sensemaking 0.22.0 → 0.22.1

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 @@
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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. 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\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();

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

@@ -1 +1 @@
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'').trim(), startLine: b.startLine + offset, endLine: rawLines.length, tokens: 0 }));\n  for (let s = 0; s < found.length; s++) {\n    if (s + 1 < found.length) found[s].endLine = found[s + 1].startLine - 1;\n    const text = rawLines.slice(found[s].startLine - 1, found[s].endLine).join('\\n');\n    found[s].tokens = Math.ceil(estimateTokens(text));\n  }\n  return found;\n}\n\nconst SECTION_COLUMNS = ['path', 'idx', 'level', 'heading', 'start_line', 'end_line', 'tokens'];\n\nexport const sections: Feature = {\n  name: 'sections',\n  async schema(db) {\n    await db.exec(`CREATE TABLE IF NOT EXISTS sections (\"path\" TEXT, idx INTEGER, level INTEGER, heading TEXT, start_line INTEGER, end_line INTEGER, tokens INTEGER, PRIMARY KEY (\"path\", idx))`);\n  },\n  extract(raw, body, _search, _data, _cfg, blocks) {\n    return sectionsFromBlocks(blocks ?? parse(body), raw, body);\n  },\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM sections WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    for (const { path, extracted } of docs) (extracted as Section[]).forEach((s, idx) => rows.push([path, idx, s.level, s.heading, s.startLine, s.endLine, s.tokens]));\n    // DO NOTHING, not a bare INSERT: reconcile's added/touched split is decided before this\n    // write's lock, so a path called \"added\" here can already have this row from a concurrent\n    // reconcile that committed first -- same file, same parse, same row. 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package/dist/cjs/features/tags.js

@@ -8,6 +8,7 @@ Object.defineProperty(exports, "tags", {
         return tags;
     }
 });
+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;
@@ -372,12 +373,14 @@ var tags = {
                                 }
                             }
                         }
-                        if (rows.length === 0) return [
-                            2
-                        ];
+                        // OR IGNORE guards the same concurrent-reconcile race sections.ts documents; remove() cleared
+                        // every touched path above, so a store with an append path needs no guard.
                         return [
                             4,
-                            db.runBatch('INSERT OR IGNORE INTO tags ("path", tag) VALUES (?, ?)', rows)
+                            (0, _sharedts.appendRows)(db, 'tags', [
+                                'path',
+                                'tag'
+                            ], 'INSERT OR IGNORE INTO tags ("path", tag) VALUES (?, ?)', rows)
                         ];
                     case 1:
                         _state.sent();

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

