sensemaking 0.22.0 → 0.22.2

package/dist/cjs/store/types.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/types.ts"],"sourcesContent":["// The backing-store interface: a minimal portable statement surface (exec/prepare), plus\n// dedicated interfaces exactly where engines diverge (lexical index, vector scan, raw sql).\n\nimport type { Config, ResolvedConfig, StoreName } from '../config/index.ts';\nimport type { ReconcileDelta } from '../features/types.ts';\nimport type { ParsedDoc } from '../scan/index.ts';\n\n// 'lexical'/'vectors': the store's LexicalIndex/VectorStore is functionally implemented, not\n// present-but-inert. 'sql-functions': the engine can register has/basename/segment as UDFs at all,\n// which turso's client cannot. The rest are finer FTS5-only behaviors; a missing one fails at open\n// or first use. An array, not a bare union, so a runtime check reads the same list the type does.\nexport const CAPABILITY_NAMES = ['phrases', 'snippets', 'lexical', 'vectors', 'sql-functions'] as const;\nexport type Capability = (typeof CAPABILITY_NAMES)[number];\n\nexport interface RunResult {\n  changes: number | bigint;\n  lastInsertRowid: number | bigint;\n}\n\n// A prepared statement's async surface: every supported engine crosses a real async boundary\n// for a query (DuckDB has no synchronous client), so run/get/all return Promises.\nexport interface Statement {\n  run(...params: unknown[]): Promise<RunResult>;\n  get(...params: unknown[]): Promise<unknown>;\n  all(...params: unknown[]): Promise<unknown[]>;\n  iterate(...params: unknown[]): AsyncIterable<unknown>;\n  columns(): Array<{ name: string }>;\n  setReadBigInts(enabled: boolean): void;\n}\n\n// Connection surface feature-owned SQL runs against inside a store's hot loops (schema,\n// reconcile), portable so a feature never imports an engine-specific client type.\nexport interface Connection {\n  exec(sql: string): Promise<void>;\n  prepare(sql: string): Promise<Statement>;\n  runBatch(sql: string, paramRows: unknown[][]): Promise<void>;\n}\n\n// One reconcile algorithm (src/store/reconcile.ts), parameterised per engine. reconcileContent is\n// the load-bearing member: it lands every content-table change and owns its own multi-step\n// strategy (sqlite FTS5 incremental, duckdb combined delete/insert, turso incremental-or-rebuild).\nexport interface ReconcileDialect {\n  // BEGIN mode for the whole reconcile: sqlite/turso 'BEGIN IMMEDIATE', duckdb 'BEGIN'.\n  beginMode(): string;\n  // Throws SenseError('COLUMN_LIMIT', ...) past this store's own column ceiling and reasoning.\n  checkColumnLimit(count: number): void;\n  // Adds `names` to frontmatter, already filtered to columns this connection doesn't have yet.\n  // sqlite/turso loop (their ADD COLUMN is metadata-only); duckdb issues one statement per call.\n  addColumns(conn: Connection, names: string[]): Promise<void>;\n  // Deletes content rows for `touched`, inserts rows for `docs`; `delta` carries the tree state a\n  // strategy may need. Must not open its own transaction, and must not return before its own\n  // multi-step strategy (e.g. turso's DROP/rebuild) completes.\n  reconcileContent(conn: Connection, touched: string[], docs: ParsedDoc[], delta: ReconcileDelta, cfg: Config): Promise<void>;\n  // Records this reconcile's write-transaction duration. sqlite/turso use it for open()'s derived\n  // busy_timeout; duckdb has no such PRAGMA and omits it.\n  recordDuration?(conn: Connection, ms: number): Promise<void>;\n  // Inserts rows whose path cannot already exist in `table` (no ON CONFLICT needed), through a\n  // faster append-only path. Optional: sqlite/turso omit it and every row goes through the upsert.\n  insertNew?(conn: Connection, table: string, columns: string[], rows: unknown[][]): Promise<void>;\n}\n\n// One open algorithm (src/store/open.ts), parameterised per engine. `Handle` is whatever this\n// store needs to close the connection and construct its Store (sqlite: {db}; duckdb:\n// {instance, duckdb}; turso: db) -- opaque to the shared orchestration, threaded through unchanged.\nexport interface OpenDialect<Handle> {\n  // Cache filename under STATE_DIR, e.g. 'cache.db'.\n  filename: string;\n  // Cache shape version, independent of the config's own `version`; bumping it rebuilds an existing tree.\n  schemaVersion: string;\n  reconcileDialect: ReconcileDialect;\n  // Opens the physical connection and applies pragmas due before any SQL runs (sqlite: busy_timeout\n  // + WAL; turso: connect-time timeout; duckdb: none).\n  connect(dbPath: string, cfg: ResolvedConfig): Promise<{ handle: Handle; conn: Connection }>;\n  // Releases the handle, for both the rebuild-and-reopen branch and error cleanup on this attempt.