@wrongstack/tools 0.320.1 → 1.0.0

package/dist/{chunk-J43O3BOX.js → chunk-N3K2SFEI.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-YOHO4DVT.js";
 import {
   loadGitignoreMatcher
-} from "./chunk-DTQ75VBC.js";
+} from "./chunk-2CTZW6JQ.js";
 
 // src/codebase-index/circuit-breaker.ts
 var CircuitOpenError = class extends Error {
@@ -463,80 +463,6 @@ function runSqliteWithRetry(fn) {
   throw lastError;
 }
 
-// src/codebase-index/vector-search.ts
-var RRF_K = 60;
-function vectorEmbeddingEnabled() {
-  return process.env["WRONGSTACK_INDEX_VECTORS"] === "1";
-}
-var VECTOR_DIMENSIONS = 384;
-var NGRAM_SIZE = 3;
-function embedText(text) {
-  const vec = new Float32Array(VECTOR_DIMENSIONS);
-  const normalized = text.toLowerCase().trim();
-  if (normalized.length === 0) return vec;
-  const target = normalized.length < NGRAM_SIZE ? ` ${normalized} `.slice(0, Math.max(NGRAM_SIZE, normalized.length + 2)) : normalized;
-  for (let i = 0; i <= target.length - NGRAM_SIZE; i++) {
-    const ngram = target.slice(i, i + NGRAM_SIZE);
-    const bucket = hashNgram(ngram) % VECTOR_DIMENSIONS;
-    vec[bucket] += 1;
-  }
-  let norm = 0;
-  for (let i = 0; i < VECTOR_DIMENSIONS; i++) {
-    norm += vec[i] * vec[i];
-  }
-  norm = Math.sqrt(norm);
-  if (norm > 0) {
-    for (let i = 0; i < VECTOR_DIMENSIONS; i++) {
-      vec[i] /= norm;
-    }
-  }
-  return vec;
-}
-function hashNgram(str) {
-  let hash = 2166136261;
-  for (let i = 0; i < str.length; i++) {
-    hash ^= str.charCodeAt(i);
-    hash = Math.imul(hash, 16777619);
-  }
-  return hash >>> 0;
-}
-function cosineSimilarity(a, b) {
-  let dot = 0;
-  const len = Math.min(a.length, b.length);
-  for (let i = 0; i < len; i++) {
-    dot += a[i] * b[i];
-  }
-  return dot;
-}
-function encodeVector(vec) {
-  return Buffer.from(vec.buffer, vec.byteOffset, vec.byteLength);
-}
-function decodeVector(buf) {
-  if (buf.byteLength === 0) return new Float32Array(0);
-  if (buf.byteLength % 4 !== 0) {
-    throw new Error(
-      `decodeVector: invalid vector byteLength ${buf.byteLength} (must be a multiple of 4)`
-    );
-  }
-  const copy = new Float32Array(buf.byteLength / 4);
-  new Uint8Array(copy.buffer).set(buf);
-  return copy;
-}
-function reciprocalRankFusion(bm25Ranks, vectorRanks, k = RRF_K) {
-  const allIds = /* @__PURE__ */ new Set([...bm25Ranks.keys(), ...vectorRanks.keys()]);
-  const scored = [];
-  for (const id of allIds) {
-    const bm25Rank = bm25Ranks.get(id);
-    const vecRank = vectorRanks.get(id);
-    let score = 0;
-    if (bm25Rank !== void 0) score += 1 / (k + bm25Rank);
-    if (vecRank !== void 0) score += 1 / (k + vecRank);
-    scored.push([id, score]);
-  }
-  scored.sort((a, b) => b[1] - a[1]);
-  return scored;
-}
-
 // src/codebase-index/writer-admin.ts
 import * as fs from "node:fs";
 import * as path from "node:path";
@@ -1698,129 +1624,78 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
   return { nodes, edges };
 }
 
-// src/codebase-index/writer-mutations.ts
-function commitBatchWithStatement(stmtFn, maxSqlVars, ftsAvailable, vectorsAvailable, allocateSymbolIds, invalidateIncomingRefsForFiles, resolveRefsForNamesUnsafe2, entries, options = {}) {
-  if (entries.length === 0 && (options.deleteForFiles?.length ?? 0) === 0) {
-    return [];
+// src/codebase-index/vector-search.ts
+var RRF_K = 60;
+function vectorEmbeddingEnabled() {
+  return process.env["WRONGSTACK_INDEX_VECTORS"] === "1";
+}
+var VECTOR_DIMENSIONS = 384;
+var NGRAM_SIZE = 3;
+function embedText(text) {
+  const vec = new Float32Array(VECTOR_DIMENSIONS);
+  const normalized = text.toLowerCase().trim();
+  if (normalized.length === 0) return vec;
+  const target = normalized.length < NGRAM_SIZE ? ` ${normalized} `.slice(0, Math.max(NGRAM_SIZE, normalized.length + 2)) : normalized;
+  for (let i = 0; i <= target.length - NGRAM_SIZE; i++) {
+    const ngram = target.slice(i, i + NGRAM_SIZE);
+    const bucket = hashNgram(ngram) % VECTOR_DIMENSIONS;
+    vec[bucket] += 1;
   }
-  const affectedNames = /* @__PURE__ */ new Set();
-  for (const entry of entries) {
-    for (const symbol of entry.symbols) affectedNames.add(symbol.name);
-    for (const ref of entry.refs) affectedNames.add(ref.toName);
+  let norm = 0;
+  for (let i = 0; i < VECTOR_DIMENSIONS; i++) {
+    norm += vec[i] * vec[i];
   }
-  if (options.deleteForFiles && options.deleteForFiles.length > 0) {
-    for (const name of invalidateIncomingRefsForFiles(options.deleteForFiles)) {
-      affectedNames.add(name);
-    }
-    let cursor = 0;
-    for (const take of inListChunks(options.deleteForFiles.length, Math.floor(maxSqlVars / 4))) {
