory walk in the query path.
 function inScope(path, include, exclude) {
     if (!include.some((g)=>matchesGlob(path, g))) return false;
     if (exclude === null || exclude === void 0 ? void 0 : exclude.some((g)=>matchesGlob(path, g))) return false;
@@ -122,36 +119,32 @@ function scopeHasEmbeddings(db, cfg, scopedPaths) {
     const rows = db.prepare('SELECT DISTINCT "path" FROM embeddings').all();
     return rows.some((r)=>scopedPaths.has(r.path));
 }
-// BM25 + link-graph expansion, fused by reciprocal rank. `via` says which signal produced
-// each row so the agent knows what evidence it is trusting.
-// Resolution precedence (built-ins <- preset <- caller overrides) lives in
-// src/config.ts:resolveSearch; `opts` here is whatever the caller (a saved search merged
-// with any CLI flag, or a bare CLI invocation) already resolved.
+// BM25 + link expansion + vectors, fused by reciprocal rank; `via` names the signal per row.
+// `opts` arrives already resolved (config.ts:resolveSearch).
 export async function search(db, cfg, terms, opts = {}) {
     var _hits_get, _chunkLines_get, _chunkSimilarity_get;
     const effective = resolveSearch(cfg, opts);
     const { k, include, exclude } = effective;
     const allPaths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
-    // A preset scope reads preset_files -- the coverage reconcile actually indexed with
-    // (fast-glob semantics); re-matching globs here with node:path's matchesGlob could
-    // silently disagree with it. Ad-hoc --include has no persisted coverage, so only that
-    // path pays the JS glob match.
-    const scopedPaths = opts.include ? new Set(allPaths.filter((p)=>inScope(p, include, exclude))) : new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
+    // A preset scope reads the coverage reconcile indexed; re-matching globs here could disagree
+    // with it. Only ad-hoc scope flags, which have no persisted coverage, pay the JS match.
+    const adHocScope = opts.include !== undefined || opts.exclude !== undefined || opts.noExclude === true;
+    const scopedPaths = adHocScope ? new Set(allPaths.filter((p)=>inScope(p, include, exclude))) : new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
     // A scope narrower than the whole index needs a bigger candidate pool before filtering, or
     // filtering can starve k even though enough in-scope matches exist further down the ranked
     // list that a plain over-fetch wouldn't have reached.
     const scopeActive = scopedPaths.size < allPaths.length;
     const fetch = scopeActive ? Math.max(k * 5, 50) : Math.max(k * 3, 30);
-    // Semantic participation: vectors run only when the effective setting allows it AND the
-    // scope actually has embedded files -- a scope covered only by semantic-false presets (or
-    // by no preset embedding at all) searches lexically, automatically, no error.
-    const semanticEnabled = effective.semantic && scopeHasEmbeddings(db, cfg, scopedPaths);
-    // Terms pass verbatim to FTS5 MATCH: bare words AND-join, operators are the caller's.
-    // Invalid syntax propagates as an error, zero matches return zero -- no silent rewrites.
-    // --where applies inside the candidate query (a post-filter over the top-N would drop
-    // matches ranked past the pool) and again on the final select for link-derived rows.
-    // An explicit --where replaces the preset's declared where rather than ANDing with it,
-    // so a caller can always widen back to the whole scope.
+    // Asking for vectors without a model is a misconfiguration, not a mode: degrading would make
+    // the same search answer differently before and after a download. semantic:false never asks.
+    const wantsVectors = !opts.probe && effective.semantic && anyPresetEmbeds(cfg);
+    if (wantsVectors && !modelPresent(cfg)) {
+        throw new SenseError('EMBED_MODEL_MISSING', `preset "${effective.presetName}" searches with vectors, but the embedding model is not available; run \`sense download\`, or set "semantic": false on that preset to search on words and links`);
+    }
+    const semanticEnabled = wantsVectors && scopeHasEmbeddings(db, cfg, scopedPaths);
+    // Terms pass verbatim to MATCH; invalid syntax errors rather than being rewritten. --where
+    // applies inside the candidate query (a post-filter would drop matches ranked past the pool)
+    // and again on the final select, for link-derived rows.
     const scope = effective.where;
     const whereJoin = scope ? `JOIN frontmatter f ON f."path" = content.path` : '';
     const whereCond = scope ? `AND (${scope})` : '';
@@ -184,10 +177,8 @@ export async function search(db, cfg, terms, opts = {}) {
     });
     const edges = featureEnabled(cfg, 'links') && matchRows.length > 0 ? linkEdges(db) : [];
     if (edges.length > 0) {
-        // `linked` gates the label only, not the score: PPR restart mass gives every seed a
-        // nonzero rank even without an incident edge, which is not link evidence — but dropping
-        // that mass from the score list reweights fusion toward connectivity and measurably
-        // wrecks ranking on link-dense corpora (FEVER hit@10 0.997 -> 0.907; fusion-tuning.md).
