fix: thread configured busyTimeoutMs through remaining read-only query call sites

src/cli/commands/embed.ts

@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { openReadonlyOrFail } from '../../db/index.js';
+import { openReadonlyOrFail, resolveBusyTimeoutMs } from '../../db/index.js';
 import { getEmbeddingMeta } from '../../db/repository/embeddings.js';
 import {
   buildEmbeddings,
@@ -13,7 +13,7 @@ import type { CommandDefinition } from '../types.js';
 
 function resolveStickyModel(dbPath: string | undefined): string | null {
   try {
-    const db = openReadonlyOrFail(dbPath);
+    const db = openReadonlyOrFail(dbPath, resolveBusyTimeoutMs(dbPath));
     try {
       const storedName = getEmbeddingMeta(db, 'model');
       if (!storedName) return null;

src/cli/shared/open-graph.ts

@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../db/index.js';
+import { openReadonlyOrFail, resolveBusyTimeoutMs } from '../../db/index.js';
 import type { BetterSqlite3Database } from '../../types.js';
 
 /**
@@ -8,6 +8,6 @@ export function openGraph(opts: { db?: string } = {}): {
   db: BetterSqlite3Database;
   close: () => void;
 } {
-  const db = openReadonlyOrFail(opts.db);
+  const db = openReadonlyOrFail(opts.db, resolveBusyTimeoutMs(opts.db));
   return { db, close: () => db.close() };
 }

src/db/connection.ts

@@ -6,7 +6,7 @@ import { DEFAULTS, loadConfig } from '../infrastructure/config.js';
 import { debug, warn } from '../infrastructure/logger.js';
 import { getNative, isNativeAvailable } from '../infrastructure/native.js';
 import { DbError, toErrorMessage } from '../shared/errors.js';
-import type { BetterSqlite3Database, NativeDatabase } from '../types.js';
+import type { BetterSqlite3Database, CodegraphConfig, NativeDatabase } from '../types.js';
 import { getDatabase } from './better-sqlite3.js';
 import { Repository } from './repository/base.js';
 import { NativeRepository } from './repository/native-repository.js';
@@ -386,6 +386,18 @@ interface ResolvedDbSettings {
   busyTimeoutMs: number;
 }
 
+/**
+ * Derive the project rootDir from a possibly-custom DB path, for loadConfig().
+ * Using findDbPath (not path.resolve(customDbPath)) ensures directory inputs like
+ * --db /path/to/repo are normalised to .codegraph/graph.db before we strip two levels.
+ * Convention: resolvedDbPath = <rootDir>/.codegraph/graph.db
+ * Shared by resolveDbSettings() and resolveBusyTimeoutMs() so rootDir derivation can't drift.
+ */
+function deriveRootDirFromDbPath(customDbPath: string | undefined): string | undefined {
+  const resolvedDbPath = customDbPath ? findDbPath(customDbPath) : undefined;
+  return resolvedDbPath ? path.dirname(path.dirname(resolvedDbPath)) : undefined;
+}
+
 /**
  * Resolve the effective engine for DB access (explicit opts.engine > config.build.engine >
  * 'auto') alongside config.db.busyTimeoutMs, in a single loadConfig() call.
@@ -400,12 +412,7 @@ function resolveDbSettings(
   customDbPath: string | undefined,
   engineOpt: 'native' | 'wasm' | 'auto' | undefined,
 ): ResolvedDbSettings {
-  // Using findDbPath (not path.resolve(customDbPath)) ensures directory inputs like
-  // --db /path/to/repo are normalised to .codegraph/graph.db before we strip two levels.
-  // Convention: resolvedDbPath = <rootDir>/.codegraph/graph.db
-  const resolvedDbPath = customDbPath ? findDbPath(customDbPath) : undefined;
-  const rootDir = resolvedDbPath ? path.dirname(path.dirname(resolvedDbPath)) : undefined;
-  const config = loadConfig(rootDir);
+  const config = loadConfig(deriveRootDirFromDbPath(customDbPath));
   // config.build.engine is already populated from CODEGRAPH_ENGINE env by applyEnvOverrides,
   // so this covers both the env-var path and the .codegraphrc.json config-file path.
   return {
@@ -414,6 +421,31 @@ function resolveDbSettings(
   };
 }
 
