sensemaking 0.21.1 → 0.22.1

package/README.md

@@ -93,7 +93,7 @@ ORDER BY bm25(content, 10.0, 5.0, 1.0) LIMIT 10
 |---|---|
 | `presets` | named bundles of `include`/`exclude` globs, `k` (result count), `signals` (which engines this scope searches with, `words`, `links`, `vectors`; every signal whose prerequisites hold, unless the preset lists them exhaustively), `where` (a standing SQL filter). A file is indexed if any preset includes it, embedded if a model is named and some covering preset's `signals` include `vectors`; `status` shows each preset's coverage. |
 | `embed` | the model vectors are built with. Naming one gives the tree vectors; omitting the block means none at all, whatever the presets say. `sense download` fetches it. |
-| `store` | backing store engine: `sqlite` (default, zero-dependency, Node's built-in SQLite), or the experimental `duckdb` and `turso`. The first command that opens such a tree installs that engine's package on its own (`@duckdb/node-api`, a one-time native download of ~110 MB; `@tursodatabase/database`, much smaller). The same commands and table names run on all three; what does not port is FTS5 syntax. Under `duckdb` and `turso`, `search` text and raw `MATCH` reject FTS5's prefix (`foo*`), boolean (`AND`/`OR`/`NOT`), `NEAR`, initial-token (`^`), and column-filter (`title:foo`) operators with a named error that says how to rephrase or set `store` to `sqlite`; bare words and quoted phrases work on all three. Raw `sql` is a per-store dialect: the tables are portable, but sqlite's FTS5 `MATCH`/`snippet()`/`bm25()` do not run under `duckdb` or `turso`, so saved queries written in FTS5 syntax are sqlite dialect, and `has`/`basename`/`segment` are registered on `sqlite` and `duckdb` but not `turso`, whose client cannot register SQL functions. `sense watch` requires `sqlite`; on the other two it errors at start naming the fix. Each store keeps its own cache file (`.sense/cache.db`, `.sense/cache.duckdb`, `.sense/cache.turso.db`); switching stores is a rebuild, not a migration. |
+| `store` | backing store engine: `sqlite` (default, zero-dependency, Node's built-in SQLite), or the experimental `duckdb` and `turso`. The first command that opens such a tree installs that engine's package on its own (`@duckdb/node-api`, a one-time native download of ~110 MB; `@tursodatabase/database`, much smaller). The same commands and table names run on all three; what does not port is FTS5 syntax. Under `duckdb` and `turso`, `search` text and raw `MATCH` reject FTS5's prefix (`foo*`), boolean (`AND`/`OR`/`NOT`), `NEAR`, initial-token (`^`), and column-filter (`title:foo`) operators with a named error that says how to rephrase or set `store` to `sqlite`; bare words and quoted phrases work on all three. Raw `sql` is a per-store dialect: the tables are portable, but sqlite's FTS5 `MATCH`/`snippet()`/`bm25()` do not run under `duckdb` or `turso`, so saved queries written in FTS5 syntax are sqlite dialect, and `has`/`basename`/`segment` are registered on `sqlite` and `duckdb` but not `turso`, whose client cannot register SQL functions. `sense watch` runs on all three; on `duckdb` and `turso`, which lock the cache file per connection, a concurrent command waits out the watcher's current cycle instead of failing. Each store keeps its own cache file (`.sense/cache.db`, `.sense/cache.duckdb`, `.sense/cache.turso.db`); switching stores is a rebuild, not a migration. |
 | `queries` | entries runnable as `sense <name>`, each naming the verb it runs: `{ sql }` for SQL (`?` binds positional args) or `{ search }` for a ranked search with its settings baked in, so `sense hot` needs no flags. Running an entry validates it: a typo'd column errors and exits nonzero, and a parameterised entry validates with any argument, since preparing precedes binding. |
 | `version` | schema version; older configs auto-migrate on load, noted on stderr. |
 

package/dist/cjs/chunk/group.js

@@ -144,13 +144,17 @@ function finalize(parts) {
     };
 }
 var NEWLINE_TOKENS = (0, _tokensts.estimateTokens)('\n');
-var SENTENCE_SEGMENTER = new Intl.Segmenter(undefined, {
-    granularity: 'sentence'
-});
-var WORD_SEGMENTER = new Intl.Segmenter(undefined, {
-    granularity: 'word'
-});
-function segmentsOf(text, segmenter) {
+// Built on first use and kept: each construction is ~3.5 ms, and only an oversize block is ever
+// split, so no command pays for a segmenter it never reaches.
+var SEGMENTERS = new Map();
+function segmentsOf(text, granularity) {
+    var segmenter = SEGMENTERS.get(granularity);
+    if (!segmenter) {
+        segmenter = new Intl.Segmenter(undefined, {
+            granularity: granularity
+        });
+        SEGMENTERS.set(granularity, segmenter);
+    }
     return Array.from(segmenter.segment(text), function(s) {
         return s.segment;
     });
@@ -194,7 +198,7 @@ function pack(segments, working) {
 // Line-split alone can't shrink a lone dense line (the CJK case): falls back to sentence then
 // word boundaries (Intl.Segmenter, the same grapheme-safe engine as segment.ts), mode-agnostic on `text`.
 function splitLineText(text, working) {
-    var sentences = segmentsOf(text, SENTENCE_SEGMENTER);
+    var sentences = segmentsOf(text, 'sentence');
     var out = [];
     var current = '';
     var tokens = 0;
@@ -213,7 +217,7 @@ function splitLineText(text, working) {
             if (sentenceTokens > working) {
                 var _out;
                 flush();
-                (_out = out).push.apply(_out, _to_consumable_array(pack(segmentsOf(sentence, WORD_SEGMENTER), working)));
+                (_out = out).push.apply(_out, _to_consumable_array(pack(segmentsOf(sentence, 'word'), working)));
                 continue;
             }
             if (current.length > 0 && tokens + sentenceTokens > working) flush();

package/dist/cjs/chunk/group.js.map

@@ -1 +1 @@
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pieceLines.join('\\n')\n      : parse(pieceLines.join('\\n'))\n          .map((b) => extractText(b.node))\n          .join('\\n');\n  return { startLine, endLine, text };\n}\n\n// A one-line piece over working can't shrink via another line-boundary pass (rule 5's gap), so it\n// splits at sentence/word boundaries instead; `final` stops group() re-deriving its text by extent (F5).\nfunction finalizePiece(pieceLines: string[], startLine: number, endLine: number, working: number, blockType: BlockType, textMode: 'extracted' | 'raw'): Part[] {\n  const p = piece(pieceLines, startLine, endLine, blockType, textMode);\n  if (pieceLines.length === 1 && estimateTokens(p.text) > working) {\n    return splitLineText(p.text, working).map((text) => ({ startLine, endLine, text, final: true }));\n  }\n  return [p];\n}\n\n// A block over 2x working size splits at line boundaries into pieces each <= working size, never\n// mid-line. `seed`: pending tokens (e.g. a heading) the first piece must join, checked against the limit.\nfunction splitOversizeBlock(lines: string[], startLine: number, endLine: number, working: number, blockType: BlockType, textMode: 'extracted' | 'raw', seed = 0): Part[] {\n  const pieces: Part[] = [];\n  let pieceLines: string[] = [];\n  let pieceStart = startLine;\n  let tokens = seed;\n  for (let line = startLine; line <= endLine; line++) {\n    const lineText = lines[line - 1];\n    const sep = pieceLines.length > 0 || tokens > 0 ? 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package/dist/cjs/commands/search.js

@@ -202,7 +202,7 @@ function _unsupported_iterable_to_array(o, minLen) {
     if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _array_like_to_array(o, minLen);
 }
 // snippet() re-tokenizes each candidate doc, superlinearly: ~10s for one 1MB doc
-// (benchmark/reports/2026-08-23-hub-release-battery.md). Past this bound, rows get the JS excerpt.
