sensemaking 0.24.6 → 0.25.0

package/dist/esm/store/open.js

@@ -1,8 +1,9 @@
 import { channel } from 'node:diagnostics_channel';
-import { mkdirSync } from 'node:fs';
+import { existsSync, mkdirSync } from 'node:fs';
 import { join } from 'node:path';
-import { featureSignature, STATE_DIR } from '../config/index.js';
+import { anyPresetEmbeds, featureSignature, STATE_DIR } from '../config/index.js';
 import { rekeyChunkText } from '../embed/handoff.js';
+import { embedPending } from '../embed/query.js';
 import { SenseError } from '../errors.js';
 import { FEATURES } from '../features/index.js';
 import { createBuilder } from './builder.js';
@@ -13,20 +14,40 @@ import { lockWaitBudgetMs } from './lock-wait.js';
 import { forcedPresetPaths, isPresetOnlyChange } from './preset-scope.js';
 import { getMeta, setMeta } from './shared.js';
 import { changedSignatureKeys, embedIdentityAdopted, signatureDiff } from './signature.js';
-// duckdb/turso hold the cache file for their connection's whole life, so a second command waits.
-// Bounded by this tree's recorded reconcile time (lock-wait.ts), not a fixed guess.
+import { stageRecorder } from './stages.js';
+import { withTransaction } from './transaction.js';
+const CORE_READY_META_KEY = 'core_ready';
 const LOCK_POLL_MS = 50;
 const lockWait = channel('sensemaking.store.lock-wait');
-async function connectUnlocked(dbPath, cfg, configDir, dialect) {
+function notReady(reason) {
+    return new SenseError('INDEX_NOT_READY', `${reason}; run "sense build" or call build(config) before opening with { build: false }`);
+}
+function normaliseConfig(cfg) {
+    // `baseDir` was the original public open() input. Keep direct API callers working while
+    // making the two ownership paths explicit for every internal operation.
+    if (!cfg.rootDir) {
+        if (!cfg.baseDir) throw new SenseError('CONFIG_INVALID', 'open requires rootDir (or legacy baseDir)');
+        cfg.rootDir = cfg.baseDir;
+    }
+    if (!cfg.configDir) cfg.configDir = cfg.rootDir;
+    return cfg;
+}
+function cachePath(cfg, dialect) {
+    var _cfg_configDir;
+    return join((_cfg_configDir = cfg.configDir) !== null && _cfg_configDir !== void 0 ? _cfg_configDir : cfg.baseDir, STATE_DIR, dialect.filename);
+}
+async function connectUnlocked(dbPath, cfg, configDir, dialect, options) {
     const budgetMs = lockWaitBudgetMs(configDir);
     const deadline = Date.now() + budgetMs;
     for(;;){
         try {
-            return await dialect.connect(dbPath, cfg);
+            return await dialect.connect(dbPath, cfg, options);
         } catch (err) {
             var _dialect_isLocked;
+            if (options.existingOnly && !existsSync(dbPath)) {
+                throw notReady(`the derived index does not exist at ${dbPath}`);
+            }
             if (!((_dialect_isLocked = dialect.isLocked) === null || _dialect_isLocked === void 0 ? void 0 : _dialect_isLocked.call(dialect, err))) throw err;
-            // Observe a real rejected native connection, never merely the start of an async open.
             if (lockWait.hasSubscribers) lockWait.publish({
                 store: cfg.store,
                 dbPath
@@ -38,7 +59,71 @@ async function connectUnlocked(dbPath, cfg, configDir, dialect) {
         }
     }
 }
-async function connectWithDialect(cfg, dialect) {
+async function assertCoreSchema(conn) {
+    for (const table of [
+        'frontmatter',
+        'content',
+        'preset_files',
+        'indexed_sources'
+    ]){
+        await (await conn.prepare(`SELECT 1 FROM ${table} LIMIT 0`)).all();
+    }
+}
+async function connectExisting(cfg, dialect, requirements) {
+    var _cfg_configDir;
+    const configDir = (_cfg_configDir = cfg.configDir) !== null && _cfg_configDir !== void 0 ? _cfg_configDir : cfg.baseDir;
+    const dbPath = cachePath(cfg, dialect);
+    if (!existsSync(dbPath)) throw notReady(`the derived index does not exist at ${dbPath}`);
+    const { handle, conn } = await connectUnlocked(dbPath, cfg, configDir, dialect, {
+        existingOnly: true,
+        observational: true
+    });
+    try {
+        let version;
+        let features;
+        let ready;
+        try {
+            version = await getMeta(conn, 'schema_version');
+            features = await getMeta(conn, 'features');
+            ready = await getMeta(conn, CORE_READY_META_KEY);
+            await assertCoreSchema(conn);
+        } catch  {
+            if (!existsSync(dbPath)) throw notReady(`the derived index was deleted while opening ${dbPath}`);
+            throw notReady(`the derived index at ${dbPath} has no compatible schema`);
+        }
+        if (version !== dialect.schemaVersion) {
+            throw notReady(`the derived index at ${dbPath} uses schema ${version !== null && version !== void 0 ? version : 'unknown'}, but this sense version requires ${dialect.schemaVersion}`);
+        }
+        const wantFeatures = featureSignature(cfg, FEATURES);
+        if (features !== wantFeatures) {
+            throw notReady(`the derived index at ${dbPath} was built for different configuration features`);
+        }
+        if (ready !== '1') {
+            throw notReady(`the derived index at ${dbPath} has an incomplete core build`);
+        }
+        if (requirements.has('lexical')) {
+            var _dialect_assertLexicalReady;
+            await ((_dialect_assertLexicalReady = dialect.assertLexicalReady) === null || _dialect_assertLexicalReady === void 0 ? void 0 : _dialect_assertLexicalReady.call(dialect, conn));
+        }
+        if (!existsSync(dbPath)) throw notReady(`the derived index was deleted while opening ${dbPath}`);
+        return {
+            handle,
+            conn,
+            cfg,
+            dbPath,
+            parsed: 0,
+            warnings: [],
+            stages: stageRecorder().take(0, 0),
+            observational: true
+        };
+    } catch (err) {
+        await dialect.close(handle, {
+            observational: true
+        });
+        throw err;
+    }
+}
+async function connectForBuild(cfg, dialect, requirements) {
     var _cfg_configDir, _cfg_rootDir;
     const configDir = (_cfg_configDir = cfg.configDir) !== null && _cfg_configDir !== void 0 ? _cfg_configDir : cfg.baseDir;
     const stateDir = join(configDir, STATE_DIR);
@@ -46,107 +131,84 @@ async function connectWithDialect(cfg, dialect) {
         recursive: true
     });
     const dbPath = join(stateDir, dialect.filename);
-    const { handle, conn } = await connectUnlocked(dbPath, cfg, configDir, dialect);
-    // A throw below must release this handle, or the leaked WAL makes the cache file undeletable on
-    // Windows. `closed` keeps the catch from double-closing a handle a rebuild branch already closed.
+    const { handle, conn } = await connectUnlocked(dbPath, cfg, configDir, dialect, {
+        existingOnly: false,
+        observational: false
+    });
     let closed = false;
-    // Created here, not inside reconcile(): invalidate()/invalidateFeatures() below share its pool
-    // with the build() call that follows them.
     const builder = createBuilder(conn, cfg, {
         rootDir: (_cfg_rootDir = cfg.rootDir) !== null && _cfg_rootDir !== void 0 ? _cfg_rootDir : cfg.baseDir,
         configDir
     }, dialect.reconcileDialect);
     try {
         await conn.exec('CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT)');
-        // Schema-version or feature-set mismatch: reconcile only reparses changed files, so an
-        // old cache can't be patched incrementally -- rebuild instead (cheap: nothing expensive lives here).
         const version = await getMeta(conn, 'schema_version');
         const features = await getMeta(conn, 'features');
+        const ready = await getMeta(conn, CORE_READY_META_KEY);
         const wantFeatures = featureSignature(cfg, FEATURES);
-        // Set only by the preset-membership branch below; reconcile treats these paths as touched
-        // despite an unchanged stamp, for this one build() call.
