sensemaking 0.17.0 → 0.18.0

package/dist/esm/{db → store/sqlite}/reconcile.js

@@ -1,10 +1,12 @@
-import { contentTokenize } from '../config/index.js';
-import { SenseError } from '../errors.js';
-import { activeFeatures } from '../features/index.js';
-import { progress } from '../output/progress.js';
-import { listFiles, parseFile, RESERVED_COLUMNS } from '../scan/index.js';
-import { segmentField } from '../text/segment.js';
-import { getColumns, getMeta, quoteIdent, setMeta } from './shared.js';
+import { contentTokenize } from '../../config/index.js';
+import { SenseError } from '../../errors.js';
+import { activeFeatures } from '../../features/index.js';
+import { progress } from '../../output/progress.js';
+import { listFiles, parseFile, RESERVED_COLUMNS } from '../../scan/index.js';
+import { reparseFiles } from '../../scan/reparse.js';
+import { segmentField } from '../../text/segment.js';
+import { getColumns, getMeta, quoteIdent, setMeta } from '../shared.js';
+import { withTransaction } from '../transaction.js';
 // Feature-owned columns (`_rank`) must stay out of the upsert: a reparse would null the last
 // computed value on every touch, not just the reconciles that recompute it.
 const CORE_FRONTMATTER_COLUMNS = new Set([
@@ -19,15 +21,25 @@ const MAX_FRONTMATTER_COLUMNS = 2000;
 // Shared by reconcile() and the tokenize-only rebuild in open(), so both prepare the same
 // literal instead of two copies drifting apart.
 const INSERT_CONTENT_SQL = `INSERT INTO content (rowid, title, summary, text, "path", title_seg, summary_seg, text_seg) VALUES ((SELECT rowid FROM frontmatter WHERE "path" = ?), ?, ?, ?, ?, ?, ?, ?)`;
-// Shared by reconcile() and the tokenize-only rebuild in open(), so content population is
-// defined once. Assumes the frontmatter row for doc.relPath already exists (rowid lookup).
-function insertContentRow(insertBody, doc, segmenting) {
-    insertBody.run(doc.relPath, doc.search.title, doc.search.summary, doc.search.text, doc.relPath, segmenting ? segmentField(doc.search.title) : '', segmenting ? segmentField(doc.search.summary) : '', segmenting ? segmentField(doc.search.text) : '');
+// A single content row's param tuple, matching INSERT_CONTENT_SQL's placeholder order.
+// Assumes the frontmatter row for doc.relPath already exists (rowid subquery).
+function contentRow(doc, segmenting) {
+    return [
+        doc.relPath,
+        doc.search.title,
+        doc.search.summary,
+        doc.search.text,
+        doc.relPath,
+        segmenting ? segmentField(doc.search.title) : '',
+        segmenting ? segmentField(doc.search.summary) : '',
+        segmenting ? segmentField(doc.search.text) : ''
+    ];
 }
-export function reconcile(db, cfg, baseDir) {
+export async function reconcile(conn, cfg, baseDir) {
     const files = listFiles(cfg, baseDir);
     const currentSet = new Set(files.map((f)=>f.relPath));
-    const existingRows = db.prepare(`SELECT "path", "_mtime", "_size" FROM frontmatter`).all();
+    const existingStmt = await conn.prepare('SELECT "path", "_mtime", "_size" FROM frontmatter');
+    const existingRows = await existingStmt.all();
     const existing = new Map(existingRows.map((r)=>[
             r.path,
             r
@@ -42,30 +54,13 @@ export function reconcile(db, cfg, baseDir) {
         warnings: []
     };
     const features = activeFeatures(cfg);
-    const seenColumns = getColumns(db);
-    const newColumns = [];
-    const parsedDocs = [];
-    const warnings = [];
+    const seenColumns = await getColumns(conn);
     // Bulk reparses (a sync, a cold build) are the long silences a query can hit; short
     // reconciles stay silent (progress() has a threshold).
     const report = progress('reparsing files', toReparse.length);
-    let parsedCount = 0;
-    for (const file of toReparse){
-        // A doc only gets extract/store from features that apply to it (currently: embed, via
-        // FileStat.embed -- true iff the config names an embedding model).
-        const fileFeatures = features.filter((feature)=>!feature.enabledForFile || feature.enabledForFile(cfg, file));
-        const { doc, warnings: fileWarnings } = parseFile(file, fileFeatures, cfg);
-        report.tick(++parsedCount);
-        warnings.push(...fileWarnings);
-        for (const key of Object.keys(doc.data)){
-            if (!seenColumns.has(key)) {
-                seenColumns.add(key);
-                newColumns.push(key);
-            }
-        }
-        parsedDocs.push(doc);
-    }
+    const { docs: parsedDocs, warnings, newColumns } = reparseFiles(toReparse, features, cfg, seenColumns, report.tick);
     report.finish();
+    for (const col of newColumns)seenColumns.add(col);
     const allColumns = [
         ...seenColumns
     ];
@@ -87,38 +82,31 @@ export function reconcile(db, cfg, baseDir) {
         added,
         vanished
     };
+    const addedSet = new Set(added);
+    const reparsedExisting = parsedDocs.map((d)=>d.relPath).filter((p)=>!addedSet.has(p));
     const txStart = Date.now();
-    db.exec('BEGIN');
-    try {
-        var _feature_afterReconcile;
-        for (const col of newColumns)db.exec(`ALTER TABLE frontmatter ADD COLUMN ${quoteIdent(col)}`);
-        // FTS5 has no upsert, so delete-before-insert into `content`; coupled to the
-        // frontmatter rowid (indexed via its PRIMARY KEY) instead of the UNINDEXED `path`
-        // column, which a per-row DELETE would otherwise scan the whole table to find.
-        const delBody = db.prepare(`DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE "path" = ?)`);
-        const delPresetFiles = db.prepare(`DELETE FROM preset_files WHERE "path" = ?`);
-        const insertPresetFile = db.prepare(`INSERT INTO preset_files ("path", preset) VALUES (?, ?)`);
+    await withTransaction(conn, async ()=>{
+        var _feature_remove, _feature_afterReconcile;
+        for (const col of newColumns)await conn.exec(`ALTER TABLE frontmatter ADD COLUMN ${quoteIdent(col)}`);
+        // content's rowid lookup depends on the frontmatter row it's coupled to, so every content
+        // delete/insert below must run after that row exists (vanished paths still have their
+        // frontmatter row at this point) and before it is removed (vanished frontmatter delete
+        // comes last).
         if (vanished.length > 0) {
-            const del = db.prepare(`DELETE FROM frontmatter WHERE "path" = ?`);
-            for (const path of vanished){
-                var _feature_remove;
-                // content delete must run first: it looks up the frontmatter rowid by path, which
-                // the frontmatter delete below would otherwise have already removed.
-                delBody.run(path);
-                del.run(path);
-                delPresetFiles.run(path);
-                for (const feature of features)(_feature_remove = feature.remove) === null || _feature_remove === void 0 ? void 0 : _feature_remove.call(feature, db, path, delta);
-            }
+            await conn.runBatch('DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE "path" = ?)', vanished.map((p)=>[
+                    p
+                ]));
+        }
+        if (reparsedExisting.length > 0) {
+            // FTS5 has no upsert, so delete-before-insert into `content`, coupled to the frontmatter
+            // rowid (indexed via its PRIMARY KEY) rather than the UNINDEXED `path` column, which a
+            // per-row DELETE would otherwise scan the whole table to find.
+            await conn.runBatch('DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE "path" = ?)', reparsedExisting.map((p)=>[