+// (benchmark/reports/2026-08-23-0.13.2-hub-release-battery.md). Past this bound, rows get the JS excerpt.
 var EXCERPT_WINDOW = 160;
 // Bare terms from an FTS5 query string: strips operators/quoting so the oversized-doc excerpt
 // scan matches the same words the query matched on, not FTS5 syntax.

package/dist/cjs/commands/search.js.map

@@ -1 +1 @@
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Past this bound, rows get the JS excerpt.\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. 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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/commands/search.ts"],"sourcesContent":["import { readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { ResolvedConfig } from '../config/index.ts';\nimport { embedConfig, featureEnabled, resolveSearch } from '../config/index.ts';\nimport { localModelMissing, MODEL_FILENAMES } from '../embed/store.ts';\nimport { SenseError } from '../errors.ts';\nimport type { Row } from '../output/output.ts';\nimport { searchError } from '../output/search-error.ts';\nimport type { LexicalHit, Store } from '../store/types.ts';\nimport { materializeScope, narrowByWhere, rawScope, scopeHasEmbeddings } from './scope.ts';\nimport { linksCandidates, vectorsCandidates, wordsCandidates } from './signals.ts';\n\n// snippet() re-tokenizes each candidate doc, superlinearly: ~10s for one 1MB doc\n// (benchmark/reports/2026-08-23-0.13.2-hub-release-battery.md). Past this bound, rows get the JS excerpt.\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    // Raw substring scan, not porter-stemmed: a doc matched only through a stemmed variant\n    // finds no occurrence here, so fall back to the doc's start, unmarked.\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, ' ')}${suffix}`, offset: start };\n}\n\nfunction lineNumberAt(text: string, offset: number): number {\n  let line = 1;\n  for (let i = 0; i < offset; i++) if (text.charCodeAt(i) === 10) line++;\n  return line;\n}\n\nasync function lineRangeFor(store: Store, path: string, line: number): Promise<string | null> {\n  const stmt = await store.prepare('SELECT start_line, end_line FROM sections WHERE \"path\" = ? AND start_line <= ? AND end_line >= ? ORDER BY start_line DESC LIMIT 1');\n  const row = (await stmt.get(path, line, line)) as { start_line: number; end_line: number } | undefined;\n  return row ? `L${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// The declared or defaulted signals compose via RRF; `via` names which ones produced each row.\n// `opts` arrives already resolved (config.ts:resolveSearch).\nexport async function search(store: Store, cfg: ResolvedConfig, terms: string, opts: SearchOptions = {}): Promise<Row[]> {\n  const effective = resolveSearch(cfg, opts);\n  const { k, signals } = effective;\n\n  const allPaths = ((await (await store.prepare('SELECT \"path\" FROM frontmatter')).all()) as Array<{ path: string }>).map((r) => r.path);\n  const scopePaths = await rawScope(store, cfg, opts, allPaths);\n  const scopeActive = scopePaths.size < allPaths.length;\n  // The set every candidate pool must be filtered to before truncation: scope narrowed by\n  // --where, the same composition scopedPaths() gives the other commands.\n  let allowedPaths: Set<string>;\n  try {\n    allowedPaths = await narrowByWhere(store, scopePaths, effective.where);\n  } catch (err) {\n    throw searchError(err as Error, terms, effective.where);\n  }\n  const fetch = Math.max(k * 3, 30);\n\n  // A downloadable HF id proceeds -- getProvider fetches it lazily on consent. Only a\n  // local path with missing files errors here, since nothing will ever fetch it for itself.\n  const wantsVectors = signals.vectors !== undefined;\n  if (wantsVectors) {\n    const e = embedConfig(cfg); // validate.ts guarantees this is set whenever \"vectors\" is declared\n    if (localModelMissing(e)) {\n      throw new SenseError('EMBED_MODEL_MISSING', `preset \"${effective.presetName}\" searches with vectors, but the local model path \"${e.model}\" is missing ${MODEL_FILENAMES}; point embed.model at a directory containing them, or drop \"vectors\" from that preset's signals to search without them`);\n    }\n  }\n  const semanticEnabled = wantsVectors && (await scopeHasEmbeddings(store, cfg, allowedPaths));\n\n  // --where applies inside the candidate query (a post-filter would drop matches ranked past\n  // the pool) and again on the final select, for link-derived rows.\n  const scope = effective.where;\n  const whereJoin = scope ? `JOIN frontmatter f ON f.\"path\" = content.path` : '';\n  const whereCond = scope ? `AND (${scope})` : '';\n  // Filtered before LIMIT, not after, or scoped notes ranking below the global top-`fetch`\n  // never reach the filter; joined against a temp table since real scopes exceed SQLITE_MAX_VARIABLE_NUMBER.\n  if (scopeActive) await materializeScope(store, '_search_scope', scopePaths);\n  const scopeCond = scopeActive ? `AND content.path IN (SELECT \"path\" FROM _search_scope)` : '';\n\n  const candidates = new Map<string, { score: number; via: string }>();\n  let matchRows: LexicalHit[] = [];\n  // A query that is only whitespace has no searchable words: zero lexical rows, and the other\n  // signals compose normally.\n  if (signals.words !== undefined && terms.trim() !== '') {\n    try {\n      matchRows = await wordsCandidates(store, candidates, terms, whereJoin, whereCond, scopeCond, fetch, signals.words);\n    } catch (err) {\n      throw searchError(err as Error, terms, scope);\n    }\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\n  if (signals.links !