+        // `ready=0` may belong to another SQLite builder, so recovery stays in place and lets the
+        // engine serialize it. It never unlinks the cache.
+        await setMeta(conn, CORE_READY_META_KEY, '0');
+        const recoverIncomplete = ready === '0' && (version === null || version === dialect.schemaVersion);
         let forcedPaths;
-        // Set only by the embed-narrow branch below; applied via builder.invalidate() after ensureSchema.
         let embedInvalidate;
-        // Set only by the feature-toggle branch below; applied via builder.invalidateFeatures() after ensureSchema.
         let featureToggles;
-        if (version !== null && version !== dialect.schemaVersion || features !== null && features !== wantFeatures) {
+        if (version !== null && version !== dialect.schemaVersion) {
+            console.error('sense: cache format changed (new sensemaking version); rebuilding the index');
+            closed = true;
+            await dialect.close(handle);
+            clearCache(cfg);
+            return connectForBuild(cfg, dialect, requirements);
+        }
+        if (recoverIncomplete) {
+            console.error('sense: recovering an incomplete index generation in place');
+        } else if (features !== null && features !== wantFeatures) {
             var _cfg_rootDir1;
-            // Indexing derives from presets, so a config edit rebuilding the cache must say so and
-            // name what changed -- silent rebuilds make derived indexing look like a hang or a bug.
-            if (version !== null && version !== dialect.schemaVersion) {
-                console.error('sense: cache format changed (new sensemaking version); rebuilding the index');
-                // Close before clearCache deletes the files out from under the still-open handle.
-                closed = true;
-                await dialect.close(handle);
-                clearCache(cfg);
-                return connectWithDialect(cfg, dialect);
-            }
             const changedKeys = changedSignatureKeys(features !== null && features !== void 0 ? features : '', wantFeatures);
-            // Null (rather than the empty set) when changedKeys isn't preset-only, or a changed
-            // preset's stored segment can't be parsed back into old include/exclude/vectors -- either
-            // way the branch below is skipped and the full rebuild stays the fallback.
             const presetForced = isPresetOnlyChange(changedKeys) ? forcedPresetPaths(cfg, (_cfg_rootDir1 = cfg.rootDir) !== null && _cfg_rootDir1 !== void 0 ? _cfg_rootDir1 : cfg.baseDir, features !== null && features !== void 0 ? features : '', changedKeys) : null;
-            // Null unless exactly one segment changed and it decomposes into a recognised embed-only
-            // case (embed-scope.ts): anything else, including embed toggled on/off, stays null.
             const embedKind = changedKeys.size === 1 && changedKeys.has('embed') ? classifyEmbedChange(features !== null && features !== void 0 ? features : '', wantFeatures) : null;
-            // Null (rather than the empty set) when changedKeys isn't feature-toggle-only, or a changed
-            // feature's stored segment can't be parsed back into old/new on-off -- either way the branch
-            // below is skipped and the full rebuild stays the fallback.
             const toggles = isFeatureOnlyChange(changedKeys) ? classifyFeatureToggles(features !== null && features !== void 0 ? features : '', wantFeatures, changedKeys) : null;
             if (changedKeys.size === 1 && changedKeys.has('embed') && embedIdentityAdopted(features !== null && features !== void 0 ? features : '', wantFeatures)) {
-                // First sight of a resolved weight identity: the model itself hasn't changed, so
-                // adopt it into meta with no rebuild and no re-embed.
                 console.error("sense: recorded the embedding model's resolved identity; vectors are unaffected");
-                await setMeta(conn, 'features', wantFeatures);
             } else if (embedKind !== null) {
-                // Chunk boundaries are file-derived, not model-derived (embed.ts's chunksOf), so neither
-                // case needs any file reparsed for any feature but embed itself.
                 embedInvalidate = embedKind;
                 console.error(embedKind === 'model' ? 'sense: config change (embed settings) invalidates only the stale vectors' : 'sense: config change (embed settings) rebuilds only the embeddings it affects');
-                await setMeta(conn, 'features', wantFeatures);
             } else if (presetForced !== null) {
-                // Membership only: which files a preset covers moved, not a file's own content, a
-                // global feature, or the embed model. reconcile() already knows how to
-                // add, update, and remove a file correctly (every cross-feature cascade included); it
-                // just needs telling which unchanged files to treat as touched (forcedPaths, above).
                 forcedPaths = presetForced;
                 const changed = signatureDiff(features !== null && features !== void 0 ? features : '', wantFeatures);
                 console.error(`sense: config change (${changed}) reparses only the files it affects`);
-                await setMeta(conn, 'features', wantFeatures);
             } else if (toggles !== null) {
-                // A feature turned off or on: reconcile.ts's activeFeatures skips a disabled feature's
-                // hooks entirely, so its rows rot while off -- invalidateFeatures drops them and, for a
-                // feature turning back on, fully re-derives across every indexed file rather than
-                // trusting rows written before or during that window.
                 featureToggles = toggles;
                 const changed = signatureDiff(features !== null && features !== void 0 ? features : '', wantFeatures);
                 console.error(`sense: config change (${changed}) reparses only the feature it affects`);
-                await setMeta(conn, 'features', wantFeatures);
             } else {
                 const changed = signatureDiff(features !== null && features !== void 0 ? features : '', wantFeatures);
                 console.error(`sense: config change (${changed}) rebuilds the index`);
                 closed = true;
                 await dialect.close(handle);
                 clearCache(cfg);
-                return connectWithDialect(cfg, dialect);
+                return connectForBuild(cfg, dialect, requirements);
             }
         }
         await dialect.ensureSchema(handle, conn, cfg);
-        // 3x the largest reconcile this cache has recorded, floored at 30s and capped at 10min.
-        // Installed before build() -- that call is the one that races a watcher's transaction.
         if (dialect.setDerivedBusyTimeout) {
             var _ref;
             const recordedMaxMs = Number((_ref = await getMeta(conn, 'reconcile_max_ms')) !== null && _ref !== void 0 ? _ref : '0');
             await dialect.setDerivedBusyTimeout(handle, conn, Math.min(Math.max(30000, 3 * recordedMaxMs), 600000));
         }
-        // Runs before build(): forcedPaths, embedInvalidate and featureToggles never target the same
-        // call (each comes from its own mutually exclusive branch above: a preset-only, embed-only, or
-        // feature-toggle-only changed-key set).
         const embedParsed = embedInvalidate ? (await builder.invalidate(embedInvalidate)).parsed : 0;
         const featureParsed = featureToggles ? (await builder.invalidateFeatures(featureToggles)).parsed : 0;
-        const { parsed, warnings, stages } = await builder.build(forcedPaths);
-        // Every open reconciles once and is done with it -- a watcher opens fresh per event instead of holding this connection (src/watch.ts).