+                    p
+                ]));
         }
         if (parsedDocs.length > 0) {
-            const insert = db.prepare(insertSql);
-            const insertBody = db.prepare(INSERT_CONTENT_SQL);
-            // A non-default tokenizer means the tree has chosen its own scheme; a phrase query over
-            // grapheme runs would be nonsense against trigram, so the sidecars stay empty.
-            const segmenting = contentTokenize(cfg) === undefined;
-            for (const doc of parsedDocs){
-                var _feature_store;
-                const values = writableColumns.map((col)=>{
+            const rows = parsedDocs.map((doc)=>writableColumns.map((col)=>{
                     var _doc_data_col;
                     if (col === 'path') return doc.relPath;
                     if (col === '_mtime') return doc.mtimeMs;
@@ -127,37 +115,54 @@ export function reconcile(db, cfg, baseDir) {
                     // Written per parse, unlike _rank, which a feature pass owns and the upsert skips.
                     if (col === '_parse_error') return doc.parseError;
                     return (_doc_data_col = doc.data[col]) !== null && _doc_data_col !== void 0 ? _doc_data_col : null;
-                });
-                // Frontmatter upsert first: content's rowid lookup below depends on this row existing.
-                insert.run(...values);
-                // Only for docs that have rows: an unconditional delete made cold crawls quadratic.
-                if (existing.has(doc.relPath)) {
-                    var _feature_remove1;
-                    delBody.run(doc.relPath);
-                    for (const feature of features)(_feature_remove1 = feature.remove) === null || _feature_remove1 === void 0 ? void 0 : _feature_remove1.call(feature, db, doc.relPath, delta);
-                }
-                insertContentRow(insertBody, doc, segmenting);
-                // A preset edit forces a full rebuild, so an unchanged doc's coverage is already
-                // correct; new docs have nothing to clear, which keeps cold builds linear.
-                if (existing.has(doc.relPath)) delPresetFiles.run(doc.relPath);
-                for (const presetName of doc.presets)insertPresetFile.run(doc.relPath, presetName);
-                for (const feature of features)(_feature_store = feature.store) === null || _feature_store === void 0 ? void 0 : _feature_store.call(feature, db, doc.relPath, doc.extracted[feature.name], delta);
-            }
+                }));
+            await conn.runBatch(insertSql, rows);
+            // A non-default tokenizer means the tree has chosen its own scheme; a phrase query over
+            // grapheme runs would be nonsense against trigram, so the sidecars stay empty.
+            const segmenting = contentTokenize(cfg) === undefined;
+            await conn.runBatch(INSERT_CONTENT_SQL, parsedDocs.map((doc)=>contentRow(doc, segmenting)));
         }
-        for (const feature of features)(_feature_afterReconcile = feature.afterReconcile) === null || _feature_afterReconcile === void 0 ? void 0 : _feature_afterReconcile.call(feature, db, delta);
-        db.exec('COMMIT');
-    } catch (err) {
-        db.exec('ROLLBACK');
-        throw err;
-    }
+        if (vanished.length > 0) await conn.runBatch('DELETE FROM frontmatter WHERE "path" = ?', vanished.map((p)=>[
+                p
+            ]));
+        // A preset edit forces a full rebuild, so an unchanged doc's coverage is already correct;
+        // new docs have nothing to clear, which keeps cold builds linear.
+        const presetTouched = [
+            ...vanished,
+            ...reparsedExisting
+        ];
+        if (presetTouched.length > 0) await conn.runBatch('DELETE FROM preset_files WHERE "path" = ?', presetTouched.map((p)=>[
+                p
+            ]));
+        const presetRows = [];
+        for (const doc of parsedDocs)for (const presetName of doc.presets)presetRows.push([
+            doc.relPath,
+            presetName
+        ]);
+        if (presetRows.length > 0) await conn.runBatch('INSERT INTO preset_files ("path", preset) VALUES (?, ?)', presetRows);
+        const removedPaths = [
+            ...vanished,
+            ...reparsedExisting
+        ];
+        if (removedPaths.length > 0) for (const feature of features)await ((_feature_remove = feature.remove) === null || _feature_remove === void 0 ? void 0 : _feature_remove.call(feature, conn, removedPaths, delta));
+        for (const feature of features){
+            var _feature_store;
+            const docsForFeature = parsedDocs.map((doc)=>({
+                    path: doc.relPath,
+                    extracted: doc.extracted[feature.name]
+                }));
+            await ((_feature_store = feature.store) === null || _feature_store === void 0 ? void 0 : _feature_store.call(feature, conn, docsForFeature, delta));
+        }
+        for (const feature of features)await ((_feature_afterReconcile = feature.afterReconcile) === null || _feature_afterReconcile === void 0 ? void 0 : _feature_afterReconcile.call(feature, conn, delta));
+    });
     // Reconcile's own write-transaction duration, for open()'s derived busy_timeout (F):
     // keep the observed max so a big watcher reconcile's lock hold is what the next open bounds its wait against.
     const durationMs = Date.now() - txStart;
-    const prevRaw = getMeta(db, 'reconcile_max_ms');
+    const prevRaw = await getMeta(conn, 'reconcile_max_ms');
     // -1, not 0, so a genuinely 0ms first reconcile (sub-millisecond, common on a tiny tree)
     // still gets recorded instead of losing to the "nothing recorded yet" default.
     const prevMax = prevRaw === null ? -1 : Number(prevRaw);
-    if (durationMs > prevMax) setMeta(db, 'reconcile_max_ms', String(durationMs));
+    if (durationMs > prevMax) await setMeta(conn, 'reconcile_max_ms', String(durationMs));
     return {
         parsed: parsedDocs.length,
         warnings
@@ -202,23 +207,20 @@ export function signatureDiff(before, after) {
 // run here -- doc.search (title/summary/text) is all content population needs. Returns
 // parseFile's per-file warnings (e.g. a bad date) so open() can surface them -- mtimes are
 // untouched, so reconcile() never reparses these files and would otherwise never emit them again.
-export function rebuildContentTable(db, cfg, baseDir) {
-    const known = new Set(db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path));
+export async function rebuildContentTable(conn, cfg, baseDir) {
+    const stmt = await conn.prepare('SELECT "path" FROM frontmatter');
+    const known = new Set((await stmt.all()).map((r)=>r.path));
     const files = listFiles(cfg, baseDir).filter((f)=>known.has(f.relPath));
     const segmenting = contentTokenize(cfg) === undefined;
-    const insertBody = db.prepare(INSERT_CONTENT_SQL);
     const warnings = [];
-    db.exec('BEGIN');
-    try {
-        for (const file of files){
-            const { doc, warnings: fileWarnings } = parseFile(file);
-            warnings.push(...fileWarnings);
-            insertContentRow(insertBody, doc, segmenting);
-        }
-        db.exec('COMMIT');
-    } catch (err) {
-        db.exec('ROLLBACK');
-        throw err;
+    const rows = [];
+    for (const file of files){
+        const { doc, warnings: fileWarnings } = parseFile(file);
+        warnings.push(...fileWarnings);
+        rows.push(contentRow(doc, segmenting));
     }
+    await withTransaction(conn, async ()=>{
+        if (rows.length > 0) await conn.runBatch(INSERT_CONTENT_SQL, rows);
+    });
     return warnings;
 }