+        // Gates the label only, not the score: restart mass ranks every seed without an incident
+        // edge, but dropping it from the score reweights fusion (FEVER hit@10 0.997 -> 0.907).
         const linked = new Set(edges.flat());
         const seeds = new Map(matchRows.map((r, i)=>[
                 r.path,
@@ -230,21 +221,19 @@ export async function search(db, cfg, terms, opts = {}) {
             }
         });
     }
-    db.exec('DROP TABLE IF EXISTS _find');
-    db.exec('CREATE TEMP TABLE _find ("path" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');
-    const insert = db.prepare('INSERT INTO _find ("path", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');
+    db.exec('DROP TABLE IF EXISTS _search');
+    db.exec('CREATE TEMP TABLE _search ("path" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');
+    const insert = db.prepare('INSERT INTO _search ("path", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');
     for (const [path, c] of candidates)insert.run(path, c.score, c.via, (_hits_get = hits.get(path)) !== null && _hits_get !== void 0 ? _hits_get : null, (_chunkLines_get = chunkLines.get(path)) !== null && _chunkLines_get !== void 0 ? _chunkLines_get : null, (_chunkSimilarity_get = chunkSimilarity.get(path)) !== null && _chunkSimilarity_get !== void 0 ? _chunkSimilarity_get : null);
-    // Every candidate list was already filtered to scopedPaths above, so _find only ever holds
-    // in-scope rows -- the final select just needs --where again, same as before, for rows
-    // whichever candidate query didn't itself apply it to (link-derived rows never touched
-    // whereCond above).
+    // Already scope-filtered above; the final select reapplies --where only for link-derived
+    // rows, which never passed through whereCond.
     const where = scope ? `WHERE (${scope})` : '';
     // lines is always present now: semantic rows carry their chunk's range, oversized-doc
     // lexical rows gain one below, everything else stays null. similarity stays semantic-only.
-    const similarityCol = semanticEnabled ? ', _find.similarity' : '';
-    const rows = db.prepare(`SELECT f."path" AS path, content.title, content.summary, _find.hit, _find.via, round(_find.score, 4) AS score, _find.lines${similarityCol}
-       FROM _find JOIN frontmatter f ON f."path" = _find."path" JOIN content ON content.path = _find."path"
-       ${where} ORDER BY _find.score DESC LIMIT ?`).all(k);
+    const similarityCol = semanticEnabled ? ', _search.similarity' : '';
+    const rows = db.prepare(`SELECT f."path" AS path, content.title, content.summary, _search.hit, _search.via, round(_search.score, 4) AS score, _search.lines${similarityCol}
+       FROM _search JOIN frontmatter f ON f."path" = _search."path" JOIN content ON content.path = _search."path"
+       ${where} ORDER BY _search.score DESC LIMIT ?`).all(k);
     if (oversized.size > 0) {
         const bareTerms = extractBareTerms(terms);
         for (const row of rows){
@@ -262,10 +251,24 @@ export async function search(db, cfg, terms, opts = {}) {
     }
     return rows;
 }
-// Indexing and embedding are both derived from presets rather than declared directly, so
-// that derivation must stay visible: how many files each preset actually matched, and how
-// many of those are covered by embedding. Read from preset_files (rebuilt at reconcile), not
-// recomputed from globs, so this always reflects what's actually on disk in the cache.
+// The scope resolver for non-search commands (path, peek, map): same coverage rule search()
+// applies (preset_files for a named preset, JS glob matching for an ad hoc include/exclude),
+// then narrowed by the resolved `where`.