@@ -1 +1 @@
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Nested tags store full (book/scifi); `tag = 'book' OR tag LIKE 'book/%'` matches the parent too.\n\n// Obsidian treats [[#Heading]] as a same-note link, not a tag.\nconst WIKILINK_RE = /\\[\\[.*?\\]\\]/g; // to the first ]], so a heading holding a lone ] still masks\n// Obsidian doesn't read tags inside HTML markup.\nconst HTML_TAG_RE = /<\\/?[a-zA-Z][^>]*>/g; // tag-shaped only: a comparison's `< 5` must not open a span\n// Anchors on start-of-line or a preceding whitespace/(/[ so `a#b` and URL fragments don't count.\nconst INLINE_TAG_RE = /(?:^|[\\s([])#([\\p{L}\\p{N}_/-]+)/gu;\n// A markdown link destination `](...)` -- `[text](#anchor)` is a same-page link, not a tag.\nconst LINK_DEST_RE = /\\]\\((?:[^()]|\\([^()]*\\))*\\)/g; // one paren-nesting level, as CommonMark destinations allow: (https://x/a_(b)#frag)\n\n// Strips a leading # (frontmatter entries may carry one) and a trailing /; rejects an\n// all-digit result -- a tag needs at least one non-digit character.\nfunction normalizeTag(raw: string): string | null {\n  const stripped = raw.replace(/^#/, '').replace(/\\/+$/, '');\n  if (!stripped || /^\\d+$/.test(stripped)) return null;\n  return stripped;\n}\n\n// data.tags: a YAML list (Obsidian also accepts a bare string). Null members and non-string\n// members are skipped rather than throwing -- `tags:\\n  -` parses to [null].\nfunction frontmatterTags(data?: Record<string, unknown>): string[] {\n  const raw = data?.tags;\n  const list = Array.isArray(raw) ? raw : typeof raw === 'string' ? [raw] : [];\n  const found: string[] = [];\n  for (const item of list) {\n    if (typeof item !== 'string') continue;\n    const tag = normalizeTag(item);\n    if (tag) found.push(tag);\n  }\n  return found;\n}\n\n// #tag tokens outside the regions maskRegions() masks (fences, code spans, wikilinks, HTML,\n// comments, link destinations); this loop only does per-line tag extraction.\nfunction inlineTags(body: string): string[] {\n  const found: string[] = [];\n  for (const line of maskRegions(body).split('\\n')) {\n    if (!line.includes('#')) continue; // most lines; skip the regex work\n    let cleaned = line;\n    if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('](')) cleaned = cleaned.replace(LINK_DEST_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('<')) cleaned = cleaned.replace(HTML_TAG_RE, (m) => ' '.repeat(m.length));\n    for (const m of cleaned.matchAll(INLINE_TAG_RE)) {\n      const tag = normalizeTag(m[1]);\n      if (tag) found.push(tag);\n    }\n  }\n  return found;\n}\n\nfunction extract(_raw: string, body: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): string[] {\n  return [...new Set([...frontmatterTags(data), ...inlineTags(body)])].sort();\n}\n\nexport const tags: Feature = {\n  name: 'tags',\n  async schema(db) {\n    await db.exec('CREATE TABLE IF NOT EXISTS tags (\"path\" TEXT, tag TEXT, PRIMARY KEY (\"path\", tag))');\n    await db.exec('CREATE INDEX IF NOT EXISTS tags_tag ON tags(tag)');\n  },\n  extract,\n  // Blanket clear-then-reinsert (store() always writes the full found list back), so remove()\n  // covers vanished and reparsed files without per-file NOT IN diffing, which cannot be one statement shared across files.