-      const bucket = padToInBucket(options.deleteForFiles.slice(cursor, cursor + take));
-      cursor += take;
-      const ph = placeholders(bucket.length);
-      if (ftsAvailable) {
-        stmtFn(
-          `DELETE FROM symbols_fts WHERE rowid IN (SELECT id FROM symbols WHERE file IN (${ph}))`
-        ).run(...bucket);
-      }
-      if (vectorsAvailable) {
-        stmtFn(
-          `DELETE FROM symbol_vectors WHERE symbol_id IN (SELECT id FROM symbols WHERE file IN (${ph}))`
-        ).run(...bucket);
-      }
-      stmtFn(
-        `DELETE FROM refs WHERE from_id IN (SELECT id FROM symbols WHERE file IN (${ph}))`
-      ).run(...bucket);
-      stmtFn(`DELETE FROM symbols WHERE file IN (${ph})`).run(...bucket);
+  norm = Math.sqrt(norm);
+  if (norm > 0) {
+    for (let i = 0; i < VECTOR_DIMENSIONS; i++) {
+      vec[i] /= norm;
     }
   }
-  const totalSymbols = entries.reduce((n, e) => n + e.symbols.length, 0);
-  let nextId = allocateSymbolIds(totalSymbols);
-  const allInserted = [];
-  const refsToInsert = [];
-  const bulkSyms = [];
-  const ftsRows = [];
-  const vectorRows = [];
-  for (const entry of entries) {
-    const insertedForEntry = [];
-    for (const s of entry.symbols) {
-      const id = nextId++;
-      bulkSyms.push({
-        id,
-        lang: s.lang,
-        kind: s.kind,
-        name: s.name,
-        file: s.file,
-        line: s.line,
-        col: s.col,
-        signature: s.signature,
-        docComment: s.docComment,
-        scope: s.scope
-      });
-      if (ftsAvailable) {
-        ftsRows.push({
-          id,
-          text: buildIndexableText(s.name, s.signature, s.docComment)
-        });
-      }
-      if (vectorsAvailable) {
-        vectorRows.push({
-          id,
-          vector: encodeVector(embedText(buildIndexableText(s.name, s.signature, s.docComment)))
-        });
-      }
-      const inserted = { ...s, id };
-      allInserted.push(inserted);
-      insertedForEntry.push(inserted);
-    }
-    refsToInsert.push(...assignRefsToSymbols(entry.refs, insertedForEntry));
+  return vec;
+}
+function hashNgram(str) {
+  let hash = 2166136261;
+  for (let i = 0; i < str.length; i++) {
+    hash ^= str.charCodeAt(i);
+    hash = Math.imul(hash, 16777619);
   }
-  bulkInsertSymbolsWithStatement((sql) => stmtFn(sql), maxSqlVars, bulkSyms);
-  bulkInsertFtsWithStatement((sql) => stmtFn(sql), maxSqlVars, ftsAvailable, ftsRows);
-  if (vectorsAvailable) {
-    bulkInsertVectorsWithStatement((sql) => stmtFn(sql), maxSqlVars, vectorRows);
+  return hash >>> 0;
+}
+function cosineSimilarity(a, b) {
+  let dot = 0;
+  const len = Math.min(a.length, b.length);
+  for (let i = 0; i < len; i++) {
+    dot += a[i] * b[i];
   }
-  bulkInsertRefsWithStatement((sql) => stmtFn(sql), maxSqlVars, refsToInsert);
-  const upsertStmt = stmtFn(
-    `INSERT INTO files(file, lang, mtime_ms, content_hash, symbol_count, last_indexed)
-     VALUES (?, ?, ?, ?, ?, ?)
-     ON CONFLICT(file) DO UPDATE SET
-       lang = excluded.lang,
-       mtime_ms = excluded.mtime_ms,
-       content_hash = excluded.content_hash,
-       symbol_count = excluded.symbol_count,
-       last_indexed = excluded.last_indexed`
-  );
-  const now = Date.now();
-  for (const entry of entries) {
-    upsertStmt.run(
-      entry.file,
-      entry.lang,
-      entry.mtimeMs,
-      entry.contentHash ?? "",
-      entry.symbolCount,
-      now
+  return dot;
+}
+function encodeVector(vec) {
+  return Buffer.from(vec.buffer, vec.byteOffset, vec.byteLength);
+}
+function decodeVector(buf) {
+  if (buf.byteLength === 0) return new Float32Array(0);
+  if (buf.byteLength % 4 !== 0) {
+    throw new Error(
+      `decodeVector: invalid vector byteLength ${buf.byteLength} (must be a multiple of 4)`
     );
   }
-  resolveRefsForNamesUnsafe2(affectedNames);
-  return allInserted;
+  const copy = new Float32Array(buf.byteLength / 4);
+  new Uint8Array(copy.buffer).set(buf);
+  return copy;
 }
-
-// src/codebase-index/writer-pragmas.ts
-import { sqliteCachePragmas } from "@wrongstack/core/utils";
-function applyIndexStorePragmas(db) {
-  try {
-    db.exec("PRAGMA journal_mode = WAL");
-    db.exec("PRAGMA synchronous = NORMAL");
-    db.exec("PRAGMA busy_timeout = 15000");
-    db.exec("PRAGMA temp_store = MEMORY");
-    const cache = sqliteCachePragmas();
-    db.exec(`PRAGMA cache_size = -${cache.cacheSizeKiB}`);
-    db.exec(`PRAGMA mmap_size = ${cache.mmapBytes}`);
-    db.exec("PRAGMA foreign_keys = ON");
-    db.exec("PRAGMA journal_size_limit = 67108864");
-    db.exec("PRAGMA wal_autocheckpoint = 1000");
-  } catch {
+function reciprocalRankFusion(bm25Ranks, vectorRanks, k = RRF_K) {