== undefined) await linksCandidates(store, candidates, matchRows, allPaths, allowedPaths, fetch, signals.links);\n\n  let chunkLines = new Map<string, string>();\n  let chunkSimilarity = new Map<string, number>();\n  if (semanticEnabled) {\n    ({ chunkLines, chunkSimilarity } = await vectorsCandidates(store, cfg, candidates, terms, fetch, allowedPaths, signals.vectors as number));\n  }\n\n  await store.exec('DROP TABLE IF EXISTS _search');\n  // DOUBLE, not REAL: sqlite's REAL is an 8-byte double but duckdb's is a 4-byte float, and the\n  // rounded score/similarity are printed at full precision in rows.\n  await store.exec('CREATE TEMP TABLE _search (\"path\" TEXT PRIMARY KEY, score DOUBLE, via TEXT, hit TEXT, lines TEXT, similarity DOUBLE)');\n  if (candidates.size > 0) {\n    await store.runBatch(\n      'INSERT INTO _search (\"path\", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)',\n      [...candidates].map(([path, c]) => [path, c.score, c.via, hits.get(path) ?? null, chunkLines.get(path) ?? null, chunkSimilarity.get(path) ?? null])\n    );\n  }\n\n  // Reapplies --where even though _search is already scope+where filtered, since the join to\n  // frontmatter is already needed for the path column.\n  const where = scope ? `WHERE (${scope})` : '';\n  // lines: semantic rows carry their chunk's range, oversized-doc lexical rows gain one\n  // below, everything else stays null; similarity stays semantic-only.\n  const similarityCol = semanticEnabled ? ', _search.similarity' : '';\n  const selectStmt = await store.prepare(\n    `SELECT f.\"path\" AS path, content.title, content.summary, _search.hit, _search.via, round(_search.score, 4) AS score, _search.lines${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  const rows = (await selectStmt.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') ? await lineRangeFor(store, row.path as string, lineNumberAt(text, offset)) : null;\n    }\n  }\n\n  return rows;\n}\n"],"names":["search","EXCERPT_WINDOW","extractBareTerms","query","cleaned","replace","split","map","tok","toLowerCase","trim","filter","length","findOccurrences","haystackLower","terms","occ","term","idx","found","indexOf","push","start","end","sort","a","b","bestWindowStart","windowSize","best","bestDistinct","bestCount","i","winEnd","seen","Set","count","j","add","size","computeExcerpt","text","Math","min","excerpt","slice","offset","out","cursor","o","prefix","suffix","lineNumberAt","line","charCodeAt","lineRangeFor","store","path","stmt","row","prepare","get","start_line","end_line","cfg","opts","effective","k","signals","allPaths","scopePaths","scopeActive","allowedPaths","err","fetch","wantsVectors","e","semanticEnabled","scope","whereJoin","whereCond","scopeCond","candidates","matchRows","hits","oversized","chunkLines","chunkSimilarity","where","similarityCol","selectStmt","rows","bareTerms","resolveSearch","all","r","rawScope","narrowByWhere","searchError","max","vectors","undefined","embedConfig","localModelMissing","SenseError","presetName","MODEL_FILENAMES","model","scopeHasEmbeddings","materializeScope","Map","words","wordsCandidates","hit","links","linksCandidates","vectorsCandidates","exec","runBatch","c","score","via","has","readFileSync","join","baseDir","lines","featureEnabled"],"mappings":";;;;+BAwHsBA;;;eAAAA;;;sBAxHO;wBACR;uBAEsC;uBACR;wBACxB;6BAEC;uBAEkD;yBACV;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAEpE,iFAAiF;AACjF,0GAA0G;AAC1G,IAAMC,iBAAiB;AAEvB,8FAA8F;AAC9F,qEAAqE;AACrE,SAASC,iBAAiBC,KAAa;IACrC,IAAMC,UAAUD,MACbE,OAAO,CAAC,MAAM,KACdA,OAAO,CAAC,UAAU,KAClBA,OAAO,CAAC,mCAAmC;IAC9C,OAAOD,QACJE,KAAK,CAAC,OACNC,GAAG,CAAC,SAACC;eAAQA,IAAIH,OAAO,CAAC,kBAAkB;OAAK,iCAAiC;KACjFE,GAAG,CAAC,SAACC;eAAQA,IAAIC,WAAW,GAAGC,IAAI;OACnCC,MAAM,CAAC,SAACH;eAAQA,IAAII,MAAM,GAAG;;AAClC;AAEA,SAASC,gBAAgBC,aAAqB,EAAEC,KAAe;IAC7D,IAAMC,MAA2D,EAAE;QAC9D,kCAAA,2BAAA;;QAAL,QAAK,YAAcD,0BAAd,SAAA,6BAAA,QAAA,yBAAA,iCAAqB;YAArB,IAAME,OAAN;YACH,IAAIC,MAAM;YACV,OAAS;gBACP,IAAMC,QAAQL,cAAcM,OAAO,CAACH,MAAMC;gBAC1C,IAAIC,UAAU,CAAC,GAAG;gBAClBH,IAAIK,IAAI,CAAC;oBAAEC,OAAOH;oBAAOI,KAAKJ,QAAQF,KAAKL,MAAM;oBAAEK,MAAAA;gBAAK;gBACxDC,MAAMC,QAAQF,KAAKL,MAAM;YAC3B;QACF;;QARK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IASL,mFAAmF;IACnF,+EAA+E;IAC/E,OAAOI,IAAIQ,IAAI,CAAC,SAACC,GAAGC;eAAMD,EAAEH,KAAK,GAAGI,EAAEJ,KAAK,IAAII,EAAEH,GAAG,GAAGE,EAAEF,GAAG;;AAC9D;AAEA,wFAAwF;AACxF,6DAA6D;AAC7D,SAASI,gBAAgBX,GAAwD,EAAEY,UAAkB;IACnG,IAAIC,OAAOb,GAAG,CAAC,EAAE,CAACM,KAAK;IACvB,IAAIQ,eAAe;IACnB,IAAIC,YAAY;IAChB,IAAK,IAAIC,IAAI,GAAGA,IAAIhB,IAAIJ,MAAM,EAAEoB,IAAK;QACnC,IAAMC,SAASjB,GAAG,CAACgB,EAAE,CAACV,KAAK,GAAGM;QAC9B,IAAMM,OAAO,IAAIC;QACjB,IAAIC,QAAQ;QACZ,IAAK,IAAIC,IAAIL,GAAGK,IAAIrB,IAAIJ,MAAM,IAAII,GAAG,CAACqB,EAAE,CAACf,KAAK,GAAGW,QAAQI,IAAK;YAC5DH,KAAKI,GAAG,CAACtB,GAAG,CAACqB,EAAE,CAACpB,IAAI;YACpBmB;QACF;QACA,IAAIF,KAAKK,IAAI,GAAGT,gBAAiBI,KAAKK,IAAI,KAAKT,gBAAgBM,QAAQL,WAAY;YACjFF,OAAOb,GAAG,CAACgB,EAAE,CAACV,KAAK;YACnBQ,eAAeI,KAAKK,IAAI;YACxBR,YAAYK;QACd;IACF;IACA,OAAOP;AACT;AAEA,uFAAuF;AACvF,uFAAuF;AACvF,SAASW,eAAeC,IAAY,EAAE1B,KAAe;IACnD,IAAMC,MAAMH,gBAAgB4B,KAAKhC,WAAW,IAAIM;IAChD,IAAIC,IAAIJ,MAAM,KAAK,GAAG;QACpB,uFAAuF;QACvF,uEAAuE;QACvE,IAAMW,MAAMmB,KAAKC,GAAG,CAACF,KAAK7B,MAAM,EAAEX;QAClC,OAAO;YAAE2C,SAAS,AAAC,GAAmDrB,OAAjDkB,KAAKI,KAAK,CAAC,GAAGtB,KAAKlB,OAAO,CAAC,QAAQ,KAAKK,IAAI,IAAkC,OAA7Ba,MAAMkB,KAAK7B,MAAM,GAAG,MAAM;YAAMkC,QAAQ;QAAE;IAClH;IACA,IAAMxB,QAAQK,gBAAgBX,KAAKf;IACnC,IAAMsB,OAAMmB,KAAKC,GAAG,CAACF,KAAK7B,MAAM,EAAEU,QAAQrB;IAC1C,IAAI8C,MAAM;IACV,IAAIC,SAAS1B;QACR,kCAAA,2BAAA;;QAAL,QAAK,YAAWN,wBAAX,SAAA,6BAAA,QAAA,yBAAA,iCAAgB;YAAhB,IAAMiC,IAAN;YACH,IAAIA,EAAE3B,KAAK,GAAGA,SAAS2B,EAAE1B,GAAG,GAAGA,MAAK;YACpC,sFAAsF;YACtF,gFAAgF;YAChF,IAAI0B,EAAE3B,KAAK,GAAG0B,QAAQ;YACtBD,OAAO,AAAC,GAAiCN,OAA/BA,KAAKI,KAAK,CAACG,QAAQC,EAAE3B,KAAK,GAAE,QAA8B,OAA3BmB,KAAKI,KAAK,CAACI,EAAE3B,KAAK,EAAE2B,EAAE1B,GAAG,GAAE;YACpEyB,SAASC,EAAE1B,GAAG;QAChB;;QAPK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IAQLwB,OAAON,KAAKI,KAAK,CAACG,QAAQzB;IAC1B,IAAM2B,SAAS5B,QAAQ,IAAI,MAAM;IACjC,IAAM6B,SAAS5B,OAAMkB,KAAK7B,MAAM,GAAG,MAAM;IACzC,OAAO;QAAEgC,SAAS,AAAC,GAAWG,OAATG,QAAoCC,OAA3BJ,IAAI1C,OAAO,CAAC,QAAQ,MAAc,OAAP8C;QAAUL,QAAQxB;IAAM;AACnF;AAEA,SAAS8B,aAAaX,IAAY,EAAEK,MAAc;IAChD,IAAIO,OAAO;IACX,IAAK,IAAIrB,IAAI,GAAGA,IAAIc,QAAQd,IAAK,IAAIS,KAAKa,UAAU,CAACtB,OAAO,IAAIqB;IAChE,OAAOA;AACT;AAEA,SAAeE,aAAaC,KAAY,EAAEC,IAAY,EAAEJ,IAAY;;YAC5DK,MACAC;;;;oBADO;;wBAAMH,MAAMI,OAAO,CAAC;;;oBAA3BF,OAAO;oBACA;;wBAAMA,KAAKG,GAAG,CAACJ,MAAMJ,MAAMA;;;oBAAlCM,MAAO;oBACb;;wBAAOA,MAAM,AAAC,IAAqBA,OAAlBA,IAAIG,UAAU,EAAC,KAAgB,OAAbH,IAAII,QAAQ,IAAK;;;;IACtD;;AAaO,SAAe/D;wCAAOwD,KAAY,EAAEQ,GAAmB,EAAEjD,KAAa;YAAEkD,MACvEC,WACEC,GAAGC,SAELC,UACAC,YACAC,aAGFC,cAGKC,MAGHC,OAIAC,cAEEC,GAKFC,uBAIAC,OACAC,WACAC,WAIAC,WAEAC,YACFC,WAMOV,MAILW,MAGAC,WAIFC,YACAC,sBAkBEC,OAGAC,eACAC,YAKAC,MAGEC,WACD,2BAAA,mBAAA,gBAAA,WAAA,OAAM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package/dist/cjs/features/embed.js