+/**
+ * Resolve the full config for a given DB path, deriving rootDir the same way
+ * resolveDbSettings()/resolveBusyTimeoutMs() do. Exported so callers that need
+ * both the busy-timeout and other config values (e.g. withReadonlyDb()) can
+ * share a single loadConfig() call instead of resolving it twice.
+ *
+ * MUST be called before opening any DB handle, for the same reason as
+ * resolveDbSettings(): loadConfig can throw (e.g. ConfigError via
+ * resolveSecrets on a malformed llm.apiKeyCommand config), and an
+ * already-open handle at that point would never be closed.
+ */
+export function resolveDbConfig(customDbPath?: string): CodegraphConfig {
+  return loadConfig(deriveRootDirFromDbPath(customDbPath));
+}
+
+/**
+ * Resolve config.db.busyTimeoutMs alone, for the ad-hoc read-only query call
+ * sites (features/*, domain/analysis/*, domain/search/*) that call
+ * openReadonlyOrFail() directly and don't need engine selection. Shares
+ * rootDir derivation with resolveDbSettings() so the two can't drift.
+ */
+export function resolveBusyTimeoutMs(customDbPath?: string): number {
+  return resolveDbConfig(customDbPath).db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs;
+}
+
 /** Open a NativeRepository via rusqlite, throwing DbError if the DB file is missing. */
 function openRepoNative(customDbPath?: string): { repo: Repository; close(): void } {
   const dbPath = findDbPath(customDbPath);

src/db/index.ts

@@ -15,6 +15,8 @@ export {
   openReadonlyWithNative,
   openRepo,
   releaseAdvisoryLock,
+  resolveBusyTimeoutMs,
+  resolveDbConfig,
 } from './connection.js';
 export { getBuildMeta, initSchema, MIGRATIONS, setBuildMeta } from './migrations.js';
 export {

src/domain/analysis/context.ts

@@ -438,12 +438,15 @@ export function contextData(
     config?: any;
   } = {},
 ) {
-  return withReadonlyDb(customDbPath, (db) => {
+  return withReadonlyDb(customDbPath, (db, config) => {
     const depth = opts.depth || 0;
     const noSource = opts.noSource || false;
     const includeTests = opts.includeTests || false;
 
-    const { noTests, displayOpts } = resolveAnalysisOpts(opts);
+    const { noTests, displayOpts } = resolveAnalysisOpts({
+      ...opts,
+      config: opts.config ?? config,
+    });
 
     const dbPath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbPath), '..');
@@ -510,11 +513,14 @@ export function explainData(
     config?: any;
   } = {},
 ) {
-  return withReadonlyDb(customDbPath, (db) => {
+  return withReadonlyDb(customDbPath, (db, config) => {
     const depth = opts.depth || 0;
     const kind = isFileLikeTarget(target) ? 'file' : 'function';
 
-    const { noTests, displayOpts } = resolveAnalysisOpts(opts);
+    const { noTests, displayOpts } = resolveAnalysisOpts({
+      ...opts,
+      config: opts.config ?? config,
+    });
 
     const dbPath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbPath), '..');

src/domain/analysis/diff-impact.ts

@@ -6,7 +6,7 @@ import { cachedStmt } from '../../db/repository/cached-stmt.js';
 import { evaluateBoundaries } from '../../features/boundaries.js';
 import { coChangeForFiles } from '../../features/cochange.js';
 import { ownersForFiles } from '../../features/owners.js';
-import { loadConfig } from '../../infrastructure/config.js';
+import { DEFAULTS, loadConfig } from '../../infrastructure/config.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { paginateResult } from '../../shared/paginate.js';
@@ -269,10 +269,17 @@ export function diffImpactData(
     config?: any;
   } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  // Resolve config before opening the DB so config.db.busyTimeoutMs can be
+  // threaded through to openReadonlyOrFail() (mirrors resolveDbSettings()'s
+  // ordering in db/connection.ts — loadConfig can throw, and an already-open
+  // handle at that point would never be closed).
+  const config = opts.config || loadConfig();
+  const db = openReadonlyOrFail(
+    customDbPath,
+    config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs,
+  );
   try {
     const noTests = opts.noTests || false;
-    const config = opts.config || loadConfig();
     const maxDepth = opts.depth || config.analysis?.impactDepth || 3;
 