+  const allIds = /* @__PURE__ */ new Set([...bm25Ranks.keys(), ...vectorRanks.keys()]);
+  const scored = [];
+  for (const id of allIds) {
+    const bm25Rank = bm25Ranks.get(id);
+    const vecRank = vectorRanks.get(id);
+    let score = 0;
+    if (bm25Rank !== void 0) score += 1 / (k + bm25Rank);
+    if (vecRank !== void 0) score += 1 / (k + vecRank);
+    scored.push([id, score]);
   }
+  scored.sort((a, b) => b[1] - a[1]);
+  return scored;
 }
 
 // src/codebase-index/writer-schema.ts
@@ -1914,15 +1789,431 @@ var SYMBOL_VECTORS_TABLE_SQL = `
   );
 `;
 
-// src/codebase-index/writer-refs.ts
-var FAMILY_MATCH_SQL = `(
-  sym.lang = refs.lang
-  OR refs.lang = ''
-  OR EXISTS (
-    SELECT 1 FROM lang_family lf1
-      JOIN lang_family lf2 ON lf1.family = lf2.family
-     WHERE lf1.lang = sym.lang AND lf2.lang = refs.lang
-  )
+// src/codebase-index/writer-init.ts
+var SYMBOLS_TEXT_DROPPED_KEY = "symbols_text_dropped";
+var NEXT_SYMBOL_ID_KEY = "next_symbol_id";
+function seedLangFamilies(stmt) {
+  const insert = stmt("INSERT OR REPLACE INTO lang_family(lang, family) VALUES (?, ?)");
+  for (const [lang, family] of LANG_FAMILY_ENTRIES) insert.run(lang, family);
+  insert.run("", LANG_FAMILY_WILDCARD);
+}
+function repairMissingColumns(db) {
+  const expected = [
+    {
+      table: "files",
+      columns: [
+        ["package", "TEXT NOT NULL DEFAULT ''"],
+        ["content_hash", "TEXT NOT NULL DEFAULT ''"]
+      ]
+    },
+    {
+      table: "refs",
+      columns: [
+        ["lang", "TEXT NOT NULL DEFAULT ''"],
+        ["module", "TEXT"],
+        ["to_file", "TEXT"]
+      ]
+    }
+  ];
+  for (const { table, columns } of expected) {
+    const rows = db.prepare(`PRAGMA table_info(${table})`).all();
+    const present = /* @__PURE__ */ new Set();
+    for (const row of rows) {
+      if (typeof row.name === "string") present.add(row.name);
+    }
+    if (present.size === 0) continue;
+    for (const [name, type] of columns) {
+      if (present.has(name)) continue;
+      db.exec(`ALTER TABLE ${table} ADD COLUMN ${name} ${type}`);
+    }
+  }
+}
+function dropDeprecatedSymbolsColumns(db, getMetadata, setMetadata) {
+  if (getMetadata(SYMBOLS_TEXT_DROPPED_KEY) !== void 0) return;
+  const present = new Set(
+    db.prepare("PRAGMA table_info(symbols)").all().flatMap(
+      (row) => typeof row.name === "string" ? [row.name] : []
+    )
+  );
+  if (present.size === 0) return;
+  if (!present.has("text")) {
+    setMetadata(SYMBOLS_TEXT_DROPPED_KEY, "1");
+    return;
+  }
+  try {
+    db.exec("ALTER TABLE symbols DROP COLUMN text");
+    setMetadata(SYMBOLS_TEXT_DROPPED_KEY, "1");
+  } catch {
+  }
+}
+function initIndexSchema(db, stmt, getMetadata, setMetadata, maxSqlVars, invalidateBm25) {
+  db.exec(METADATA_TABLE_SQL);
+  const storedRows = stmt("SELECT value FROM metadata WHERE key = ?").all("version");
+  const storedVersion = storedRows.length ? Number(storedRows[0]?.value) : null;
+  if (storedVersion !== null && storedVersion !== SCHEMA_VERSION) {
+    db.exec(`
+      DROP TABLE IF EXISTS symbols;
+      DROP TABLE IF EXISTS files;
+      DROP TABLE IF EXISTS refs;
+      DROP TABLE IF EXISTS symbol_vectors;
+    `);
+    db.exec("DROP TABLE IF EXISTS symbols_fts");
+    stmt("UPDATE metadata SET value = ? WHERE key = ?").run(String(SCHEMA_VERSION), "version");
+  } else if (storedVersion === null) {
+    stmt("INSERT INTO metadata(key, value) VALUES (?, ?)").run("version", String(SCHEMA_VERSION));
+  }
+  db.exec(CORE_TABLES_SQL);
+  db.exec(REFS_TABLE_SQL);
+  repairMissingColumns(db);
+  dropDeprecatedSymbolsColumns(db, getMetadata, setMetadata);
+  for (const sql of FILE_INDEX_SQL) db.exec(sql);
+  for (const sql of SYMBOL_INDEX_SQL) db.exec(sql);
+  for (const sql of REFS_INDEX_SQL) db.exec(sql);
+  db.exec(LANG_FAMILY_TABLE_SQL);
+  seedLangFamilies(stmt);
+  let ftsAvailable = false;
+  try {
+    const ftsSchema = stmt(
+      "SELECT sql FROM sqlite_master WHERE type='table' AND name='symbols_fts'"
+    ).get();
+    if (ftsSchema?.sql?.includes("unicode61")) {
+      db.exec("DROP TABLE IF EXISTS symbols_fts");
+    }
+    db.exec(SYMBOLS_FTS_SQL);
+    ftsAvailable = true;
+    const symbolCount = Number(
+      stmt("SELECT COUNT(*) AS n FROM symbols").get()?.n ?? 0
+    );
+    const ftsCount = Number(
+      stmt("SELECT COUNT(*) AS n FROM symbols_fts").get()?.n ?? 0
+    );
+    if (symbolCount !== ftsCount) {
+      db.exec("DELETE FROM symbols_fts");
+      if (vectorEmbeddingEnabled() && stmt("SELECT 1 FROM sqlite_master WHERE type='table' AND name='symbol_vectors'").get() !== void 0) {
+        db.exec("DELETE FROM symbol_vectors");
+      }