+export function scopedPaths(db, cfg, overrides) {
+    const effective = resolveSearch(cfg, overrides);
+    const { include, exclude, where } = effective;
+    const allPaths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
+    const adHocScope = overrides.include !== undefined || overrides.exclude !== undefined || overrides.noExclude === true;
+    const paths = adHocScope ? new Set(allPaths.filter((p)=>inScope(p, include, exclude))) : new Set(db.prepare('SELECT "path" FROM preset_files WHERE preset = ?').all(effective.presetName).map((r)=>r.path));
+    if (!where) return paths;
+    const whereRows = db.prepare(`SELECT "path" FROM frontmatter f WHERE (${where})`).all();
+    const wherePaths = new Set(whereRows.map((r)=>r.path));
+    return new Set([
+        ...paths
+    ].filter((p)=>wherePaths.has(p)));
+}
+// Indexing derives from presets, so the derivation stays visible. Read from preset_files, not
+// recomputed from globs, so it reflects the cache rather than the config.
 export function presetCoverage(db, cfg) {
     const embedActive = anyPresetEmbeds(cfg);
     return presetNames(cfg).map((name)=>{
@@ -292,23 +295,32 @@ function chunk(items, size) {
     for(let i = 0; i < items.length; i += size)out.push(items.slice(i, i + size));
     return out;
 }
-// mapTree: what is this tree. Fixed-size output regardless of tree size.
-export function mapTree(db, cfg) {
-    const docs = db.prepare('SELECT COUNT(*) AS count, COALESCE(SUM("_size"), 0) AS bytes FROM frontmatter').get();
+// Materializes the resolved scope into a temp table (same shape as traverse.ts's
+// allowed_nodes) so every mapTree query can join/filter against it cheaply.
+function setupMapScope(db, paths) {
+    db.exec('DROP TABLE IF EXISTS _map_scope');
+    db.exec('CREATE TEMP TABLE _map_scope ("path" TEXT PRIMARY KEY)');
+    db.prepare('INSERT INTO _map_scope SELECT DISTINCT value FROM json_each(?1)').run(JSON.stringify([
+        ...paths
+    ]));
+}
+// What is this scope: fixed-size output regardless of tree size. Coverage and features stay
+// global -- they describe the tree, not the current question.
+export function mapTree(db, cfg, overrides = {}) {
+    setupMapScope(db, scopedPaths(db, cfg, overrides));
+    const scopeWhere = 'WHERE "path" IN (SELECT "path" FROM _map_scope)';
+    const scopeAnd = 'AND f."path" IN (SELECT "path" FROM _map_scope)';
+    const docs = db.prepare(`SELECT COUNT(*) AS count, COALESCE(SUM("_size"), 0) AS bytes FROM frontmatter ${scopeWhere}`).get();
     const columns = db.prepare('PRAGMA table_info(frontmatter)').all().map((r)=>r.name).filter((name)=>!INTERNAL_COLUMNS.has(name));
-    // Observed storage class, not a declared one: these columns are added dynamically and
-    // SQLite types per value, so a field can be text in most notes and numeric in a few.
-    // Listing every distinct type makes both the type and any drift visible.
-    // One aggregate scan per chunk of columns rather than one scan per column: COUNT already
-    // ignores NULL, and FILTER keeps typeof() looking only at the non-null rows COUNT counted,
-    // matching the old per-column `WHERE ... IS NOT NULL` exactly.
+    // Observed types, not declared: SQLite types per value, so a field can be text in most notes
+    // and numeric in a few. One aggregate scan per chunk of columns; FILTER matches COUNT's nulls.
     const allFields = [];
     for (const group of chunk(columns, MAP_COLUMN_CHUNK)){
         const exprs = group.map((name, i)=>{
             const quoted = `"${name.split('"').join('""')}"`;
             return `COUNT(${quoted}) AS n${i}, GROUP_CONCAT(DISTINCT typeof(${quoted})) FILTER (WHERE ${quoted} IS NOT NULL) AS t${i}`;
         });
-        const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter`).get();
+        const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter ${scopeWhere}`).get();
         group.forEach((name, i)=>{
             var _result_;
             return allFields.push({
@@ -320,8 +332,8 @@ export function mapTree(db, cfg) {
     }
     allFields.sort((a, b)=>b.coverage - a.coverage);
     const fields = allFields.slice(0, 20);
-    const hubs = featureEnabled(cfg, 'rank') ? db.prepare(`SELECT f."path" AS path, round(f."_rank" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f."path" WHERE f."_rank" IS NOT NULL ORDER BY f."_rank" DESC LIMIT 8`).all() : [];
-    const recent = db.prepare(`SELECT "path", datetime("_mtime" / 1000, 'unixepoch') AS modified FROM frontmatter ORDER BY "_mtime" DESC LIMIT 5`).all();
+    const hubs = featureEnabled(cfg, 'rank') ? db.prepare(`SELECT f."path" AS path, round(f."_rank" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f."path" WHERE f."_rank" IS NOT NULL ${scopeAnd} ORDER BY f."_rank" DESC LIMIT 8`).all() : [];
+    const recent = db.prepare(`SELECT "path", datetime("_mtime" / 1000, 'unixepoch') AS modified FROM frontmatter ${scopeWhere} ORDER BY "_mtime" DESC LIMIT 5`).all();
     return {
         docs,
         fields,
@@ -332,20 +344,24 @@ export function mapTree(db, cfg) {
         recent
     };
 }
+// Note resolution shared by peek and path: an exact path, or a unique basename (case
+// insensitive, .md stripped).