\n  close(handle: Handle): Promise<void>;\n  // True when connect() failed because another process holds the cache file, which the orchestration\n  // retries. Each engine words it differently, so the match is the dialect's own (`native-not-emulated`).\n  // Absent for sqlite, whose file lock is shared and whose concurrent-open failure is a different defect.\n  // Matching on message text is forced, not chosen: measured 2026-09-02, duckdb throws a plain Error\n  // whose only own properties are stack and message, and turso sets code to the constant\n  // 'GenericFailure' on every failure alike with rawCode undefined. Neither exposes anything a\n  // predicate could switch on, so each dialect pins its engine's wordings and unit-tests them.\n  isLocked?(err: Error): boolean;\n  // Schema DDL beyond frontmatter/preset_files/meta (content table, feature hooks); sole owner of\n  // whether it wraps itself in a write transaction (sqlite: yes, guards a cold-open ALTER race; duckdb/turso: no).\n  ensureSchema(handle: Handle, conn: Connection, cfg: Config): Promise<void>;\n  // Installs the derived busy_timeout PRAGMA right before reconcile (sqlite/turso); absent for\n  // duckdb, which has no such PRAGMA.\n  setDerivedBusyTimeout?(handle: Handle, conn: Connection, ms: number): Promise<void>;\n  createStore(handle: Handle, conn: Connection, cfg: ResolvedConfig): Store;\n}\n\nexport interface FieldStat {\n  field: string;\n  coverage: number;\n  type: string;\n}\n\nexport interface DocumentStore {\n  // Frontmatter column names (including internal ones; callers filter).\n  columns(): Promise<string[]>;\n  // Per-column coverage (non-null count) and observed type set, aggregated in one SQL query,\n  // never one row per note. `scopeWhere` is a caller-built WHERE fragment, per LexicalQueryOptions.\n  fieldStats(columns: string[], scopeWhere: string): Promise<FieldStat[]>;\n}\n\nexport interface LexicalHit {\n  path: string;\n  hit: string | null;\n}\n\nexport interface LexicalQueryOptions {\n  whereJoin: string;\n  whereCond: string;\n  scopeCond: string;\n  limit: number;\n}\n\nexport interface LexicalIndex {\n  // Ranked word-match query with excerpt, scoped by the caller-built SQL fragments (the same\n  // fragments narrowByWhere/materializeScope produce elsewhere).\n  query(terms: string, opts: LexicalQueryOptions): Promise<LexicalHit[]>;\n}\n\nexport interface VectorCandidate {\n  path: string;\n  lines: string;\n  similarity: number;\n}\n\nexport interface VectorSimilar {\n  path: string;\n  similarity: number;\n}\n\nexport interface VectorWriteRow {\n  path: string;\n  chunk: number;\n  scale: number;\n  vector: Buffer;\n}\n\nexport interface VectorStore {\n  // Rows whose vector is NULL: never embedded, or added since.\n  pending(): Promise<Array<{ path: string; chunk: number }>>;\n  // One batch write per call (never per row) so a provider's embedding batch stays inside a\n  // single store method.\n  writeVectors(rows: VectorWriteRow[]): Promise<void>;\n  candidates(queryVector: Float32Array, storeDims: number, fetch: number, allowed?: Set<string>): Promise<VectorCandidate[]>;\n  similar(path: string, opts: { exclude: Set<string>; allowed?: Set<string>; k: number }): Promise<VectorSimilar[]>;\n  hasVector(path: string): Promise<boolean>;\n}\n\n// The `sense sql` passthrough: string in, streamed rows out. Each store registers the same\n// sense-supplied functions and applies its own read-bigints/error-translation behavior.\nexport interface RawStatement {\n  columns(): Array<{ name: string }>;\n  iterate(...params: unknown[]): AsyncIterable<unknown>;\n}\n\nexport interface SqlSession {\n  prepare(sql: string): Promise<RawStatement>;\n}\n\nexport interface Store {\n  readonly name: StoreName;\n  readonly capabilities: ReadonlySet<Capability>;\n  exec(sql: string): Promise<void>;\n  prepare(sql: string): Promise<Statement>;\n  // One crossing, N rows: every external write loop (search's candidate insert, graph ring's\n  // temp-table writes) goes through this instead of looping over `run()`. Same contract as Connection.runBatch.\n  runBatch(sql: string, paramRows: unknown[][]): Promise<void>;\n  // Pins one snapshot across multi-statement reads; `map` and `peek` use it. A network-bound\n  // write (search's embedding top-up) must stay outside it. Nesting joins the enclosing transaction.\n  transaction<T>(fn: () => Promise<T>): Promise<T>;\n  docs: DocumentStore;\n  lexical: LexicalIndex;\n  vectors: VectorStore;\n  raw: SqlSession;\n  // Engine-level facts for `sense status` (e.g. a derived busy_timeout PRAGMA reading); each\n  // store owns what it reports and how it is worded. Empty when there is nothing to report.\n  engineStatus(): Promise<Record<string, string>>;\n  close(): Promise<void>;\n}\n"],"names":["CAPABILITY_NAMES"],"mappings":"AAAA,yFAAyF;AACzF,4FAA4F;;;;;+BAU/EA;;;eAAAA;;;AAAN,IAAMA,mBAAmB;IAAC;IAAW;IAAY;IAAW;IAAW;CAAgB"}