+        const { parsed, warnings, stages } = recoverIncomplete ? await builder.recover() : await builder.build(forcedPaths);
+        await withTransaction(conn, async ()=>{
+            await setMeta(conn, 'features', wantFeatures);
+            await setMeta(conn, CORE_READY_META_KEY, '1');
+        });
+        // Lexical preparation is a separate capability stage. A failure leaves core usable and the
+        // dialect's own lexical marker stale, so unrelated map/peek/path/sql commands stay available.
+        if (requirements.has('lexical')) {
+            var _dialect_prepareLexical;
+            await ((_dialect_prepareLexical = dialect.prepareLexical) === null || _dialect_prepareLexical === void 0 ? void 0 : _dialect_prepareLexical.call(dialect, conn));
+        }
         await builder.close();
         return {
             handle,
@@ -155,7 +217,8 @@ async function connectWithDialect(cfg, dialect) {
             dbPath,
             parsed: parsed + embedParsed + featureParsed,
             warnings,
-            stages
+            stages,
+            observational: false
         };
     } catch (err) {
         await builder.close();
@@ -163,28 +226,56 @@ async function connectWithDialect(cfg, dialect) {
         throw err;
     }
 }
-// A store's open(): connects (see connectWithDialect above), then wraps the resulting connection
-// in the Store interface. The builder's pool closes right after the initial build.
-export async function openWithDialect(cfg, dialect) {
-    // `baseDir` was the original public open() input. Keep direct API callers working while
-    // making the two ownership paths explicit for every internal operation.
-    if (!cfg.rootDir) {
-        if (!cfg.baseDir) throw new SenseError('CONFIG_INVALID', 'open requires rootDir (or legacy baseDir)');
-        cfg.rootDir = cfg.baseDir;
+// A static provider can resolve its identity while embedding. Publish it only after vectors
+// succeed and only when the durable signature still matches the prepared generation.
+export async function prepareDocumentEmbeddings(store, cfg, allowed) {
+    const preparedSignature = await getMeta(store, 'features');
+    await embedPending(store, cfg, allowed);
+    const actualSignature = featureSignature(cfg, FEATURES);
+    if (preparedSignature === actualSignature) return;
+    const changedKeys = changedSignatureKeys(preparedSignature !== null && preparedSignature !== void 0 ? preparedSignature : '', actualSignature);
+    if (preparedSignature === null || changedKeys.size !== 1 || !changedKeys.has('embed') || !embedIdentityAdopted(preparedSignature, actualSignature)) {
+        throw notReady('the index configuration changed while vectors were being prepared');
+    }
+    const update = await store.prepare('UPDATE meta SET value = ? WHERE key = ? AND value = ?');
+    const result = await update.run(actualSignature, 'features', preparedSignature);
+    if (Number(result.changes) !== 1) throw notReady('another build changed the index configuration while vectors were being prepared');
+}
+export async function openWithDialect(input, dialect, options = {}) {
+    var _options_requirements;
+    const cfg = normaliseConfig(input);
+    const buildEnabled = options.build !== false;
+    const defaultRequirements = new Set(buildEnabled ? [
+        'core',
+        'lexical'
+    ] : [
+        'core'
+    ]);
+    if (buildEnabled && anyPresetEmbeds(cfg)) defaultRequirements.add('vectors');
+    const requirements = (_options_requirements = options.requirements) !== null && _options_requirements !== void 0 ? _options_requirements : defaultRequirements;
+    const connected = buildEnabled ? await connectForBuild(cfg, dialect, requirements) : await connectExisting(cfg, dialect, requirements);
+    let store;
+    try {
+        store = dialect.createStore(connected.handle, connected.conn, connected.cfg, {
+            observational: connected.observational
+        });
+        rekeyChunkText(connected.conn, store);
+        if (requirements.has('vectors') && buildEnabled) await prepareDocumentEmbeddings(store, connected.cfg);
+        return {
+            store,
+            cfg: connected.cfg,
+            dbPath: connected.dbPath,
+            parsed: connected.parsed,
+            warnings: connected.warnings,
+            stages: connected.stages
+        };
+    } catch (err) {
+        if (store) await store.close();
+        else await dialect.close(connected.handle, {
+            observational: connected.observational
+        });
+        throw err;
     }
-    if (!cfg.configDir) cfg.configDir = cfg.rootDir;
-    const { handle, conn, cfg: resolvedCfg, dbPath, parsed, warnings, stages } = await connectWithDialect(cfg, dialect);
-    const store = dialect.createStore(handle, conn, resolvedCfg);
-    // reconcile ran before this object existed, so its chunk text is keyed by the connection.
-    rekeyChunkText(conn, store);
-    return {
-        store,
-        cfg: resolvedCfg,
-        dbPath,
-        parsed,
-        warnings,
-        stages
-    };
 }
 export async function docCount(store) {
     const stmt = await store.prepare('SELECT COUNT(*) AS n FROM frontmatter');

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/open.ts"],"sourcesContent":["import { channel } from 'node:diagnostics_channel';\nimport { mkdirSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { ResolvedConfig } from '../config/index.ts';\nimport { featureSignature, STATE_DIR } from '../config/index.ts';\nimport { rekeyChunkText } from '../embed/handoff.ts';\nimport { SenseError } from '../errors.ts';\nimport { FEATURES } from '../features/index.ts';\nimport { createBuilder } from './builder.ts';\nimport { clearCache } from './cache.ts';\nimport type { EmbedChangeKind } from './embed-scope.ts';\nimport { classifyEmbedChange } from './embed-scope.ts';\nimport type { FeatureToggle } from './feature-scope.ts';\nimport { classifyFeatureToggles, isFeatureOnlyChange } from './feature-scope.ts';\nimport { lockWaitBudgetMs } from './lock-wait.ts';\nimport { forcedPresetPaths, isPresetOnlyChange } from './preset-scope.ts';\nimport { getMeta, setMeta } from './shared.ts';\nimport { changedSignatureKeys, embedIdentityAdopted, signatureDiff } from './signature.ts';\nimport type { Stages } from './stages.ts';\nimport type { Connection, OpenDialect, Store } from './types.ts';\n\n// One open algorithm shared by every store, parameterised by a per-engine OpenDialect (types.ts).\n// Ordering is universal, not a dialect concern: connect, meta table, schema-version and\n// feature-signature comparison (rebuild, adopt, or partial rebuild), any extra rebuild trigger,\n// ensureSchema, the derived busy_timeout PRAGMA, reconcile, then the store itself.\n\nexport interface OpenResult {\n  store: Store;\n  cfg: ResolvedConfig;\n  dbPath: string;\n  parsed: number;\n  warnings: string[];\n  // Per-stage wall time for this open's build pass (stages.ts), not for any narrow embed or\n  // feature invalidation that ran beside it -- on a cold build there is none, so it is the whole cost.\n  stages: Stages;\n}\n\ninterface ConnectResult<Handle> {\n  handle: Handle;\n  conn: Connection;\n  cfg: ResolvedConfig;\n  dbPath: string;\n  parsed: number;\n  warnings: string[];\n  stages: Stages;\n}\n\n// duckdb/turso hold the cache file for their connection's whole life, so a second command waits.\n// Bounded by this tree's recorded reconcile time (lock-wait.ts), not a fixed guess.\nconst LOCK_POLL_MS = 50;\nconst lockWait = channel('sensemaking.store.lock-wait');\n\nasync function connectUnlocked<Handle>(dbPath: string, cfg: ResolvedConfig, configDir: string, dialect: OpenDialect<Handle>): Promise<{ handle: Handle; conn: Connection }> {\n  const budgetMs = lockWaitBudgetMs(configDir);\n  const deadline = Date.now() + budgetMs;\n  for (;;) {\n    try {\n      return await dialect.connect(dbPath, cfg);\n    } catch (err) {\n      if (!dialect.isLocked?.