cognium-ai 4.10.0 → 4.11.0

package/README.md

@@ -215,7 +215,7 @@ jobs:
 | OWASP Benchmark (Java) | 100% (1415/1415) |
 | Juliet Test Suite (14 CWEs) | 100% (243/243) |
 | SecuriBench Micro | 97.7% TPR, 6.7% FPR |
-| CWE-Bench-Java (120 CVEs) | 50.8% static (61/120), **86.7% +LLM Discovery** (104/120, Claude Opus) — IRIS-paper strict methodology |
+| CWE-Bench-Java (120 CVEs) | mode `static` 50.8% (61/120) · mode `discovery` **86.7%** (104/120, Claude Opus; LLM told the CWE — research recall) · mode `product-verify` 20% (24/120, 4.0.1 / gpt-4o-mini; `cognium-ai scan --llm --llm-verify`) — IRIS-paper strict methodology |
 | OWASP NodeGoat / Juice Shop / DVJA | 100% |
 | NodeJS Synthetic (25 tests) | 92.9% Score (96.2% TPR, 11.1% FPR) |
 | CWE-Bench-Rust (30 tests) | 94.4% TPR, 0% FPR |
@@ -223,7 +223,7 @@ jobs:
 | Go Synthetic (29 tests) | 84.2% TPR, 30% FPR |
 | Vulnerability-goapp (13 tests) | cmdi/xss/pathtraver 100%; sqli pending [circle-ir#2](https://github.com/cogniumhq/circle-ir/issues/2) |
 
-CWE-Bench-Java reference: **CodeQL 22.5%**, IRIS+GPT-4 45.8% — cognium-ai with Claude Opus is **2.85× CodeQL**.
+CWE-Bench-Java reference: **CodeQL 22.5%**, IRIS+GPT-4 45.8% — cognium-ai in discovery mode with Claude Opus is **2.85× CodeQL**. CWE-Bench-Java numbers carry a **mode label** (cognium-ai#303): `static` = no LLM; `discovery` = the built-in runner's `--llm-discovery`, where the LLM is *told the CWE* and asked where the fix is (a research recall metric); `product-verify` = what customers run, `cognium-ai scan --llm --llm-verify`, scored IRIS-strict by `npm run benchmark:cwe:product`. The three are not interchangeable — product-verify measured **24/120** on 4.0.1 / gpt-4o-mini (Aug 2026) against discovery's ~104/120.
 
 ## License
 

package/dist/cli/commands/analyze.d.ts

@@ -5,6 +5,7 @@
  */
 import { type CircleIR, type TaintConfig } from 'circle-ir';
 import type { CliArgs } from '../args.js';
+import { type EffectiveOptions } from '../effective-options.js';
 export interface AnalysisOptions {
     taintConfig?: TaintConfig;
     discoverPatterns?: boolean;
@@ -15,5 +16,24 @@ export interface AnalysisOptions {
     llmApiKey?: string;
 }
 export declare function runAnalysis(filePath: string, options?: AnalysisOptions): Promise<CircleIR>;
+export type AnalyzeLanguage = 'java' | 'csharp' | 'javascript' | 'typescript' | 'python' | 'rust' | 'c' | 'cpp' | 'go' | 'bash' | 'html';
+/**
+ * Languages the multi-agent `--bundle` runner accepts. Anything else must fail
+ * loud rather than be coerced to `java` (cognium-ai#348 — `.cs` was silently
+ * parsed as Java).
+ */
+export declare const BUNDLE_LANGUAGES: readonly AnalyzeLanguage[];
+export declare function resolveBundleLanguage(filePath: string): 'java' | 'c' | 'cpp';
+/**
+ * cognium-ai#348 — the default `cognium-ai <path>` action coupled LLM
+ * verification to `--no-llm` only, so `--no-llm-verify` (advertised via
+ * addCommonOptions and honored by `scan` / `trust`) still ran the verifier.
+ * Same resolution as scan.ts: verify follows `eff.llm.verify`, gated on --llm.
+ */
+export declare function resolveAnalyzeLLMFlags(args: Pick<CliArgs, 'noLlm'>, eff: Pick<EffectiveOptions, 'llm'>): {
+    enableEnrichment: boolean;
+    enableVerification: boolean;
+};
+export declare function detectLanguageFromFile(filePath: string): AnalyzeLanguage;
 export declare function executeAnalyze(args: CliArgs): Promise<number>;
 //# sourceMappingURL=analyze.d.ts.map