\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM tags WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    for (const { path, extracted } of docs) for (const tag of extracted as string[]) rows.push([path, tag]);\n    if (rows.length === 0) return;\n    await db.runBatch('INSERT OR IGNORE INTO tags (\"path\", tag) VALUES (?, ?)', rows);\n  },\n};\n"],"names":["tags","WIKILINK_RE","HTML_TAG_RE","INLINE_TAG_RE","LINK_DEST_RE","normalizeTag","raw","stripped","replace","test","frontmatterTags","data","list","Array","isArray","found","item","tag","push","inlineTags","body","maskRegions","split","line","includes","cleaned","m","repeat","length","matchAll","extract","_raw","_search","Set","sort","name","schema","db","exec","remove","paths","runBatch","map","p","store","docs","rows","path","extracted"],"mappings":";;;;+BA2DaA;;;eAAAA;;;wBA3De;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAG5B,0FAA0F;AAC1F,kJAAkJ;AAElJ,+DAA+D;AAC/D,IAAMC,cAAc,gBAAgB,6DAA6D;AACjG,iDAAiD;AACjD,IAAMC,cAAc,uBAAuB,6DAA6D;AACxG,iGAAiG;AACjG,IAAMC,gBAAgB;AACtB,4FAA4F;AAC5F,IAAMC,eAAe,gCAAgC,oFAAoF;AAEzI,sFAAsF;AACtF,oEAAoE;AACpE,SAASC,aAAaC,GAAW;IAC/B,IAAMC,WAAWD,IAAIE,OAAO,CAAC,MAAM,IAAIA,OAAO,CAAC,QAAQ;IACvD,IAAI,CAACD,YAAY,QAAQE,IAAI,CAACF,WAAW,OAAO;IAChD,OAAOA;AACT;AAEA,4FAA4F;AAC5F,6EAA6E;AAC7E,SAASG,gBAAgBC,IAA8B;IACrD,IAAML,MAAMK,iBAAAA,2BAAAA,KAAMX,IAAI;IACtB,IAAMY,OAAOC,MAAMC,OAAO,CAACR,OAAOA,MAAM,OAAOA,QAAQ,WAAW;QAACA;KAAI,GAAG,EAAE;IAC5E,IAAMS,QAAkB,EAAE;QACrB,kCAAA,2BAAA;;QAAL,QAAK,YAAcH,yBAAd,SAAA,6BAAA,QAAA,yBAAA,iCAAoB;YAApB,IAAMI,OAAN;YACH,IAAI,OAAOA,SAAS,UAAU;YAC9B,IAAMC,MAAMZ,aAAaW;YACzB,IAAIC,KAAKF,MAAMG,IAAI,CAACD;QACtB;;QAJK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IAKL,OAAOF;AACT;AAEA,4FAA4F;AAC5F,6EAA6E;AAC7E,SAASI,WAAWC,IAAY;IAC9B,IAAML,QAAkB,EAAE;QACrB,kCAAA,2BAAA;;QAAL,QAAK,YAAcM,IAAAA,qBAAW,EAACD,MAAME,KAAK,CAAC,0BAAtC,SAAA,6BAAA,QAAA,yBAAA,iCAA6C;YAA7C,IAAMC,OAAN;YACH,IAAI,CAACA,KAAKC,QAAQ,CAAC,MAAM,UAAU,kCAAkC;YACrE,IAAIC,UAAUF;YACd,IAAIE,QAAQD,QAAQ,CAAC,OAAOC,UAAUA,QAAQjB,OAAO,CAACP,aAAa,SAACyB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;YAC7F,IAAIH,QAAQD,QAAQ,CAAC,OAAOC,UAAUA,QAAQjB,OAAO,CAACJ,cAAc,SAACsB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;YAC9F,IAAIH,QAAQD,QAAQ,CAAC,MAAMC,UAAUA,QAAQjB,OAAO,CAACN,aAAa,SAACwB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;gBACvF,mCAAA,4BAAA;;gBAAL,QAAK,aAAWH,QAAQI,QAAQ,CAAC1B,mCAA5B,UAAA,8BAAA,SAAA,0BAAA,kCAA4C;oBAA5C,IAAMuB,IAAN;oBACH,IAAMT,MAAMZ,aAAaqB,CAAC,CAAC,EAAE;oBAC7B,IAAIT,KAAKF,MAAMG,IAAI,CAACD;gBACtB;;gBAHK;gBAAA;;;yBAAA,8BAAA;wBAAA;;;wBAAA;8BAAA;;;;QAIP;;QAVK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IAWL,OAAOF;AACT;AAEA,SAASe,QAAQC,IAAY,EAAEX,IAAY,EAAEY,OAA4C,EAAErB,IAA8B;IACvH,OAAO,AAAC,qBAAG,IAAIsB,IAAI,AAAC,qBAAGvB,gBAAgBC,cAAO,qBAAGQ,WAAWC,UAASc,IAAI;AAC3E;AAEO,IAAMlC,OAAgB;IAC3BmC,MAAM;IACAC,QAAN,SAAMA,OAAOC,EAAE;;;;;wBACb;;4BAAMA,GAAGC,IAAI,CAAC;;