(err as Error)) throw err;\n      // Observe a real rejected native connection, never merely the start of an async open.\n      if (lockWait.hasSubscribers) lockWait.publish({ store: cfg.store, dbPath });\n      if (Date.now() >= deadline) {\n        throw new SenseError('STORE_BUSY', `another sense process is using this tree's ${cfg.store} cache (${dbPath}) and did not release it within ${Math.round(budgetMs / 1000)}s; wait for that command to finish, or set \"store\" to \"sqlite\" in sense.config.json, which serves concurrent commands`);\n      }\n      await new Promise((resolve) => setTimeout(resolve, LOCK_POLL_MS));\n    }\n  }\n}\n\nasync function connectWithDialect<Handle>(cfg: ResolvedConfig, dialect: OpenDialect<Handle>): Promise<ConnectResult<Handle>> {\n  const configDir = cfg.configDir ?? cfg.baseDir;\n  const stateDir = join(configDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, dialect.filename);\n\n  const { handle, conn } = await connectUnlocked(dbPath, cfg, configDir, dialect);\n  // A throw below must release this handle, or the leaked WAL makes the cache file undeletable on\n  // Windows. `closed` keeps the catch from double-closing a handle a rebuild branch already closed.\n  let closed = false;\n  // Created here, not inside reconcile(): invalidate()/invalidateFeatures() below share its pool\n  // with the build() call that follows them.\n  const builder = createBuilder(conn, cfg, { rootDir: cfg.rootDir ?? cfg.baseDir, configDir }, dialect.reconcileDialect);\n  try {\n    await conn.exec('CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT)');\n\n    // Schema-version or feature-set mismatch: reconcile only reparses changed files, so an\n    // old cache can't be patched incrementally -- rebuild instead (cheap: nothing expensive lives here).\n    const version = await getMeta(conn, 'schema_version');\n    const features = await getMeta(conn, 'features');\n    const wantFeatures = featureSignature(cfg, FEATURES);\n    // Set only by the preset-membership branch below; reconcile treats these paths as touched\n    // despite an unchanged stamp, for this one build() call.\n    let forcedPaths: Set<string> | undefined;\n    // Set only by the embed-narrow branch below; applied via builder.invalidate() after ensureSchema.\n    let embedInvalidate: EmbedChangeKind | undefined;\n    // Set only by the feature-toggle branch below; applied via builder.invalidateFeatures() after ensureSchema.\n    let featureToggles: FeatureToggle[] | undefined;\n    if ((version !== null && version !== dialect.schemaVersion) || (features !== null && features !== wantFeatures)) {\n      // Indexing derives from presets, so a config edit rebuilding the cache must say so and\n      // name what changed -- silent rebuilds make derived indexing look like a hang or a bug.\n      if (version !== null && version !== dialect.schemaVersion) {\n        console.error('sense: cache format changed (new sensemaking version); rebuilding the index');\n        // Close before clearCache deletes the files out from under the still-open handle.\n        closed = true;\n        await dialect.close(handle);\n        clearCache(cfg);\n        return connectWithDialect(cfg, dialect);\n      }\n      const changedKeys = changedSignatureKeys(features ?? '', wantFeatures);\n      // Null (rather than the empty set) when changedKeys isn't preset-only, or a changed\n      // preset's stored segment can't be parsed back into old include/exclude/vectors -- either\n      // way the branch below is skipped and the full rebuild stays the fallback.\n      const presetForced = isPresetOnlyChange(changedKeys) ? forcedPresetPaths(cfg, cfg.rootDir ?? cfg.baseDir, features ?? '', changedKeys) : null;\n      // Null unless exactly one segment changed and it decomposes into a recognised embed-only\n      // case (embed-scope.ts): anything else, including embed toggled on/off, stays null.\n      const embedKind = changedKeys.size === 1 && changedKeys.has('embed') ? classifyEmbedChange(features ?? '', wantFeatures) : null;\n      // Null (rather than the empty set) when changedKeys isn't feature-toggle-only, or a changed\n      // feature's stored segment can't be parsed back into old/new on-off -- either way the branch\n      // below is skipped and the full rebuild stays the fallback.\n      const toggles = isFeatureOnlyChange(changedKeys) ? classifyFeatureToggles(features ?? '', wantFeatures, changedKeys) : null;\n      if (changedKeys.size === 1 && changedKeys.has('embed') && embedIdentityAdopted(features ?? '', wantFeatures)) {\n        // First sight of a resolved weight identity: the model itself hasn't changed, so\n        // adopt it into meta with no rebuild and no re-embed.\n        console.error(\"sense: recorded the embedding model's resolved identity; vectors are unaffected\");\n        await setMeta(conn, 'features', wantFeatures);\n      } else if (embedKind !== null) {\n        // Chunk boundaries are file-derived, not model-derived (embed.ts's chunksOf), so neither\n        // case needs any file reparsed for any feature but embed itself.\n        embedInvalidate = embedKind;\n        console.error(embedKind === 'model' ? 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'', wantFeatures);\n      const presetForced = isPresetOnlyChange(changedKeys) ? forcedPresetPaths(cfg, cfg.rootDir ?? cfg.baseDir, features ?? '', changedKeys) : null;\n      const embedKind = changedKeys.size === 1 && changedKeys.has('embed') ? classifyEmbedChange(features ?? '', wantFeatures) : null;\n      const toggles = isFeatureOnlyChange(changedKeys) ? classifyFeatureToggles(features ?? '', wantFeatures, changedKeys) : null;\n      if (changedKeys.size === 1 && changedKeys.has('embed') && embedIdentityAdopted(features ?? '', wantFeatures)) {\n        console.error(\"sense: recorded the embedding model's resolved identity; vectors are unaffected\");\n      } else if (embedKind !== null) {\n        embedInvalidate = embedKind;\n        console.error(embedKind === 'model' ? 'sense: config change (embed settings) invalidates only the stale vectors' : 'sense: config change (embed settings) rebuilds only the embeddings it affects');\n      } else if (presetForced !== null) {\n        forcedPaths = presetForced;\n        const changed = signatureDiff(features ?? '', wantFeatures);\n        console.error(`sense: config change (${changed}) reparses only the files it affects`);\n      } else if (toggles !== null) {\n        featureToggles = toggles;\n        const changed = signatureDiff(features ?? '', wantFeatures);\n        console.error(`sense: config change (${changed}) reparses only the feature it affects`);\n      } else {\n        const changed = signatureDiff(features ?? '', wantFeatures);\n        console.error(`sense: config change (${changed}) rebuilds the index`);\n        closed = true;\n        await dialect.close(handle);\n        clearCache(cfg);\n        return connectForBuild(cfg, dialect, requirements);\n      }\n    }\n\n    await dialect.ensureSchema(handle, conn, cfg);\n\n    if (dialect.setDerivedBusyTimeout) {\n      const recordedMaxMs = Number((await getMeta(conn, 'reconcile_max_ms')) ?? '0');\n      await dialect.setDerivedBusyTimeout(handle, conn, Math.min(Math.max(30000, 3 * recordedMaxMs), 600_000));\n    }\n\n    const embedParsed = embedInvalidate ? (await builder.invalidate(embedInvalidate)).parsed : 0;\n    const featureParsed = featureToggles ? 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package/dist/esm/store/reconcile.js

@@ -134,6 +134,18 @@ export async function reconcile(conn, cfg, paths, dialect, pool, forcedPaths) {
         // After the upsert, so every doc already has the frontmatter row sqlite's content rowid
         // couples to. ON CONFLICT DO UPDATE preserves that rowid, so a reparse keeps its identity.
         await stages.time('text-index', ()=>dialect.reconcileContent(conn, contentTouched, parsedDocs, delta, cfg));
+        // Exact source text belongs to the same indexed generation as content and section ranges.