@@ -13,6 +13,7 @@ var _indexts1 = require("../config/index.js");
 var _handoffts = require("../embed/handoff.js");
 var _identityts = require("../embed/identity.js");
 var _frontmatterts = require("../scan/frontmatter.js");
+var _sharedts = require("../store/shared.js");
 function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) {
     try {
         var info = gen[key](arg);
@@ -255,9 +256,16 @@ var embed = {
                         if (rows.length === 0) return [
                             2
                         ];
+                        // scale and vector are written by the embed pass, not here, so they are not in the column list
+                        // and take the table's own default on the append path.
                         return [
                             4,
-                            db.runBatch('INSERT INTO embeddings ("path", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows)
+                            (0, _sharedts.appendRows)(db, 'embeddings', [
+                                'path',
+                                'chunk',
+                                'start_line',
+                                'end_line'
+                            ], 'INSERT INTO embeddings ("path", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows)
                         ];
                     case 1:
                         _state.sent();

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/embed.ts"],"sourcesContent":["import type { Block, Chunk } from '../chunk/index.ts';\nimport { CHUNK_VERSION, chunkFromBlocks, parse } from '../chunk/index.ts';\nimport { embedConfig } from '../config/index.ts';\nimport { stashChunkText } from '../embed/handoff.ts';\nimport { modelIdentity } from '../embed/identity.ts';\nimport { countLines } from '../scan/frontmatter.ts';\nimport type { Feature } from './types.ts';\n\n// int8 vectors with a per-vector scale, NULL vector = not yet embedded: reconcile writes dirty\n// rows and embedding tops up on the next search, so staleness costs recall.\n\nexport type { Chunk };\n\n// The title/summary prefix mirrors bm25 field weighting. Chunks the body, not the raw file, so\n// `offset` shifts line numbers back onto raw and a range stays a direct Read range.\nfunction chunksOf(blocks: Block[], body: string, search?: { title: string; summary: string }, offset = 0, chunkTokens?: number): Chunk[] {\n  const prefix = [search?.title, search?.summary].filter(Boolean).join('\\n');\n  // A hardcoded option change here must bump src/chunk/version.ts's CHUNK_VERSION, the signature\n  // for every chunker input not already carried in config.\n  return chunkFromBlocks(blocks, body, chunkTokens !== undefined ? { targetTokens: chunkTokens } : undefined).map((c) => ({\n    startLine: c.startLine + offset,\n    endLine: c.endLine + offset,\n    text: prefix ? `${prefix}\\n${c.text}` : c.text,\n  }));\n}\n\nexport const embed: Feature = {\n  name: 'embed',\n  async schema(db) {\n    await db.exec(`CREATE TABLE IF NOT EXISTS embeddings (\"path\" TEXT, chunk INTEGER, start_line INTEGER, end_line INTEGER, scale REAL, vector BLOB, PRIMARY KEY (\"path\", chunk))`);\n  },\n  extract(raw, body, search, _data, cfg, blocks) {\n    // Lines the frontmatter occupies, so body line 1 maps back to its raw line number.\n    // blocks comes from parseFile's shared parse; falls back to parsing body for a direct call.\n    return chunksOf(blocks ?? parse(body), body, search, countLines(raw) - countLines(body), cfg?.embed?.chunkTokens);\n  },\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM embeddings WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  // A tree with no embedding model never had extract() run for the doc (reconcile.ts's per-file\n  // filter skips it), so extracted is undefined here -- those docs contribute no rows.\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    const texts = new Map<string, string[]>();\n    for (const { path, extracted } of docs) {\n      if (!extracted) continue;\n      const chunks = extracted as Chunk[];\n      chunks.forEach((c, idx) => rows.push([path, idx, c.startLine, c.endLine]));\n      texts.set(\n        path,\n        chunks.map((c) => c.text)\n      );\n    }\n    if (rows.length === 0) return;\n    await db.runBatch('INSERT INTO embeddings (\"path\", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows);\n    // The text extract() just computed, handed to the embed pass that follows in this same\n    // process rather than re-derived from the file there (src/embed/handoff.ts).\n    stashChunkText(db, texts);\n  },\n  enabledForFile(_cfg, file) {\n    return file.embed;\n  },\n  // Keyed so a rebuild notice can name it \"embed settings\". 