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/types.ts"],"sourcesContent":["// The backing-store interface: a minimal portable statement surface (exec/prepare), plus\n// dedicated interfaces exactly where engines diverge (lexical index, vector scan, raw sql).\n\nimport type { Config, ResolvedConfig, StoreName } from '../config/index.ts';\nimport type { ReconcileDelta } from '../features/types.ts';\nimport type { ParsedDoc } from '../scan/index.ts';\n\n// 'lexical'/'vectors': the store's LexicalIndex/VectorStore is functionally implemented, not\n// present-but-inert. 'sql-functions': the engine can register has/basename/segment as UDFs at all,\n// which turso's client cannot. The rest are finer FTS5-only behaviors; a missing one fails at open\n// or first use. An array, not a bare union, so a runtime check reads the same list the type does.\nexport const CAPABILITY_NAMES = ['phrases', 'snippets', 'lexical', 'vectors', 'sql-functions'] as const;\nexport type Capability = (typeof CAPABILITY_NAMES)[number];\n\nexport interface RunResult {\n  changes: number | bigint;\n  lastInsertRowid: number | bigint;\n}\n\n// A prepared statement's async surface: every supported engine crosses a real async boundary\n// for a query (DuckDB has no synchronous client), so run/get/all return Promises.\nexport interface Statement {\n  run(...params: unknown[]): Promise<RunResult>;\n  get(...params: unknown[]): Promise<unknown>;\n  all(...params: unknown[]): Promise<unknown[]>;\n  iterate(...params: unknown[]): AsyncIterable<unknown>;\n  columns(): Array<{ name: string }>;\n  setReadBigInts(enabled: boolean): void;\n}\n\n// Connection surface feature-owned SQL runs against inside a store's hot loops (schema,\n// reconcile), portable so a feature never imports an engine-specific client type.\nexport interface Connection {\n  exec(sql: string): Promise<void>;\n  prepare(sql: string): Promise<Statement>;\n  runBatch(sql: string, paramRows: unknown[][]): Promise<void>;\n  // Bulk-inserts rows that cannot conflict, through a path that binds no per-value parameters.\n  // Optional: a store that has nothing faster than its own INSERT omits it and callers fall back\n  // (appendRows in shared.ts). `columns` names the values each row carries; a table column the\n  // caller does not write takes its default.\n  appendRows?(table: string, columns: string[], rows: unknown[][]): Promise<void>;\n}\n\n// One reconcile algorithm (src/store/reconcile.ts), parameterised per engine. reconcileContent is\n// the load-bearing member: it lands every content-table change and owns its own multi-step\n// strategy (sqlite FTS5 incremental, duckdb combined delete/insert, turso incremental-or-rebuild).\nexport interface ReconcileDialect {\n  // BEGIN mode for the whole reconcile: sqlite/turso 'BEGIN IMMEDIATE', duckdb 'BEGIN'.\n  beginMode(): string;\n  // Throws SenseError('COLUMN_LIMIT', ...) past this store's own column ceiling and reasoning.\n  checkColumnLimit(count: number): void;\n  // Adds `names` to frontmatter, already filtered to columns this connection doesn't have yet.\n  // sqlite/turso loop (their ADD COLUMN is metadata-only); duckdb issues one statement per call.\n  addColumns(conn: Connection, names: string[]): Promise<void>;\n  // Deletes content rows for `touched`, inserts rows for `docs`; `delta` carries the tree state a\n  // strategy may need. Must not open its own transaction, and must not return before its own\n  // multi-step strategy (e.g. turso's DROP/rebuild) completes.\n  reconcileContent(conn: Connection, touched: string[], docs: ParsedDoc[], delta: ReconcileDelta, cfg: Config): Promise<void>;\n  // Records this reconcile's write-transaction duration. sqlite/turso use it for open()'s derived\n  // busy_timeout; duckdb has no such PRAGMA and omits it.\n  recordDuration?(conn: Connection, ms: number): Promise<void>;\n}\n\n// One open algorithm (src/store/open.ts), parameterised per engine. `Handle` is whatever this\n// store needs to close the connection and construct its Store (sqlite: {db}; duckdb:\n// {instance, duckdb}; turso: db) -- opaque to the shared orchestration, threaded through unchanged.\nexport interface OpenDialect<Handle> {\n  // Cache filename under STATE_DIR, e.g. 'cache.db'.\n  filename: string;\n  // Cache shape version, independent of the config's own `version`; bumping it rebuilds an existing tree.\n  schemaVersion: string;\n  reconcileDialect: ReconcileDialect;\n  // Opens the physical connection and applies pragmas due before any SQL runs (sqlite: busy_timeout\n  // + WAL; turso: connect-time timeout; duckdb: none).\n  connect(dbPath: string, cfg: ResolvedConfig): Promise<{ handle: Handle; conn: Connection }>;\n  // Releases the handle, for both the rebuild-and-reopen branch and error cleanup on this attempt.