package/dist/esm/store/sqlite/reconcile.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/sqlite/reconcile.ts"],"sourcesContent":["import type { Config } from '../../config/index.ts';\nimport { contentTokenize } from '../../config/index.ts';\nimport { SenseError } from '../../errors.ts';\nimport { activeFeatures } from '../../features/index.ts';\nimport type { ExtractedDoc, ReconcileDelta } from '../../features/types.ts';\nimport { progress } from '../../output/progress.ts';\nimport type { ParsedDoc } from '../../scan/index.ts';\nimport { listFiles, parseFile, RESERVED_COLUMNS } from '../../scan/index.ts';\nimport { reparseFiles } from '../../scan/reparse.ts';\nimport { segmentField } from '../../text/segment.ts';\nimport { getColumns, getMeta, quoteIdent, setMeta } from '../shared.ts';\nimport { withTransaction } from '../transaction.ts';\nimport type { Connection } from '../types.ts';\n\n// Feature-owned columns (`_rank`) must stay out of the upsert: a reparse would null the last\n// computed value on every touch, not just the reconciles that recompute it.\nconst CORE_FRONTMATTER_COLUMNS = new Set(['path', '_mtime', '_ctime', '_size', '_parse_error']);\n\n// SQLite's compile-time SQLITE_MAX_COLUMN, default 2000 (https://www.sqlite.org/limits.html).\nconst MAX_FRONTMATTER_COLUMNS = 2000;\n\n// Shared by reconcile() and the tokenize-only rebuild in open(), so both prepare the same\n// literal instead of two copies drifting apart.\nconst INSERT_CONTENT_SQL = `INSERT INTO content (rowid, title, summary, text, \"path\", title_seg, summary_seg, text_seg) VALUES ((SELECT rowid FROM frontmatter WHERE \"path\" = ?), ?, ?, ?, ?, ?, ?, ?)`;\n\n// A single content row's param tuple, matching INSERT_CONTENT_SQL's placeholder order.\n// Assumes the frontmatter row for doc.relPath already exists (rowid subquery).\nfunction contentRow(doc: ParsedDoc, segmenting: boolean): unknown[] {\n  return [doc.relPath, doc.search.title, doc.search.summary, doc.search.text, doc.relPath, segmenting ? segmentField(doc.search.title) : '', segmenting ? segmentField(doc.search.summary) : '', segmenting ? segmentField(doc.search.text) : ''];\n}\n\nexport async function reconcile(conn: Connection, cfg: Config, baseDir: string): Promise<{ parsed: number; warnings: string[] }> {\n  const files = listFiles(cfg, baseDir);\n  const currentSet = new Set(files.map((f) => f.relPath));\n\n  const existingStmt = await conn.prepare('SELECT \"path\", \"_mtime\", \"_size\" FROM frontmatter');\n  const existingRows = (await existingStmt.all()) as Array<{ path: string; _mtime: number; _size: number }>;\n  const existing = new Map(existingRows.map((r) => [r.path, r]));\n  const vanished = existingRows.filter((r) => !currentSet.has(r.path)).map((r) => r.path);\n\n  const toReparse = files.filter((f) => {\n    const row = existing.get(f.relPath);\n    return !row || row._mtime !== f.mtimeMs || row._size !== f.size;\n  });\n\n  if (vanished.length === 0 && toReparse.length === 0) return { parsed: 0, warnings: [] };\n\n  const features = activeFeatures(cfg);\n  const seenColumns = await getColumns(conn);\n\n  // Bulk reparses (a sync, a cold build) are the long silences a query can hit; short\n  // reconciles stay silent (progress() has a threshold).\n  const report = progress('reparsing files', toReparse.length);\n  const { docs: parsedDocs, warnings, newColumns } = reparseFiles(toReparse, features, cfg, seenColumns, report.tick);\n  report.finish();\n  for (const col of newColumns) seenColumns.add(col);\n\n  const allColumns = [...seenColumns];\n  // Fence before ALTERing: SQLite's own failure past this point is a raw\n  // \"too many columns on sqlite_altertab_frontmatter\" with no indication of the boundary or the levers.\n  if (allColumns.length > MAX_FRONTMATTER_COLUMNS) {\n    throw new SenseError(\n      'COLUMN_LIMIT',\n      `frontmatter would need ${allColumns.length} columns, crossing SQLite's compile-time SQLITE_MAX_COLUMN limit (default ${MAX_FRONTMATTER_COLUMNS}; see https://www.sqlite.org/limits.html). Narrow the presets' include globs so fewer/other files are indexed, or fix whatever is generating unbounded frontmatter keys.`\n    );\n  }\n  // Columns the frontmatter upsert actually writes: core + parsed frontmatter keys, never a\n  // feature-owned reserved column (see CORE_FRONTMATTER_COLUMNS above).\n  const writableColumns = allColumns.filter((c) => CORE_FRONTMATTER_COLUMNS.has(c) || !RESERVED_COLUMNS.has(c));\n  // ON CONFLICT UPDATE (not OR REPLACE) keeps the row's rowid stable across reparses --\n  // content rows are coupled to that rowid below.\n  const insertSql = `INSERT INTO frontmatter (${writableColumns.map(quoteIdent).join(', ')}) VALUES (${writableColumns.map(() => '?').join(', ')}) ON CONFLICT(\"path\") DO UPDATE SET ${writableColumns\n    .filter((c) => c !== 'path')\n    .map((c) => `${quoteIdent(c)} = excluded.${quoteIdent(c)}`)\n    .join(', ')}`;\n\n  const added = toReparse.filter((f) => !existing.has(f.relPath)).map((f) => f.relPath);\n  const delta: ReconcileDelta = { files, reparsed: parsedDocs.map((d) => d.relPath), added, vanished };\n  const addedSet = new Set(added);\n  const reparsedExisting = parsedDocs.map((d) => d.relPath).filter((p) => !addedSet.has(p));\n\n  const txStart = Date.now();\n  await withTransaction(conn, async () => {\n    for (const col of newColumns) await conn.exec(`ALTER TABLE frontmatter ADD COLUMN ${quoteIdent(col)}`);\n\n    // content's rowid lookup depends on the frontmatter row it's coupled to, so every content\n    // delete/insert below must run after that row exists (vanished paths still have their\n    // frontmatter row at this point) and before it is removed (vanished frontmatter delete\n    // comes last).