code-auditor-mcp 3.4.14 → 3.4.16

package/dist/utils/fileDiscovery.js

@@ -7,8 +7,19 @@
  */
 import { promises as fs } from 'fs';
 import path from 'path';
-// Default directories to exclude from analysis
-export const DEFAULT_EXCLUDED_DIRS = [
+/**
+ * Spec 44 — the excluded-directory split. The two halves of the default
+ * exclusion set behave differently under file accounting:
+ *
+ * - **Infra** dirs are toolchain artifacts (never source). They are pruned
+ *   silently and recorded only as an aggregate `infraPruned` line, because
+ *   enumerating `node_modules` per-file is impossible at scale.
+ * - **Content** dirs (docs, specs, tmp, …) are small and genuinely "source the
+ *   user might have meant to include". They are enumerated per-file and each
+ *   file is recorded `dropped: directory pruned` — which is what makes an
+ *   `.mdx` under `docs/` appear in the report instead of vanishing.
+ */
+export const DEFAULT_EXCLUDED_INFRA_DIRS = [
     'node_modules',
     '.next',
     'dist',
@@ -18,20 +29,78 @@ export const DEFAULT_EXCLUDED_DIRS = [
     '.turbo',
     'out',
     '.cache',
-    'tmp',
-    'temp',
     '.vscode',
     '.idea',
-    // Documentation, specs, and backups — rarely contain production source code
-    'docs',
-    'specs',
-    'backup',
-    'backups',
     // The tool's own on-disk index (CodeIndexDB). A prior audit run writes
     // `.code-index/index.db` into the project root; it must never be re-scanned
     // as source on a subsequent run (Bug #3).
     '.code-index',
 ];
+// Documentation, specs, and backups — rarely contain production source code,
+// but enumerated per-file under accounting so they are reported, not silent.
+export const DEFAULT_EXCLUDED_CONTENT_DIRS = [
+    'tmp',
+    'temp',
+    'docs',
+    'specs',
+    'backup',
+    'backups',
+];
+// Backward-compatible union — still the default `excludeDirs` for discovery.
+export const DEFAULT_EXCLUDED_DIRS = [
+    ...DEFAULT_EXCLUDED_INFRA_DIRS,
+    ...DEFAULT_EXCLUDED_CONTENT_DIRS,
+];
+/**
+ * Spec 45 R1 — the per-entry anchoring choice. Each directory basename in
+ * `DEFAULT_EXCLUDED_DIRS` is either *any-depth* or *root-anchored* depending on
+ * whether the name is an unambiguous toolchain/transient marker (never a source
+ * route) or an ambiguous one (could be user source when nested).
+ *
+ * ANY-DEPTH (13 entries) — toolchain artifacts wherever they appear; nested
+ * occurrences are never source, so they are excluded at every depth below the
+ * scan root:
+ *
+ *   - `node_modules` — package deps; monorepo workspaces are still deps.
+ *   - `.git` — VCS metadata; submodules are still VCS.
+ *   - `.next` — Next.js build output (reserved name).
+ *   - `dist`, `out` — build/export output.
+ *   - `coverage` — test coverage report.
+ *   - `.turbo` — Turborepo cache.
+ *   - `.cache` — cache (recall's `scripts/.cache` holds generated build JSON).
+ *   - `.vscode`, `.idea` — editor state.
+ *   - `.code-index` — the tool's own SQLite index (Bug #3); a prior scoped run
+ *     can leave `src/agents/.code-index` nested.
+ *   - `tmp`, `temp` — transient (recall's `scripts/.wrangler/tmp` is Wrangler
+ *     build cache; never source).
+ *
+ * ROOT-ANCHORED (5 entries) — ambiguous: they can be a real file-router route
+ * or user source when nested under `src/`, so they are excluded only as the
+ * first component below the scan root. File-based routers (Astro, Next,
+ * SvelteKit, Nuxt) make `src/pages/docs/…` and `src/pages/…/build/…` real
+ * routes:
+ *
+ *   - `build` — a nested `src/pages/…/build/…` dir is a route; root `build` is
+ *     build output.
+ *   - `docs` — `src/pages/docs/…` is a route (recall's two R1 source files);
+ *     root `docs` is documentation.
+ *   - `specs`, `backup`, `backups` — can be in-repo source.
+ */
+export const DEFAULT_EXCLUDED_ANY_DEPTH_DIRS = new Set([
+    'node_modules',
+    '.git',
+    '.next',
+    'dist',
+    'out',
+    'coverage',
+    '.turbo',
+    '.cache',
+    '.vscode',
+    '.idea',
+    '.code-index',
+    'tmp',
+    'temp',
+]);
 /**
  * Basenames the tool itself writes into the project, which must never be
  * re-discovered as source on a subsequent run (Bug #3 — "exclude the tool's
@@ -47,31 +116,107 @@ export const DEFAULT_EXCLUDED_FILES = new Set([
     'audit-report.sarif',
 ]);
 // Supported file extensions
-export const TYPESCRIPT_EXTENSIONS = ['.ts', '.tsx'];
-export const JAVASCRIPT_EXTENSIONS = ['.js', '.jsx'];