package/dist/cli/commands/analyze.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"analyze.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/analyze.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,EAAW,KAAK,QAAQ,EAAE,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AASrE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C,OAAO,EAAuB,KAAK,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAQrF,MAAM,WAAW,eAAe;IAC9B,WAAW,CAAC,EAAE,WAAW,CAAC;IAC1B,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,WAAW,CAC/B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,eAAoB,GAC5B,OAAO,CAAC,QAAQ,CAAC,CAQnB;AAMD,MAAM,MAAM,eAAe,GACvB,MAAM,GAAG,QAAQ,GAAG,YAAY,GAAG,YAAY,GAAG,QAAQ,GAAG,MAAM,GACnE,GAAG,GAAG,KAAK,GAAG,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;AAEzC;;;;GAIG;AACH,eAAO,MAAM,gBAAgB,EAAE,SAAS,eAAe,EAAyB,CAAC;AAEjF,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,GAAG,KAAK,CAS5E;AAED;;;;;GAKG;AACH,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,EAC5B,GAAG,EAAE,IAAI,CAAC,gBAAgB,EAAE,KAAK,CAAC,GACjC;IAAE,gBAAgB,EAAE,OAAO,CAAC;IAAC,kBAAkB,EAAE,OAAO,CAAA;CAAE,CAM5D;AAED,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,eAAe,CAiBxE;AAqFD,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA8LnE"}