\n  close(handle: Handle): Promise<void>;\n  // True when connect() failed because another process holds the cache file, which the orchestration\n  // retries. Each engine words it differently, so the match is the dialect's own (`native-not-emulated`).\n  // Absent for sqlite, whose file lock is shared and whose concurrent-open failure is a different defect.\n  // Matching on message text is forced, not chosen: measured 2026-09-02, duckdb throws a plain Error\n  // whose only own properties are stack and message, and turso sets code to the constant\n  // 'GenericFailure' on every failure alike with rawCode undefined. Neither exposes anything a\n  // predicate could switch on, so each dialect pins its engine's wordings and unit-tests them.\n  isLocked?(err: Error): boolean;\n  // Schema DDL beyond frontmatter/preset_files/meta (content table, feature hooks); sole owner of\n  // whether it wraps itself in a write transaction (sqlite: yes, guards a cold-open ALTER race; duckdb/turso: no).\n  ensureSchema(handle: Handle, conn: Connection, cfg: Config): Promise<void>;\n  // Installs the derived busy_timeout PRAGMA right before reconcile (sqlite/turso); absent for\n  // duckdb, which has no such PRAGMA.\n  setDerivedBusyTimeout?(handle: Handle, conn: Connection, ms: number): Promise<void>;\n  createStore(handle: Handle, conn: Connection, cfg: ResolvedConfig): Store;\n}\n\nexport interface FieldStat {\n  field: string;\n  coverage: number;\n  type: string;\n}\n\nexport interface DocumentStore {\n  // Frontmatter column names (including internal ones; callers filter).\n  columns(): Promise<string[]>;\n  // Per-column coverage (non-null count) and observed type set, aggregated in one SQL query,\n  // never one row per note. `scopeWhere` is a caller-built WHERE fragment, per LexicalQueryOptions.\n  fieldStats(columns: string[], scopeWhere: string): Promise<FieldStat[]>;\n}\n\nexport interface LexicalHit {\n  path: string;\n  hit: string | null;\n}\n\nexport interface LexicalQueryOptions {\n  whereJoin: string;\n  whereCond: string;\n  scopeCond: string;\n  limit: number;\n}\n\nexport interface LexicalIndex {\n  // Ranked word-match query with excerpt, scoped by the caller-built SQL fragments (the same\n  // fragments narrowByWhere/materializeScope produce elsewhere).\n  query(terms: string, opts: LexicalQueryOptions): Promise<LexicalHit[]>;\n}\n\nexport interface VectorCandidate {\n  path: string;\n  lines: string;\n  similarity: number;\n}\n\nexport interface VectorSimilar {\n  path: string;\n  similarity: number;\n}\n\nexport interface VectorWriteRow {\n  path: string;\n  chunk: number;\n  scale: number;\n  vector: Buffer;\n}\n\nexport interface VectorStore {\n  // Rows whose vector is NULL: never embedded, or added since.\n  pending(): Promise<Array<{ path: string; chunk: number }>>;\n  // One batch write per call (never per row) so a provider's embedding batch stays inside a\n  // single store method.\n  writeVectors(rows: VectorWriteRow[]): Promise<void>;\n  candidates(queryVector: Float32Array, storeDims: number, fetch: number, allowed?: Set<string>): Promise<VectorCandidate[]>;\n  similar(path: string, opts: { exclude: Set<string>; allowed?: Set<string>; k: number }): Promise<VectorSimilar[]>;\n  hasVector(path: string): Promise<boolean>;\n}\n\n// The `sense sql` passthrough: string in, streamed rows out. Each store registers the same\n// sense-supplied functions and applies its own read-bigints/error-translation behavior.\nexport interface RawStatement {\n  columns(): Array<{ name: string }>;\n  iterate(...params: unknown[]): AsyncIterable<unknown>;\n}\n\nexport interface SqlSession {\n  prepare(sql: string): Promise<RawStatement>;\n}\n\nexport interface Store {\n  readonly name: StoreName;\n  readonly capabilities: ReadonlySet<Capability>;\n  exec(sql: string): Promise<void>;\n  prepare(sql: string): Promise<Statement>;\n  // One crossing, N rows: every external write loop (search's candidate insert, graph ring's\n  // temp-table writes) goes through this instead of looping over `run()`. Same contract as Connection.runBatch.\n  runBatch(sql: string, paramRows: unknown[][]): Promise<void>;\n  // Pins one snapshot across multi-statement reads; `map` and `peek` use it. A network-bound\n  // write (search's embedding top-up) must stay outside it. Nesting joins the enclosing transaction.\n  transaction<T>(fn: () => Promise<T>): Promise<T>;\n  docs: DocumentStore;\n  lexical: LexicalIndex;\n  vectors: VectorStore;\n  raw: SqlSession;\n  // Engine-level facts for `sense status` (e.g. a derived busy_timeout PRAGMA reading); each\n  // store owns what it reports and how it is worded. Empty when there is nothing to report.\n  engineStatus(): Promise<Record<string, string>>;\n  close(): Promise<void>;\n}\n"],"names":["CAPABILITY_NAMES"],"mappings":"AAAA,yFAAyF;AACzF,4FAA4F;;;;;+BAU/EA;;;eAAAA;;;AAAN,IAAMA,mBAAmB;IAAC;IAAW;IAAY;IAAW;IAAW;CAAgB"}

