sensemaking 0.22.0 → 0.22.2

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` 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. |
+| `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. Indexing speed is the other axis, and it does not follow from any of the above: sqlite builds a cold index fastest and turso slowest, by a wide margin on a large tree, and no setting closes that gap, since turso's engine costs more per write and more again to maintain each index. What turso buys instead is concurrent writers, non-blocking I/O and encryption, none of which a one-shot command uses, so reach for it for those rather than for speed. Per-store figures: [BENCHMARKING.md](BENCHMARKING.md). |
 | `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/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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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;
@@ -507,45 +508,6 @@ function writeResolved(db, rows) {
         });
     })();
 }
-// A new or deleted file can change any note's resolution, so re-resolve the whole table.
-// Fallback for cold builds and large deltas -- see afterReconcile's threshold.
-function resolveAll(db, files) {
-    return _async_to_generator(function() {
-        var pathSet, byBase, stmt, rows, changed;
-        return _ts_generator(this, function(_state) {
-            switch(_state.label){
-                case 0:
-                    pathSet = new Set(files.map(function(f) {
-                        return f.relPath;
-                    }));
-                    byBase = buildByBase(files);
-                    return [
-                        4,
-                        db.prepare('SELECT src, target, dst, embed FROM links')
-                    ];
-                case 1:
-                    stmt = _state.sent();
-                    return [
-                        4,
-                        stmt.all()
-                    ];
-                case 2:
-                    rows = _state.sent();
-                    changed = resolveRows(rows, pathSet, byBase);
-                    return [
-                        4,
-                        writeResolved(db, changed)
-                    ];
-                case 3:
-                    _state.sent();
-                    return [
-                        2,
-                        changed.length > 0
-                    ];
-            }
-        });
-    })();
-}
 // Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit
 // (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.
 function selectIn(db, column, keys) {
@@ -756,6 +718,26 @@ 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();
+// Cold build only: whether store() resolved at least one row to a non-null dst, so afterReconcile
+// can report linksChanged without re-reading the table it just wrote.
+var coldResolved = new WeakMap();
+// dst stays NULL here on an incremental store (resolution runs afterward); a cold build resolves
+// it inline in store() instead, through the *_RESOLVED column list and SQL below.
+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 LINK_COLUMNS_RESOLVED = [
+    'src',
+    'target',
+    'target_base',
+    'dst',
+    'embed'
+];
+var UPSERT_LINK_SQL_RESOLVED = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, ?, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base';
 var links = {
     name: 'links',
     schema: function schema(db) {
@@ -830,7 +812,7 @@ 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, cold, resolveNew, pathSet, byBase, resolvedLink, appendable, upsertRows, _iteratorNormalCompletion, _didIteratorError, _iteratorError, _iterator, _step, _step_value, path, targets, _iteratorNormalCompletion1, _didIteratorError1, _iteratorError1, _iterator1, _step1, _step_value1, target, embed, targetBase, dst;
             return _ts_generator(this, function(_state) {
                 switch(_state.label){
                     case 0:
@@ -878,8 +860,25 @@ var links = {
                         removedWithLinks.set(delta, true);
                         _state.label = 3;
                     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.
+                        // Cold build: every path is in `added`, so pathSet/byBase cover the same complete tree
+                        // afterReconcile's large branch would otherwise re-derive; resolve dst here instead.
+                        cold = delta.files.length === 0 || delta.added.length === delta.files.length;
+                        if (cold) {
+                            pathSet = new Set(delta.files.map(function(f) {
+                                return f.relPath;
+                            }));
+                            byBase = buildByBase(delta.files);
+                            resolveNew = function resolveNew(src, target) {
+                                return resolveTarget(src, target, pathSet, byBase);
+                            };
+                        }
+                        resolvedLink = false;
+                        // Upsert preserves dst on surviving rows; a cold build resolves new rows, else they start 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 {
@@ -889,10 +888,32 @@ 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([
+                                        targetBase = target.startsWith('#') ? null : baseKey(cleanTarget(target));
+                                        if (!addedSet.has(path)) {
+                                            upsertRows.push([
+                                                path,
+                                                target,
+                                                targetBase,
+                                                embed ? 1 : 0
+                                            ]);
+                                            continue;
+                                        }
+                                        if (!resolveNew) {
+                                            appendable.push([
+                                                path,
+                                                target,
+                                                targetBase,
+                                                embed ? 1 : 0
+                                            ]);
+                                            continue;
+                                        }
+                                        dst = resolveNew(path, target);
+                                        if (dst !== null) resolvedLink = true;
+                                        appendable.push([
                                             path,
                                             target,
-                                            target.startsWith('#') ? null : baseKey(cleanTarget(target)),
+                                            targetBase,
+                                            dst,
                                             embed ? 1 : 0
                                         ]);
                                     }
@@ -925,18 +946,25 @@ var links = {
                                 }
                             }
                         }
+                        return [
+                            4,
+                            (0, _sharedts.appendRows)(db, 'links', resolveNew ? LINK_COLUMNS_RESOLVED : LINK_COLUMNS, resolveNew ? UPSERT_LINK_SQL_RESOLVED : 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:
+                        if (cold) coldResolved.set(delta, resolvedLink);
                         return [
                             2
                         ];
@@ -946,7 +974,7 @@ var links = {
     },
     afterReconcile: function afterReconcile(db, delta) {
         return _async_to_generator(function() {
-            var _removedWithLinks_get, removeHadLinks, large, dstChanged, _tmp;
+            var _removedWithLinks_get, removeHadLinks, large, _coldResolved_get, dstChanged;
             return _ts_generator(this, function(_state) {
                 switch(_state.label){
                     case 0:
@@ -956,30 +984,20 @@ var links = {
                         // A cold build is the only case a full pass wins. Measured 2026-09-01 on 6,566 notes, resolve
                         // time alone: full is flat near 90ms at any churn, incremental 7ms at 10 files and 30ms at 2,000.