+      const rows = stmt(
+        "SELECT id, name, signature, doc_comment FROM symbols ORDER BY id"
+      ).all();
+      bulkInsertFtsWithStatement(
+        stmt,
+        maxSqlVars,
+        ftsAvailable,
+        rows.map((row) => ({
+          id: row.id,
+          text: buildIndexableText(row.name, row.signature, row.doc_comment)
+        }))
+      );
+      invalidateBm25();
+    }
+  } catch {
+    ftsAvailable = false;
+  }
+  let vectorsAvailable = false;
+  try {
+    if (vectorEmbeddingEnabled()) {
+      db.exec(SYMBOL_VECTORS_TABLE_SQL);
+      vectorsAvailable = true;
+    } else {
+      db.exec("DROP TABLE IF EXISTS symbol_vectors");
+      vectorsAvailable = false;
+    }
+  } catch {
+    vectorsAvailable = false;
+  }
+  ensureNextSymbolIdSeeded(stmt);
+  return { ftsAvailable, vectorsAvailable };
+}
+function ensureNextSymbolIdSeeded(stmt) {
+  const existing = stmt("SELECT value FROM metadata WHERE key = ?").get(NEXT_SYMBOL_ID_KEY);
+  if (existing?.value !== void 0) return;
+  const maxRows = stmt("SELECT MAX(id) AS m FROM symbols").all();
+  const next = (maxRows[0]?.m ?? 0) + 1;
+  stmt("INSERT OR REPLACE INTO metadata(key, value) VALUES (?, ?)").run(
+    NEXT_SYMBOL_ID_KEY,
+    String(next)
+  );
+}
+function allocateSymbolIds(stmt, count, getMaxSymbolId) {
+  if (count <= 0) return getMaxSymbolId() + 1;
+  ensureNextSymbolIdSeeded(stmt);
+  const row = stmt("SELECT value FROM metadata WHERE key = ?").get(NEXT_SYMBOL_ID_KEY);
+  const start = Math.max(1, Number(row?.value ?? 1) || 1);
+  stmt("INSERT OR REPLACE INTO metadata(key, value) VALUES (?, ?)").run(
+    NEXT_SYMBOL_ID_KEY,
+    String(start + count)
+  );
+  return start;
+}
+
+// src/codebase-index/writer-maintenance.ts
+var FTS_CHURN_KEY = "fts_churn_since_maintain";
+function optimizeStore(db) {
+  try {
+    db.exec("PRAGMA optimize");
+  } catch {
+  }
+}
+function recordFtsChurn(ftsAvailable, getMetadata, setMetadata, rows) {
+  if (rows <= 0 || !ftsAvailable) return;
+  try {
+    const current = Number(getMetadata(FTS_CHURN_KEY) ?? "0") || 0;
+    setMetadata(FTS_CHURN_KEY, String(current + rows));
+  } catch {
+  }
+}
+function optimizeFtsIfNeeded(stmt, ftsAvailable, getMetadata, setMetadata, runWithRetry, options = {}) {
+  if (!ftsAvailable) return false;
+  try {
+    const minChurnRatio = options.minChurnRatio ?? 0.1;
+    const minChurnRows = options.minChurnRows ?? 5e3;
+    const churn = Number(getMetadata(FTS_CHURN_KEY) ?? "0") || 0;
+    const liveRows = Number(
+      stmt("SELECT COUNT(*) AS n FROM symbols").get()?.n ?? 0
+    );
+    if (churn < Math.max(minChurnRows, liveRows * minChurnRatio)) return false;
+    runWithRetry(() => {
+      stmt(`INSERT INTO symbols_fts(symbols_fts) VALUES('optimize')`).run();
+    });
+    setMetadata(FTS_CHURN_KEY, "0");
+    return true;
+  } catch {
+    return false;
+  }
+}
+function checkpointWal(db) {
+  try {
+    const probe = db.prepare("PRAGMA wal_checkpoint(PASSIVE)").get();
+    if (Number(probe?.busy ?? 1) !== 0) return false;
+    const done = db.prepare("PRAGMA wal_checkpoint(TRUNCATE)").get();
+    return Number(done?.busy ?? 1) === 0;
+  } catch {
+    return false;
+  }
+}
+function compactIfNeeded(db, stmt, runWithRetry, options = {}) {
+  const minBytes = options.minBytes ?? 256 * 1024 * 1024;
+  const minFreeRatio = options.minFreeRatio ?? 0.35;
+  try {
+    const pageCount = Number(
+      stmt("PRAGMA page_count").get()?.page_count ?? 0
+    );
+    const pageSize = Number(
+      stmt("PRAGMA page_size").get()?.page_size ?? 0
+    );
+    const freePages = Number(
+      stmt("PRAGMA freelist_count").get()?.freelist_count ?? 0
+    );
+    if (pageCount <= 0 || pageSize <= 0 || pageCount * pageSize < minBytes || freePages / pageCount < minFreeRatio) {
+      return false;
+    }
+    runWithRetry(() => {
+      db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
+      db.exec("VACUUM");
+      db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
+    });
+    return true;
+  } catch {
+    return false;
+  }
+}
+
+// src/codebase-index/writer-mutations.ts
+function commitBatchWithStatement(stmtFn, maxSqlVars, ftsAvailable, vectorsAvailable, allocateSymbolIds2, invalidateIncomingRefsForFiles, resolveRefsForNamesUnsafe2, entries, options = {}) {
+  if (entries.length === 0 && (options.deleteForFiles?.length ?? 0) === 0) {
+    return [];
+  }
+  const affectedNames = /* @__PURE__ */ new Set();
+  for (const entry of entries) {
+    for (const symbol of entry.symbols) affectedNames.add(symbol.name);
+    for (const ref of entry.refs) affectedNames.add(ref.toName);
+  }
+  if (options.deleteForFiles && options.deleteForFiles.length > 0) {