+        // The upsert also covers an added path another writer committed while this build waited.
+        if (contentTouched.length > 0) await conn.runBatch('DELETE FROM indexed_sources WHERE "path" = ?', contentTouched.map((p)=>[
+                p
+            ]));
+        await appendRows(conn, 'indexed_sources', [
+            'path',
+            'text'
+        ], 'INSERT INTO indexed_sources ("path", text) VALUES (?, ?) ON CONFLICT("path") DO UPDATE SET text = excluded.text', parsedDocs.map((doc)=>[
+                doc.relPath,
+                doc.source
+            ]));
         // 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.
         await stages.time('presets', async ()=>{

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/reconcile.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { activeFeatures } from '../features/index.ts';\nimport type { ExtractedDoc, ReconcileDelta } from '../features/types.ts';\nimport { progress } from '../output/progress.ts';\nimport { listFiles, RESERVED_COLUMNS } from '../scan/index.ts';\nimport type { ParsePool } from '../scan/pool.ts';\nimport { reparseFiles } from '../scan/reparse.ts';\nimport { recordLockWaitMs } from './lock-wait.ts';\nimport { appendRows, getColumns, quoteIdent } from './shared.ts';\nimport { featureStage, type Stages, stageRecorder } from './stages.ts';\nimport { withTransaction } from './transaction.ts';\nimport type { Connection, ReconcileDialect } from './types.ts';\n\n// One reconcile algorithm shared by every store, parameterised by a per-engine ReconcileDialect\n// (types.ts). Ordering is universal, not a dialect concern: ALTER, then the frontmatter upsert,\n// then reconcileContent, then preset_files, then the vanished-frontmatter delete, then feature hooks\n// -- a vanished path's content delete (inside reconcileContent) must precede its frontmatter\n// delete, since sqlite's delete SQL resolves the row via its frontmatter rowid.\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.\nexport const CORE_FRONTMATTER_COLUMNS = new Set(['path', '_mtime', '_ctime', '_size', '_parse_error']);\n\nexport interface ReconcilePaths {\n  rootDir: string;\n  configDir: string;\n}\n\nexport async function reconcile(conn: Connection, cfg: Config, paths: ReconcilePaths, dialect: ReconcileDialect, pool?: ParsePool, forcedPaths?: ReadonlySet<string>): Promise<{ parsed: number; warnings: string[]; stages: Stages }> {\n  const { rootDir, configDir } = paths;\n  const start = process.hrtime.bigint();\n  const features = activeFeatures(cfg);\n  const stages = stageRecorder(features.map((f) => f.name));\n  const elapsed = () => Number(process.hrtime.bigint() - start) / 1e6;\n  const files = await stages.time('list', () => listFiles(cfg, rootDir));\n  const currentSet = new Set(files.map((f) => f.relPath));\n\n  const existingRows = await stages.time('existing', async () => {\n    const existingStmt = await conn.prepare('SELECT \"path\", \"_mtime\", \"_size\" FROM frontmatter');\n    return (await existingStmt.all()) as Array<{ path: string; _mtime: number; _size: number }>;\n  });\n  const existing = new Map(existingRows.map((r) => [r.path, r]));\n  // A path whose coverage moved between presets (forcedPaths) but is no longer covered at all is\n  // already caught below by !currentSet.has, since it can only be forced by having existed under\n  // an old preset's match, which means it was reconciled into `existing` already.\n  const vanished = existingRows.filter((r) => !currentSet.has(r.path)).map((r) => r.path);\n\n  // forcedPaths treats an unchanged file as touched because its preset coverage moved, not its\n  // stamp -- reconcile still owns add/update/remove and every cross-feature cascade for it.\n  const toReparse = files.filter((f) => {\n    const row = existing.get(f.relPath);\n    return !row || row._mtime !== f.mtimeMs || row._size !== f.size || (forcedPaths?.has(f.relPath) ?? false);\n  });\n\n  if (vanished.length === 0 && toReparse.length === 0) return { parsed: 0, warnings: [], stages: stages.take(elapsed(), 0) };\n\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  // Pool wall time, dispatch to drain, so this stage shares a clock with every other one.\n  const { docs: parsedDocs, warnings, newColumns, workerParseMs } = await stages.time('parse', () => reparseFiles(toReparse, features, cfg, seenColumns, report.tick, { pool }));\n  report.finish();\n  for (const col of newColumns) seenColumns.add(col);\n\n  const allColumns = [...seenColumns];\n  // Fence before ALTERing: a store's own failure past this point is a raw, engine-specific\n  // error with no indication of the boundary or the levers -- dialect.checkColumnLimit names both.\n  dialect.checkColumnLimit(allColumns.length);\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 DO UPDATE (not OR REPLACE) keeps the row's rowid stable across reparses --\n  // sqlite's content rows are coupled to that rowid.\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  // Paths whose content (and, per feature, other rows) need clearing: gone entirely, or about to\n  // be reinserted fresh. Disjoint from `added`, which has nothing to clear.\n  const touched = [...vanished, ...reparsedExisting];\n\n  const txStart = Date.now();\n  await withTransaction(\n    conn,\n    async () => {\n      // Re-read inside the write transaction: newColumns came from a read taken before it opened, so a\n      // concurrent reconcile may have added some of them since. ALTER has no IF NOT EXISTS.\n      const present = await getColumns(conn);\n      const missingColumns = newColumns.filter((col) => !present.has(col));\n      if (missingColumns.length > 0) await stages.time('alter', () => dialect.addColumns(conn, missingColumns));\n\n      // Revalidated once the lock is held, before this process's own frontmatter upsert below:\n      // `added` came from a path read taken before this transaction's lock, so a path still\n      // called \"added\" here may already have a content row from a concurrent reconcile that\n      // committed while this one waited. One SELECT, not a DELETE per added file -- with no\n      // contention it returns the same set `existing` already ruled out, so nothing extra clears.