\n    if (vanished.length > 0) {\n      await conn.runBatch(\n        'DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE \"path\" = ?)',\n        vanished.map((p) => [p])\n      );\n    }\n    if (reparsedExisting.length > 0) {\n      // FTS5 has no upsert, so delete-before-insert into `content`, coupled to the frontmatter\n      // rowid (indexed via its PRIMARY KEY) rather than the UNINDEXED `path` column, which a\n      // per-row DELETE would otherwise scan the whole table to find.\n      await conn.runBatch(\n        'DELETE FROM content WHERE rowid = (SELECT rowid FROM frontmatter WHERE \"path\" = ?)',\n        reparsedExisting.map((p) => [p])\n      );\n    }\n\n    if (parsedDocs.length > 0) {\n      const rows = parsedDocs.map((doc) =>\n        writableColumns.map((col) => {\n          if (col === 'path') return doc.relPath;\n          if (col === '_mtime') return doc.mtimeMs;\n          if (col === '_ctime') return doc.ctimeMs;\n          if (col === '_size') return doc.size;\n          // Written per parse, unlike _rank, which a feature pass owns and the upsert skips.\n          if (col === '_parse_error') return doc.parseError;\n          return doc.data[col] ?? null;\n        })\n      );\n      await conn.runBatch(insertSql, rows);\n\n      // A non-default tokenizer means the tree has chosen its own scheme; a phrase query over\n      // grapheme runs would be nonsense against trigram, so the sidecars stay empty.\n      const segmenting = contentTokenize(cfg) === undefined;\n      await conn.runBatch(\n        INSERT_CONTENT_SQL,\n        parsedDocs.map((doc) => contentRow(doc, segmenting))\n      );\n    }\n\n    if (vanished.length > 0)\n      await conn.runBatch(\n        'DELETE FROM frontmatter WHERE \"path\" = ?',\n        vanished.map((p) => [p])\n      );\n\n    // A preset edit forces a full rebuild, so an unchanged doc's coverage is already correct;\n    // new docs have nothing to clear, which keeps cold builds linear.\n    const presetTouched = [...vanished, ...reparsedExisting];\n    if (presetTouched.length > 0)\n      await conn.runBatch(\n        'DELETE FROM preset_files WHERE \"path\" = ?',\n        presetTouched.map((p) => [p])\n      );\n    const presetRows: unknown[][] = [];\n    for (const doc of parsedDocs) for (const presetName of doc.presets) presetRows.push([doc.relPath, presetName]);\n    if (presetRows.length > 0) await conn.runBatch('INSERT INTO preset_files (\"path\", preset) VALUES (?, ?)', presetRows);\n\n    const removedPaths = [...vanished, ...reparsedExisting];\n    if (removedPaths.length > 0) for (const feature of features) await feature.remove?.(conn, removedPaths, delta);\n    for (const feature of features) {\n      const docsForFeature: ExtractedDoc[] = parsedDocs.map((doc) => ({ path: doc.relPath, extracted: doc.extracted[feature.name] }));\n      await feature.store?.(conn, docsForFeature, delta);\n    }\n    for (const feature of features) await feature.afterReconcile?.(conn, delta);\n  });\n\n  // Reconcile's own write-transaction duration, for open()'s derived busy_timeout (F):\n  // keep the observed max so a big watcher reconcile's lock hold is what the next open bounds its wait against.\n  const durationMs = Date.now() - txStart;\n  const prevRaw = await getMeta(conn, 'reconcile_max_ms');\n  // -1, not 0, so a genuinely 0ms first reconcile (sub-millisecond, common on a tiny tree)\n  // still gets recorded instead of losing to the \"nothing recorded yet\" default.\n  const prevMax = prevRaw === null ? -1 : Number(prevRaw);\n  if (durationMs > prevMax) await setMeta(conn, 'reconcile_max_ms', String(durationMs));\n\n  return { parsed: parsedDocs.length, warnings };\n}\n\n// Segment keys that moved between two feature signatures (see config.featureSignature's\n// format: global features, embed provider, tokenize, then one segment per preset).\nexport function changedSignatureKeys(before: string, after: string): Set<string> {\n  const keyOf = (part: string) => (part.startsWith('preset:') ? part.split(':').slice(0, 2).join(':') : part.split(':')[0]);\n  const parse = (sig: string) => new Map(sig.split('|').map((part) => [keyOf(part), part]));\n  const a = parse(before);\n  const b = parse(after);\n  const changed = new Set<string>();\n  for (const [key, val] of b) if (a.get(key) !== val) changed.add(key);\n  for (const key of a.keys()) if (!b.has(key)) changed.add(key);\n  return changed;\n}\n\n// Whether the embed segment only gained its resolved weight identity: same provider and\n// model, no identity recorded before, one now -- adopted into meta without a rebuild.\nexport function embedIdentityAdopted(before: string, after: string): boolean {\n  const embedPart = (sig: string) => sig.split('|').find((p) => p.startsWith('embed:'));\n  const b = embedPart(before);\n  const a = embedPart(after);\n  if (b === undefined || a === undefined) return false;\n  const at = a.indexOf('@');\n  return b.indexOf('@') === -1 && at !== -1 && a.slice(0, at) === b;\n}\n\n// Names what moved, for the rebuild notice.\nexport function signatureDiff(before: string, after: string): string {\n  const changed = changedSignatureKeys(before, after);\n  const label = (key: string) => (key === 'embed' ? 'embed settings' : key === 'tokenize' ? 'content tokenizer' : key.startsWith('preset:') ? `preset \"${key.slice(7)}\"` : 'features');\n  return changed.size === 0 ? 'features' : [...changed].map(label).join(', ');\n}\n\n// The tokenize-only rebuild in open(): content is dropped and repopulated from files already\n// listed in frontmatter, which itself is untouched. Frontmatter, links, sections, and\n// embeddings are file-derived and tokenizer-independent, so they survive. No feature extractors\n// run here -- doc.search (title/summary/text) is all content population needs. 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package/dist/esm/store/sqlite/sql-functions.js