+    for (const name of invalidateIncomingRefsForFiles(options.deleteForFiles)) {
+      affectedNames.add(name);
+    }
+    let cursor = 0;
+    for (const take of inListChunks(options.deleteForFiles.length, Math.floor(maxSqlVars / 4))) {
+      const bucket = padToInBucket(options.deleteForFiles.slice(cursor, cursor + take));
+      cursor += take;
+      const ph = placeholders(bucket.length);
+      if (ftsAvailable) {
+        stmtFn(
+          `DELETE FROM symbols_fts WHERE rowid IN (SELECT id FROM symbols WHERE file IN (${ph}))`
+        ).run(...bucket);
+      }
+      if (vectorsAvailable) {
+        stmtFn(
+          `DELETE FROM symbol_vectors WHERE symbol_id IN (SELECT id FROM symbols WHERE file IN (${ph}))`
+        ).run(...bucket);
+      }
+      stmtFn(
+        `DELETE FROM refs WHERE from_id IN (SELECT id FROM symbols WHERE file IN (${ph}))`
+      ).run(...bucket);
+      stmtFn(`DELETE FROM symbols WHERE file IN (${ph})`).run(...bucket);
+    }
+  }
+  const totalSymbols = entries.reduce((n, e) => n + e.symbols.length, 0);
+  let nextId = allocateSymbolIds2(totalSymbols);
+  const allInserted = [];
+  const refsToInsert = [];
+  const bulkSyms = [];
+  const ftsRows = [];
+  const vectorRows = [];
+  for (const entry of entries) {
+    const insertedForEntry = [];
+    for (const s of entry.symbols) {
+      const id = nextId++;
+      bulkSyms.push({
+        id,
+        lang: s.lang,
+        kind: s.kind,
+        name: s.name,
+        file: s.file,
+        line: s.line,
+        col: s.col,
+        signature: s.signature,
+        docComment: s.docComment,
+        scope: s.scope
+      });
+      if (ftsAvailable) {
+        ftsRows.push({
+          id,
+          text: buildIndexableText(s.name, s.signature, s.docComment)
+        });
+      }
+      if (vectorsAvailable) {
+        vectorRows.push({
+          id,
+          vector: encodeVector(embedText(buildIndexableText(s.name, s.signature, s.docComment)))
+        });
+      }
+      const inserted = { ...s, id };
+      allInserted.push(inserted);
+      insertedForEntry.push(inserted);
+    }
+    refsToInsert.push(...assignRefsToSymbols(entry.refs, insertedForEntry));
+  }
+  bulkInsertSymbolsWithStatement((sql) => stmtFn(sql), maxSqlVars, bulkSyms);
+  bulkInsertFtsWithStatement((sql) => stmtFn(sql), maxSqlVars, ftsAvailable, ftsRows);
+  if (vectorsAvailable) {
+    bulkInsertVectorsWithStatement((sql) => stmtFn(sql), maxSqlVars, vectorRows);
+  }
+  bulkInsertRefsWithStatement((sql) => stmtFn(sql), maxSqlVars, refsToInsert);
+  const upsertStmt = stmtFn(
+    `INSERT INTO files(file, lang, mtime_ms, content_hash, symbol_count, last_indexed)
+     VALUES (?, ?, ?, ?, ?, ?)
+     ON CONFLICT(file) DO UPDATE SET
+       lang = excluded.lang,
+       mtime_ms = excluded.mtime_ms,
+       content_hash = excluded.content_hash,
+       symbol_count = excluded.symbol_count,
+       last_indexed = excluded.last_indexed`
+  );
+  const now = Date.now();
+  for (const entry of entries) {
+    upsertStmt.run(
+      entry.file,
+      entry.lang,
+      entry.mtimeMs,
+      entry.contentHash ?? "",
+      entry.symbolCount,
+      now
+    );
+  }
+  resolveRefsForNamesUnsafe2(affectedNames);
+  return allInserted;
+}
+function insertSymbolsWithStatement(stmtFn, maxSqlVars, ftsAvailable, vectorsAvailable, allocateSymbolIds2, symbols) {
+  let nextId = allocateSymbolIds2(symbols.length);
+  const result = [];
+  const bulk = [];
+  const ftsRows = [];
+  const vectorRows = [];
+  for (const s of symbols) {
+    const id = nextId++;
+    bulk.push({
+      id,
+      lang: s.lang,
+      kind: s.kind,
+      name: s.name,
+      file: s.file,
+      line: s.line,
+      col: s.col,
+      signature: s.signature,
+      docComment: s.docComment,
+      scope: s.scope
+    });
+    if (ftsAvailable) {
+      ftsRows.push({ id, text: buildIndexableText(s.name, s.signature, s.docComment) });
+    }
+    if (vectorsAvailable) {
+      vectorRows.push({
+        id,
+        vector: encodeVector(embedText(buildIndexableText(s.name, s.signature, s.docComment)))
+      });
+    }
+    result.push({ ...s, id });
+  }
+  bulkInsertSymbolsWithStatement((sql) => stmtFn(sql), maxSqlVars, bulk);
+  bulkInsertFtsWithStatement((sql) => stmtFn(sql), maxSqlVars, ftsAvailable, ftsRows);
+  if (vectorsAvailable) {
+    bulkInsertVectorsWithStatement((sql) => stmtFn(sql), maxSqlVars, vectorRows);
+  }
+  return result;
+}
+function upsertFileWithStatement(stmtFn, meta) {
+  stmtFn(
+    `INSERT INTO files(file, lang, mtime_ms, content_hash, symbol_count, last_indexed)
+     VALUES (?, ?, ?, ?, ?, ?)