package/dist/cli/commands/analyze.js

@@ -8,6 +8,7 @@ import * as path from 'path';
 import { analyze } from 'circle-ir';
 import { ensureAnalyzerInitialized, analyzeFile, runBundle, runBundleOnFiles, registerSecurityAgents, } from 'circle-ir-ai';
 import { loadCogniumConfig, convertCogniumConfigToPassOptions } from '../config.js';
+import { getEffectiveOptions } from '../effective-options.js';
 import { runSwarmAnalysis } from './swarm.js';
 import { formatOutput } from '../formatters/index.js';
 export async function runAnalysis(filePath, options = {}) {
@@ -21,10 +22,34 @@ export async function runAnalysis(filePath, options = {}) {
         language = 'cpp';
     return analyze(code, filePath, language, { taintConfig: options.taintConfig });
 }
-// ---------------------------------------------------------------------------
-// executeAnalyze — CLI entry for `cognium-ai <path>` (no subcommand)
-// ---------------------------------------------------------------------------
-function detectLanguageFromFile(filePath) {
+/**
+ * Languages the multi-agent `--bundle` runner accepts. Anything else must fail
+ * loud rather than be coerced to `java` (cognium-ai#348 — `.cs` was silently
+ * parsed as Java).
+ */
+export const BUNDLE_LANGUAGES = ['java', 'c', 'cpp'];
+export function resolveBundleLanguage(filePath) {
+    const detected = detectLanguageFromFile(filePath);
+    if (!BUNDLE_LANGUAGES.includes(detected)) {
+        throw new Error(`--bundle supports ${BUNDLE_LANGUAGES.join('|')} sources; ${path.basename(filePath)} ` +
+            `is ${detected}. Use \`cognium-ai scan\` for ${detected}.`);
+    }
+    return detected;
+}
+/**
+ * cognium-ai#348 — the default `cognium-ai <path>` action coupled LLM
+ * verification to `--no-llm` only, so `--no-llm-verify` (advertised via
+ * addCommonOptions and honored by `scan` / `trust`) still ran the verifier.
+ * Same resolution as scan.ts: verify follows `eff.llm.verify`, gated on --llm.
+ */
+export function resolveAnalyzeLLMFlags(args, eff) {
+    const llmEnabled = !args.noLlm;
+    return {
+        enableEnrichment: llmEnabled,
+        enableVerification: llmEnabled ? eff.llm.verify : false,
+    };
+}
+export function detectLanguageFromFile(filePath) {
     const ext = path.extname(filePath).toLowerCase();
     switch (ext) {
         case '.java': return 'java';
@@ -39,6 +64,13 @@ function detectLanguageFromFile(filePath) {
         case '.py': return 'python';
         case '.rs': return 'rust';
         case '.go': return 'go';
+        // cognium-ai#348 — `.cs` fell through to `java` (no case); bash/html likewise.
+        case '.cs':
+        case '.csx': return 'csharp';
+        case '.sh':
+        case '.bash': return 'bash';
+        case '.html':
+        case '.htm': return 'html';
         case '.c':
         case '.h': return 'c';
         case '.cpp':
@@ -145,6 +177,10 @@ export async function executeAnalyze(args) {
     // Effective include/exclude (CLI overrides config)
     const include = args.include.length > 0 ? args.include : (cogniumConfig?.include ?? []);
     const exclude = args.exclude.length > 0 ? args.exclude : (cogniumConfig?.exclude ?? []);
+    // cognium-ai#348 — resolve --llm-verify/--no-llm-verify (CLI > config > on)
+    // exactly as scan/trust do, instead of coupling verification to --no-llm.
+    const eff = getEffectiveOptions(args, targetPath);
+    const llmFlags = resolveAnalyzeLLMFlags(args, eff);
     try {
         if (args.bundle) {
             registerSecurityAgents();
@@ -180,8 +216,8 @@ export async function executeAnalyze(args) {
             }
             else {
                 const sourceCode = fs.readFileSync(targetPath, 'utf-8');
-                const detectedLang = detectLanguageFromFile(targetPath);
-                const bundleLang = (['java', 'c', 'cpp'].includes(detectedLang) ? detectedLang : 'java');
+                // cognium-ai#348 — no silent coercion of non-Java sources to `java`.
+                const bundleLang = resolveBundleLanguage(targetPath);
                 const bundleResult = await runBundle(args.bundle, sourceCode, targetPath, {
                     language: bundleLang,
                 });
@@ -212,8 +248,10 @@ export async function executeAnalyze(args) {
                 exclude,
                 quiet: args.quiet,
                 maxConcurrency: args.threads,
-                enableEnrichment: !args.noLlm,
-                enableVerification: !args.noLlm,
+                enableEnrichment: llmFlags.enableEnrichment,
+                enableVerification: llmFlags.enableVerification,
+                // cognium-ai#348 — honor --language on the default action (was ignored).
+                language: args.language ?? undefined,
                 cacheEnabled: args.cache,
                 cacheDir: args.cacheDir ?? undefined,
                 clearCache: args.clearCache,
@@ -237,9 +275,9 @@ export async function executeAnalyze(args) {
         const sourceCode = fs.readFileSync(targetPath, 'utf-8');
         const detectedLang = detectLanguageFromFile(targetPath);
         const mastraResult = await analyzeFile(targetPath, sourceCode, {
-            language: detectedLang,
-            enableEnrichment: !args.noLlm,
-            enableVerification: !args.noLlm,
+            language: args.language ?? detectedLang,
+            enableEnrichment: llmFlags.enableEnrichment,
+            enableVerification: llmFlags.enableVerification,
             disabledPasses: mergedDisabledPasses.length > 0 ? mergedDisabledPasses : undefined,
         });
         const result = {

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package/dist/cli/commands/health.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"health.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/health.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AASH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAI1C;;GAEG;AACH,wBAAsB,aAAa,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAqFlE"}
+{"version":3,"file":"health.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/health.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AASH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAK1C;;GAEG;AACH,wBAAsB,aAAa,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA8FlE"}