\n      let contentTouched = touched;\n      if (added.length > 0)\n        contentTouched = await stages.time('added-recheck', async () => {\n          const currentPathsStmt = await conn.prepare('SELECT \"path\" FROM frontmatter');\n          const currentPaths = new Set(((await currentPathsStmt.all()) as Array<{ path: string }>).map((r) => r.path));\n          const staleAdded = added.filter((p) => currentPaths.has(p));\n          return staleAdded.length > 0 ? [...touched, ...staleAdded] : touched;\n        });\n\n      if (parsedDocs.length > 0) {\n        const toRow = (doc: (typeof parsedDocs)[number]) =>\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        // A path in `added` has no existing frontmatter row, so it can never conflict; the rest\n        // genuinely can, and keep the upsert.\n        await stages.time('fm-upsert', async () => {\n          const newDocs = parsedDocs.filter((d) => addedSet.has(d.relPath));\n          const updateDocs = parsedDocs.filter((d) => !addedSet.has(d.relPath));\n          await appendRows(conn, 'frontmatter', writableColumns, insertSql, newDocs.map(toRow));\n          if (updateDocs.length > 0) await conn.runBatch(insertSql, updateDocs.map(toRow));\n        });\n      }\n\n      // After the upsert, so every doc already has the frontmatter row sqlite's content rowid\n      // couples to. ON CONFLICT DO UPDATE preserves that rowid, so a reparse keeps its identity.\n      await stages.time('text-index', () => dialect.reconcileContent(conn, contentTouched, parsedDocs, delta, cfg));\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      await stages.time('presets', async () => {\n        if (touched.length > 0)\n          await conn.runBatch(\n            'DELETE FROM preset_files WHERE \"path\" = ?',\n            touched.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        // DO NOTHING, not a bare INSERT: the added/touched split above comes from a read taken\n        // before this transaction's lock, so a path this process calls \"added\" can already have\n        // its (path, preset) row committed by a concurrent reconcile -- the row would be identical either way.\n        await appendRows(conn, 'preset_files', ['path', 'preset'], 'INSERT INTO preset_files (\"path\", preset) VALUES (?, ?) ON CONFLICT(\"path\", preset) DO NOTHING', presetRows);\n      });\n\n      // Before the feature hooks, never after: rank's afterReconcile reads frontmatter as PageRank's\n      // node set, so a lingering vanished row would dilute rank mass across every surviving note.\n      if (vanished.length > 0)\n        await stages.time('vanished', () =>\n          conn.runBatch(\n            'DELETE FROM frontmatter WHERE \"path\" = ?',\n            vanished.map((p) => [p])\n          )\n        );\n\n      // Timed per feature per hook, so link resolution and PageRank are named stages without\n      // links.ts or rank.ts knowing anything about this, and a new feature is visible for free.\n      if (touched.length > 0) for (const feature of features) await stages.time(featureStage(feature.name, 'remove'), () => feature.remove?.(conn, touched, delta));\n      for (const feature of features) {\n        const docsForFeature: ExtractedDoc[] = parsedDocs.map((doc) => ({ path: doc.relPath, 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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/reconcile.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { activeFeatures } from '../features/index.ts';\nimport type { ExtractedDoc, ReconcileDelta } from '../features/types.ts';\nimport { progress } from '../output/progress.ts';\nimport { listFiles, RESERVED_COLUMNS } from '../scan/index.ts';\nimport type { ParsePool } from '../scan/pool.ts';\nimport { reparseFiles } from '../scan/reparse.ts';\nimport { recordLockWaitMs } from './lock-wait.ts';\nimport { appendRows, getColumns, quoteIdent } from './shared.ts';\nimport { featureStage, type Stages, stageRecorder } from './stages.ts';\nimport { withTransaction } from './transaction.ts';\nimport type { Connection, ReconcileDialect } from './types.ts';\n\n// One reconcile algorithm shared by every store, parameterised by a per-engine ReconcileDialect\n// (types.ts). Ordering is universal, not a dialect concern: ALTER, then the frontmatter upsert,\n// then reconcileContent, then preset_files, then the vanished-frontmatter delete, then feature hooks\n// -- a vanished path's content delete (inside reconcileContent) must precede its frontmatter\n// delete, since sqlite's delete SQL resolves the row via its frontmatter rowid.\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.\nexport const CORE_FRONTMATTER_COLUMNS = new Set(['path', '_mtime', '_ctime', '_size', '_parse_error']);\n\nexport interface ReconcilePaths {\n  rootDir: string;\n  configDir: string;\n}\n\nexport async function reconcile(conn: Connection, cfg: Config, paths: ReconcilePaths, dialect: ReconcileDialect, pool?: ParsePool, forcedPaths?: ReadonlySet<string>): Promise<{ parsed: number; warnings: string[]; stages: Stages }> {\n  const { rootDir, configDir } = paths;\n  const start = process.hrtime.bigint();\n  const features = activeFeatures(cfg);\n  const stages = stageRecorder(features.map((f) => f.name));\n  const elapsed = () => Number(process.hrtime.bigint() - start) / 1e6;\n  const files = await stages.time('list', () => listFiles(cfg, rootDir));\n  const currentSet = new Set(files.map((f) => f.relPath));\n\n  const existingRows = await stages.time('existing', async () => {\n    const existingStmt = await conn.prepare('SELECT \"path\", \"_mtime\", \"_size\" FROM frontmatter');\n    return (await existingStmt.all()) as Array<{ path: string; _mtime: number; _size: number }>;\n  });\n  const existing = new Map(existingRows.map((r) => [r.path, r]));\n  // A path whose coverage moved between presets (forcedPaths) but is no longer covered at all is\n  // already caught below by !currentSet.has, since it can only be forced by having existed under\n  // an old preset's match, which means it was reconciled into `existing` already.\n  const vanished = existingRows.filter((r) => !currentSet.has(r.path)).map((r) => r.path);\n\n  // forcedPaths treats an unchanged file as touched because its preset coverage moved, not its\n  // stamp -- reconcile still owns add/update/remove and every cross-feature cascade for it.\n  const toReparse = files.filter((f) => {\n    const row = existing.get(f.relPath);\n    return !row || row._mtime !== f.mtimeMs || row._size !