package/dist/esm/features/embed.js

@@ -3,6 +3,7 @@ import { embedConfig } from '../config/index.js';
 import { stashChunkText } from '../embed/handoff.js';
 import { modelIdentity } from '../embed/identity.js';
 import { countLines } from '../scan/frontmatter.js';
+import { appendRows } from '../store/shared.js';
 // The title/summary prefix mirrors bm25 field weighting. Chunks the body, not the raw file, so
 // `offset` shifts line numbers back onto raw and a range stays a direct Read range.
 function chunksOf(blocks, body, search, offset = 0, chunkTokens) {
@@ -54,7 +55,14 @@ export const embed = {
             texts.set(path, chunks.map((c)=>c.text));
         }
         if (rows.length === 0) return;
-        await db.runBatch('INSERT INTO embeddings ("path", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows);
+        // scale and vector are written by the embed pass, not here, so they are not in the column list
+        // and take the table's own default on the append path.
+        await appendRows(db, 'embeddings', [
+            'path',
+            'chunk',
+            'start_line',
+            'end_line'
+        ], 'INSERT INTO embeddings ("path", chunk, start_line, end_line, scale, vector) VALUES (?, ?, ?, ?, NULL, NULL)', rows);
         // The text extract() just computed, handed to the embed pass that follows in this same
         // process rather than re-derived from the file there (src/embed/handoff.ts).
         stashChunkText(db, texts);

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

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

@@ -1,4 +1,5 @@
 import posix from 'node:path/posix';
+import { appendRows } from '../store/shared.js';
 import { maskRegions } from './fences.js';
 // links(src, target, target_base, dst, embed): target as written, target_base its indexed baseKey, dst the resolved path or NULL (a queryable dead link).
 // embed distinguishes `![[x]]`/`![](x.md)` from `[[x]]`/`[](x.md)` -- Obsidian's grain: a target both linked and embedded in one note is two rows.
@@ -119,17 +120,6 @@ async function writeResolved(db, rows) {
             r.target
         ]));
 }
-// A new or deleted file can change any note's resolution, so re-resolve the whole table.
-// Fallback for cold builds and large deltas -- see afterReconcile's threshold.
-async function resolveAll(db, files) {
-    const pathSet = new Set(files.map((f)=>f.relPath));
-    const byBase = buildByBase(files);
-    const stmt = await db.prepare('SELECT src, target, dst, embed FROM links');
-    const rows = await stmt.all();
-    const changed = resolveRows(rows, pathSet, byBase);
-    await writeResolved(db, changed);
-    return changed.length > 0;
-}
 // Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit
 // (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.
 async function selectIn(db, column, keys) {
@@ -185,6 +175,26 @@ export async function linkEdges(db) {
 // Records whether remove()/store() deleted any link row, since afterReconcile runs after both
 // and dstChanged alone misses the reparsed-to-zero-links case. Keyed on delta so state dies with it.
 const removedWithLinks = new WeakMap();
+// Cold build only: whether store() resolved at least one row to a non-null dst, so afterReconcile
+// can report linksChanged without re-reading the table it just wrote.
+const coldResolved = new WeakMap();
+// dst stays NULL here on an incremental store (resolution runs afterward); a cold build resolves
+// it inline in store() instead, through the *_RESOLVED column list and SQL below.
+const LINK_COLUMNS = [
+    'src',
+    'target',
+    'target_base',
+    'embed'
+];
+const UPSERT_LINK_SQL = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base';
+const LINK_COLUMNS_RESOLVED = [
+    'src',
+    'target',
+    'target_base',
+    'dst',
+    'embed'
+];
+const UPSERT_LINK_SQL_RESOLVED = 'INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, ?, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base';
 export const links = {
     name: 'links',
     async schema (db) {
@@ -228,20 +238,58 @@ export const links = {
                 ]));
             removedWithLinks.set(delta, true);
         }
-        // Upsert preserves dst on surviving rows; only new rows start at NULL. A same-note anchor
-        // gets no target_base, so SQL's `IN` excludes it from resolveIncremental's lookup.
+        // Cold build: every path is in `added`, so pathSet/byBase cover the same complete tree
+        // afterReconcile's large branch would otherwise re-derive; resolve dst here instead.
+        const cold = delta.files.length === 0 || delta.added.length === delta.files.length;
+        let resolveNew;
+        if (cold) {
+            const pathSet = new Set(delta.files.map((f)=>f.relPath));
+            const byBase = buildByBase(delta.files);
+            resolveNew = (src, target)=>resolveTarget(src, target, pathSet, byBase);
+        }
+        let resolvedLink = false;
+        // Upsert preserves dst on surviving rows; a cold build resolves new rows, else they start NULL.
+        // A same-note anchor gets no target_base, so SQL's `IN` excludes it from resolveIncremental's lookup.
+        // Split, unlike the other features: this hook has no remove() pass behind it (see above), so
+        // only a path in `added` is guaranteed to have no row yet. The rest genuinely conflict and the
+        // upsert is what preserves their `dst`.
+        const appendable = [];
         const upsertRows = [];
         for (const [path, targets] of byPath){
-            for (const { target, embed } of targets)upsertRows.push([
-                path,
-                target,
-                target.startsWith('#') ? null : baseKey(cleanTarget(target)),
-                embed ? 1 : 0
-            ]);
-        }
-        if (upsertRows.length > 0) {
-            await db.runBatch('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base', upsertRows);
+            for (const { target, embed } of targets){
+                const targetBase = target.startsWith('#') ? null : baseKey(cleanTarget(target));
+                if (!addedSet.has(path)) {
+                    upsertRows.push([
+                        path,
+                        target,
+                        targetBase,
+                        embed ? 1 : 0
+                    ]);
+                    continue;
+                }
+                if (!resolveNew) {
+                    appendable.push([
+                        path,
+                        target,
+                        targetBase,
+                        embed ? 1 : 0
+                    ]);
+                    continue;
+                }
+                const dst = resolveNew(path, target);
+                if (dst !== null) resolvedLink = true;
+                appendable.push([
+                    path,
+                    target,
+                    targetBase,
+                    dst,
+                    embed ? 1 : 0
+                ]);
+            }
         }
+        await appendRows(db, 'links', resolveNew ? LINK_COLUMNS_RESOLVED : LINK_COLUMNS, resolveNew ? UPSERT_LINK_SQL_RESOLVED : UPSERT_LINK_SQL, appendable);
+        if (upsertRows.length > 0) await db.runBatch(UPSERT_LINK_SQL, upsertRows);
+        if (cold) coldResolved.set(delta, resolvedLink);
     },
     async afterReconcile (db, delta) {
         var _removedWithLinks_get;
@@ -251,7 +299,13 @@ export const links = {
         // A cold build is the only case a full pass wins. Measured 2026-09-01 on 6,566 notes, resolve
         // time alone: full is flat near 90ms at any churn, incremental 7ms at 10 files and 30ms at 2,000.
         const large = delta.files.length === 0 || delta.added.length === delta.files.length;
-        const dstChanged = large ? await resolveAll(db, delta.files) : await resolveIncremental(db, delta);
+        // store() already resolved dst inline on this cold build (same test), so nothing is left to update.
+        if (large) {
+            var _coldResolved_get;
+            delta.linksChanged = ((_coldResolved_get = coldResolved.get(delta)) !== null && _coldResolved_get !== void 0 ? _coldResolved_get : false) || removeHadLinks;
+            return;
+        }
+        const dstChanged = await resolveIncremental(db, delta);
         delta.linksChanged = dstChanged || removeHadLinks;
     }
 };