     const dbPath = findDbPath(customDbPath);

src/domain/analysis/exports.ts

@@ -32,8 +32,11 @@ export function exportsData(
     config?: any;
   } = {},
 ) {
-  return withReadonlyDb(customDbPath, (db) => {
-    const { noTests, displayOpts } = resolveAnalysisOpts(opts);
+  return withReadonlyDb(customDbPath, (db, config) => {
+    const { noTests, displayOpts } = resolveAnalysisOpts({
+      ...opts,
+      config: opts.config ?? config,
+    });
 
     const dbFilePath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbFilePath), '..');

src/domain/analysis/module-map.ts

@@ -1,5 +1,10 @@
 import path from 'node:path';
-import { openReadonlyOrFail, openReadonlyWithNative, testFilterSQL } from '../../db/index.js';
+import {
+  openReadonlyOrFail,
+  openReadonlyWithNative,
+  resolveBusyTimeoutMs,
+  testFilterSQL,
+} from '../../db/index.js';
 import { loadConfig } from '../../infrastructure/config.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
@@ -307,7 +312,7 @@ function getComplexitySummary(db: BetterSqlite3Database, testFilter: string) {
 // ---------------------------------------------------------------------------
 
 export function moduleMapData(customDbPath: string, limit = 20, opts: { noTests?: boolean } = {}) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
 

src/domain/analysis/query-helpers.ts

@@ -1,19 +1,25 @@
-import { openReadonlyOrFail, openRepo, type Repository } from '../../db/index.js';
-import { loadConfig } from '../../infrastructure/config.js';
+import { openReadonlyOrFail, openRepo, type Repository, resolveDbConfig } from '../../db/index.js';
+import { DEFAULTS, loadConfig } from '../../infrastructure/config.js';
 import type { BetterSqlite3Database, CodegraphConfig } from '../../types.js';
 
 /**
  * Open a readonly DB connection, run `fn`, and close the DB on completion.
  * Eliminates the duplicated `openReadonlyOrFail` + `try/finally/db.close()` pattern
  * that appears in every analysis query function.
+ *
+ * Resolves the config once and passes it to `fn` so callers that also need
+ * `resolveAnalysisOpts` can reuse it as `opts.config` instead of triggering a
+ * second `loadConfig()` for the same rootDir (#1763 review).
  */
 export function withReadonlyDb<T>(
   customDbPath: string | undefined,
-  fn: (db: BetterSqlite3Database) => T,
+  fn: (db: BetterSqlite3Database, config: CodegraphConfig) => T,
 ): T {
-  const db = openReadonlyOrFail(customDbPath);
+  const config = resolveDbConfig(customDbPath);
+  const busyTimeoutMs = config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs;
+  const db = openReadonlyOrFail(customDbPath, busyTimeoutMs);
   try {
-    return fn(db);
+    return fn(db, config);
   } finally {
     db.close();
   }

src/domain/analysis/roles.ts

@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../db/index.js';
+import { openReadonlyOrFail, resolveBusyTimeoutMs } from '../../db/index.js';
 import { buildFileConditionSQL } from '../../db/query-builder.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { DEAD_ROLE_PREFIX } from '../../shared/kinds.js';
@@ -13,7 +13,7 @@ export interface DynamicCallCount {
 
 /** Return a count of flagged dynamic call sink edges, grouped by kind. */
 export function dynamicCallsData(customDbPath: string): DynamicCallCount[] {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     return db
       .prepare(
@@ -39,7 +39,7 @@ export function rolesData(
     offset?: number;
   } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
     const filterRole = opts.role || null;

src/domain/analysis/symbol-lookup.ts

@@ -13,6 +13,7 @@ import {
   listFunctionNodes,
   openReadonlyOrFail,
   Repository,
+  resolveBusyTimeoutMs,
 } from '../../db/index.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
@@ -95,7 +96,7 @@ export function queryNameData(
   customDbPath: string,
   opts: { noTests?: boolean; limit?: number; offset?: number } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
     let nodes = db.prepare(`SELECT * FROM nodes WHERE name LIKE ?`).all(`%${name}%`) as NodeRow[];
@@ -195,7 +196,7 @@ export function whereData(
   customDbPath: string,
   opts: { noTests?: boolean; file?: boolean; limit?: number; offset?: number } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
     const fileMode = opts.file || false;
@@ -219,7 +220,7 @@ export function listFunctionsData(
     offset?: number;
   } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
 