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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/embed.ts"],"sourcesContent":["import type { Block, Chunk } from '../chunk/index.ts';\nimport { CHUNK_VERSION, chunkFromBlocks, parse } from '../chunk/index.ts';\nimport { embedConfig } from '../config/index.ts';\nimport { stashChunkText } from '../embed/handoff.ts';\nimport { modelIdentity } from '../embed/identity.ts';\nimport { countLines } from '../scan/frontmatter.ts';\nimport { appendRows } from '../store/shared.ts';\nimport type { Feature } from './types.ts';\n\n// int8 vectors with a per-vector scale, NULL vector = not yet embedded: reconcile writes dirty\n// rows and embedding tops up on the next search, so staleness costs recall.\n\nexport type { Chunk };\n\n// The title/summary prefix mirrors bm25 field weighting. Chunks the body, not the raw file, so\n// `offset` shifts line numbers back onto raw and a range stays a direct Read range.\nfunction chunksOf(blocks: Block[], body: string, search?: { title: string; summary: string }, offset = 0, chunkTokens?: number): Chunk[] {\n  const prefix = [search?.title, search?.summary].filter(Boolean).join('\\n');\n  // A hardcoded option change here must bump src/chunk/version.ts's CHUNK_VERSION, the signature\n  // for every chunker input not already carried in config.\n  return chunkFromBlocks(blocks, body, chunkTokens !== undefined ? { targetTokens: chunkTokens } : undefined).map((c) => ({\n    startLine: c.startLine + offset,\n    endLine: c.endLine + offset,\n    text: prefix ? `${prefix}\\n${c.text}` : c.text,\n  }));\n}\n\nexport const embed: Feature = {\n  name: 'embed',\n  async schema(db) {\n    await db.exec(`CREATE TABLE IF NOT EXISTS embeddings (\"path\" TEXT, chunk INTEGER, start_line INTEGER, end_line INTEGER, scale REAL, vector BLOB, PRIMARY KEY (\"path\", chunk))`);\n  },\n  extract(raw, body, search, _data, cfg, blocks) {\n    // Lines the frontmatter occupies, so body line 1 maps back to its raw line number.\n    // blocks comes from parseFile's shared parse; falls back to parsing body for a direct call.\n    return chunksOf(blocks ?? parse(body), body, search, countLines(raw) - countLines(body), cfg?.embed?.chunkTokens);\n  },\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM embeddings WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  // A tree with no embedding model never had extract() run for the doc (reconcile.ts's per-file\n  // filter skips it), so extracted is undefined here -- those docs contribute no rows.\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    const texts = new Map<string, string[]>();\n    for (const { path, extracted } of docs) {\n      if (!extracted) continue;\n      const chunks = extracted as Chunk[];\n      chunks.forEach((c, idx) => rows.push([path, idx, c.startLine, c.endLine]));\n      texts.set(\n        path,\n        chunks.map((c) => c.text)\n      );\n    }\n    if (rows.length === 0) return;\n    // scale and vector are written by the embed pass, not here, so they are not in the column list\n    // and take the table's own default on the append path.\n    await appendRows(db, 'embeddings', ['path', 'chunk', 'start_line', 'end_line'], 'INSERT INTO embeddings (\"path\", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows);\n    // The text extract() just computed, handed to the embed pass that follows in this same\n    // process rather than re-derived from the file there (src/embed/handoff.ts).\n    stashChunkText(db, texts);\n  },\n  enabledForFile(_cfg, file) {\n    return file.embed;\n  },\n  // Keyed so a rebuild notice can name it \"embed settings\". 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package/dist/cjs/features/links.js

@@ -23,6 +23,7 @@ _export(exports, {
     }
 });
 var _posix = /*#__PURE__*/ _interop_require_default(require("node:path/posix"));
+var _sharedts = require("../store/shared.js");
 var _fencests = require("./fences.js");
 function _array_like_to_array(arr, len) {
     if (len == null || len > arr.length) len = arr.length;
@@ -756,6 +757,15 @@ function linkEdges(db) {
 // Records whether remove()/store() deleted any link row, since afterReconcile runs after both
 // and dstChanged alone misses the reparsed-to-zero-links case. Keyed on delta so state dies with it.
 var removedWithLinks = new WeakMap();
+// dst is written by resolution, not by store(), so it is absent from the column list and takes the
+// table's default on the append path.
+var LINK_COLUMNS = [
+    'src',
+    'target',
+    'target_base',
+    'embed'
+];
+var UPSERT_LINK_SQL = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base';
 var links = {
     name: 'links',
     schema: function schema(db) {
@@ -830,7 +840,7 @@ var links = {
     },
     store: function store(db, docs, delta) {
         return _async_to_generator(function() {
-            var byPath, addedSet, reparsedExisting, existingRows, staleRows, upsertRows, _iteratorNormalCompletion, _didIteratorError, _iteratorError, _iterator, _step, _step_value, path, targets, _iteratorNormalCompletion1, _didIteratorError1, _iteratorError1, _iterator1, _step1, _step_value1, target, embed;
+            var byPath, addedSet, reparsedExisting, existingRows, staleRows, appendable, upsertRows, _iteratorNormalCompletion, _didIteratorError, _iteratorError, _iterator, _step, _step_value, path, targets, _iteratorNormalCompletion1, _didIteratorError1, _iteratorError1, _iterator1, _step1, _step_value1, target, embed, row;
             return _ts_generator(this, function(_state) {
                 switch(_state.label){
                     case 0:
@@ -880,6 +890,10 @@ var links = {
                     case 3:
                         // Upsert preserves dst on surviving rows; only new rows start at NULL. A same-note anchor
                         // gets no target_base, so SQL's `IN` excludes it from resolveIncremental's lookup.
+                        // Split, unlike the other features: this hook has no remove() pass behind it (see above), so
+                        // only a path in `added` is guaranteed to have no row yet. The rest genuinely conflict and the
+                        // upsert is what preserves their `dst`.