@@ -0,0 +1,23 @@
+import { segmentMatch } from '../../text/segment.js';
+import { basenameImpl, hasImpl } from '../sql-functions.js';
+export function registerFunctions(db, segmenting) {
+    db.function('has', {
+        deterministic: true,
+        varargs: false
+    }, hasImpl);
+    db.function('basename', {
+        deterministic: true,
+        varargs: true
+    }, basenameImpl);
+    // Raw `content MATCH '<unspaced text>'` cannot be rewritten behind the author's back, and
+    // matches nothing, so the same transform is available to hand-written SQL by name. `segmenting`
+    // is the same config predicate commands.ts's search() gates on (contentTokenize(cfg) ===
+    // undefined), passed in by open() rather than read back from persisted state.
+    db.function('segment', {
+        deterministic: true,
+        varargs: false
+    }, (terms)=>{
+        const text = terms === null || terms === undefined ? '' : String(terms);
+        return segmenting ? segmentMatch(text) : text;
+    });
+}

package/dist/esm/store/sqlite/sql-functions.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/sqlite/sql-functions.ts"],"sourcesContent":["import type { DatabaseSync } from 'node:sqlite';\nimport { segmentMatch } from '../../text/segment.ts';\nimport { basenameImpl, hasImpl } from '../sql-functions.ts';\n\nexport function registerFunctions(db: DatabaseSync, segmenting: boolean): void {\n  db.function('has', { deterministic: true, varargs: false }, hasImpl);\n\n  db.function('basename', { deterministic: true, varargs: true }, basenameImpl);\n\n  // Raw `content MATCH '<unspaced text>'` cannot be rewritten behind the author's back, and\n  // matches nothing, so the same transform is available to hand-written SQL by name. `segmenting`\n  // is the same config predicate commands.ts's search() gates on (contentTokenize(cfg) ===\n  // undefined), passed in by open() rather than read back from persisted state.\n  db.function('segment', { deterministic: true, varargs: false }, (terms: unknown): string => {\n    const text = terms === null || terms === undefined ? '' : String(terms);\n    return segmenting ? segmentMatch(text) : text;\n  });\n}\n"],"names":["segmentMatch","basenameImpl","hasImpl","registerFunctions","db","segmenting","function","deterministic","varargs","terms","text","undefined","String"],"mappings":"AACA,SAASA,YAAY,QAAQ,wBAAwB;AACrD,SAASC,YAAY,EAAEC,OAAO,QAAQ,sBAAsB;AAE5D,OAAO,SAASC,kBAAkBC,EAAgB,EAAEC,UAAmB;IACrED,GAAGE,QAAQ,CAAC,OAAO;QAAEC,eAAe;QAAMC,SAAS;IAAM,GAAGN;IAE5DE,GAAGE,QAAQ,CAAC,YAAY;QAAEC,eAAe;QAAMC,SAAS;IAAK,GAAGP;IAEhE,0FAA0F;IAC1F,gGAAgG;IAChG,yFAAyF;IACzF,8EAA8E;IAC9EG,GAAGE,QAAQ,CAAC,WAAW;QAAEC,eAAe;QAAMC,SAAS;IAAM,GAAG,CAACC;QAC/D,MAAMC,OAAOD,UAAU,QAAQA,UAAUE,YAAY,KAAKC,OAAOH;QACjE,OAAOJ,aAAaL,aAAaU,QAAQA;IAC3C;AACF"}