+export const TYPESCRIPT_EXTENSIONS = ['.ts', '.tsx', '.mts', '.cts'];
+export const JAVASCRIPT_EXTENSIONS = ['.js', '.jsx', '.mjs', '.cjs'];
 export const JSON_EXTENSIONS = ['.json'];
 export const GO_EXTENSIONS = ['.go'];
 export const CSS_EXTENSIONS = ['.css', '.scss'];
+// Markup extensions that carry `<style>` blocks (Spec 42 R1). Discovered so the
+// style indexer can extract their embedded stylesheets; the pipeline itself has
+// no language adapter for them, so they are consumed only by syncStyleIndex.
+export const MARKUP_EXTENSIONS = ['.astro', '.vue', '.svelte'];
+// Markup/component extensions the style extractor reads (embedded <style> blocks
+// and class attributes). This is the single source of truth for the extractor's
+// markup dispatch — the gates in styleIndexer.ts and the dispatch in
+// styleExtractor.ts derive from it so a newly supported dialect is handled
+// everywhere at once instead of silently dropped from one list. `.html` is
+// included because scoped runs may pass HTML files, even though `.html` is NOT
+// discovered by default (recall-protocol's ~11,928 spec-dump `.html` files would
+// blow up a full audit).
+export const STYLE_MARKUP_EXTENSIONS = ['.html', ...MARKUP_EXTENSIONS];
+// Dialects the style indexer cannot yet read (Sass/SCSS indented syntax, Less,
+// Stylus). Not discovered as source — the indexer records them as *unread*
+// stylesheet sources (Spec 42 R2) so undefined-class never asserts on a class
+// that could be defined in one of these.
+export const UNREAD_STYLE_EXTENSIONS = ['.less', '.styl', '.sass'];
 // Raw-source extensions — no tree-sitter grammar, included for visitors that
 // read sourceCode directly (e.g. SQL migrations, TOML config, Prisma schemas)
 export const SQL_EXTENSIONS = ['.sql'];
 export const TOML_EXTENSIONS = ['.toml'];
 export const PRISMA_EXTENSIONS = ['.prisma'];
 export const RAW_EXTENSIONS = [...SQL_EXTENSIONS, ...TOML_EXTENSIONS, ...PRISMA_EXTENSIONS];
-export const ALL_EXTENSIONS = [...TYPESCRIPT_EXTENSIONS, ...JAVASCRIPT_EXTENSIONS, ...JSON_EXTENSIONS, ...GO_EXTENSIONS, ...CSS_EXTENSIONS, ...RAW_EXTENSIONS];
+// NOTE: .html is deliberately NOT here — recall-protocol has ~11,928 .html
+// files (spec dumps) and reading them all would blow up the audit. Markup
+// extensions are added because they are real component files with styles.
+export const ALL_EXTENSIONS = [...TYPESCRIPT_EXTENSIONS, ...JAVASCRIPT_EXTENSIONS, ...JSON_EXTENSIONS, ...GO_EXTENSIONS, ...CSS_EXTENSIONS, ...RAW_EXTENSIONS, ...MARKUP_EXTENSIONS];
+// Every extension the analysis layer understands as source — style-bearing
+// (TS/JS/markup/CSS) plus non-style (JSON/Go/SQL/TOML/Prisma), with `.html`
+// added since scoped runs may pass it even though it is not discovered by
+// default. Single source of truth for the style extractor's "loud" default
+// branch: an extension that reaches it unhandled is recorded as an unread
+// source (Spec 42 R2) *only* when it is NOT in this set, so a genuinely unknown
+// dialect (`.mdx`, `.md`, …) surfaces instead of a silent zero while legitimate
+// non-style source and `.css`/`.scss` (handled by the AST pipeline) stay silent.
+export const KNOWN_SOURCE_EXTENSIONS = [...ALL_EXTENSIONS, '.html'];
 /**
- * Check if a path should be excluded based on directory names.
- * Only checks directory components *below* the scan root to avoid
- * false matches against filesystem roots like /tmp or /temp.
+ * Classify a path against the excluded-directory split (Spec 44 + Spec 45 R1).
+ *
+ * Only checks directory components *below* the scan root to avoid false
+ * matches against filesystem roots like /tmp or /temp. A component that is a
+ * default *infra* dir prunes silently (aggregate); every other excluded
+ * component — default *content* dirs and any user-supplied dir — is enumerated
+ * per-file so nothing is silently dropped.
+ *
+ * Spec 45 R1: a basename matches only as the *first* component below the scan
+ * root, unless it is one of the `DEFAULT_EXCLUDED_ANY_DEPTH_DIRS` entries
+ * (unambiguous toolchain/transient names — see the per-entry list on that
+ * constant), which match at any depth. This keeps `src/pages/docs/…` and
+ * `src/pages/…/build/…` as source instead of silently pruning them, while still
+ * pruning nested `node_modules`, `.cache`, `.code-index`, and `tmp`.
  */
-function shouldExcludeDir(filePath, excludeDirs, scanRoot) {
+function classifyExcludedDir(filePath, excludeDirs, scanRoot) {