@@ -241,7 +242,7 @@ export function childrenData(
   customDbPath: string,
   opts: { noTests?: boolean; file?: string; kind?: string; limit?: number; offset?: number } = {},
 ) {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   try {
     const noTests = opts.noTests || false;
 

src/domain/search/search/hybrid.ts

@@ -1,5 +1,5 @@
 import { openReadonlyOrFail } from '../../../db/index.js';
-import { loadConfig } from '../../../infrastructure/config.js';
+import { DEFAULTS, loadConfig } from '../../../infrastructure/config.js';
 import type { BetterSqlite3Database, CodegraphConfig } from '../../../types.js';
 import { hasFtsIndex } from '../stores/fts5.js';
 import { ftsSearchData } from './keyword.js';
@@ -184,7 +184,10 @@ export async function hybridSearchData(
   const k = opts.rrfK ?? searchCfg.rrfK ?? 60;
   const topK = (opts.limit ?? searchCfg.topK ?? 15) * 5;
 
-  const checkDb = openReadonlyOrFail(customDbPath) as BetterSqlite3Database;
+  const checkDb = openReadonlyOrFail(
+    customDbPath,
+    config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs,
+  ) as BetterSqlite3Database;
   const ftsAvailable = hasFtsIndex(checkDb);
   checkDb.close();
   if (!ftsAvailable) return null;

src/domain/search/search/keyword.ts

@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../../db/index.js';
+import { openReadonlyOrFail, resolveBusyTimeoutMs } from '../../../db/index.js';
 import { buildFileConditionSQL } from '../../../db/query-builder.js';
 import type { BetterSqlite3Database } from '../../../types.js';
 import { normalizeSymbol } from '../../queries.js';
@@ -41,7 +41,10 @@ export function ftsSearchData(
 ): FtsSearchResult | null {
   const limit = opts.limit || 15;
 
-  const db = openReadonlyOrFail(customDbPath) as BetterSqlite3Database;
+  const db = openReadonlyOrFail(
+    customDbPath,
+    resolveBusyTimeoutMs(customDbPath),
+  ) as BetterSqlite3Database;
 
   try {
     if (!hasFtsIndex(db)) {

src/domain/search/search/prepare.ts

@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../../db/index.js';
+import { openReadonlyOrFail, resolveBusyTimeoutMs } from '../../../db/index.js';
 import { buildFileConditionSQL } from '../../../db/query-builder.js';
 import { getEmbeddingCount, getEmbeddingMeta } from '../../../db/repository/embeddings.js';
 import { info } from '../../../infrastructure/logger.js';
@@ -43,7 +43,10 @@ export function prepareSearch(
   customDbPath: string | undefined,
   opts: PrepareSearchOpts = {},
 ): PreparedSearch | null {
-  const db = openReadonlyOrFail(customDbPath) as BetterSqlite3Database;
+  const db = openReadonlyOrFail(
+    customDbPath,
+    resolveBusyTimeoutMs(customDbPath),
+  ) as BetterSqlite3Database;
 
   try {
     const count = getEmbeddingCount(db);

src/features/ast.ts

@@ -8,7 +8,7 @@ import {
 import { buildExtensionSet } from '../ast-analysis/shared.js';
 import { walkWithVisitors } from '../ast-analysis/visitor.js';
 import { createAstStoreVisitor } from '../ast-analysis/visitors/ast-store-visitor.js';
-import { bulkNodeIdsByFile, openReadonlyOrFail } from '../db/index.js';
+import { bulkNodeIdsByFile, openReadonlyOrFail, resolveBusyTimeoutMs } from '../db/index.js';
 import { buildFileConditionSQL } from '../db/query-builder.js';
 import { debug } from '../infrastructure/logger.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
@@ -304,7 +304,7 @@ export function astQueryData(
     limit: number;
   };
 } {
-  const db = openReadonlyOrFail(customDbPath);
+  const db = openReadonlyOrFail(customDbPath, resolveBusyTimeoutMs(customDbPath));
   const { kind, file, noTests, limit, offset } = opts;
 
   let where = 'WHERE 1=1';