package/dist/esm/store/sqlite/store.d.ts

@@ -0,0 +1,5 @@
+import type { DatabaseSync } from 'node:sqlite';
+import type { Config } from '../../config/index.js';
+import type { Capability, Connection, Store } from '../types.js';
+export declare const CAPABILITIES: ReadonlySet<Capability>;
+export declare function createStore(db: DatabaseSync, conn: Connection, cfg: Config, baseDir: string): Store;

package/dist/esm/store/sqlite/store.js

@@ -0,0 +1,82 @@
+import { contentTokenize } from '../../config/index.js';
+import { getColumns } from '../shared.js';
+import { withTransaction } from '../transaction.js';
+import { queryLexical } from './lexical.js';
+import { reconcile } from './reconcile.js';
+import { hasVectorRow, pendingRows, scanCandidates, scanSimilar, writeVectorBatch } from './vectors.js';
+export const CAPABILITIES = new Set([
+    'phrases',
+    'snippets',
+    'watch-concurrency',
+    'lexical',
+    'vectors'
+]);
+// Wraps the synchronous DatabaseSync connection in the async Store interface, sharing one
+// Connection instance (conn) with open()'s own reconcile call so transaction depth (see
+// transaction.ts) is tracked against the same object everywhere.
+export function createStore(db, conn, cfg, baseDir) {
+    return {
+        name: 'sqlite',
+        capabilities: CAPABILITIES,
+        async exec (sql) {
+            await conn.exec(sql);
+        },
+        async prepare (sql) {
+            return conn.prepare(sql);
+        },
+        async runBatch (sql, paramRows) {
+            await conn.runBatch(sql, paramRows);
+        },
+        async transaction (fn) {
+            return withTransaction(conn, fn);
+        },
+        async reconcile () {
+            return reconcile(conn, cfg, baseDir);
+        },
+        docs: {
+            async columns () {
+                return [
+                    ...await getColumns(conn)
+                ];
+            }
+        },
+        lexical: {
+            async query (terms, opts) {
+                return queryLexical(conn, terms, opts, contentTokenize(cfg) === undefined);
+            }
+        },
+        vectors: {
+            async pending () {
+                return pendingRows(conn);
+            },
+            async writeVectors (rows) {
+                await writeVectorBatch(conn, rows);
+            },
+            async candidates (qv, storeDims, fetch, allowed) {
+                return scanCandidates(conn, qv, storeDims, fetch, allowed);
+            },
+            async similar (path, opts) {
+                return scanSimilar(conn, path, opts);
+            },
+            async hasVector (path) {
+                return hasVectorRow(conn, path);
+            }
+        },
+        raw: {
+            async prepare (sql) {
+                const stmt = db.prepare(sql);
+                stmt.setReadBigInts(true); // int64 past 2^53 arrives as BigInt instead of throwing at step time
+                return {
+                    columns: ()=>stmt.columns(),
+                    // sense sql streams through an async iterator wrapping the sync iterate().
+                    iterate: async function*(...params) {
+                        yield* stmt.iterate(...params);
+                    }
+                };
+            }
+        },
+        async close () {
+            db.close();
+        }
+    };
+}

package/dist/esm/store/sqlite/store.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/sqlite/store.ts"],"sourcesContent":["import type { DatabaseSync } from 'node:sqlite';\nimport type { Config } from '../../config/index.ts';\nimport { contentTokenize } from '../../config/index.ts';\nimport { getColumns } from '../shared.ts';\nimport { withTransaction } from '../transaction.ts';\nimport type { Capability, Connection, Statement, Store, VectorWriteRow } from '../types.ts';\nimport { queryLexical } from './lexical.ts';\nimport { reconcile } from './reconcile.ts';\nimport { hasVectorRow, pendingRows, scanCandidates, scanSimilar, writeVectorBatch } from './vectors.ts';\n\nexport const CAPABILITIES: ReadonlySet<Capability> = new Set(['phrases', 'snippets', 'watch-concurrency', 'lexical', 'vectors']);\n\n// Wraps the synchronous DatabaseSync connection in the async Store interface, sharing one\n// Connection instance (conn) with open()'s own reconcile call so transaction depth (see\n// transaction.ts) is tracked against the same object everywhere.\nexport function createStore(db: DatabaseSync, conn: Connection, cfg: Config, baseDir: string): Store {\n  return {\n    name: 'sqlite',\n    capabilities: CAPABILITIES,\n    async exec(sql: string): Promise<void> {\n      await conn.exec(sql);\n    },\n    async prepare(sql: string): Promise<Statement> {\n      return conn.prepare(sql);\n    },\n    async runBatch(sql: string, paramRows: unknown[][]): Promise<void> {\n      await conn.runBatch(sql, paramRows);\n    },\n    async transaction<T>(fn: () => Promise<T>): Promise<T> {\n      return withTransaction(conn, fn);\n    },\n    async reconcile() {\n      return reconcile(conn, cfg, baseDir);\n    },\n    docs: {\n      async columns() {\n        return [...(await getColumns(conn))];\n      },\n    },\n    lexical: {\n      async query(terms, opts) {\n        return queryLexical(conn, terms, opts, contentTokenize(cfg) === undefined);\n      },\n    },\n    vectors: {\n      async pending() {\n        return pendingRows(conn);\n      },\n      async writeVectors(rows: VectorWriteRow[]) {\n        await writeVectorBatch(conn, rows);\n      },\n      async candidates(qv, storeDims, fetch, allowed) {\n        return scanCandidates(conn, qv, storeDims, fetch, allowed);\n      },\n      async similar(path, opts) {\n        return scanSimilar(conn, path, opts);\n      },\n      async hasVector(path) {\n        return hasVectorRow(conn, path);\n      },\n    },\n    raw: {\n      async prepare(sql: string) {\n        const stmt = db.prepare(sql);\n        stmt.setReadBigInts(true); 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package/dist/esm/store/sqlite/vectors.d.ts