     // Get the relative path below scanRoot
     const relPath = path.relative(scanRoot, filePath);
     // If the path is outside scanRoot (shouldn't happen), don't exclude
     if (relPath.startsWith('..'))
-        return false;
+        return null;
     const parts = relPath.split(path.sep);
-    return parts.some(part => excludeDirs.includes(part));
+    for (let i = 0; i < parts.length; i++) {
+        const part = parts[i];
+        if (!excludeDirs.includes(part))
+            continue;
+        // Root-anchored entries match only at the first component; any-depth
+        // entries (`node_modules`, `.git`) match anywhere below the scan root.
+        if (i !== 0 && !DEFAULT_EXCLUDED_ANY_DEPTH_DIRS.has(part))
+            continue;
+        if (DEFAULT_EXCLUDED_INFRA_DIRS.includes(part))
+            return { kind: 'infra', dir: part };
+        return { kind: 'content', dir: part };
+    }
+    return null;
+}
+/**
+ * Recursively list every file under a directory, any extension. Used only for
+ * *content* exclude dirs (small, enumerated per-file under accounting).
+ */
+async function enumerateAllFiles(dir) {
+    const out = [];
+    try {
+        const entries = await fs.readdir(dir, { withFileTypes: true });
+        for (const entry of entries) {
+            const fullPath = path.join(dir, entry.name);
+            if (entry.isDirectory()) {
+                out.push(...(await enumerateAllFiles(fullPath)));
+            }
+            else if (entry.isFile()) {
+                out.push(fullPath);
+            }
+        }
+    }
+    catch {
+        // Unreadable subtree — skip (mirrors the walk's EACCES tolerance).
+    }
+    return out;
 }
 /**
  * Recursively find files matching criteria
@@ -82,7 +227,21 @@ async function findFilesRecursive(dir, options) {
         const entries = await fs.readdir(dir, { withFileTypes: true });
         for (const entry of entries) {
             const fullPath = path.join(dir, entry.name);
-            if (shouldExcludeDir(fullPath, options.excludeDirs, options.scanRoot)) {
+            const excl = classifyExcludedDir(fullPath, options.excludeDirs, options.scanRoot);
+            if (excl) {
+                const rule = DEFAULT_EXCLUDED_DIRS.includes(excl.dir) ? 'DEFAULT_EXCLUDED_DIRS' : 'excludeDirs';
+                if (excl.kind === 'infra') {
+                    // Aggregate — never per-file (node_modules is not enumerable at scale).
+                    options.fileAccounting?.recordInfraPruned(excl.dir, rule);
+                }
+                else if (entry.isDirectory() && options.fileAccounting) {
+                    // Content dir — enumerated per-file, each dropped: directory pruned.
+                    // This is what makes `.mdx` under `docs/` appear (Spec 44 acceptance 5).
+                    const contentFiles = await enumerateAllFiles(fullPath);
+                    for (const f of contentFiles) {
+                        options.fileAccounting.recordDropped('directory pruned', f, { directory: excl.dir, rule });
+                    }
+                }
                 continue;
             }
             if (entry.isDirectory()) {
@@ -99,6 +258,18 @@ async function findFilesRecursive(dir, options) {
                         results.push(fullPath);
                     }
                 }
+                else if (ext !== '') {
+                    // Record the extension discovery skipped so the report can answer
+                    // "what isn't being analyzed here" (Spec 43 R5 follow-up) rather than
+                    // silently dropping the file at discovery.
+                    options.onSkippedExtension?.(ext, fullPath);
+                    // Spec 44 reason 2 — a file with a known (or unknown) extension that
+                    // is simply not in the discovery set.
+                    options.fileAccounting?.recordDropped('extension not known', fullPath, {
+                        ext,
+                        kind: KNOWN_SOURCE_EXTENSIONS.includes(ext) ? 'known-but-not-discovered' : 'unknown',
+                    });
+                }
             }
         }
     }
@@ -119,13 +290,24 @@ export async function findFiles(rootDir = process.cwd(), options = {}) {
     const files = await findFilesRecursive(rootDir, {
         extensions,
         excludeDirs,
-        scanRoot: rootDir
+        scanRoot: rootDir,
+        ...(options.onSkippedExtension ? { onSkippedExtension: options.onSkippedExtension } : {}),