                         large = delta.files.length === 0 || delta.added.length === delta.files.length;
-                        if (!large) return [
-                            3,
-                            2
-                        ];
-                        return [
-                            4,
-                            resolveAll(db, delta.files)
-                        ];
-                    case 1:
-                        _tmp = _state.sent();
-                        return [
-                            3,
-                            4
-                        ];
-                    case 2:
+                        // store() already resolved dst inline on this cold build (same test), so nothing is left to update.
+                        if (large) {
+                            ;
+                            delta.linksChanged = ((_coldResolved_get = coldResolved.get(delta)) !== null && _coldResolved_get !== void 0 ? _coldResolved_get : false) || removeHadLinks;
+                            return [
+                                2
+                            ];
+                        }
                         return [
                             4,
                             resolveIncremental(db, delta)
                         ];
-                    case 3:
-                        _tmp = _state.sent();
-                        _state.label = 4;
-                    case 4:
-                        dstChanged = _tmp;
+                    case 1:
+                        dstChanged = _state.sent();
                         delta.linksChanged = dstChanged || removeHadLinks;
                         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) ?? [];\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    const upsertRows: unknown[][] = [];\n    for (const [path, targets] of byPath) {\n      for (const { target, embed } of targets) upsertRows.push([path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0]);\n    }\n    if (upsertRows.length > 0) {\n      await db.runBatch('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) 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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// 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// Cold build only: whether store() resolved at least one row to a non-null dst, so afterReconcile\n// can report linksChanged without re-reading the table it just wrote.\nconst coldResolved = new WeakMap<ReconcileDelta, boolean>();\n\n// dst stays NULL here on an incremental store (resolution runs afterward); a cold build resolves\n// it inline in store() instead, through the *_RESOLVED column list and SQL below.\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';\nconst LINK_COLUMNS_RESOLVED = ['src', 'target', 'target_base', 'dst', 'embed'];\nconst UPSERT_LINK_SQL_RESOLVED = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, ?, ?) 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    // Cold build: every path is in `added`, so pathSet/byBase cover the same complete tree\n    // afterReconcile's large branch would otherwise re-derive; resolve dst here instead.\n    const cold = delta.files.length === 0 || delta.added.length === delta.files.length;\n    let resolveNew: ((src: string, target: string) => string | null) | undefined;\n    if (cold) {\n      const pathSet = new Set(delta.files.map((f) => f.relPath));\n      const byBase = buildByBase(delta.files);\n      resolveNew = (src, target) => resolveTarget(src, target, pathSet, byBase);\n    }\n    let resolvedLink = false;\n\n    // Upsert preserves dst on surviving rows; a cold build resolves new rows, else they start NULL.\n    // A same-note anchor 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 targetBase = target.startsWith('#') ? null : baseKey(cleanTarget(target));\n        if (!addedSet.has(path)) {\n          upsertRows.push([path, target, targetBase, embed ? 1 : 0]);\n          continue;\n        }\n        if (!resolveNew) {\n          appendable.push([path, target, targetBase, embed ? 1 : 0]);\n          continue;\n        }\n        const dst = resolveNew(path, target);\n        if (dst !== null) resolvedLink = true;\n        appendable.push([path, target, targetBase, dst, embed ? 1 : 0]);\n      }\n    }\n    await appendRows(db, 'links', resolveNew ? LINK_COLUMNS_RESOLVED : LINK_COLUMNS, resolveNew ? 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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    // store() already resolved dst inline on this cold build (same test), so nothing is left to update.\n    if (large) {\n      delta.linksChanged = (coldResolved.get(delta) ?? false) || removeHadLinks;\n      return;\n    }\n\n    const dstChanged = 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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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/sections.ts"],"sourcesContent":["import type { Block } from '../chunk/index.ts';\nimport { estimateTokens, parse } from '../chunk/index.ts';\nimport { countLines } from '../scan/frontmatter.ts';\nimport { appendRows } from '../store/shared.ts';\nimport type { Feature } from './types.ts';\n\n// sections(path, idx, level, heading, start_line, end_line, tokens): the heading outline,\n// 1-indexed over the raw file so a row is a direct Read range; tokens is estimateTokens (D5), CJK-aware.\n\nexport interface Section {\n  level: number;\n  heading: string;\n  startLine: number;\n  endLine: number;\n  tokens: number;\n}\n\n// Heading blocks parse() already found (mdast/CommonMark fences), offset back onto the raw file;\n// a section runs to just before the next heading, or EOF.\nfunction sectionsFromBlocks(blocks: Block[], raw: string, body: string): Section[] {\n  const rawLines = raw.split('\\n');\n  const offset = rawLines.length - countLines(body);\n  const found: Section[] = blocks.filter((b) => b.type === 'heading').map((b) => ({ level: b.depth ?? 1, heading: (b.text ?? '').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 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/tags.ts"],"sourcesContent":["import { 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; 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+{"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; 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package/dist/cjs/store/builder.js

@@ -323,9 +323,8 @@ function invalidateFeatureTable(conn, cfg, baseDir, dialect, pool, toggle) {
                     paths = docs.map(function(d) {
                         return d.relPath;
                     });
-                    // Every path counts as added, not just touched: the table was just dropped, so there is nothing
-                    // stale to diff against, and links' own afterReconcile takes its cold-build (resolveAll) path
-                    // only when added.length equals files.length.
+                    // Every path counts as added, not just touched: nothing stale to diff against. Links resolves
+                    // dst inside store() itself when added.length equals files.length (a cold build).
                     delta = {
                         files: files,
                         reparsed: paths,