+                        appendable = [];
                         upsertRows = [];
                         _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
                         try {
@@ -889,12 +903,14 @@ var links = {
                                 try {
                                     for(_iterator1 = targets[Symbol.iterator](); !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
                                         _step_value1 = _step1.value, target = _step_value1.target, embed = _step_value1.embed;
-                                        upsertRows.push([
+                                        row = [
                                             path,
                                             target,
                                             target.startsWith('#') ? null : baseKey(cleanTarget(target)),
                                             embed ? 1 : 0
-                                        ]);
+                                        ];
+                                        if (addedSet.has(path)) appendable.push(row);
+                                        else upsertRows.push(row);
                                     }
                                 } catch (err) {
                                     _didIteratorError1 = true;
@@ -925,18 +941,24 @@ var links = {
                                 }
                             }
                         }
+                        return [
+                            4,
+                            (0, _sharedts.appendRows)(db, 'links', LINK_COLUMNS, UPSERT_LINK_SQL, appendable)
+                        ];
+                    case 4:
+                        _state.sent();
                         if (!(upsertRows.length > 0)) return [
                             3,
-                            5
+                            6
                         ];
                         return [
                             4,
-                            db.runBatch('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base', upsertRows)
+                            db.runBatch(UPSERT_LINK_SQL, upsertRows)
                         ];
-                    case 4:
-                        _state.sent();
-                        _state.label = 5;
                     case 5:
+                        _state.sent();
+                        _state.label = 6;
+                    case 6:
                         return [
                             2
                         ];

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/links.ts"],"sourcesContent":["import posix from 'node:path/posix';\nimport type { FileStat } from '../scan/index.ts';\nimport type { Connection } from '../store/types.ts';\nimport { maskRegions } from './fences.ts';\nimport type { ExtractedDoc, Feature, ReconcileDelta } from './types.ts';\n\n// links(src, target, target_base, dst, embed): target as written, target_base its indexed baseKey, dst the resolved path or NULL (a queryable dead link).\n// embed distinguishes `![[x]]`/`![](x.md)` from `[[x]]`/`[](x.md)` -- Obsidian's grain: a target both linked and embedded in one note is two rows.\n\n// Alias stripped after |; a leading # keeps the anchor as the target (self-link needs a\n// heading name), else the anchor splits off. 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'1' : '0'}`;\n    if (seen.has(key)) return;\n    seen.add(key);\n    results.push({ target, embed });\n  };\n  // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still\n  // matches; anchor and alias split off in parseWikilinkInner.\n  for (const m of body.matchAll(/\\[\\[(.*?)\\]\\]/g)) {\n    const target = parseWikilinkInner(m[1]);\n    if (target) add(target, body[(m.index ?? 0) - 1] === '!');\n  }\n  // Any internal destination, not only .md-suffixed: \\](Zektor) resolves like [[Zektor]] and\n  // \\](#anchor) is a self-edge. External URLs and titled links (dest stops at whitespace) skip.\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(((?:[^()\\s]|\\([^()\\s]*\\))+)(?:\\s+(?:\"[^)]*\"|'[^)]*'))?\\)/g)) {\n    const dest = m[2].trim();\n    // External: a URI scheme prefix (mailto:, tel:, data:, https:...), protocol-relative\n    // //host, a www. shorthand, or a scheme anywhere (the malformed double-paren case).\n    if (!dest || dest.includes('://')) continue;\n    if (/^([a-z][a-z0-9+.-]*:|\\/\\/|www\\.)/i.test(dest)) continue;\n    const target = dest.startsWith('#') ? dest : dest.split('#')[0];\n    if (target) add(target, m[1] === '!');\n  }\n  for (const value of Object.values(data ?? {})) {\n    for (const item of Array.isArray(value) ? value : [value]) {\n      if (typeof item !== 'string') continue;\n      const m = /^\\[\\[(.*)\\]\\]$/.exec(item.trim());\n      if (!m) continue;\n      const target = parseWikilinkInner(m[1]);\n      if (target) add(target, false);\n    }\n  }\n  return results;\n}\n\nfunction cleanTarget(target: string): string {\n  return target.replace(/\\\\/g, '/').replace(/^\\.\\//, '');\n}\n\nfunction baseKey(path: string): string {\n  return posix.basename(path).replace(/\\.md$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking note's\n// directory, then basename match (shortest path wins ties, verified against a cold-loaded vault).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.\n  if (target.startsWith('#')) return src;\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  const candidates = byBase.get(baseKey(clean));\n  if (!candidates) return null;\n  // The linking note itself wins a basename collision (Obsidian resolves to self before the\n  // shortest-path rule -- cold-load verified on the hub corpus).\n  return candidates.includes(src) ? src : candidates[0];\n}\n\n// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own\n// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  const paths = files.map((f) => f.relPath).sort((a, b) => a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));\n  for (const path of paths) {\n    const key = baseKey(path);\n    const list = byBase.get(key);\n    if (list) list.push(path);\n    else byBase.set(key, [path]);\n  }\n  return byBase;\n}\n\ninterface LinkRow {\n  src: string;\n  target: string;\n  dst: string | null;\n  embed: number;\n}\n\n// resolveTarget applied to `rows`, returning only the rows whose dst changed, so the caller\n// can write them in one runBatch call.\nfunction resolveRows(rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): LinkRow[] {\n  const changed: LinkRow[] = [];\n  for (const row of rows) {\n    const dst = resolveTarget(row.src, row.target, pathSet, byBase);\n    if (dst !== row.dst) changed.push({ ...row, dst });\n  }\n  return changed;\n}\n\nasync function writeResolved(db: Connection, rows: LinkRow[]): Promise<void> {\n  if (rows.length === 0) return;\n  await db.runBatch(\n    'UPDATE links SET dst = ? 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AND target = ?',\n    rows.map((r) => [r.dst, r.src, r.target])\n  );\n}\n\n// A new or deleted file can change any note's resolution, so re-resolve the whole table.\n// Fallback for cold builds and large deltas -- see afterReconcile's threshold.\nasync function resolveAll(db: Connection, files: FileStat[]): Promise<boolean> {\n  const pathSet = new Set(files.map((f) => f.relPath));\n  const byBase = buildByBase(files);\n  const stmt = await db.prepare('SELECT src, target, dst, embed FROM links');\n  const rows = (await stmt.all()) as unknown as LinkRow[];\n  const changed = resolveRows(rows, pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\n// Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit\n// (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.\nasync function selectIn(db: Connection, column: string, keys: string[]): Promise<LinkRow[]> {\n  const rows: LinkRow[] = [];\n  for (let i = 0; i < keys.length; i += 500) {\n    const chunk = keys.slice(i, i + 500);\n    const stmt = await db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${chunk.map(() => '?').join(', ')})`);\n    rows.push(...((await stmt.all(...chunk)) as unknown as LinkRow[]));\n  }\n  return rows;\n}\n\n// Re-resolves only what this reconcile could have touched: re-stored sources, links whose\n// target basename matches an added/vanished file, and links whose dst vanished -- all indexed.