== f.size || (forcedPaths?.has(f.relPath) ?? false);\n  });\n\n  if (vanished.length === 0 && toReparse.length === 0) return { parsed: 0, warnings: [], stages: stages.take(elapsed(), 0) };\n\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  // Pool wall time, dispatch to drain, so this stage shares a clock with every other one.\n  const { docs: parsedDocs, warnings, newColumns, workerParseMs } = await stages.time('parse', () => reparseFiles(toReparse, features, cfg, seenColumns, report.tick, { pool }));\n  report.finish();\n  for (const col of newColumns) seenColumns.add(col);\n\n  const allColumns = [...seenColumns];\n  // Fence before ALTERing: a store's own failure past this point is a raw, engine-specific\n  // error with no indication of the boundary or the levers -- dialect.checkColumnLimit names both.\n  dialect.checkColumnLimit(allColumns.length);\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 DO UPDATE (not OR REPLACE) keeps the row's rowid stable across reparses --\n  // sqlite's content rows are coupled to that rowid.\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  // Paths whose content (and, per feature, other rows) need clearing: gone entirely, or about to\n  // be reinserted fresh. Disjoint from `added`, which has nothing to clear.\n  const touched = [...vanished, ...reparsedExisting];\n\n  const txStart = Date.now();\n  await withTransaction(\n    conn,\n    async () => {\n      // Re-read inside the write transaction: newColumns came from a read taken before it opened, so a\n      // concurrent reconcile may have added some of them since. ALTER has no IF NOT EXISTS.\n      const present = await getColumns(conn);\n      const missingColumns = newColumns.filter((col) => !present.has(col));\n      if (missingColumns.length > 0) await stages.time('alter', () => dialect.addColumns(conn, missingColumns));\n\n      // Revalidated once the lock is held, before this process's own frontmatter upsert below:\n      // `added` came from a path read taken before this transaction's lock, so a path still\n      // called \"added\" here may already have a content row from a concurrent reconcile that\n      // committed while this one waited. One SELECT, not a DELETE per added file -- with no\n      // contention it returns the same set `existing` already ruled out, so nothing extra clears.\n      let contentTouched = touched;\n      if (added.length > 0)\n        contentTouched = await stages.time('added-recheck', async () => {\n          const currentPathsStmt = await conn.prepare('SELECT \"path\" FROM frontmatter');\n          const currentPaths = new Set(((await currentPathsStmt.all()) as Array<{ path: string }>).map((r) => r.path));\n          const staleAdded = added.filter((p) => currentPaths.has(p));\n          return staleAdded.length > 0 ? [...touched, ...staleAdded] : touched;\n        });\n\n      if (parsedDocs.length > 0) {\n        const toRow = (doc: (typeof parsedDocs)[number]) =>\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        // A path in `added` has no existing frontmatter row, so it can never conflict; the rest\n        // genuinely can, and keep the upsert.\n        await stages.time('fm-upsert', async () => {\n          const newDocs = parsedDocs.filter((d) => addedSet.has(d.relPath));\n          const updateDocs = parsedDocs.filter((d) => !addedSet.has(d.relPath));\n          await appendRows(conn, 'frontmatter', writableColumns, insertSql, newDocs.map(toRow));\n          if (updateDocs.length > 0) await conn.runBatch(insertSql, updateDocs.map(toRow));\n        });\n      }\n\n      // After the upsert, so every doc already has the frontmatter row sqlite's content rowid\n      // couples to. ON CONFLICT DO UPDATE preserves that rowid, so a reparse keeps its identity.\n      await stages.time('text-index', () => dialect.reconcileContent(conn, contentTouched, parsedDocs, delta, cfg));\n\n      // Exact source text belongs to the same indexed generation as content and section ranges.\n      // The upsert also covers an added path another writer committed while this build waited.\n      if (contentTouched.length > 0)\n        await conn.runBatch(\n          'DELETE FROM indexed_sources WHERE \"path\" = ?',\n          contentTouched.map((p) => [p])\n        );\n      await appendRows(\n        conn,\n        'indexed_sources',\n        ['path', 'text'],\n        'INSERT INTO indexed_sources (\"path\", text) VALUES (?, ?) ON CONFLICT(\"path\") DO UPDATE SET text = excluded.text',\n        parsedDocs.map((doc) => [doc.relPath, doc.source])\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      await stages.time('presets', async () => {\n        if (touched.length > 0)\n          await conn.runBatch(\n            'DELETE FROM preset_files WHERE \"path\" = ?',\n            touched.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        // DO NOTHING, not a bare INSERT: the added/touched split above comes from a read taken\n        // before this transaction's lock, so a path this process calls \"added\" can already have\n        // its (path, preset) row committed by a concurrent reconcile -- the row would be identical either way.\n        await appendRows(conn, 'preset_files', ['path', 'preset'], 'INSERT INTO preset_files (\"path\", preset) VALUES (?, ?) ON CONFLICT(\"path\", preset) DO NOTHING', presetRows);\n      });\n\n      // Before the feature hooks, never after: rank's afterReconcile reads frontmatter as PageRank's\n      // node set, so a lingering vanished row would dilute rank mass across every surviving note.\n      if (vanished.length > 0)\n        await stages.time('vanished', () =>\n          conn.runBatch(\n            'DELETE FROM frontmatter WHERE \"path\" = ?',\n            vanished.map((p) => [p])\n          )\n        );\n\n      // Timed per feature per hook, so link resolution and PageRank are named stages without\n      // links.ts or rank.ts knowing anything about this, and a new feature is visible for free.\n      if (touched.length > 0) for (const feature of features) await stages.time(featureStage(feature.name, 'remove'), () => feature.remove?.(conn, touched, delta));\n      for (const feature of features) {\n        const docsForFeature: ExtractedDoc[] = parsedDocs.map((doc) => ({ path: doc.relPath, extracted: doc.extracted[feature.name] }));\n        await stages.time(featureStage(feature.name, 'store'), () => feature.store?.