package/dist/cli/commands/health.js

@@ -7,11 +7,15 @@ import * as fs from 'fs';
 import { calculateHealthScore, formatHealthReport, } from 'circle-ir-ai';
 import { getEffectiveOptions } from '../effective-options.js';
 import { resolveProjectProfileForEngine } from '../project-profile.js';
+import { applyIsolateParseEnv, buildInnerScanOptions } from '../inner-scan-options.js';
 /**
  * Execute health score command.
  */
 export async function executeHealth(args) {
     const targetPath = args.directory || process.cwd();
+    // cognium-ai#348 — health advertises --isolate-parse (addCommonOptions
+    // discovery) but never read it. Same env handoff as scan/trust.
+    applyIsolateParseEnv(args);
     if (!fs.existsSync(targetPath)) {
         console.error(`Error: Path not found: ${targetPath}`);
         return 1;
@@ -25,7 +29,7 @@ export async function executeHealth(args) {
     // vulnerability counts match `cognium-ai scan --llm` on the same
     // repo. Without this the inner scan ran static-only regardless of
     // LLM configuration.
-    const llmEnabled = !args.noLlm;
+    // (enableLLM itself is resolved inside buildInnerScanOptions.)
     // cognium-ai#130: thread projectProfile via the inner ScanOptions
     // since circle-ir-ai 2.19.0's HealthScoreOptions doesn't expose
     // projectProfile directly — it delegates to the security scanner.
@@ -38,10 +42,11 @@ export async function executeHealth(args) {
         includePerformance: args.healthPerformance,
         includePatterns: eff.include.length > 0 ? eff.include : undefined,
         excludePatterns: eff.exclude.length > 0 ? eff.exclude : undefined,
-        scanOptions: {
-            enableLLM: llmEnabled,
-            projectProfile: projectProfile,
-        },
+        // cognium-ai#348 — forward every advertised scan flag (--no-llm-verify,
+        // --language, --file-timeout, --max-scan-time, -t, include/exclude) into
+        // the inner security scan, matching scan.ts and post-#324 trust.ts. Before
+        // this only enableLLM + projectProfile reached the engine.
+        scanOptions: buildInnerScanOptions(args, eff, projectProfile),
         onProgress: args.quiet ? undefined : (phase, progress) => {
             console.error(`[${phase}] ${Math.round(progress * 100)}%`);
         },

package/dist/cli/commands/health.js.map

@@ -1 +1 @@
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package/dist/cli/commands/quality.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"quality.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/quality.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAU1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA0FnE"}
+{"version":3,"file":"quality.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/quality.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAW1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAkGnE"}

package/dist/cli/commands/quality.js

@@ -14,6 +14,7 @@ import * as fs from 'fs';
 import { runQualityScore as calculateQualityScore, formatQualityReport, generateQualityBadge, } from 'circle-ir-ai';
 import { getEffectiveOptions } from '../effective-options.js';
 import { resolveProjectProfileForEngine } from '../project-profile.js';
+import { applyIsolateParseEnv, buildInnerScanOptions } from '../inner-scan-options.js';
 export async function executeQuality(args) {
     const targetPath = args.directory || args.file;
     if (!targetPath) {
@@ -25,15 +26,17 @@ export async function executeQuality(args) {
         console.error(`Error: Path not found: ${targetPath}`);
         return 1;
     }
+    // cognium-ai#348 — quality advertises --isolate-parse but never read it.
+    applyIsolateParseEnv(args);
     // #56: honor cognium.config.json include/exclude (and CLI flags),
     // matching how scan / analyze / dead-code already do via
     // getEffectiveOptions(). Without this, the file walk only applied
     // built-in regex skips (node_modules, .git, etc.) and the reported
     // Files/LOC ignored user excludes entirely.
     const eff = getEffectiveOptions(args, targetPath);
-    // #44: forward LLM enable through to the inner security scan via
-    // QualityScoreOptions.scanOptions → HealthScoreOptions.scanOptions.
-    const llmEnabled = !args.noLlm;
+    // #44: LLM enable is forwarded to the inner security scan via
+    // QualityScoreOptions.scanOptions → HealthScoreOptions.scanOptions
+    // (resolved inside buildInnerScanOptions below).
     // cognium-ai#130: thread projectProfile via inner ScanOptions (the
     // quality calculator delegates the security scan).
     const projectProfile = await resolveProjectProfileForEngine(targetPath, eff.profile);
@@ -46,10 +49,11 @@ export async function executeQuality(args) {
                 },
             includePatterns: eff.include.length > 0 ? eff.include : undefined,
             excludePatterns: eff.exclude.length > 0 ? eff.exclude : undefined,
-            scanOptions: {
-                enableLLM: llmEnabled,
-                projectProfile: projectProfile,
-            },
+            // cognium-ai#348 — forward --language / --file-timeout / --max-scan-time
+            // / -t / include/exclude (and the LLM verify switch) into the inner
+            // security scan, matching scan.ts and trust.ts. Before this only
+            // enableLLM + projectProfile reached the engine.
+            scanOptions: buildInnerScanOptions(args, eff, projectProfile),
         });
         if (args.format === 'json') {
             const jsonOutput = JSON.stringify(result, null, 2);

