fix: derive loadConfig() rootDir from --db path in read-only query functions

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';
@@ -417,6 +417,24 @@ function deriveRootDirFromDbPath(customDbPath: string | undefined): string | und
   return resolvedDbPath ? path.dirname(path.dirname(resolvedDbPath)) : undefined;
 }
 
+/**
+ * Load config with rootDir derived from the resolved DB path, rather than
+ * process.cwd(). This is the single entry point every read-only query
+ * function should use to call loadConfig() when it has (or can resolve) a
+ * `--db` path — so `--db /other/repo/.codegraph/graph.db` reads *that*
+ * repo's `.codegraphrc.json` instead of the invoking directory's. Shared by
+ * resolveDbSettings() and resolveBusyTimeoutMs() (below) plus the ad-hoc
+ * read-only query call sites (features/*, domain/analysis/*, domain/search/*)
+ * so rootDir derivation can't drift between them (issue #1881).
+ *
+ * MUST be called before opening any DB handle: 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 resolveConfigForDbPath(customDbPath?: string): CodegraphConfig {
+  return loadConfig(deriveRootDirFromDbPath(customDbPath));
+}
+
 /**
  * Resolve the effective engine for DB access (explicit opts.engine > config.build.engine >
  * 'auto') alongside config.db.busyTimeoutMs, in a single loadConfig() call.
@@ -431,7 +449,7 @@ function resolveDbSettings(
   customDbPath: string | undefined,
   engineOpt: 'native' | 'wasm' | 'auto' | undefined,
 ): ResolvedDbSettings {
-  const config = loadConfig(deriveRootDirFromDbPath(customDbPath));
+  const config = resolveConfigForDbPath(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 {
@@ -452,8 +470,7 @@ function resolveDbSettings(
  * already-open handle at that point would never be closed.
  */
 export function resolveBusyTimeoutMs(customDbPath?: string): number {
-  const config = loadConfig(deriveRootDirFromDbPath(customDbPath));
-  return config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs;
+  return resolveConfigForDbPath(customDbPath).db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs;
 }
 
 /** Open a NativeRepository via rusqlite, throwing DbError if the DB file is missing. */

src/db/index.ts

@@ -16,6 +16,7 @@ export {
   openRepo,
   releaseAdvisoryLock,
   resolveBusyTimeoutMs,
+  resolveConfigForDbPath,
 } from './connection.js';
 export { getBuildMeta, initSchema, MIGRATIONS, setBuildMeta } from './migrations.js';
 export {

src/domain/analysis/diff-impact.ts

@@ -1,7 +1,7 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { findDbPath, openReadonlyOrFail } from '../../db/index.js';
+import { findDbPath, openReadonlyOrFail, resolveConfigForDbPath } from '../../db/index.js';
 import { cachedStmt } from '../../db/repository/cached-stmt.js';
 import { evaluateBoundaries } from '../../features/boundaries.js';
 import { coChangeForFiles } from '../../features/cochange.js';
@@ -272,8 +272,10 @@ export function diffImpactData(
   // 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();
+  // handle at that point would never be closed). Derives rootDir from
+  // customDbPath (not process.cwd()) so `--db /other/repo/...` reads that
+  // repo's .codegraphrc.json (issue #1881).
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   const db = openReadonlyOrFail(
     customDbPath,
     config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs,

src/domain/search/search/hybrid.ts

@@ -1,5 +1,5 @@
-import { openReadonlyOrFail } from '../../../db/index.js';
-import { DEFAULTS, loadConfig } from '../../../infrastructure/config.js';
+import { openReadonlyOrFail, resolveConfigForDbPath } from '../../../db/index.js';
+import { DEFAULTS } from '../../../infrastructure/config.js';
 import type { BetterSqlite3Database, CodegraphConfig } from '../../../types.js';
 import { hasFtsIndex } from '../stores/fts5.js';
 import { ftsSearchData } from './keyword.js';
@@ -178,7 +178,9 @@ export async function hybridSearchData(
   customDbPath: string | undefined,
   opts: SemanticSearchOpts = {},
 ): Promise<HybridSearchResult | null> {
-  const config = opts.config || loadConfig();
+  // Derive rootDir from customDbPath (not process.cwd()) so `--db /other/repo/...`
+  // reads that repo's .codegraphrc.json (issue #1881).
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   const searchCfg = config.search || ({} as CodegraphConfig['search']);
   const limit = opts.limit ?? searchCfg.topK ?? 15;
   const k = opts.rrfK ?? searchCfg.rrfK ?? 60;