\nasync function resolveIncremental(db: Connection, delta: ReconcileDelta): Promise<boolean> {\n  const pathSet = new Set(delta.files.map((f) => f.relPath));\n  const byBase = buildByBase(delta.files);\n\n  const changedBasenames = new Set<string>();\n  for (const p of delta.added) changedBasenames.add(baseKey(p));\n  for (const p of delta.vanished) changedBasenames.add(baseKey(p));\n\n  // \\0 can't appear in a path or target, so the key never collides; a space can.\n  const candidates = new Map<string, LinkRow>();\n  const collect = (rows: LinkRow[]) => {\n    for (const row of rows) candidates.set(`${row.src}\\0${row.target}\\0${row.embed}`, row);\n  };\n  collect(await selectIn(db, 'src', delta.reparsed));\n  collect(await selectIn(db, 'target_base', [...changedBasenames]));\n  collect(await selectIn(db, 'dst', delta.vanished));\n\n  const changed = resolveRows([...candidates.values()], pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\n// One edge per (src, target); an embed row is excluded only when the same pair also exists as\n// a link. 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Keyed on delta so state dies with it.\nconst removedWithLinks = new WeakMap<ReconcileDelta, boolean>();\n\nexport const links: Feature = {\n  name: 'links',\n  async schema(db) {\n    await db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');\n    await db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    await db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');\n  },\n  extract,\n  // Reparsed docs are diffed in store() instead of wiped here: delete-and-reinsert resets dst\n  // to NULL, making every touch-only reparse look like an edge change and recompute PageRank.\n  async remove(db, paths, delta) {\n    const vanishedSet = new Set(delta.vanished);\n    const vanished = paths.filter((p) => vanishedSet.has(p));\n    if (vanished.length === 0) return;\n    const existingRows = await selectIn(db, 'src', vanished);\n    await db.runBatch(\n      'DELETE FROM links WHERE src = ?',\n      vanished.map((p) => [p])\n    );\n    if (existingRows.length > 0) removedWithLinks.set(delta, true);\n  },\n  async store(db, docs: ExtractedDoc[], delta) {\n    const byPath = new Map(docs.map((d) => [d.path, d.extracted as Array<{ target: string; embed: boolean }>]));\n    const addedSet = new Set(delta.added);\n    const reparsedExisting = docs.map((d) => d.path).filter((p) => !addedSet.has(p));\n\n    // Stale rows (target/embed pairs missing from the new parse) are diffed in JS from one\n    // bulk SELECT, so this pass costs one query plus one batched DELETE regardless of file count.\n    const existingRows = await selectIn(db, 'src', reparsedExisting);\n    const staleRows = existingRows.filter((row) => {\n      const targets = byPath.get(row.src) ?? 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Null = not a link.\nfunction parseWikilinkInner(inner: string): string | null {\n  const beforeAlias = inner.split('|')[0].trim();\n  if (beforeAlias.startsWith('#')) return beforeAlias.length > 1 ? beforeAlias : null;\n  const target = beforeAlias.split('#')[0].trim();\n  return target || null;\n}\n\n// A frontmatter value counts only when it is exactly a wikilink (\"[[X]]\") -- mid-string and\n// ![[...]] forms don't count there, per Obsidian's rule (probe-verified).\nfunction extract(_raw: string, rawBody: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): Array<{ target: string; embed: boolean }> {\n  const body = /\\[\\[|\\]\\(/.test(rawBody) ? maskRegions(rawBody) : rawBody;\n  const seen = new Set<string>();\n  const results: Array<{ target: string; embed: boolean }> = [];\n  const add = (target: string, embed: boolean) => {\n    const key = `${target}\\0${embed ? '1' : '0'}`;\n    if (seen.has(key)) return;\n    seen.add(key);\n    results.push({ target, embed });\n  };\n  // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still\n  // matches; anchor and alias split off in parseWikilinkInner.\n  for (const m of body.matchAll(/\\[\\[(.*?)\\]\\]/g)) {\n    const target = parseWikilinkInner(m[1]);\n    if (target) add(target, body[(m.index ?? 0) - 1] === '!');\n  }\n  // Any internal destination, not only .md-suffixed: \\](Zektor) resolves like [[Zektor]] and\n  // \\](#anchor) is a self-edge. External URLs and titled links (dest stops at whitespace) skip.\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(((?:[^()\\s]|\\([^()\\s]*\\))+)(?:\\s+(?:\"[^)]*\"|'[^)]*'))?\\)/g)) {\n    const dest = m[2].trim();\n    // External: a URI scheme prefix (mailto:, tel:, data:, https:...), protocol-relative\n    // //host, a www. shorthand, or a scheme anywhere (the malformed double-paren case).\n    if (!dest || dest.includes('://')) continue;\n    if (/^([a-z][a-z0-9+.-]*:|\\/\\/|www\\.)/i.test(dest)) continue;\n    const target = dest.startsWith('#') ? dest : dest.split('#')[0];\n    if (target) add(target, m[1] === '!');\n  }\n  for (const value of Object.values(data ?? {})) {\n    for (const item of Array.isArray(value) ? value : [value]) {\n      if (typeof item !== 'string') continue;\n      const m = /^\\[\\[(.*)\\]\\]$/.exec(item.trim());\n      if (!m) continue;\n      const target = parseWikilinkInner(m[1]);\n      if (target) add(target, false);\n    }\n  }\n  return results;\n}\n\nfunction cleanTarget(target: string): string {\n  return target.replace(/\\\\/g, '/').replace(/^\\.\\//, '');\n}\n\nfunction baseKey(path: string): string {\n  return posix.basename(path).replace(/\\.md$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking note's\n// directory, then basename match (shortest path wins ties, verified against a cold-loaded vault).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.\n  if (target.startsWith('#')) return src;\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  const candidates = byBase.get(baseKey(clean));\n  if (!candidates) return null;\n  // The linking note itself wins a basename collision (Obsidian resolves to self before the\n  // shortest-path rule -- cold-load verified on the hub corpus).\n  return candidates.includes(src) ? src : candidates[0];\n}\n\n// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own\n// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  const paths = files.map((f) => f.relPath).sort((a, b) => a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));\n  for (const path of paths) {\n    const key = baseKey(path);\n    const list = byBase.get(key);\n    if (list) list.push(path);\n    else byBase.set(key, [path]);\n  }\n  return byBase;\n}\n\ninterface LinkRow {\n  src: string;\n  target: string;\n  dst: string | null;\n  embed: number;\n}\n\n// resolveTarget applied to `rows`, returning only the rows whose dst changed, so the caller\n// can write them in one runBatch call.\nfunction resolveRows(rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): LinkRow[] {\n  const changed: LinkRow[] = [];\n  for (const row of rows) {\n    const dst = resolveTarget(row.src, row.target, pathSet, byBase);\n    if (dst !== row.dst) changed.push({ ...row, dst });\n  }\n  return changed;\n}\n\nasync function writeResolved(db: Connection, rows: LinkRow[]): Promise<void> {\n  if (rows.length === 0) return;\n  await db.runBatch(\n    'UPDATE links SET dst = ? WHERE src = ? AND target = ?',\n    rows.map((r) => [r.dst, r.src, r.target])\n  );\n}\n\n// A new or deleted file can change any note's resolution, so re-resolve the whole table.\n// Fallback for cold builds and large deltas -- see afterReconcile's threshold.\nasync function resolveAll(db: Connection, files: FileStat[]): Promise<boolean> {\n  const pathSet = new Set(files.map((f) => f.relPath));\n  const byBase = buildByBase(files);\n  const stmt = await db.prepare('SELECT src, target, dst, embed FROM links');\n  const rows = (await stmt.all()) as unknown as LinkRow[];\n  const changed = resolveRows(rows, pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\n// Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit\n// (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.\nasync function selectIn(db: Connection, column: string, keys: string[]): Promise<LinkRow[]> {\n  const rows: LinkRow[] = [];\n  for (let i = 0; i < keys.length; i += 500) {\n    const chunk = keys.slice(i, i + 500);\n    const stmt = await db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${chunk.map(() => '?').join(', ')})`);\n    rows.push(...