+     ON CONFLICT(file) DO UPDATE SET
+       lang = excluded.lang,
+       mtime_ms = excluded.mtime_ms,
+       content_hash = excluded.content_hash,
+       symbol_count = excluded.symbol_count,
+       last_indexed = excluded.last_indexed`
+  ).run(
+    meta.file,
+    meta.lang,
+    meta.mtimeMs,
+    meta.contentHash ?? "",
+    meta.symbolCount,
+    meta.lastIndexed
+  );
+}
+function setFilePackagesWithStatement(stmtFn, entries) {
+  if (entries.size === 0) return;
+  const update = stmtFn("UPDATE files SET package = ? WHERE file = ?");
+  for (const [file, label] of entries) update.run(label, file);
+}
+
+// src/codebase-index/writer-pragmas.ts
+import { sqliteCachePragmas } from "@wrongstack/core/utils";
+function applyIndexStorePragmas(db) {
+  try {
+    db.exec("PRAGMA journal_mode = WAL");
+    db.exec("PRAGMA synchronous = NORMAL");
+    db.exec("PRAGMA busy_timeout = 15000");
+    db.exec("PRAGMA temp_store = MEMORY");
+    const cache = sqliteCachePragmas();
+    db.exec(`PRAGMA cache_size = -${cache.cacheSizeKiB}`);
+    db.exec(`PRAGMA mmap_size = ${cache.mmapBytes}`);
+    db.exec("PRAGMA foreign_keys = ON");
+    db.exec("PRAGMA journal_size_limit = 67108864");
+    db.exec("PRAGMA wal_autocheckpoint = 1000");
+  } catch {
+  }
+}
+
+// src/codebase-index/writer-refs.ts
+var FAMILY_MATCH_SQL = `(
+  sym.lang = refs.lang
+  OR refs.lang = ''
+  OR EXISTS (
+    SELECT 1 FROM lang_family lf1
+      JOIN lang_family lf2 ON lf1.family = lf2.family
+     WHERE lf1.lang = sym.lang AND lf2.lang = refs.lang
+  )
   OR ? IN (
     SELECT family FROM lang_family WHERE lang = refs.lang
   )
@@ -2517,180 +2808,26 @@ var IndexStore = class _IndexStore {
       this.db.exec("ROLLBACK");
     }
   }
-  seedLangFamilies() {
-    const insert = this.stmt("INSERT OR REPLACE INTO lang_family(lang, family) VALUES (?, ?)");
-    for (const [lang, family] of LANG_FAMILY_ENTRIES) insert.run(lang, family);
-    insert.run("", LANG_FAMILY_WILDCARD);
-  }
-  repairMissingColumns() {
-    const expected = [
-      {
-        table: "files",
-        columns: [
-          ["package", "TEXT NOT NULL DEFAULT ''"],
-          ["content_hash", "TEXT NOT NULL DEFAULT ''"]
-        ]
-      },
-      {
-        table: "refs",
-        columns: [
-          ["lang", "TEXT NOT NULL DEFAULT ''"],
-          ["module", "TEXT"],
-          ["to_file", "TEXT"]
-        ]
-      }
-    ];
-    for (const { table, columns } of expected) {
-      const rows = this.db.prepare(`PRAGMA table_info(${table})`).all();
-      const present = /* @__PURE__ */ new Set();
-      for (const row of rows) {
-        if (typeof row.name === "string") present.add(row.name);
-      }
-      if (present.size === 0) continue;
-      for (const [name, type] of columns) {
-        if (present.has(name)) continue;
-        this.db.exec(`ALTER TABLE ${table} ADD COLUMN ${name} ${type}`);
-      }
-    }
-  }
-  /**
-   * P4: `symbols.text` duplicated name + signature + doc_comment (~19 MB on
-   * the live index) and is derived on demand now. In-place DROP COLUMN — no
-   * SCHEMA_VERSION bump, so no wipe-and-reparse. Best-effort: a busy or
-   * SQLite-without-DROP-COLUMN open leaves the column in place, where new
-   * inserts simply default it to '' and the next open retries.
-   */
-  dropDeprecatedSymbolsColumns() {
-    if (this.getMetadata(_IndexStore.SYMBOLS_TEXT_DROPPED_KEY) !== void 0) return;
-    const present = new Set(
-      this.db.prepare("PRAGMA table_info(symbols)").all().flatMap(
-        (row) => typeof row.name === "string" ? [row.name] : []
-      )
-    );
-    if (present.size === 0) return;
-    if (!present.has("text")) {
-      this.setMetadata(_IndexStore.SYMBOLS_TEXT_DROPPED_KEY, "1");
-      return;
-    }
-    try {
-      this.db.exec("ALTER TABLE symbols DROP COLUMN text");
-      this.setMetadata(_IndexStore.SYMBOLS_TEXT_DROPPED_KEY, "1");
-    } catch {
-    }
-  }
   initSchema() {
-    this.db.exec(METADATA_TABLE_SQL);
-    const storedRows = this.stmt("SELECT value FROM metadata WHERE key = ?").all("version");
-    const storedVersion = storedRows.length ? Number(storedRows[0]?.value) : null;
-    if (storedVersion !== null && storedVersion !== SCHEMA_VERSION) {
-      this.db.exec(`
-        DROP TABLE IF EXISTS symbols;
-        DROP TABLE IF EXISTS files;
-        DROP TABLE IF EXISTS refs;
-        DROP TABLE IF EXISTS symbol_vectors;
-      `);
-      this.db.exec("DROP TABLE IF EXISTS symbols_fts");
-      this.stmt("UPDATE metadata SET value = ? WHERE key = ?").run(
-        String(SCHEMA_VERSION),
-        "version"
-      );
-    } else if (storedVersion === null) {
-      this.stmt("INSERT INTO metadata(key, value) VALUES (?, ?)").run(
-        "version",
-        String(SCHEMA_VERSION)
-      );
-    }
-    this.db.exec(CORE_TABLES_SQL);
-    this.db.exec(REFS_TABLE_SQL);
-    this.repairMissingColumns();
-    this.dropDeprecatedSymbolsColumns();
-    for (const sql of FILE_INDEX_SQL) this.db.exec(sql);
-    for (const sql of SYMBOL_INDEX_SQL) this.db.exec(sql);
-    for (const sql of REFS_INDEX_SQL) this.db.exec(sql);
-    this.db.exec(LANG_FAMILY_TABLE_SQL);
-    this.seedLangFamilies();
-    try {
-      const ftsSchema = this.stmt(
-        "SELECT sql FROM sqlite_master WHERE type='table' AND name='symbols_fts'"
-      ).get();
-      if (ftsSchema?.sql?.includes("unicode61")) {
-        this.db.exec("DROP TABLE IF EXISTS symbols_fts");
-      }
-      this.db.exec(SYMBOLS_FTS_SQL);
-      this.ftsAvailable = true;
-      const symbolCount = Number(