src/features/audit.ts

@@ -1,9 +1,8 @@
-import path from 'node:path';
-import { openReadonlyOrFail } from '../db/index.js';
+import { openReadonlyOrFail, resolveConfigForDbPath } from '../db/index.js';
 import { normalizeFileFilter } from '../db/query-builder.js';
 import { bfsTransitiveCallers } from '../domain/analysis/impact.js';
 import { explainData } from '../domain/queries.js';
-import { DEFAULTS, loadConfig } from '../infrastructure/config.js';
+import { DEFAULTS } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { toErrorMessage } from '../shared/errors.js';
@@ -35,13 +34,7 @@ function resolveThresholds(
   config: unknown,
 ): Record<string, ThresholdEntry> {
   try {
-    const cfg =
-      config ||
-      (() => {
-        const dbDir = customDbPath ? path.dirname(customDbPath) : process.cwd();
-        const repoRoot = path.resolve(dbDir, '..');
-        return loadConfig(repoRoot);
-      })();
+    const cfg = config || resolveConfigForDbPath(customDbPath);
     const userRules = (cfg as Record<string, unknown>).manifesto || {};
     const resolved: Record<string, ThresholdEntry> = {};
     for (const def of FUNCTION_RULES) {
@@ -144,7 +137,10 @@ export function auditData(
   opts: AuditDataOpts = {},
 ): AuditResult {
   const noTests = opts.noTests || false;
-  const config = opts.config || loadConfig();
+  // Derive rootDir from customDbPath (not process.cwd()) so `--db /other/repo/...`
+  // reads that repo's .codegraphrc.json (issue #1881) — matches resolveThresholds()
+  // below, which already derived rootDir correctly.
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   const maxDepth =
     opts.depth ||
     (config as unknown as { analysis?: { auditDepth?: number } }).analysis?.auditDepth ||

src/features/complexity-query.ts

@@ -5,9 +5,9 @@
  * pagination) from compute-time concerns (AST traversal, metric algorithms).
  */
 
-import { openReadonlyOrFail } from '../db/index.js';
+import { openReadonlyOrFail, resolveConfigForDbPath } from '../db/index.js';
 import { buildFileConditionSQL } from '../db/query-builder.js';
-import { DEFAULTS, loadConfig } from '../infrastructure/config.js';
+import { DEFAULTS } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { paginateResult } from '../shared/paginate.js';
@@ -281,14 +281,19 @@ interface ComplexityQueryOpts {
 }
 
 /** Resolve query flags + effective manifesto thresholds from opts/config/DEFAULTS. */
-function resolveComplexityQueryOptions(opts: ComplexityQueryOpts): {
+function resolveComplexityQueryOptions(
+  customDbPath: string | undefined,
+  opts: ComplexityQueryOpts,
+): {
   sort: string;
   noTests: boolean;
   aboveThreshold: boolean;
   thresholds: any;
   busyTimeoutMs: number;
 } {
-  const config = opts.config || loadConfig(process.cwd());
+  // Derive rootDir from customDbPath (not process.cwd()) so `--db /other/repo/...`
+  // reads that repo's .codegraphrc.json (issue #1881).
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   return {
     sort: opts.sort || 'cognitive',
     noTests: opts.noTests || false,
@@ -330,7 +335,7 @@ export function complexityData(
   // resolveDbSettings()'s ordering in db/connection.ts, since loadConfig can
   // throw and an already-open handle at that point would never be closed.
   const { sort, noTests, aboveThreshold, thresholds, busyTimeoutMs } =
-    resolveComplexityQueryOptions(opts);
+    resolveComplexityQueryOptions(customDbPath, opts);
   const db = openReadonlyOrFail(customDbPath, busyTimeoutMs);
   try {
     const { where, params } = buildComplexityWhere({