@@ -0,0 +1,13 @@
+import type { Connection, VectorCandidate, VectorSimilar, VectorWriteRow } from '../types.js';
+export declare function pendingRows(conn: Connection): Promise<Array<{
+    path: string;
+    chunk: number;
+}>>;
+export declare function writeVectorBatch(conn: Connection, rows: VectorWriteRow[]): Promise<void>;
+export declare function scanCandidates(conn: Connection, qv: Float32Array, storeDims: number, fetch: number, allowed?: Set<string>): Promise<VectorCandidate[]>;
+export declare function scanSimilar(conn: Connection, path: string, opts: {
+    exclude: Set<string>;
+    allowed?: Set<string>;
+    k: number;
+}): Promise<VectorSimilar[]>;
+export declare function hasVectorRow(conn: Connection, path: string): Promise<boolean>;

package/dist/esm/store/sqlite/vectors.js

@@ -0,0 +1,90 @@
+// Seed chunks that participate in a `related` scan; see similar() for the measurement.
+const TARGET_CHUNK_CAP = 16;
+// Dequantised int8 dot products land a little either side of a true cosine, so an identical
+// pair prints 1.001 and undermines a column whose whole job is being a bounded number.
+function asCosine(score) {
+    return Math.round(Math.min(1, Math.max(-1, score)) * 1000) / 1000;
+}
+export async function pendingRows(conn) {
+    const stmt = await conn.prepare('SELECT "path", chunk FROM embeddings WHERE vector IS NULL ORDER BY "path", chunk');
+    return await stmt.all();
+}
+// One runBatch call per provider batch: the caller (embed/query.ts) already batches by the
+// provider's batchCap, so this is one crossing per batch, never per row.
+export async function writeVectorBatch(conn, rows) {
+    if (rows.length === 0) return;
+    await conn.runBatch('UPDATE embeddings SET scale = ?, vector = ? WHERE "path" = ? AND chunk = ?', rows.map((row)=>[
+            row.scale,
+            row.vector,
+            row.path,
+            row.chunk
+        ]));
+}
+// Best chunk per file by cosine, its line range riding along: the JS loop over stored int8
+// BLOBs this store's scan strategy is (a native store scans differently, same contract).
+export async function scanCandidates(conn, qv, storeDims, fetch, allowed) {
+    const stmt = await conn.prepare('SELECT "path", start_line, end_line, scale, vector FROM embeddings WHERE vector IS NOT NULL');
+    const rows = await stmt.all();
+    const best = new Map();
+    for (const row of rows){
+        if (allowed && !allowed.has(row.path)) continue;
+        const q = new Int8Array(row.vector.buffer, row.vector.byteOffset, Math.min(storeDims, row.vector.byteLength));
+        let dot = 0;
+        for(let d = 0; d < q.length; d++)dot += q[d] * qv[d];
+        const score = dot * row.scale;
+        const existing = best.get(row.path);
+        if (!existing || score > existing.score) best.set(row.path, {
+            score,
+            lines: `L${row.start_line}-${row.end_line}`
+        });
+    }
+    return [
+        ...best.entries()
+    ].sort((a, b)=>b[1].score - a[1].score).slice(0, fetch).map(([path, b])=>({
+            path,
+            lines: b.lines,
+            similarity: asCosine(b.score)
+        }));
+}
+// Note-to-note similarity is the max cosine over (target chunk, other chunk) pairs, one linear
+// scan of stored vectors.
+export async function scanSimilar(conn, path, opts) {
+    // Cost is target_chunks x stored_chunks, so a heading-dense seed multiplies a full-corpus
+    // scan (12.7s at 201 chunks/note). Sample evenly, so late sections still get a vote.
+    const targetStmt = await conn.prepare('SELECT scale, vector FROM embeddings WHERE "path" = ? AND vector IS NOT NULL ORDER BY chunk');
+    const targetRows = await targetStmt.all(path);
+    if (targetRows.length === 0) return [];
+    const step = Math.max(1, Math.ceil(targetRows.length / TARGET_CHUNK_CAP));
+    const target = targetRows.filter((_, i)=>i % step === 0).map((row)=>({
+            v: new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength),
+            scale: row.scale
+        }));
+    const stmt = await conn.prepare('SELECT "path", scale, vector FROM embeddings WHERE vector IS NOT NULL');
+    const rows = await stmt.all();
+    const best = new Map();
+    for (const row of rows){
+        if (row.path === path || opts.exclude.has(row.path) || opts.allowed && !opts.allowed.has(row.path)) continue;
+        const other = new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength);
+        for (const t of target){
+            let dot = 0;
+            const len = Math.min(t.v.length, other.length);
+            for(let d = 0; d < len; d++)dot += t.v[d] * other[d];
+            const score = dot * t.scale * row.scale;
+            const existing = best.get(row.path);
+            if (existing === undefined || score > existing) best.set(row.path, score);
+        }
+    }
+    return [
+        ...best.entries()
+    ].sort((a, b)=>b[1] - a[1]).slice(0, opts.k).map(([p, score])=>({
+            path: p,
+            similarity: asCosine(score)
+        }));
+}
+// Whether a note has any chunk with a vector. Distinguishes "nothing is near this note" from
+// "this note has no text", which look the same in an empty result.
+export async function hasVectorRow(conn, path) {
+    const stmt = await conn.prepare('SELECT 1 AS ok FROM embeddings WHERE "path" = ? AND vector IS NOT NULL LIMIT 1');
+    const row = await stmt.get(path);
+    return row !== undefined;
+}