;wBAAd;wBACA;;4BAAMD,GAAGC,IAAI,CAAC;;;wBAAd;;;;;;QACF;;IACAR,SAAAA;IAGMS,QAFN,4FAA4F;IAC5F,yHAAyH;IACzH,SAAMA,OAAOF,EAAE,EAAEG,KAAK;;;;;wBACpB,IAAIA,MAAMZ,MAAM,KAAK,GAAG;;;wBACxB;;4BAAMS,GAAGI,QAAQ,CACf,qCACAD,MAAME,GAAG,CAAC,SAACC;uCAAM;oCAACA;iCAAE;;;;wBAFtB;;;;;;QAIF;;IACMC,OAAN,SAAMA,MAAMP,EAAE,EAAEQ,IAAI;;gBACZC,MACuC,2BAAA,mBAAA,gBAAxC,4BAAA,oBAAA,iBAAA,WAAA,oBAAQC,MAAMC,WAA0B,YAAA,QAAM/B;;;;wBAD7C6B;wBACuC,kCAAA,2BAAA,4BAAxC,mCAAA,4BAAA;;4BAAL,IAAK,YAA6BD,2BAA7B,8BAAA,QAAA,yBAAA;8CAAA,aAAQE,mBAAAA,MAAMC,wBAAAA;;oCAAqB,IAAK,aAAaA,gCAAb,6BAAA,SAAA,0BAAA;wCAAM/B,MAAN;wCAAoC6B,KAAK5B,IAAI;4CAAE6B;4CAAM9B;;;;oCAArD;oCAAA;;;6CAAA,6BAAA;4CAAA;;;4CAAA;kDAAA;;;;;;4BAAxC;4BAAA;;;qCAAA,8BAAA;oCAAA;;;oCAAA;0CAAA;;;;wBACL,IAAI6B,KAAKlB,MAAM,KAAK,GAAG;;;wBACvB;;4BAAMS,GAAGI,QAAQ,CAAC,0DAA0DK;;;wBAA5E;;;;;;QACF;;AACF"}
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/tags.ts"],"sourcesContent":["import { appendRows } from '../store/shared.ts';\nimport { maskRegions } from './fences.ts';\nimport type { Feature } from './types.ts';\n\n// tags(path, tag): Obsidian's file.tags grain -- frontmatter list/string tags plus inline\n// #tags, deduplicated, source not distinguished. Nested tags store full (book/scifi); `tag = 'book' OR tag LIKE 'book/%'` matches the parent too.\n\n// Obsidian treats [[#Heading]] as a same-note link, not a tag.\nconst WIKILINK_RE = /\\[\\[.*?\\]\\]/g; // to the first ]], so a heading holding a lone ] still masks\n// Obsidian doesn't read tags inside HTML markup.\nconst HTML_TAG_RE = /<\\/?[a-zA-Z][^>]*>/g; // tag-shaped only: a comparison's `< 5` must not open a span\n// Anchors on start-of-line or a preceding whitespace/(/[ so `a#b` and URL fragments don't count.\nconst INLINE_TAG_RE = /(?:^|[\\s([])#([\\p{L}\\p{N}_/-]+)/gu;\n// A markdown link destination `](...)` -- `[text](#anchor)` is a same-page link, not a tag.\nconst LINK_DEST_RE = /\\]\\((?:[^()]|\\([^()]*\\))*\\)/g; // one paren-nesting level, as CommonMark destinations allow: (https://x/a_(b)#frag)\n\n// Strips a leading # (frontmatter entries may carry one) and a trailing /; rejects an\n// all-digit result -- a tag needs at least one non-digit character.\nfunction normalizeTag(raw: string): string | null {\n  const stripped = raw.replace(/^#/, '').replace(/\\/+$/, '');\n  if (!stripped || /^\\d+$/.test(stripped)) return null;\n  return stripped;\n}\n\n// data.tags: a YAML list (Obsidian also accepts a bare string). Null members and non-string\n// members are skipped rather than throwing -- `tags:\\n  -` parses to [null].\nfunction frontmatterTags(data?: Record<string, unknown>): string[] {\n  const raw = data?.tags;\n  const list = Array.isArray(raw) ? raw : typeof raw === 'string' ? [raw] : [];\n  const found: string[] = [];\n  for (const item of list) {\n    if (typeof item !== 'string') continue;\n    const tag = normalizeTag(item);\n    if (tag) found.push(tag);\n  }\n  return found;\n}\n\n// #tag tokens outside the regions maskRegions() masks (fences, code spans, wikilinks, HTML,\n// comments, link destinations); this loop only does per-line tag extraction.