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

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

@@ -1,5 +1,6 @@
 import { estimateTokens, parse } from '../chunk/index.js';
 import { countLines } from '../scan/frontmatter.js';
+import { appendRows } from '../store/shared.js';
 // Heading blocks parse() already found (mdast/CommonMark fences), offset back onto the raw file;
 // a section runs to just before the next heading, or EOF.
 function sectionsFromBlocks(blocks, raw, body) {
@@ -22,6 +23,15 @@ function sectionsFromBlocks(blocks, raw, body) {
     }
     return found;
 }
+const SECTION_COLUMNS = [
+    'path',
+    'idx',
+    'level',
+    'heading',
+    'start_line',
+    'end_line',
+    'tokens'
+];
 export const sections = {
     name: 'sections',
     async schema (db) {
@@ -47,10 +57,10 @@ export const sections = {
                 s.endLine,
                 s.tokens
             ]));
-        if (rows.length === 0) return;
         // DO NOTHING, not a bare INSERT: reconcile's added/touched split is decided before this
         // write's lock, so a path called "added" here can already have this row from a concurrent
-        // reconcile that committed first -- same file, same parse, same row.
-        await db.runBatch('INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?) ON CONFLICT("path", idx) DO NOTHING', rows);
+        // reconcile that committed first -- same file, same parse, same row. A store with an append
+        // path has no second writer, and remove() cleared every touched path above, so it skips the guard.
+        await appendRows(db, 'sections', SECTION_COLUMNS, 'INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?) ON CONFLICT("path", idx) DO NOTHING', rows);
     }
 };

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

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

@@ -1,3 +1,4 @@
+import { appendRows } from '../store/shared.js';
 import { maskRegions } from './fences.js';
 // tags(path, tag): Obsidian's file.tags grain -- frontmatter list/string tags plus inline
 // #tags, deduplicated, source not distinguished. Nested tags store full (book/scifi); `tag = 'book' OR tag LIKE 'book/%'` matches the parent too.
@@ -77,7 +78,11 @@ export const tags = {
             path,
             tag
         ]);
-        if (rows.length === 0) return;
-        await db.runBatch('INSERT OR IGNORE INTO tags ("path", tag) VALUES (?, ?)', rows);
+        // OR IGNORE guards the same concurrent-reconcile race sections.ts documents; remove() cleared
+        // every touched path above, so a store with an append path needs no guard.
+        await appendRows(db, 'tags', [
+            'path',
+            'tag'
+        ], 'INSERT OR IGNORE INTO tags ("path", tag) VALUES (?, ?)', rows);
     }
 };

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

@@ -1 +1 @@
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package/dist/esm/store/builder.js

@@ -76,9 +76,8 @@ async function invalidateFeatureTable(conn, cfg, baseDir, dialect, pool, toggle)
             extracted: d.extracted[feature.name]
         }));
     const paths = docs.map((d)=>d.relPath);
-    // Every path counts as added, not just touched: the table was just dropped, so there is nothing
-    // stale to diff against, and links' own afterReconcile takes its cold-build (resolveAll) path
-    // only when added.length equals files.length.
+    // Every path counts as added, not just touched: nothing stale to diff against. Links resolves
+    // dst inside store() itself when added.length equals files.length (a cold build).
     const delta = {
         files,
         reparsed: paths,