package/dist/esm/store/sqlite/vectors.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/sqlite/vectors.ts"],"sourcesContent":["import type { Connection, VectorCandidate, VectorSimilar, VectorWriteRow } from '../types.ts';\n\n// Seed chunks that participate in a `related` scan; see similar() for the measurement.\nconst TARGET_CHUNK_CAP = 16;\n\n// Dequantised int8 dot products land a little either side of a true cosine, so an identical\n// pair prints 1.001 and undermines a column whose whole job is being a bounded number.\nfunction asCosine(score: number): number {\n  return Math.round(Math.min(1, Math.max(-1, score)) * 1000) / 1000;\n}\n\nexport async function pendingRows(conn: Connection): Promise<Array<{ path: string; chunk: number }>> {\n  const stmt = await conn.prepare('SELECT \"path\", chunk FROM embeddings WHERE vector IS NULL ORDER BY \"path\", chunk');\n  return (await stmt.all()) as Array<{ path: string; chunk: number }>;\n}\n\n// One runBatch call per provider batch: the caller (embed/query.ts) already batches by the\n// provider's batchCap, so this is one crossing per batch, never per row.\nexport async function writeVectorBatch(conn: Connection, rows: VectorWriteRow[]): Promise<void> {\n  if (rows.length === 0) return;\n  await conn.runBatch(\n    'UPDATE embeddings SET scale = ?, vector = ? WHERE \"path\" = ? AND chunk = ?',\n    rows.map((row) => [row.scale, row.vector, row.path, row.chunk])\n  );\n}\n\n// Best chunk per file by cosine, its line range riding along: the JS loop over stored int8\n// BLOBs this store's scan strategy is (a native store scans differently, same contract).\nexport async function scanCandidates(conn: Connection, qv: Float32Array, storeDims: number, fetch: number, allowed?: Set<string>): Promise<VectorCandidate[]> {\n  const stmt = await conn.prepare('SELECT \"path\", start_line, end_line, scale, vector FROM embeddings WHERE vector IS NOT NULL');\n  const rows = (await stmt.all()) as Array<{\n    path: string;\n    start_line: number;\n    end_line: number;\n    scale: number;\n    vector: Uint8Array;\n  }>;\n\n  const best = new Map<string, { score: number; lines: string }>();\n  for (const row of rows) {\n    if (allowed && !allowed.has(row.path)) continue;\n    const q = new Int8Array(row.vector.buffer, row.vector.byteOffset, Math.min(storeDims, row.vector.byteLength));\n    let dot = 0;\n    for (let d = 0; d < q.length; d++) dot += q[d] * qv[d];\n    const score = dot * row.scale;\n    const existing = best.get(row.path);\n    if (!existing || score > existing.score) best.set(row.path, { score, lines: `L${row.start_line}-${row.end_line}` });\n  }\n  return [...best.entries()]\n    .sort((a, b) => b[1].score - a[1].score)\n    .slice(0, fetch)\n    .map(([path, b]) => ({ path, lines: b.lines, similarity: asCosine(b.score) }));\n}\n\n// Note-to-note similarity is the max cosine over (target chunk, other chunk) pairs, one linear\n// scan of stored vectors.\nexport async function scanSimilar(conn: Connection, path: string, opts: { exclude: Set<string>; allowed?: Set<string>; k: number }): Promise<VectorSimilar[]> {\n  // Cost is target_chunks x stored_chunks, so a heading-dense seed multiplies a full-corpus\n  // scan (12.7s at 201 chunks/note). Sample evenly, so late sections still get a vote.\n  const targetStmt = await conn.prepare('SELECT scale, vector FROM embeddings WHERE \"path\" = ? AND vector IS NOT NULL ORDER BY chunk');\n  const targetRows = (await targetStmt.all(path)) as Array<{ scale: number; vector: Uint8Array }>;\n  if (targetRows.length === 0) return [];\n  const step = Math.max(1, Math.ceil(targetRows.length / TARGET_CHUNK_CAP));\n  const target = targetRows.filter((_, i) => i % step === 0).map((row) => ({ v: new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength), scale: row.scale }));\n\n  const stmt = await conn.prepare('SELECT \"path\", scale, vector FROM embeddings WHERE vector IS NOT NULL');\n  const rows = (await stmt.all()) as Array<{ path: string; scale: number; vector: Uint8Array }>;\n  const best = new Map<string, number>();\n  for (const row of rows) {\n    if (row.path === path || opts.exclude.has(row.path) || (opts.allowed && !opts.allowed.has(row.path))) continue;\n    const other = new Int8Array(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength);\n    for (const t of target) {\n      let dot = 0;\n      const len = Math.min(t.v.length, other.length);\n      for (let d = 0; d < len; d++) dot += t.v[d] * other[d];\n      const score = dot * t.scale * row.scale;\n      const existing = best.get(row.path);\n      if (existing === undefined || score > existing) best.set(row.path, score);\n    }\n  }\n\n  return [...best.entries()]\n    .sort((a, b) => b[1] - a[1])\n    .slice(0, opts.k)\n    .map(([p, score]) => ({ path: p, similarity: asCosine(score) }));\n}\n\n// Whether a note has any chunk with a vector. 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package/dist/esm/store/transaction.d.ts

@@ -0,0 +1,5 @@
+interface ExecConnection {
+    exec(sql: string): Promise<void>;
+}
+export declare function withTransaction<T>(conn: ExecConnection, fn: () => Promise<T>): Promise<T>;
+export {};