+export function resolveNote(paths, arg) {
+    const exact = paths.find((p)=>p === arg);
+    if (exact) return exact;
+    const base = posix.basename(arg).replace(/\.md$/i, '').toLowerCase();
+    const matches = paths.filter((p)=>posix.basename(p).replace(/\.md$/i, '').toLowerCase() === base);
+    if (matches.length === 1) return matches[0];
+    if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `"${arg}" is ambiguous: ${matches.join(', ')}`);
+    throw new SenseError('NOTE_NOT_FOUND', `no note matches "${arg}"`);
+}
 const PEEK_LIST_LIMIT = 20;
 // peek: everything about one note except its prose -- frontmatter, outline with line
 // ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.
-export function peek(db, cfg, pathArg) {
+export function peek(db, cfg, pathArg, overrides = {}) {
     var _row__size;
     const paths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
-    let path = paths.find((p)=>p === pathArg);
-    if (!path) {
-        const base = posix.basename(pathArg).replace(/\.md$/i, '').toLowerCase();
-        const matches = paths.filter((p)=>posix.basename(p).replace(/\.md$/i, '').toLowerCase() === base);
-        if (matches.length === 1) path = matches[0];
-        else if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `"${pathArg}" is ambiguous: ${matches.join(', ')}`);
-        else throw new SenseError('NOTE_NOT_FOUND', `no note matches "${pathArg}"`);
-    }
+    const path = resolveNote(paths, pathArg);
     const row = db.prepare('SELECT * FROM frontmatter WHERE "path" = ?').get(path);
     const frontmatter = {};
     for (const [key, value] of Object.entries(row)){
@@ -357,6 +373,7 @@ export function peek(db, cfg, pathArg) {
     let backlinks = [];
     let unresolved = [];
     let backlinksTotal = 0;
+    const _allowed = scopedPaths(db, cfg, overrides);
     if (featureEnabled(cfg, 'links')) {
         const out = db.prepare('SELECT target, dst FROM links WHERE src = ? ORDER BY target').all(path);
         outbound = [
@@ -384,3 +401,29 @@ export function peek(db, cfg, pathArg) {
         ].filter((name)=>!featureEnabled(cfg, name))
     };
 }
+// Notes most similar by cosine, excluding self and everything already linked either way.
+// Its own command, not a peek section: a full embeddings scan is ~480ms at 26k notes.
+export async function relatedNotes(db, cfg, pathArg, overrides, k) {
+    const paths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
+    const path = resolveNote(paths, pathArg);
+    const outbound = db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL').all(path).map((r)=>r.dst);
+    const backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ?').all(path).map((r)=>r.src);
+    const exclude = new Set([
+        path,
+        ...outbound,
+        ...backlinks
+    ]);
+    const allowed = scopedPaths(db, cfg, overrides);
+    if (!scopeHasEmbeddings(db, cfg, allowed)) return [];
+    // 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.