-        this.stmt("SELECT COUNT(*) AS n FROM symbols").get()?.n ?? 0
-      );
-      const ftsCount = Number(
-        this.stmt("SELECT COUNT(*) AS n FROM symbols_fts").get()?.n ?? 0
-      );
-      if (symbolCount !== ftsCount) {
-        this.db.exec("DELETE FROM symbols_fts");
-        if (vectorEmbeddingEnabled() && this.stmt(
-          "SELECT 1 FROM sqlite_master WHERE type='table' AND name='symbol_vectors'"
-        ).get() !== void 0) {
-          this.db.exec("DELETE FROM symbol_vectors");
-        }
-        const rows = this.stmt(
-          "SELECT id, name, signature, doc_comment FROM symbols ORDER BY id"
-        ).all();
-        bulkInsertFtsWithStatement(
-          (sql) => this.stmt(sql),
-          _IndexStore.MAX_SQL_VARS,
-          this.ftsAvailable,
-          rows.map((row) => ({
-            id: row.id,
-            text: buildIndexableText(row.name, row.signature, row.doc_comment)
-          }))
-        );
-        this.invalidateBm25();
-      }
-    } catch {
-      this.ftsAvailable = false;
-    }
-    try {
-      if (vectorEmbeddingEnabled()) {
-        this.db.exec(SYMBOL_VECTORS_TABLE_SQL);
-        this.vectorsAvailable = true;
-      } else {
-        this.db.exec("DROP TABLE IF EXISTS symbol_vectors");
-        this.vectorsAvailable = false;
-      }
-    } catch {
-      this.vectorsAvailable = false;
-    }
-    this.ensureNextSymbolIdSeeded();
-  }
-  static NEXT_SYMBOL_ID_KEY = "next_symbol_id";
-  static MAX_SQL_VARS = 900;
-  /** P2: persisted FTS-mutation churn counter — see {@link optimizeFtsIfNeeded}. */
-  static FTS_CHURN_KEY = "fts_churn_since_maintain";
-  /** P4: one-shot marker that the deprecated symbols.text column is gone. */
-  static SYMBOLS_TEXT_DROPPED_KEY = "symbols_text_dropped";
-  ensureNextSymbolIdSeeded() {
-    const existing = this.stmt("SELECT value FROM metadata WHERE key = ?").get(
-      _IndexStore.NEXT_SYMBOL_ID_KEY
-    );
-    if (existing?.value !== void 0) return;
-    const maxRows = this.stmt("SELECT MAX(id) AS m FROM symbols").all();
-    const next = (maxRows[0]?.m ?? 0) + 1;
-    this.stmt("INSERT OR REPLACE INTO metadata(key, value) VALUES (?, ?)").run(
-      _IndexStore.NEXT_SYMBOL_ID_KEY,
-      String(next)
+    const { ftsAvailable, vectorsAvailable } = initIndexSchema(
+      this.db,
+      (sql) => this.stmt(sql),
+      (key) => this.getMetadata(key),
+      (key, value) => this.setMetadata(key, value),
+      _IndexStore.MAX_SQL_VARS,
+      () => this.invalidateBm25()
     );
+    this.ftsAvailable = ftsAvailable;
+    this.vectorsAvailable = vectorsAvailable;
   }
+  static NEXT_SYMBOL_ID_KEY = NEXT_SYMBOL_ID_KEY;
+  static MAX_SQL_VARS = 900;
   allocateSymbolIds(count) {
-    if (count <= 0) return this.getMaxSymbolId() + 1;
-    this.ensureNextSymbolIdSeeded();
-    const row = this.stmt("SELECT value FROM metadata WHERE key = ?").get(
-      _IndexStore.NEXT_SYMBOL_ID_KEY
-    );
-    const start = Math.max(1, Number(row?.value ?? 1) || 1);
-    this.stmt("INSERT OR REPLACE INTO metadata(key, value) VALUES (?, ?)").run(
-      _IndexStore.NEXT_SYMBOL_ID_KEY,
-      String(start + count)
+    return allocateSymbolIds(
+      (sql) => this.stmt(sql),
+      count,
+      () => this.getMaxSymbolId()
     );
-    return start;
   }
   invalidateIncomingRefsForFiles(files) {
     if (files.length === 0) return /* @__PURE__ */ new Set();
@@ -2720,52 +2857,14 @@ var IndexStore = class _IndexStore {
     return this.runWithRetry(() => {
       const ownsTransaction = this.beginWriteTransaction();
       try {
-        let nextId = this.allocateSymbolIds(symbols.length);
-        const result = [];
-        const bulk = [];
-        const ftsRows = [];
-        const vectorRows = [];
-        for (const s of symbols) {
-          const id = nextId++;
-          bulk.push({
-            id,
-            lang: s.lang,
-            kind: s.kind,
-            name: s.name,
-            file: s.file,
-            line: s.line,
-            col: s.col,
-            signature: s.signature,
-            docComment: s.docComment,
-            scope: s.scope
-          });
-          if (this.ftsAvailable) {
-            ftsRows.push({ id, text: buildIndexableText(s.name, s.signature, s.docComment) });
-          }
-          if (this.vectorsAvailable) {
-            vectorRows.push({
-              id,
-              vector: encodeVector(
-                embedText(buildIndexableText(s.name, s.signature, s.docComment))
-              )
-            });
-          }
-          result.push({ ...s, id });
-        }
-        bulkInsertSymbolsWithStatement((sql) => this.stmt(sql), _IndexStore.MAX_SQL_VARS, bulk);
-        bulkInsertFtsWithStatement(
+        const result = insertSymbolsWithStatement(
           (sql) => this.stmt(sql),
           _IndexStore.MAX_SQL_VARS,
           this.ftsAvailable,
-          ftsRows
+          this.vectorsAvailable,
+          this.allocateSymbolIds.bind(this),
+          symbols
         );
-        if (this.vectorsAvailable) {
-          bulkInsertVectorsWithStatement(
-            (sql) => this.stmt(sql),
-            _IndexStore.MAX_SQL_VARS,
-            vectorRows
-          );
-        }
         this.recordFtsChurn(symbols.length);
         this.commitWriteTransaction(ownsTransaction);
         return result;
@@ -2836,25 +2935,7 @@ var IndexStore = class _IndexStore {
     });
   }
   upsertFile(meta) {
-    this.runWithRetry(() => {
-      this.stmt(
-        `INSERT INTO files(file, lang, mtime_ms, content_hash, symbol_count, last_indexed)
-         VALUES (?, ?, ?, ?, ?, ?)