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/builder.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { embed } from '../features/embed.ts';\nimport { FEATURES } from '../features/index.ts';\nimport { rank } from '../features/rank.ts';\nimport type { ReconcileDelta } from '../features/types.ts';\nimport { listFiles } from '../scan/index.ts';\nimport { ParsePool } from '../scan/pool.ts';\nimport { reparseFiles } from '../scan/reparse.ts';\nimport type { EmbedChangeKind } from './embed-scope.ts';\nimport type { FeatureToggle } from './feature-scope.ts';\nimport { NARROW_FEATURE_TABLE } from './feature-scope.ts';\nimport { reconcile } from './reconcile.ts';\nimport { getColumns } from './shared.ts';\nimport type { Stages } from './stages.ts';\nimport { withTransaction } from './transaction.ts';\nimport type { Connection, ReconcileDialect } from './types.ts';\n\n// Owns bringing a store's index current: the write half `Store` (types.ts) deliberately does not\n// carry. 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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/store/builder.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { embed } from '../features/embed.ts';\nimport { FEATURES } from '../features/index.ts';\nimport { rank } from '../features/rank.ts';\nimport type { ReconcileDelta } from '../features/types.ts';\nimport { listFiles } from '../scan/index.ts';\nimport { ParsePool } from '../scan/pool.ts';\nimport { reparseFiles } from '../scan/reparse.ts';\nimport type { EmbedChangeKind } from './embed-scope.ts';\nimport type { FeatureToggle } from './feature-scope.ts';\nimport { NARROW_FEATURE_TABLE } from './feature-scope.ts';\nimport { reconcile } from './reconcile.ts';\nimport { getColumns } from './shared.ts';\nimport type { Stages } from './stages.ts';\nimport { withTransaction } from './transaction.ts';\nimport type { Connection, ReconcileDialect } from './types.ts';\n\n// Owns bringing a store's index current: the write half `Store` (types.ts) deliberately does not\n// carry. A one-shot open calls build() once; a watcher calls it repeatedly on the same instance.\nexport interface Builder {\n  // forcedPaths (open.ts's preset-only narrow rebuild) applies to this call alone, not future ones.\n  build(forcedPaths?: ReadonlySet<string>): Promise<{ parsed: number; warnings: string[]; stages: Stages }>;\n  // Narrow embed invalidation (open.ts, embed-scope.ts's classifyEmbedChange): 'model' nulls every\n  // vector/scale in place; 'chunk' rebuilds every embedding row. Neither touches another table.\n  invalidate(kind: EmbedChangeKind): Promise<{ parsed: number }>;\n  // Narrow feature-toggle invalidation (open.ts, feature-scope.ts's classifyFeatureToggles): a\n  // toggle drops (or, turning back on, fully re-derives) that feature's own table; rank instead\n  // nulls or recomputes its `_rank` column, since rows written while a feature was off are\n  // untrustworthy (reconcile.ts's activeFeatures skips a disabled feature's hooks entirely).\n  invalidateFeatures(toggles: FeatureToggle[]): Promise<{ parsed: number }>;\n  // Releases the parse worker pool, if this lifetime ever created one; never the connection.\n  close(): Promise<void>;\n  // Pools this lifetime has constructed, so reuse is observable rather than inferred.\n  readonly poolsCreated: number;\n}\n\n// 'model': the provider or model name moved but chunk boundaries did not, so only the vector\n// values are stale. No reparse, and no table but embeddings is touched.\nasync function nullEmbedVectors(conn: Connection, dialect: ReconcileDialect): Promise<{ parsed: number }> {\n  await withTransaction(conn, () => conn.exec('UPDATE embeddings SET vector = NULL, scale = NULL'), dialect.beginMode());\n  return { parsed: 0 };\n}\n\n// 'chunk': chunkTokens or the chunk version moved, so chunk boundaries genuinely changed. Rebuilds\n// every embedding row through the embed feature's own remove/store, touching no other table.\nasync function rebuildEmbeddings(conn: Connection, cfg: Config, baseDir: string, dialect: ReconcileDialect, pool: ParsePool): Promise<{ parsed: number }> {\n  const existingStmt = await conn.prepare('SELECT \"path\" FROM frontmatter');\n  const existingPaths = new Set((await existingStmt.all()).map((r) => (r as { path: string }).path));\n  // A file added since the last build has no row yet; leaving it for build() to insert avoids a\n  // primary-key collision between this INSERT and build()'s own insert for the same new file.\n  const files = listFiles(cfg, baseDir).filter((f) => f.embed && existingPaths.has(f.relPath));\n  if (files.length === 0) return { parsed: 0 };\n\n  const { docs } = await reparseFiles(files, [embed], cfg, new Set(), undefined, { pool });\n  const paths = docs.map((d) => d.relPath);\n  const delta: ReconcileDelta = { files, reparsed: paths, added: [], vanished: [] };\n  await withTransaction(\n    conn,\n    async () => {\n      await embed.remove?.(conn, paths, delta);\n      await embed.store?.(\n        conn,\n        docs.map((d) => ({ path: d.relPath, extracted: d.extracted.embed })),\n        delta\n      );\n    },\n    dialect.beginMode()\n  );\n  return { parsed: docs.length };\n}\n\n// One feature's own table, dropped and (turning on) fully re-derived across every indexed file.