\nfunction inlineTags(body: string): string[] {\n  const found: string[] = [];\n  for (const line of maskRegions(body).split('\\n')) {\n    if (!line.includes('#')) continue; // most lines; skip the regex work\n    let cleaned = line;\n    if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('](')) cleaned = cleaned.replace(LINK_DEST_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('<')) cleaned = cleaned.replace(HTML_TAG_RE, (m) => ' '.repeat(m.length));\n    for (const m of cleaned.matchAll(INLINE_TAG_RE)) {\n      const tag = normalizeTag(m[1]);\n      if (tag) found.push(tag);\n    }\n  }\n  return found;\n}\n\nfunction extract(_raw: string, body: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): string[] {\n  return [...new Set([...frontmatterTags(data), ...inlineTags(body)])].sort();\n}\n\nexport const tags: Feature = {\n  name: 'tags',\n  async schema(db) {\n    await db.exec('CREATE TABLE IF NOT EXISTS tags (\"path\" TEXT, tag TEXT, PRIMARY KEY (\"path\", tag))');\n    await db.exec('CREATE INDEX IF NOT EXISTS tags_tag ON tags(tag)');\n  },\n  extract,\n  // Blanket clear-then-reinsert (store() always writes the full found list back), so remove()\n  // covers vanished and reparsed files without per-file NOT IN diffing, which cannot be one statement shared across files.\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM tags WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    for (const { path, extracted } of docs) for (const tag of extracted as string[]) rows.push([path, tag]);\n    // OR IGNORE guards the same concurrent-reconcile race sections.ts documents; remove() cleared\n    // every touched path above, so a store with an append path needs no guard.\n    await appendRows(db, 'tags', ['path', 'tag'], 'INSERT OR IGNORE INTO tags (\"path\", tag) VALUES (?, ?)', rows);\n  },\n};\n"],"names":["tags","WIKILINK_RE","HTML_TAG_RE","INLINE_TAG_RE","LINK_DEST_RE","normalizeTag","raw","stripped","replace","test","frontmatterTags","data","list","Array","isArray","found","item","tag","push","inlineTags","body","maskRegions","split","line","includes","cleaned","m","repeat","length","matchAll","extract","_raw","_search","Set","sort","name","schema","db","exec","remove","paths","runBatch","map","p","store","docs","rows","path","extracted","appendRows"],"mappings":";;;;+BA4DaA;;;eAAAA;;;wBA5Dc;wBACC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAG5B,0FAA0F;AAC1F,kJAAkJ;AAElJ,+DAA+D;AAC/D,IAAMC,cAAc,gBAAgB,6DAA6D;AACjG,iDAAiD;AACjD,IAAMC,cAAc,uBAAuB,6DAA6D;AACxG,iGAAiG;AACjG,IAAMC,gBAAgB;AACtB,4FAA4F;AAC5F,IAAMC,eAAe,gCAAgC,oFAAoF;AAEzI,sFAAsF;AACtF,oEAAoE;AACpE,SAASC,aAAaC,GAAW;IAC/B,IAAMC,WAAWD,IAAIE,OAAO,CAAC,MAAM,IAAIA,OAAO,CAAC,QAAQ;IACvD,IAAI,CAACD,YAAY,QAAQE,IAAI,CAACF,WAAW,OAAO;IAChD,OAAOA;AACT;AAEA,4FAA4F;AAC5F,6EAA6E;AAC7E,SAASG,gBAAgBC,IAA8B;IACrD,IAAML,MAAMK,iBAAAA,2BAAAA,KAAMX,IAAI;IACtB,IAAMY,OAAOC,MAAMC,OAAO,CAACR,OAAOA,MAAM,OAAOA,QAAQ,WAAW;QAACA;KAAI,GAAG,EAAE;IAC5E,IAAMS,QAAkB,EAAE;QACrB,kCAAA,2BAAA;;QAAL,QAAK,YAAcH,yBAAd,SAAA,6BAAA,QAAA,yBAAA,iCAAoB;YAApB,IAAMI,OAAN;YACH,IAAI,OAAOA,SAAS,UAAU;YAC9B,IAAMC,MAAMZ,aAAaW;YACzB,IAAIC,KAAKF,MAAMG,IAAI,CAACD;QACtB;;QAJK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IAKL,OAAOF;AACT;AAEA,4FAA4F;AAC5F,6EAA6E;AAC7E,SAASI,WAAWC,IAAY;IAC9B,IAAML,QAAkB,EAAE;QACrB,kCAAA,2BAAA;;QAAL,QAAK,YAAcM,IAAAA,qBAAW,EAACD,MAAME,KAAK,CAAC,0BAAtC,SAAA,6BAAA,QAAA,yBAAA,iCAA6C;YAA7C,IAAMC,OAAN;YACH,IAAI,CAACA,KAAKC,QAAQ,CAAC,MAAM,UAAU,kCAAkC;YACrE,IAAIC,UAAUF;YACd,IAAIE,QAAQD,QAAQ,CAAC,OAAOC,UAAUA,QAAQjB,OAAO,CAACP,aAAa,SAACyB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;YAC7F,IAAIH,QAAQD,QAAQ,CAAC,OAAOC,UAAUA,QAAQjB,OAAO,CAACJ,cAAc,SAACsB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;YAC9F,IAAIH,QAAQD,QAAQ,CAAC,MAAMC,UAAUA,QAAQjB,OAAO,CAACN,aAAa,SAACwB;uBAAM,IAAIC,MAAM,CAACD,EAAEE,MAAM;;gBACvF,mCAAA,4BAAA;;gBAAL,QAAK,aAAWH,QAAQI,QAAQ,CAAC1B,mCAA5B,UAAA,8BAAA,SAAA,0BAAA,kCAA4C;oBAA5C,IAAMuB,IAAN;oBACH,IAAMT,MAAMZ,aAAaqB,CAAC,CAAC,EAAE;oBAC7B,IAAIT,KAAKF,MAAMG,IAAI,CAACD;gBACtB;;gBAHK;gBAAA;;;yBAAA,8BAAA;wBAAA;;;wBAAA;8BAAA;;;;QAIP;;QAVK;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IAWL,OAAOF;AACT;AAEA,SAASe,QAAQC,IAAY,EAAEX,IAAY,EAAEY,OAA4C,EAAErB,IAA8B;IACvH,OAAO,AAAC,qBAAG,IAAIsB,IAAI,AAAC,qBAAGvB,gBAAgBC,cAAO,qBAAGQ,WAAWC,UAASc,IAAI;AAC3E;AAEO,IAAMlC,OAAgB;IAC3BmC,MAAM;IACAC,QAAN,SAAMA,OAAOC,EAAE;;;;;wBACb;;4BAAMA,GAAGC,IAAI,CAAC;;;wBAAd;wBACA;;4BAAMD,GAAGC,IAAI,CAAC;;;wBAAd;;;;;;QACF;;IACAR,SAAAA;IAGMS,QAFN,4FAA4F;IAC5F,yHAAyH;IACzH,SAAMA,OAAOF,EAAE,EAAEG,KAAK;;;;;wBACpB,IAAIA,MAAMZ,MAAM,KAAK,GAAG;;;wBACxB;;4BAAMS,GAAGI,QAAQ,CACf,qCACAD,MAAME,GAAG,CAAC,SAACC;uCAAM;oCAACA;iCAAE;;;;wBAFtB;;;;;;QAIF;;IACMC,OAAN,SAAMA,MAAMP,EAAE,EAAEQ,IAAI;;gBACZC,MACuC,2BAAA,mBAAA,gBAAxC,4BAAA,oBAAA,iBAAA,WAAA,oBAAQC,MAAMC,WAA0B,YAAA,QAAM/B;;;;wBAD7C6B;wBACuC,kCAAA,2BAAA,4BAAxC,mCAAA,4BAAA;;4BAAL,IAAK,YAA6BD,2BAA7B,8BAAA,QAAA,yBAAA;8CAAA,aAAQE,mBAAAA,MAAMC,wBAAAA;;oCAAqB,IAAK,aAAaA,gCAAb,6BAAA,SAAA,0BAAA;wCAAM/B,MAAN;wCAAoC6B,KAAK5B,IAAI;4CAAE6B;4CAAM9B;;;;oCAArD;oCAAA;;;6CAAA,6BAAA;4CAAA;;;4CAAA;kDAAA;;;;;;4BAAxC;4BAAA;;;qCAAA,8BAAA;oCAAA;;;oCAAA;0CAAA;;;;wBACL,8FAA8F;wBAC9F,2EAA2E;wBAC3E;;4BAAMgC,IAAAA,oBAAU,EAACZ,IAAI;gCAAS;gCAAQ;+BAAQ,0DAA0DS;;;wBAAxG;;;;;;QACF;;AACF"}

package/dist/cjs/store/duckdb/connection.js

@@ -19,8 +19,10 @@ _export(exports, {
         return storeValueToJs;
     }
 });
+var _sharedts = require("../shared.js");
 var _transactionts = require("../transaction.js");
 var _batchts = require("./batch.js");
+var _nativets = require("./native.js");
 function _array_like_to_array(arr, len) {
     if (len == null || len > arr.length) len = arr.length;
     for(var i = 0, arr2 = new Array(len); i < len; i++)arr2[i] = arr[i];
@@ -610,6 +612,124 @@ function createConnection(duckdb) {
                 });
             })();
         },
+        appendRows: // The appender writes columnar vectors with no per-parameter binding, which is the cost
+        // runBatch pays: measured 7.2x on frontmatter at 6,566 rows. Alignment is against the table's
+        // own physical column order, read fresh, so a column the caller does not write (a
+        // feature-owned "_rank", say) takes appendDefault() rather than shifting every value one slot.