+    if (!modelPresent(cfg)) {
+        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)');
+    }
+    await embedPending(db, cfg, cfg.baseDir);
+    return similarNotes(db, cfg, path, {
+        exclude,
+        allowed,
+        k
+    });
+}

package/dist/esm/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 } from './config.ts';\nimport { anyPresetEmbeds, featureEnabled, featureStates, presetNames, resolveSearch } from './config.ts';\nimport { SenseError } from './errors.ts';\nimport { semanticCandidates } 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// FTS5 snippet() re-tokenizes the whole doc per candidate row, superlinearly: measured\n// 2ms at 4KB docs but 189ms at 64KB for one query's pool, and ~10s for a single 1MB doc\n// (plans/performance-findings.md finding A). 16KB keeps the whole pool's snippet cost in\n// the low-ms range; bigger docs get the JS-computed excerpt, linear and only for the rows\n// actually returned.\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); replaces the preset's include/exclude\n  semantic?: boolean; // false opts out of vector participation regardless of the preset\n}\n\n// node:path's matchesGlob is experimental (stable behind an unstable-API flag) as of the\n// engines floor (Node >=22.16); scope filtering only ever needs single-pattern matching, so\n// it's used here in JS rather than pulling fast-glob's directory walk into 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-graph expansion, fused by reciprocal rank. `via` says which signal produced\n// each row so the agent knows what evidence it is trusting.\n// Resolution precedence (built-ins <- preset <- caller overrides) lives in\n// src/config.ts:resolveSearch; `opts` here is whatever the caller (a saved search merged\n// with any CLI flag, or a bare CLI invocation) already resolved.\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 preset_files -- the coverage reconcile actually indexed with\n  // (fast-glob semantics); re-matching globs here with node:path's matchesGlob could\n  // silently disagree with it. Ad-hoc --include has no persisted coverage, so only that\n  // path pays the JS glob match.\n  const scopedPaths = opts.include ? 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  // Semantic participation: vectors run only when the effective setting allows it AND the\n  // scope actually has embedded files -- a scope covered only by semantic-false presets (or\n  // by no preset embedding at all) searches lexically, automatically, no error.\n  const semanticEnabled = effective.semantic && scopeHasEmbeddings(db, cfg, scopedPaths);\n\n  // Terms pass verbatim to FTS5 MATCH: bare words AND-join, operators are the caller's.\n  // Invalid syntax propagates as an error, zero matches return zero -- no silent rewrites.\n  // --where applies inside the candidate query (a post-filter over the top-N would drop\n  // matches ranked past the pool) and again on the final select for link-derived rows.\n  // An explicit --where replaces the preset's declared where rather than ANDing with it,\n  // so a caller can always widen back to the whole scope.\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    // `linked` gates the label only, not the score: PPR restart mass gives every seed a\n    // nonzero rank even without an incident edge, which is not link evidence — but dropping\n    // that mass from the score list reweights fusion toward connectivity and measurably\n    // wrecks ranking on link-dense corpora (FEVER hit@10 0.997 -> 0.907; fusion-tuning.md).\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 _find');\n  db.exec('CREATE TEMP TABLE _find (\"path\" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');\n  const insert = db.prepare('INSERT INTO _find (\"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  // Every candidate list was already filtered to scopedPaths above, so _find only ever holds\n  // in-scope rows -- the final select just needs --where again, same as before, for rows\n  // whichever candidate query didn't itself apply it to (link-derived rows never touched\n  // whereCond above).\n  const where = scope ? `WHERE (${scope})` : '';\n  // lines is always present now: semantic rows carry their chunk's range, oversized-doc\n  // lexical rows gain one below, everything else stays null. similarity stays semantic-only.\n  const similarityCol = semanticEnabled ? ', _find.similarity' : '';\n  const rows = db\n    .prepare(\n      `SELECT f.\"path\" AS path, content.title, content.summary, _find.hit, _find.via, round(_find.score, 4) AS score, _find.lines${similarityCol}\n       FROM _find JOIN frontmatter f ON f.\"path\" = _find.\"path\" JOIN content ON content.path = _find.\"path\"\n       ${where} ORDER BY _find.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\nexport interface PresetCoverage {\n  name: string;\n  files: number;\n  embedded: number;\n}\n\n// Indexing and embedding are both derived from presets rather than declared directly, so\n// that derivation must stay visible: how many files each preset actually matched, and how\n// many of those are covered by embedding. Read from preset_files (rebuilt at reconcile), not\n// recomputed from globs, so this always reflects what's actually on disk in the cache.\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// mapTree: what is this tree. Fixed-size output regardless of tree size.