+        ...(options.fileAccounting ? { fileAccounting: options.fileAccounting } : {})
     });
     // Apply additional filtering
-    let filtered = filterFiles(files, {
+    const filtered = filterFiles(files, {
         includePaths: options.includePaths,
-        excludePaths: options.excludePaths
+        excludePaths: options.excludePaths,
+        fileAccounting: options.fileAccounting
     });
+    // Spec 44 — every candidate that survives discovery filtering is "touched"
+    // (it will be classified analyzed/dropped in stage 2). Recording it here —
+    // after include/exclude filtering — means a positive-selection `includePaths`
+    // narrows the universe instead of producing touched-but-dropped entries.
+    if (options.fileAccounting) {
+        for (const f of filtered)
+            options.fileAccounting.recordTouched(f);
+    }
     // Sort for consistent output
     return filtered.sort();
 }
@@ -170,13 +352,20 @@ export async function findFilesByPattern(rootDir = process.cwd(), pattern, optio
         extensions,
         excludeDirs,
         pattern: regex,
-        scanRoot: rootDir
+        scanRoot: rootDir,
+        ...(options.onSkippedExtension ? { onSkippedExtension: options.onSkippedExtension } : {}),
+        ...(options.fileAccounting ? { fileAccounting: options.fileAccounting } : {})
     });
     // Apply additional filtering
-    let filtered = filterFiles(files, {
+    const filtered = filterFiles(files, {
         includePaths: options.includePaths,
-        excludePaths: options.excludePaths
+        excludePaths: options.excludePaths,
+        fileAccounting: options.fileAccounting
     });
+    if (options.fileAccounting) {
+        for (const f of filtered)
+            options.fileAccounting.recordTouched(f);
+    }
     return filtered.sort();
 }
 /**
@@ -184,7 +373,8 @@ export async function findFilesByPattern(rootDir = process.cwd(), pattern, optio
  */
 export function filterFiles(files, options = {}) {
     let filtered = [...files];
-    // Apply include patterns
+    // Apply include patterns (positive selection — narrows the universe; a file
+    // removed here is simply not "touched", not dropped).
     if (options.includePaths && options.includePaths.length > 0) {
         filtered = filtered.filter(file => {
             return options.includePaths.some(pattern => {
@@ -196,13 +386,22 @@ export function filterFiles(files, options = {}) {
     }
     // Apply exclude patterns
     if (options.excludePaths && options.excludePaths.length > 0) {
-        filtered = filtered.filter(file => {
-            return !options.excludePaths.some(pattern => {
+        const kept = [];
+        for (const file of filtered) {
+            const matched = options.excludePaths.find(pattern => {
                 // Convert glob patterns to regex
                 const regex = globToRegex(pattern);
                 return regex.test(file);
             });
-        });
+            if (matched) {
+                // Spec 44 reason 1 — a user `excludePaths` prune, rule = the glob.
+                options.fileAccounting?.recordDropped('directory pruned', file, { rule: matched });
+            }
+            else {
+                kept.push(file);
+            }
+        }
+        filtered = kept;
     }
     return filtered;
 }
@@ -258,4 +457,22 @@ export async function isReadableFile(filePath) {
  * Alias for findFiles to match expected import
  */
 export const discoverFiles = findFiles;
+/**
+ * Discover files and simultaneously record the extensions discovery skipped.
+ * Mirrors `findFiles` (same defaults and filtering), but the returned
+ * `skippedExtensions` is aggregated during the recursive walk — before
+ * `includePaths`/`excludePaths` filtering — so it reflects the full scan, not
+ * just the filtered subset. Sorted by count descending, then extension.
+ */
+export async function discoverFilesDetailed(rootDir = process.cwd(), options = {}) {
+    const counts = new Map();
+    const onSkippedExtension = (ext) => {
+        counts.set(ext, (counts.get(ext) ?? 0) + 1);
+    };
+    const files = await findFiles(rootDir, { ...options, onSkippedExtension });
+    const skippedExtensions = [...counts.entries()]
+        .map(([ext, count]) => ({ ext, count }))
+        .sort((a, b) => b.count - a.count || a.ext.localeCompare(b.ext));
+    return { files, skippedExtensions };
+}
 //# sourceMappingURL=fileDiscovery.js.map