\n// Rows left over from before this feature was disabled are untrustworthy by construction (files\n// added, edited, or deleted got no remove/store for it), so this never diffs against them --\n// dropping every row and reparsing the whole tree is the only safe path back to consistent state.\nasync function invalidateFeatureTable(conn: Connection, cfg: Config, baseDir: string, dialect: ReconcileDialect, pool: ParsePool, toggle: FeatureToggle): Promise<{ parsed: number }> {\n  const table = NARROW_FEATURE_TABLE[toggle.name];\n  const feature = FEATURES.find((f) => f.name === toggle.name);\n  if (!feature) throw new Error(`invalidateFeatureTable: no registered feature named \"${toggle.name}\"`);\n\n  if (!toggle.turnedOn) {\n    await withTransaction(conn, () => conn.exec(`DELETE FROM ${table}`), dialect.beginMode());\n    return { parsed: 0 };\n  }\n\n  const files = listFiles(cfg, baseDir);\n  const { docs } = await reparseFiles(files, [feature], cfg, new Set(), undefined, { pool });\n  const docsForFeature = docs.map((d) => ({ path: d.relPath, extracted: d.extracted[feature.name] }));\n  const paths = docs.map((d) => d.relPath);\n  // Every path counts as added, not just touched: nothing stale to diff against. Links resolves\n  // dst inside store() itself when added.length equals files.length (a cold build).\n  const delta: ReconcileDelta = { files, reparsed: paths, added: paths, vanished: [] };\n  await withTransaction(\n    conn,\n    async () => {\n      await conn.exec(`DELETE FROM ${table}`);\n      await feature.store?.(conn, docsForFeature, delta);\n      await feature.afterReconcile?.(conn, delta);\n    },\n    dialect.beginMode()\n  );\n  return { parsed: docs.length };\n}\n\n// rank has no table of its own: frontmatter._rank is the only state it owns. Guarded on column\n// presence, since links can toggle off while rank has never been enabled for this tree.\nasync function nullRank(conn: Connection, dialect: ReconcileDialect): Promise<void> {\n  const columns = await getColumns(conn);\n  if (!columns.has('_rank')) return;\n  await withTransaction(conn, () => conn.exec('UPDATE frontmatter SET \"_rank\" = NULL'), dialect.beginMode());\n}\n\n// Whole-tree and reparse-free: PageRank is computed from the links table, not from files, so\n// turning rank back on needs no reparseFiles pass at all.\nasync function rerunRank(conn: Connection, dialect: ReconcileDialect): Promise<void> {\n  const delta: ReconcileDelta = { files: [], reparsed: [], added: [], vanished: [] };\n  await withTransaction(\n    conn,\n    async () => {\n      await rank.afterReconcile?.(conn, delta);\n    },\n    dialect.beginMode()\n  );\n}\n\nasync function invalidateFeatureToggles(conn: Connection, cfg: Config, baseDir: string, dialect: ReconcileDialect, pool: ParsePool, toggles: FeatureToggle[]): Promise<{ parsed: number }> {\n  const byName = new Map(toggles.map((toggle) => [toggle.name, toggle]));\n  let parsed = 0;\n\n  // links first, if present: rank's rerun below (whether from its own toggle or the co-change\n  // rankToggle carries) must read the links table after it is back in its new state.\n  const linksToggle = byName.get('links');\n  if (linksToggle) {\n    parsed += (await invalidateFeatureTable(conn, cfg, baseDir, dialect, pool, linksToggle)).parsed;\n    // Unconditional, per rank's dependency on links: nulling is a no-op (guarded) when rank was\n    // never enabled for this tree, so this is safe even when no feature:rank segment changed.\n    if (!linksToggle.turnedOn) await nullRank(conn, dialect);\n  }\n\n  // rank's effective on/off (featureEnabled's links dependency) only appears as a changed\n  // `feature:rank` segment when it actually flips -- whether that's rank's own config or a\n  // links toggle taking it along -- so honoring it here is complete on its own.\n  const rankToggle = byName.get('rank');\n  if (rankToggle) {\n    if (rankToggle.turnedOn) await rerunRank(conn, dialect);\n    else await nullRank(conn, dialect);\n  }\n\n  for (const toggle of toggles) {\n    if (toggle.name === 'links' || toggle.name === 'rank') continue;\n    parsed += (await invalidateFeatureTable(conn, cfg, baseDir, dialect, pool, toggle)).parsed;\n  }\n  return { parsed };\n}\n\n// The pool is created at most once, lazily, on whichever build() or invalidate() call first\n// needs it, and reused by every later call on this instance.\nexport function createBuilder(conn: Connection, cfg: Config, baseDir: string, dialect: ReconcileDialect): Builder {\n  const pool = new ParsePool();\n  return {\n    build: (forcedPaths) => reconcile(conn, cfg, baseDir, dialect, pool, forcedPaths),\n    invalidate: (kind) => (kind === 'model' ? nullEmbedVectors(conn, dialect) : rebuildEmbeddings(conn, cfg, baseDir, dialect, pool)),\n    invalidateFeatures: (toggles) => invalidateFeatureToggles(conn, cfg, baseDir, dialect, pool, toggles),\n    close: () => pool.close(),\n    get poolsCreated() {\n      return pool.poolsCreated;\n    },\n  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