-         ON CONFLICT(file) DO UPDATE SET
-           lang = excluded.lang,
-           mtime_ms = excluded.mtime_ms,
-           content_hash = excluded.content_hash,
-           symbol_count = excluded.symbol_count,
-           last_indexed = excluded.last_indexed`
-      ).run(
-        meta.file,
-        meta.lang,
-        meta.mtimeMs,
-        meta.contentHash ?? "",
-        meta.symbolCount,
-        meta.lastIndexed
-      );
-    });
+    this.runWithRetry(() => upsertFileWithStatement((sql) => this.stmt(sql), meta));
   }
   getFileMeta(file) {
     return getFileMetaWithStatement((sql) => this.stmt(sql), file);
@@ -2863,11 +2944,7 @@ var IndexStore = class _IndexStore {
     return getAllFileMetasWithStatement((sql) => this.stmt(sql));
   }
   setFilePackages(entries) {
-    if (entries.size === 0) return;
-    this.runWithRetry(() => {
-      const update = this.stmt("UPDATE files SET package = ? WHERE file = ?");
-      for (const [file, label] of entries) update.run(label, file);
-    });
+    this.runWithRetry(() => setFilePackagesWithStatement((sql) => this.stmt(sql), entries));
   }
   getNamespaceDeclarations() {
     return getNamespaceDeclarationsWithStatement((sql) => this.stmt(sql));
@@ -3089,10 +3166,7 @@ var IndexStore = class _IndexStore {
     });
   }
   optimize() {
-    try {
-      this.db.exec("PRAGMA optimize");
-    } catch {
-    }
+    optimizeStore(this.db);
   }
   /**
    * P2: churn-gated FTS5 segment maintenance.
@@ -3110,23 +3184,14 @@ var IndexStore = class _IndexStore {
    * it ran, safe to call from the daemon's single-threaded idle path.
    */
   optimizeFtsIfNeeded(options = {}) {
-    if (!this.ftsAvailable) return false;
-    try {
-      const minChurnRatio = options.minChurnRatio ?? 0.1;
-      const minChurnRows = options.minChurnRows ?? 5e3;
-      const churn = Number(this.getMetadata(_IndexStore.FTS_CHURN_KEY) ?? "0") || 0;
-      const liveRows = Number(
-        this.stmt("SELECT COUNT(*) AS n FROM symbols").get()?.n ?? 0
-      );
-      if (churn < Math.max(minChurnRows, liveRows * minChurnRatio)) return false;
-      this.runWithRetry(() => {
-        this.stmt(`INSERT INTO symbols_fts(symbols_fts) VALUES('optimize')`).run();
-      });
-      this.setMetadata(_IndexStore.FTS_CHURN_KEY, "0");
-      return true;
-    } catch {
-      return false;
-    }
+    return optimizeFtsIfNeeded(
+      (sql) => this.stmt(sql),
+      this.ftsAvailable,
+      (key) => this.getMetadata(key),
+      (key, value) => this.setMetadata(key, value),
+      (fn) => this.runWithRetry(fn),
+      options
+    );
   }
   /**
    * Best-effort churn bookkeeping for {@link optimizeFtsIfNeeded}. Counts the
@@ -3135,12 +3200,12 @@ var IndexStore = class _IndexStore {
    * survives store open/close cycles in the daemon pool.
    */
   recordFtsChurn(rows) {
-    if (rows <= 0 || !this.ftsAvailable) return;
-    try {
-      const current = Number(this.getMetadata(_IndexStore.FTS_CHURN_KEY) ?? "0") || 0;
-      this.setMetadata(_IndexStore.FTS_CHURN_KEY, String(current + rows));
-    } catch {
-    }
+    recordFtsChurn(
+      this.ftsAvailable,
+      (key) => this.getMetadata(key),
+      (key, value) => this.setMetadata(key, value),
+      rows
+    );
   }
   /**
    * P4.14: best-effort WAL checkpoint for idle-time maintenance.
@@ -3154,40 +3219,15 @@ var IndexStore = class _IndexStore {
    * never wait on readers here: busy means "retry at the next idle window".
    */
   checkpointWal() {
-    try {
-      const probe = this.db.prepare("PRAGMA wal_checkpoint(PASSIVE)").get();
-      if (Number(probe?.busy ?? 1) !== 0) return false;
-      const done = this.db.prepare("PRAGMA wal_checkpoint(TRUNCATE)").get();
-      return Number(done?.busy ?? 1) === 0;
-    } catch {
-      return false;
-    }
+    return checkpointWal(this.db);
   }
   compactIfNeeded(options = {}) {
-    const minBytes = options.minBytes ?? 256 * 1024 * 1024;
-    const minFreeRatio = options.minFreeRatio ?? 0.35;
-    try {
-      const pageCount = Number(
-        this.stmt("PRAGMA page_count").get()?.page_count ?? 0
-      );
-      const pageSize = Number(
-        this.stmt("PRAGMA page_size").get()?.page_size ?? 0
-      );
-      const freePages = Number(
-        this.stmt("PRAGMA freelist_count").get()?.freelist_count ?? 0
-      );
-      if (pageCount <= 0 || pageSize <= 0 || pageCount * pageSize < minBytes || freePages / pageCount < minFreeRatio) {
-        return false;
-      }
-      this.runWithRetry(() => {
-        this.db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
-        this.db.exec("VACUUM");
-        this.db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
-      });
-      return true;
-    } catch {
-      return false;
-    }
+    return compactIfNeeded(
+      this.db,
+      (sql) => this.stmt(sql),
+      (fn) => this.runWithRetry(fn),
+      options
+    );
   }
   findIncomingCallsByName(symbolName, file, limit = 100) {
     return findIncomingCallsByName((sql) => this.stmt(sql), symbolName, file, limit);
@@ -4608,4 +4648,4 @@ export {
   incomingCallsService,
   outgoingCallsService
 };
-//# sourceMappingURL=chunk-J43O3BOX.js.map
+//# sourceMappingURL=chunk-N3K2SFEI.js.map