package/dist/utils/fileDiscovery.js.map

@@ -1 +1 @@
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package/dist/workers/auditJobRunner.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=auditJobRunner.d.ts.map

package/dist/workers/auditJobRunner.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"auditJobRunner.d.ts","sourceRoot":"","sources":["../../src/workers/auditJobRunner.ts"],"names":[],"mappings":""}

package/dist/workers/auditJobRunner.js

@@ -0,0 +1,37 @@
+import { initParsers, initializeLanguages } from '../languages/index.js';
+import { runAuditJob } from '../mcpAuditJobs.js';
+import { CodeIndexDB } from '../codeIndexDB.js';
+/**
+ * Forkable entrypoint for Spec 41 `--detach`.
+ *
+ * Reads jobId / args / defaults from argv, initializes parsers, and runs the
+ * shared `runAuditJob` path — the same path MCP's `audit.start` schedules via
+ * setTimeout. There is no second runner: the child exists only to give `--detach`
+ * a detached process whose stderr the parent captures to a per-run log.
+ *
+ * `runAuditJob` records lifecycle state (including failure) on the run row and
+ * resolves normally, so this process exits non-zero only when `runAuditJob`
+ * itself rejects before its own try/catch takes over (e.g. a broken argv).
+ */
+async function main() {
+    const [, , jobId, argsJson, defaultsJson] = process.argv;
+    if (!jobId || !argsJson || !defaultsJson) {
+        console.error('usage: auditJobRunner <jobId> <argsJson> <defaultsJson>');
+        process.exitCode = 2;
+        return;
+    }
+    initializeLanguages();
+    await initParsers();
+    // This process is a fresh fork of a parent that already opened CodeIndexDB.
+    // fork() copies the singleton (including `isInitialized = true` and a native
+    // better-sqlite3 handle that does not survive the fork), so `getInstance`
+    // would short-circuit and hand back a dead connection. Reset the singleton so
+    // runAuditJob opens a fresh per-project connection.
+    CodeIndexDB.resetInstance();
+    await runAuditJob(jobId, JSON.parse(argsJson), JSON.parse(defaultsJson));
+}
+main().catch((err) => {
+    console.error(err instanceof Error ? (err.stack ?? err.message) : String(err));
+    process.exitCode = 1;
+});
+//# sourceMappingURL=auditJobRunner.js.map

package/dist/workers/auditJobRunner.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"auditJobRunner.js","sourceRoot":"","sources":["../../src/workers/auditJobRunner.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AACzE,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAEhD;;;;;;;;;;;GAWG;AACH,KAAK,UAAU,IAAI;IACjB,MAAM,CAAC,EAAE,AAAD,EAAG,KAAK,EAAE,QAAQ,EAAE,YAAY,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC;IACzD,IAAI,CAAC,KAAK,IAAI,CAAC,QAAQ,IAAI,CAAC,YAAY,EAAE,CAAC;QACzC,OAAO,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;QACzE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,mBAAmB,EAAE,CAAC;IACtB,MAAM,WAAW,EAAE,CAAC;IAEpB,4EAA4E;IAC5E,6EAA6E;IAC7E,0EAA0E;IAC1E,8EAA8E;IAC9E,oDAAoD;IACpD,WAAW,CAAC,aAAa,EAAE,CAAC;IAE5B,MAAM,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,QAAQ,CAA4B,EAAE,IAAI,CAAC,KAAK,CAAC,YAAY,CAAU,CAAC,CAAC;AAC/G,CAAC;AAED,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE;IACnB,OAAO,CAAC,KAAK,CAAC,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC;IAC/E,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;AACvB,CAAC,CAAC,CAAC"}