src/features/manifesto.ts

@@ -1,7 +1,7 @@
-import { openReadonlyOrFail } from '../db/index.js';
+import { openReadonlyOrFail, resolveConfigForDbPath } from '../db/index.js';
 import { buildFileConditionSQL } from '../db/query-builder.js';
 import { findCycles } from '../domain/graph/cycles.js';
-import { DEFAULTS, loadConfig } from '../infrastructure/config.js';
+import { DEFAULTS } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { paginateResult } from '../shared/paginate.js';
 import type { BetterSqlite3Database, CodegraphConfig, ThresholdRule } from '../types.js';
@@ -482,8 +482,10 @@ export function manifestoData(
   // 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(process.cwd());
+  // handle at that point would never be closed). Derives rootDir from
+  // customDbPath (not process.cwd()) so `--db /other/repo/...` reads that
+  // repo's .codegraphrc.json (issue #1881).
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   const db = openReadonlyOrFail(
     customDbPath,
     config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs,

src/features/structure-query.ts

@@ -11,9 +11,10 @@ import {
   openReadonlyOrFail,
   openReadonlyWithNative,
   resolveBusyTimeoutMs,
+  resolveConfigForDbPath,
   testFilterSQL,
 } from '../db/index.js';
-import { DEFAULTS, loadConfig } from '../infrastructure/config.js';
+import { DEFAULTS } from '../infrastructure/config.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { normalizePath } from '../shared/constants.js';
 import { paginateResult } from '../shared/paginate.js';
@@ -384,8 +385,10 @@ export function moduleBoundariesData(
   // 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();
+  // handle at that point would never be closed). Derives rootDir from
+  // customDbPath (not process.cwd()) so `--db /other/repo/...` reads that
+  // repo's .codegraphrc.json (issue #1881).
+  const config = opts.config || resolveConfigForDbPath(customDbPath);
   const db = openReadonlyOrFail(
     customDbPath,
     config.db?.busyTimeoutMs ?? DEFAULTS.db.busyTimeoutMs,

tests/unit/busy-timeout-query-sites.test.ts

@@ -101,11 +101,10 @@ describe('configured busyTimeoutMs reaches PRAGMA busy_timeout at ad-hoc read-on
   });
 
   it('manifestoData (config load reordered to before the db opens) applies the configured busy_timeout', () => {
-    // manifestoData resolves its config via loadConfig(process.cwd()) — a
-    // pre-existing, cwd-based resolution this fix intentionally preserves
-    // (only the *timing* of the call moved, not what it resolves) — so the
-    // project config must be visible from process.cwd() here, not from dbPath.
-    const cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(tmpDir);
+    // manifestoData resolves its config from the resolved DB path's rootDir
+    // (issue #1881 fix), not process.cwd() — so an unrelated cwd must not
+    // affect resolution.
+    const cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(os.tmpdir());
     const capture = captureBusyTimeoutPragmas();
     try {
       manifestoData(dbPath);
@@ -117,10 +116,9 @@ describe('configured busyTimeoutMs reaches PRAGMA busy_timeout at ad-hoc read-on
   });
 
   it('hybridSearchData (already loaded config before the db opens) applies the configured busy_timeout', async () => {
-    // Same pre-existing cwd-based config resolution as manifestoData (bare
-    // loadConfig() defaults to process.cwd()) — preserved, not introduced, by
-    // this fix.
-    const cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(tmpDir);
+    // Same DB-path-derived config resolution as manifestoData (issue #1881
+    // fix) — an unrelated cwd must not affect resolution.
+    const cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(os.tmpdir());
     const capture = captureBusyTimeoutPragmas();
     try {
       await hybridSearchData('nonexistent-query', dbPath);