+        function appendRows(table, columns, rows) {
+            return _async_to_generator(function() {
+                var variantValue, infoStmt, physical, rowIndexOf;
+                return _ts_generator(this, function(_state) {
+                    switch(_state.label){
+                        case 0:
+                            if (rows.length === 0) return [
+                                2
+                            ];
+                            return [
+                                4,
+                                (0, _nativets.duckdbApi)()
+                            ];
+                        case 1:
+                            variantValue = _state.sent().variantValue;
+                            return [
+                                4,
+                                conn.prepare("PRAGMA table_info(".concat((0, _sharedts.quoteIdent)(table), ")"))
+                            ];
+                        case 2:
+                            infoStmt = _state.sent();
+                            return [
+                                4,
+                                infoStmt.all()
+                            ];
+                        case 3:
+                            physical = _state.sent();
+                            rowIndexOf = new Map(columns.map(function(name, i) {
+                                return [
+                                    name,
+                                    i
+                                ];
+                            }));
+                            return [
+                                4,
+                                (0, _transactionts.withTransaction)(conn, function() {
+                                    return _async_to_generator(function() {
+                                        var appender, _iteratorNormalCompletion, _didIteratorError, _iteratorError, _iterator, _step, row, _iteratorNormalCompletion1, _didIteratorError1, _iteratorError1, _iterator1, _step1, column, idx, value;
+                                        return _ts_generator(this, function(_state) {
+                                            switch(_state.label){
+                                                case 0:
+                                                    return [
+                                                        4,
+                                                        duckdb.createAppender(table)
+                                                    ];
+                                                case 1:
+                                                    appender = _state.sent();
+                                                    try {
+                                                        _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
+                                                        try {
+                                                            for(_iterator = rows[Symbol.iterator](); !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
+                                                                row = _step.value;
+                                                                _iteratorNormalCompletion1 = true, _didIteratorError1 = false, _iteratorError1 = undefined;
+                                                                try {
+                                                                    for(_iterator1 = physical[Symbol.iterator](); !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
+                                                                        column = _step1.value;
+                                                                        idx = rowIndexOf.get(column.name);
+                                                                        value = idx === undefined ? undefined : row[idx];
+                                                                        if (idx === undefined) appender.appendDefault();
+                                                                        else if (value === null || value === undefined) appender.appendNull();
+                                                                        else if (column.type === 'VARIANT') appender.appendVariant(variantValue(value));
+                                                                        else appender.appendValue(value);
+                                                                    }
+                                                                } catch (err) {
+                                                                    _didIteratorError1 = true;
+                                                                    _iteratorError1 = err;
+                                                                } finally{
+                                                                    try {
+                                                                        if (!_iteratorNormalCompletion1 && _iterator1.return != null) {
+                                                                            _iterator1.return();
+                                                                        }
+                                                                    } finally{
+                                                                        if (_didIteratorError1) {
+                                                                            throw _iteratorError1;
+                                                                        }
+                                                                    }
+                                                                }
+                                                                appender.endRow();
+                                                            }
+                                                        } catch (err) {
+                                                            _didIteratorError = true;
+                                                            _iteratorError = err;
+                                                        } finally{
+                                                            try {
+                                                                if (!_iteratorNormalCompletion && _iterator.return != null) {
+                                                                    _iterator.return();
+                                                                }
+                                                            } finally{
+                                                                if (_didIteratorError) {
+                                                                    throw _iteratorError;
+                                                                }
+                                                            }
+                                                        }
+                                                        appender.flushSync();
+                                                    } finally{
+                                                        appender.closeSync();
+                                                    }
+                                                    return [
+                                                        2
+                                                    ];
+                                            }
+                                        });
+                                    })();
+                                })
+                            ];
+                        case 4:
+                            _state.sent();
+                            return [
+                                2
+                            ];
+                    }
+                });
+            })();
+        },
         runBatch: // One crossing regardless of row count: rewriteBatch folds recognized shapes into a multi-row statement (batch.ts),
         // else falls back to a bind-and-run loop, one call either way. Joins the caller's transaction when there is one, else opens its own.
         function runBatch(sql, paramRows) {