((await stmt.all(...chunk)) as unknown as LinkRow[]));\n  }\n  return rows;\n}\n\n// Re-resolves only what this reconcile could have touched: re-stored sources, links whose\n// target basename matches an added/vanished file, and links whose dst vanished -- all indexed.\nasync function resolveIncremental(db: Connection, delta: ReconcileDelta): Promise<boolean> {\n  const pathSet = new Set(delta.files.map((f) => f.relPath));\n  const byBase = buildByBase(delta.files);\n\n  const changedBasenames = new Set<string>();\n  for (const p of delta.added) changedBasenames.add(baseKey(p));\n  for (const p of delta.vanished) changedBasenames.add(baseKey(p));\n\n  // \\0 can't appear in a path or target, so the key never collides; a space can.\n  const candidates = new Map<string, LinkRow>();\n  const collect = (rows: LinkRow[]) => {\n    for (const row of rows) candidates.set(`${row.src}\\0${row.target}\\0${row.embed}`, row);\n  };\n  collect(await selectIn(db, 'src', delta.reparsed));\n  collect(await selectIn(db, 'target_base', [...changedBasenames]));\n  collect(await selectIn(db, 'dst', delta.vanished));\n\n  const changed = resolveRows([...candidates.values()], pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\n// One edge per (src, target); an embed row is excluded only when the same pair also exists as\n// a link. Self-edges are dropped so PageRank mass is not self-recycled.\nexport const LINK_EDGES_SQL = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0 AND src != dst\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1 AND src != dst\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;\n\nexport function toEdges(rows: Array<{ src: string; dst: string }>): [string, string][] {\n  return rows.map((r) => [r.src, r.dst]);\n}\n\n// Resolved edges, for rank (inside reconcile's afterReconcile pass).\nexport async function linkEdges(db: Connection): Promise<[string, string][]> {\n  const stmt = await db.prepare(LINK_EDGES_SQL);\n  return toEdges((await stmt.all()) as Array<{ src: string; dst: string }>);\n}\n\n// Records whether remove()/store() deleted any link row, since afterReconcile runs after both\n// and dstChanged alone misses the reparsed-to-zero-links case. Keyed on delta so state dies with it.\nconst removedWithLinks = new WeakMap<ReconcileDelta, boolean>();\n\n// dst is written by resolution, not by store(), so it is absent from the column list and takes the\n// table's default on the append path.\nconst LINK_COLUMNS = ['src', 'target', 'target_base', 'embed'];\nconst UPSERT_LINK_SQL = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base';\n\nexport const links: Feature = {\n  name: 'links',\n  async schema(db) {\n    await db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');\n    await db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    await db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');\n  },\n  extract,\n  // Reparsed docs are diffed in store() instead of wiped here: delete-and-reinsert resets dst\n  // to NULL, making every touch-only reparse look like an edge change and recompute PageRank.\n  async remove(db, paths, delta) {\n    const vanishedSet = new Set(delta.vanished);\n    const vanished = paths.filter((p) => vanishedSet.has(p));\n    if (vanished.length === 0) return;\n    const existingRows = await selectIn(db, 'src', vanished);\n    await db.runBatch(\n      'DELETE FROM links WHERE src = ?',\n      vanished.map((p) => [p])\n    );\n    if (existingRows.length > 0) removedWithLinks.set(delta, true);\n  },\n  async store(db, docs: ExtractedDoc[], delta) {\n    const byPath = new Map(docs.map((d) => [d.path, d.extracted as Array<{ target: string; embed: boolean }>]));\n    const addedSet = new Set(delta.added);\n    const reparsedExisting = docs.map((d) => d.path).filter((p) => !addedSet.has(p));\n\n    // Stale rows (target/embed pairs missing from the new parse) are diffed in JS from one\n    // bulk SELECT, so this pass costs one query plus one batched DELETE regardless of file count.\n    const existingRows = await selectIn(db, 'src', reparsedExisting);\n    const staleRows = existingRows.filter((row) => {\n      const targets = byPath.get(row.src) ?? [];\n      return !targets.some((t) => t.target === row.target && (t.embed ? 1 : 0) === row.embed);\n    });\n    if (staleRows.length > 0) {\n      await db.runBatch(\n        'DELETE FROM links WHERE src = ? AND target = ? AND embed = ?',\n        staleRows.map((r) => [r.src, r.target, r.embed])\n      );\n      removedWithLinks.set(delta, true);\n    }\n\n    // Upsert preserves dst on surviving rows; only new rows start at NULL. A same-note anchor\n    // gets no target_base, so SQL's `IN` excludes it from resolveIncremental's lookup.\n    // Split, unlike the other features: this hook has no remove() pass behind it (see above), so\n    // only a path in `added` is guaranteed to have no row yet. The rest genuinely conflict and the\n    // upsert is what preserves their `dst`.\n    const appendable: unknown[][] = [];\n    const upsertRows: unknown[][] = [];\n    for (const [path, targets] of byPath) {\n      for (const { target, embed } of targets) {\n        const row = [path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0];\n        if (addedSet.has(path)) appendable.push(row);\n        else upsertRows.push(row);\n      }\n    }\n    await appendRows(db, 'links', LINK_COLUMNS, UPSERT_LINK_SQL, appendable);\n    if (upsertRows.length > 0) await db.runBatch(UPSERT_LINK_SQL, upsertRows);\n  },\n  async afterReconcile(db, delta) {\n    // Any deleted rows mean the edge set shrank -- whether the file vanished or was reparsed\n    // down to fewer/no links.\n    const removeHadLinks = removedWithLinks.get(delta) ?? false;\n\n    // A cold build is the only case a full pass wins. Measured 2026-09-01 on 6,566 notes, resolve\n    // time alone: full is flat near 90ms at any churn, incremental 7ms at 10 files and 30ms at 2,000.\n    const large = delta.files.length === 0 || delta.added.length === delta.files.length;\n\n    const dstChanged = large ? await resolveAll(db, delta.files) : await resolveIncremental(db, delta);\n    delta.linksChanged = dstChanged || removeHadLinks;\n  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package/dist/cjs/features/sections.js

@@ -10,6 +10,7 @@ Object.defineProperty(exports, "sections", {
 });
 var _indexts = require("../chunk/index.js");
 var _frontmatterts = require("../scan/frontmatter.js");
+var _sharedts = require("../store/shared.js");
 function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) {
     try {
         var info = gen[key](arg);
@@ -159,6 +160,15 @@ function sectionsFromBlocks(blocks, raw, body) {
     }
     return found;
 }
+var SECTION_COLUMNS = [
+    'path',
+    'idx',
+    'level',
+    'heading',
+    'start_line',
+    'end_line',
+    'tokens'
+];
 var sections = {
     name: 'sections',
     schema: function schema(db) {
@@ -245,15 +255,13 @@ var sections = {
                                 }
                             }
                         }
-                        if (rows.length === 0) return [
-                            2
-                        ];
                         // DO NOTHING, not a bare INSERT: reconcile's added/touched split is decided before this
                         // write's lock, so a path called "added" here can already have this row from a concurrent
-                        // reconcile that committed first -- same file, same parse, same row.
+                        // reconcile that committed first -- same file, same parse, same row. A store with an append
+                        // path has no second writer, and remove() cleared every touched path above, so it skips the guard.
                         return [
                             4,
-                            db.runBatch('INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?) ON CONFLICT("path", idx) DO NOTHING', rows)
+                            (0, _sharedts.appendRows)(db, 'sections', SECTION_COLUMNS, 'INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?) ON CONFLICT("path", idx) DO NOTHING', rows)
                         ];
                     case 1:
                         _state.sent();