package/dist/workers/auditWorker.js

@@ -1,6 +1,7 @@
 import { createAuditRunner } from '../auditRunner.js';
 import { AuditAbortedError, AuditHandoffError } from '../types.js';
 import { initParsers } from '../languages/index.js';
+import { CodeIndexDB } from '../codeIndexDB.js';
 import { continuationConfigAfterHandoff, toAuditRunnerOptions, } from './auditWorkerProtocol.js';
 const abortControllers = new Map();
 /** One audit at a time per process so the parent can safely recycle workers on timeout. */
@@ -25,6 +26,10 @@ async function handleRun(message) {
         const base = toAuditRunnerOptions(message.config);
         const runner = createAuditRunner({
             ...base,
+            // The parent (runAuditJob) is the single ledger writer; a worker writing
+            // the ledger concurrently contends with the parent's syncFileIndex
+            // (SQLITE_BUSY) and pollutes listRuns with stray completed rows.
+            writeToLedger: false,
             abortSignal: ac.signal,
             progressCallback: (progress) => {
                 send({
@@ -36,6 +41,15 @@ async function handleRun(message) {
             },
         });
         const result = await runner.run();
+        // Close this worker's DB connection before signaling the parent. The
+        // parent (runAuditJob) proceeds straight into syncFileIndex the moment it
+        // receives worker-result; if this worker is then SIGTERM'd by
+        // disposeAllWorkers while its syncStyleIndex-opened connection is still
+        // open, the abrupt exit leaves the shared WAL -shm in a state that makes
+        // the parent's next write fail with "database is locked". Closing here —
+        // before the send — guarantees the connection is gone by the time the
+        // parent reads the message.
+        CodeIndexDB.resetInstance();
         send({
             kind: 'worker-result',
             requestId,
@@ -44,6 +58,9 @@ async function handleRun(message) {
         });
     }
     catch (error) {
+        // Same rationale as the success path: never leave a DB connection open
+        // across the worker's (imminent) SIGTERM, whichever way this shard ends.
+        CodeIndexDB.resetInstance();
         if (error instanceof AuditHandoffError) {
             send({
                 kind: 'worker-handoff',
@@ -118,6 +135,15 @@ process.on('message', (raw) => {
 });
 // ── Initialize parsers then signal readiness ──────────────────────────────
 async function main() {
+    // This process is a fresh exec of a forked parent (auditJobRunner) that may
+    // have left a module-level singleton on its stack before exec. The child does
+    // not inherit the parent's SQLite fd (better-sqlite3 opens it O_CLOEXEC), but
+    // the singleton module state — `isInitialized = true` and a stale native
+    // handle — does carry over if the parent initialized the parser before
+    // forking. Reset the singleton immediately so this worker drops any inherited
+    // module state and the worker's own audit-runner opens a fresh per-process
+    // connection.
+    CodeIndexDB.resetInstance();
     await initParsers();
     send({
         kind: 'worker-ready',

package/dist/workers/auditWorker.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "code-auditor-mcp",
-  "version": "3.4.14",
+  "version": "3.4.16",
   "description": "Architectural invariants and code quality analysis, enforced inside your AI agent's edit loop. MCP server + CLI + Claude Code plugin. TypeScript, JavaScript, Go.",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -33,7 +33,7 @@
     "verify:dist": "npm pack --silent && bash scripts/verify-dist.sh && rm -f code-auditor-mcp-*.tgz",
     "verify:self": "node scripts/verify-self.mjs",
     "verify:gate-budget": "node scripts/verify-gate-budget.mjs",
-    "verify:close": "npm run test && npm run test:integration && npm run verify:dist && npm run verify:self && npm run verify:gate-budget"
+    "verify:close": "npm run test && npm run test:integration && npm run verify:gate-budget && npm run verify:dist && npm run verify:self"
   },
   "keywords": [
     "mcp",

package/plugin/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "code-auditor",
   "description": "Diff-scoped code quality auditing on every edit. Indexes your codebase, enforces invariants, and feeds violations back to the agent so fixes happen inline.",
-  "version": "3.4.13",
+  "version": "3.4.16",
   "author": {
     "name": "Ben Hammond",
     "email": "ben@benhammond.tech"