(conn, docsForFeature, delta));\n      }\n      for (const feature of features) await stages.time(featureStage(feature.name, 'after'), () => feature.afterReconcile?.(conn, delta));\n    },\n    dialect.beginMode()\n  );\n\n  const durationMs = Date.now() - txStart;\n  // Every store, not just the ones with a PRAGMA to derive: connectUnlocked's lock-wait budget needs it too.\n  recordLockWaitMs(configDir, durationMs);\n  if (dialect.recordDuration) await stages.time('meta', () => dialect.recordDuration?.(conn, durationMs));\n\n  return { parsed: parsedDocs.length, warnings, stages: stages.take(elapsed(), durationMs, workerParseMs) };\n}\n"],"names":["activeFeatures","progress","listFiles","RESERVED_COLUMNS","reparseFiles","recordLockWaitMs","appendRows","getColumns","quoteIdent","featureStage","stageRecorder","withTransaction","CORE_FRONTMATTER_COLUMNS","Set","reconcile","conn","cfg","paths","dialect","pool","forcedPaths","rootDir","configDir","start","process","hrtime","bigint","features","stages","map","f","name","elapsed","Number","files","time","currentSet","relPath","existingRows","existingStmt","prepare","all","existing","Map","r","path","vanished","filter","has","toReparse","row","get","_mtime","mtimeMs","_size","size","length","parsed","warnings","take","seenColumns","report","docs","parsedDocs","newColumns","workerParseMs","tick","finish","col","add","allColumns","checkColumnLimit","writableColumns","c","insertSql","join","added","delta","reparsed","d","addedSet","reparsedExisting","p","touched","txStart","Date","now","present","missingColumns","addColumns","contentTouched","currentPathsStmt","currentPaths","staleAdded","toRow","doc","ctimeMs","parseError","data","newDocs","updateDocs","runBatch","reconcileContent","source","presetRows","presetName","presets","push","feature","remove","docsForFeature","extracted","store","afterReconcile","beginMode","durationMs","recordDuration"],"mappings":"AACA,SAASA,cAAc,QAAQ,uBAAuB;AAEtD,SAASC,QAAQ,QAAQ,wBAAwB;AACjD,SAASC,SAAS,EAAEC,gBAAgB,QAAQ,mBAAmB;AAE/D,SAASC,YAAY,QAAQ,qBAAqB;AAClD,SAASC,gBAAgB,QAAQ,iBAAiB;AAClD,SAASC,UAAU,EAAEC,UAAU,EAAEC,UAAU,QAAQ,cAAc;AACjE,SAASC,YAAY,EAAeC,aAAa,QAAQ,cAAc;AACvE,SAASC,eAAe,QAAQ,mBAAmB;AAGnD,gGAAgG;AAChG,gGAAgG;AAChG,qGAAqG;AACrG,6FAA6F;AAC7F,gFAAgF;AAEhF,6FAA6F;AAC7F,4EAA4E;AAC5E,OAAO,MAAMC,2BAA2B,IAAIC,IAAI;IAAC;IAAQ;IAAU;IAAU;IAAS;CAAe,EAAE;AAOvG,OAAO,eAAeC,UAAUC,IAAgB,EAAEC,GAAW,EAAEC,KAAqB,EAAEC,OAAyB,EAAEC,IAAgB,EAAEC,WAAiC;IAClK,MAAM,EAAEC,OAAO,EAAEC,SAAS,EAAE,GAAGL;IAC/B,MAAMM,QAAQC,QAAQC,MAAM,CAACC,MAAM;IACnC,MAAMC,WAAW3B,eAAegB;IAChC,MAAMY,SAASlB,cAAciB,SAASE,GAAG,CAAC,CAACC,IAAMA,EAAEC,IAAI;IACvD,MAAMC,UAAU,IAAMC,OAAOT,QAAQC,MAAM,CAACC,MAAM,KAAKH,SAAS;IAChE,MAAMW,QAAQ,MAAMN,OAAOO,IAAI,CAAC,QAAQ,IAAMjC,UAAUc,KAAKK;IAC7D,MAAMe,aAAa,IAAIvB,IAAIqB,MAAML,GAAG,CAAC,CAACC,IAAMA,EAAEO,OAAO;IAErD,MAAMC,eAAe,MAAMV,OAAOO,IAAI,CAAC,YAAY;QACjD,MAAMI,eAAe,MAAMxB,KAAKyB,OAAO,CAAC;QACxC,OAAQ,MAAMD,aAAaE,GAAG;IAChC;IACA,MAAMC,WAAW,IAAIC,IAAIL,aAAaT,GAAG,CAAC,CAACe,IAAM;YAACA,EAAEC,IAAI;YAAED;SAAE;IAC5D,+FAA+F;IAC/F,+FAA+F;IAC/F,gFAAgF;IAChF,MAAME,WAAWR,aAAaS,MAAM,CAAC,CAACH,IAAM,CAACR,WAAWY,GAAG,CAACJ,EAAEC,IAAI,GAAGhB,GAAG,CAAC,CAACe,IAAMA,EAAEC,IAAI;IAEtF,6FAA6F;IAC7F,0FAA0F;IAC1F,MAAMI,YAAYf,MAAMa,MAAM,CAAC,CAACjB;;QAC9B,MAAMoB,MAAMR,SAASS,GAAG,CAACrB,EAAEO,OAAO;QAClC,OAAO,CAACa,OAAOA,IAAIE,MAAM,KAAKtB,EAAEuB,OAAO,IAAIH,IAAII,KAAK,KAAKxB,EAAEyB,IAAI,aAAKnC,wBAAAA,kCAAAA,YAAa4B,GAAG,CAAClB,EAAEO,OAAO,wCAAK;IACrG;IAEA,IAAIS,SAASU,MAAM,KAAK,KAAKP,UAAUO,MAAM,KAAK,GAAG,OAAO;QAAEC,QAAQ;QAAGC,UAAU,EAAE;QAAE9B,QAAQA,OAAO+B,IAAI,CAAC3B,WAAW;IAAG;IAEzH,MAAM4B,cAAc,MAAMrD,WAAWQ;IAErC,oFAAoF;IACpF,uDAAuD;IACvD,MAAM8C,SAAS5D,SAAS,mBAAmBgD,UAAUO,MAAM;IAC3D,wFAAwF;IACxF,MAAM,EAAEM,MAAMC,UAAU,EAAEL,QAAQ,EAAEM,UAAU,EAAEC,aAAa,EAAE,GAAG,MAAMrC,OAAOO,IAAI,CAAC,SAAS,IAAM/B,aAAa6C,WAAWtB,UAAUX,KAAK4C,aAAaC,OAAOK,IAAI,EAAE;YAAE/C;QAAK;IAC3K0C,OAAOM,MAAM;IACb,KAAK,MAAMC,OAAOJ,WAAYJ,YAAYS,GAAG,CAACD;IAE9C,MAAME,aAAa;WAAIV;KAAY;IACnC,yFAAyF;IACzF,iGAAiG;IACjG1C,QAAQqD,gBAAgB,CAACD,WAAWd,MAAM;IAC1C,0FAA0F;IAC1F,sEAAsE;IACtE,MAAMgB,kBAAkBF,WAAWvB,MAAM,CAAC,CAAC0B,IAAM7D,yBAAyBoC,GAAG,CAACyB,MAAM,CAACtE,iBAAiB6C,GAAG,CAACyB;IAC1G,yFAAyF;IACzF,mDAAmD;IACnD,MAAMC,YAAY,CAAC,yBAAyB,EAAEF,gBAAgB3C,GAAG,CAACrB,YAAYmE,IAAI,CAAC,MAAM,UAAU,EAAEH,gBAAgB3C,GAAG,CAAC,IAAM,KAAK8C,IAAI,CAAC,MAAM,oCAAoC,EAAEH,gBAClLzB,MAAM,CAAC,CAAC0B,IAAMA,MAAM,QACpB5C,GAAG,CAAC,CAAC4C,IAAM,GAAGjE,WAAWiE,GAAG,YAAY,EAAEjE,WAAWiE,IAAI,EACzDE,IAAI,CAAC,OAAO;IAEf,MAAMC,QAAQ3B,UAAUF,MAAM,CAAC,CAACjB,IAAM,CAACY,SAASM,GAAG,CAAClB,EAAEO,OAAO,GAAGR,GAAG,CAAC,CAACC,IAAMA,EAAEO,OAAO;IACpF,MAAMwC,QAAwB;QAAE3C;QAAO4C,UAAUf,WAAWlC,GAAG,CAAC,CAACkD,IAAMA,EAAE1C,OAAO;QAAGuC;QAAO9B;IAAS;IACnG,MAAMkC,WAAW,IAAInE,IAAI+D;IACzB,MAAMK,mBAAmBlB,WAAWlC,GAAG,CAAC,CAACkD,IAAMA,EAAE1C,OAAO,EAAEU,MAAM,CAAC,CAACmC,IAAM,CAACF,SAAShC,GAAG,CAACkC;IACtF,+FAA+F;IAC/F,0EAA0E;IAC1E,MAAMC,UAAU;WAAIrC;WAAamC;KAAiB;IAElD,MAAMG,UAAUC,KAAKC,GAAG;IACxB,MAAM3E,gBACJI,MACA;QACE,iGAAiG;QACjG,sFAAsF;QACtF,MAAMwE,UAAU,MAAMhF,WAAWQ;QACjC,MAAMyE,iBAAiBxB,WAAWjB,MAAM,CAAC,CAACqB,MAAQ,CAACmB,QAAQvC,GAAG,CAACoB;QAC/D,IAAIoB,eAAehC,MAAM,GAAG,GAAG,MAAM5B,OAAOO,IAAI,CAAC,SAAS,IAAMjB,QAAQuE,UAAU,CAAC1E,MAAMyE;QAEzF,yFAAyF;QACzF,sFAAsF;QACtF,sFAAsF;QACtF,sFAAsF;QACtF,4FAA4F;QAC5F,IAAIE,iBAAiBP;QACrB,IAAIP,MAAMpB,MAAM,GAAG,GACjBkC,iBAAiB,MAAM9D,OAAOO,IAAI,CAAC,iBAAiB;YAClD,MAAMwD,mBAAmB,MAAM5E,KAAKyB,OAAO,CAAC;YAC5C,MAAMoD,eAAe,IAAI/E,IAAI,AAAE,CAAA,MAAM8E,iBAAiBlD,GAAG,EAAC,EAA+BZ,GAAG,CAAC,CAACe,IAAMA,EAAEC,IAAI;YAC1G,MAAMgD,aAAajB,MAAM7B,MAAM,CAAC,CAACmC,IAAMU,aAAa5C,GAAG,CAACkC;YACxD,OAAOW,WAAWrC,MAAM,GAAG,IAAI;mBAAI2B;mBAAYU;aAAW,GAAGV;QAC/D;QAEF,IAAIpB,WAAWP,MA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package/dist/esm/store/sqlite/open.d.ts

@@ -1,12 +1,12 @@
 import { DatabaseSync } from 'node:sqlite';
 import type { ResolvedConfig } from '../../config/index.js';
-import type { OpenResult } from '../open.js';
+import type { InternalOpenOptions, OpenResult } from '../open.js';
 import type { OpenDialect } from '../types.js';
 export declare const DB_FILENAME = "cache.db";
-export declare const SCHEMA_VERSION = "20";
+export declare const SCHEMA_VERSION = "21";
 export type { OpenResult };
 interface SqliteHandle {
     db: DatabaseSync;
 }
 export declare const sqliteOpenDialect: OpenDialect<SqliteHandle>;
-export declare function openSqlite(cfg: ResolvedConfig): Promise<OpenResult>;
+export declare function openSqlite(cfg: ResolvedConfig, options?: InternalOpenOptions): Promise<OpenResult>;