\nexport function mapTree(db: DatabaseSync, cfg: ResolvedConfig): TreeMap {\n  const docs = db.prepare('SELECT COUNT(*) AS count, COALESCE(SUM(\"_size\"), 0) AS bytes FROM frontmatter').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 storage class, not a declared one: these columns are added dynamically and\n  // SQLite types per value, so a field can be text in most notes and numeric in a few.\n  // Listing every distinct type makes both the type and any drift visible.\n  // One aggregate scan per chunk of columns rather than one scan per column: COUNT already\n  // ignores NULL, and FILTER keeps typeof() looking only at the non-null rows COUNT counted,\n  // matching the old per-column `WHERE ... IS NOT NULL` exactly.\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 ${exprs.join(', ')} FROM frontmatter`).get() as Record<string, number | string | null>;\n    group.forEach((name, i) => allFields.push({ field: name, coverage: result[`n${i}`] as number, type: (result[`t${i}`] as string) ?? '' }));\n  }\n  allFields.sort((a, b) => (b.coverage as number) - (a.coverage as number));\n  const fields = allFields.slice(0, 20);\n\n  const hubs = featureEnabled(cfg, 'rank') ? (db.prepare(`SELECT f.\"path\" AS path, round(f.\"_rank\" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f.\"path\" WHERE f.\"_rank\" IS NOT NULL ORDER BY f.\"_rank\" DESC LIMIT 8`).all() as Row[]) : [];\n\n  const recent = db.prepare(`SELECT \"path\", datetime(\"_mtime\" / 1000, 'unixepoch') AS modified FROM frontmatter ORDER BY \"_mtime\" DESC LIMIT 5`).all() as Row[];\n\n  return { docs, fields, fieldsTotal: allFields.length, features: featureStates(cfg), presets: presetCoverage(db, cfg), hubs, recent };\n}\n\nexport interface Peek {\n  path: string;\n  tokens: number;\n  frontmatter: Row;\n  sections: Row[];\n  outbound: string[];\n  backlinks: string[];\n  unresolved: string[];\n  // Totals before truncation: a hub can have thousands of backlinks (or a note thousands of\n  // headings), and peek's whole point is bounded output. Query the sections/links tables\n  // directly for the full list.\n  sectionsTotal: number;\n  outboundTotal: number;\n  backlinksTotal: number;\n  unresolvedTotal: number;\n  off: FeatureName[]; // disabled features whose blocks are omitted (not empty)\n}\n\nconst PEEK_LIST_LIMIT = 20;\n\n// peek: everything about one note except its prose -- frontmatter, outline with line\n// ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.\nexport function peek(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string): Peek {\n  const paths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  let path = paths.find((p) => p === pathArg);\n  if (!path) {\n    const base = posix.basename(pathArg).replace(/\\.md$/i, '').toLowerCase();\n    const matches = paths.filter((p) => posix.basename(p).replace(/\\.md$/i, '').toLowerCase() === base);\n    if (matches.length === 1) path = matches[0];\n    else if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `\"${pathArg}\" is ambiguous: ${matches.join(', ')}`);\n    else throw new SenseError('NOTE_NOT_FOUND', `no note matches \"${pathArg}\"`);\n  }\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') ? (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  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    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  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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') ? (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    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  const allowed = scopedPaths(db, cfg, overrides);\n  if (!scopeHasEmbeddings(db, cfg, allowed)) return [];\n  // Vectors are the only signal, so [] would read as \"nothing is related\" rather than \"no\n  // model\". Top up pending rows too, or a fresh index answers 0 until some search runs.\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  await embedPending(db, cfg, cfg.baseDir);\n  return similarNotes(db, cfg, path, { exclude, allowed, k 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package/dist/esm/config.d.ts

@@ -1,6 +1,6 @@
 export declare const CONFIG_FILENAME = "sense.config.json";
 export declare const STATE_DIR = ".sense";
-export declare const SUPPORTED_CONFIG_VERSION = 3;
+export declare const SUPPORTED_CONFIG_VERSION = 4;
 declare const FEATURE_NAMES: readonly ["links", "sections", "rank", "embed"];
 export type FeatureName = (typeof FEATURE_NAMES)[number];
 export interface EmbedConfig {
@@ -21,11 +21,11 @@ export interface SavedSearch {
     search: string;
     preset?: string;
     include?: string[];
+    exclude?: string[];
     where?: string;
     k?: number;
-    semantic?: boolean;
 }
-export type SavedQuery = string | {
+export type SavedQuery = {
     sql: string;
 } | SavedSearch;
 export interface Config {
@@ -47,6 +47,7 @@ export interface ResolvedConfig extends Config {
     migratedFrom?: number;
 }
 export declare function presetNames(cfg: Config): string[];
+export declare function embedEnabled(cfg: Config): boolean;
 export declare function presetSemanticEnabled(cfg: Config, name: string): boolean;
 export declare function anyPresetEmbeds(cfg: Config): boolean;
 export declare function featureEnabled(cfg: Config, name: FeatureName): boolean;
@@ -71,7 +72,8 @@ export interface SearchOverrides {
     k?: number;
     where?: string;
     include?: string[];
-    semantic?: boolean;
+    exclude?: string[];
+    noExclude?: boolean;
 }
 export interface EffectiveSearch {
     presetName: string;