package/dist/cli/commands/quality.js.map

@@ -1 +1 @@
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package/dist/cli/commands/scan.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/scan.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAGH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAanD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAU1C;;;;;;;;;;;;GAYG;AACH,eAAO,MAAM,sBAAsB,EAAE,SAAS,iBAAiB,EAE9D,CAAC;AAEF;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,iBAAiB,EAAE,CAGrE;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAwYhE"}
+{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/scan.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAGH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAanD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAW1C;;;;;;;;;;;;GAYG;AACH,eAAO,MAAM,sBAAsB,EAAE,SAAS,iBAAiB,EAE9D,CAAC;AAEF;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,iBAAiB,EAAE,CAGrE;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAoZhE"}

package/dist/cli/commands/scan.js

@@ -14,6 +14,7 @@ import { applyFindingsCap } from '../findings-cap.js';
 import { capSeverityByExploitability, capVerifierInflation } from '../severity-policy.js';
 import { enrichScanSarif } from '../formatters/scan-sarif-enrich.js';
 import { resolveProjectProfileForEngine } from '../project-profile.js';
+import { armScanWatchdog, watchdogEnabled } from '../scan-watchdog.js';
 /**
  * Languages `scan` collects by default (no explicit `--language`). These are the
  * languages circle-ir runs security passes on. `c` / `cpp` are supported by the
@@ -198,7 +199,20 @@ export async function executeScan(args) {
         // cognium-ai#166 L1 — zero the process-wide truncation counter so
         // the snapshot after the scan reflects only this run.
         resetTruncationCount();
-        const rawResult = await scanDirectory(targetPath, options);
+        // cognium-ai#315 — a worker-thread deadline that survives a wedged main loop:
+        // guarantees PARTIAL JSON + [DEGRADED] + exit at maxScanMs + grace even when
+        // the cooperative #252 budget never gets to run.
+        const watchdog = options.maxScanMs !== undefined && watchdogEnabled()
+            ? await armScanWatchdog({ target: targetPath, maxScanMs: options.maxScanMs, outputPath: args.output, format: args.format })
+            : null;
+        let rawResult;
+        try {
+            rawResult = await scanDirectory(targetPath, options);
+        }
+        finally {
+            if (watchdog)
+                await watchdog.disarm();
+        }
         const truncationCount = snapshotTruncationCount();
         // cognium-ai#217/#228 — surface a `degraded: llm-unavailable` signal when
         // the LLM breaker tripped during this scan, so the output (and the harness)

package/dist/cli/commands/scan.js.map

@@ -1 +1 @@
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package/dist/cli/commands/swarm.d.ts

@@ -2,10 +2,34 @@
  * Swarm Command - Parallel multi-file analysis using Mastra
  */
 import { type SwarmResult } from 'circle-ir-ai';
+import { type SupportedLanguage } from '../file-collection.js';
+/**
+ * cognium-ai#348 — languages the default `cognium-ai <path>` walk collects.
+ *
+ * The engine's `analyzeFilesSwarm` detects a file's language from its
+ * extension and only takes a *request-level* `language` override (no per-file
+ * field), and its detector knows java/js/ts/tsx/py/rs/go/c/cpp — any other
+ * extension falls back to `java`. So the default walk is restricted to the
+ * scanned languages the swarm can route on its own; `csharp` / `bash` / `html`
+ * are collected only when `--language` names one of them (the request-level
+ * override then routes them correctly). `c` / `cpp` are not walked at all:
+ * `scan` already rejects them (#312 — no tree-sitter-c/cpp WASM shipped) and
+ * the old default include list produced PARSER_FAIL on every `.c`/`.h`.
+ *
+ * Pinned against DEFAULT_SCAN_LANGUAGES by `autofix-348-default-action.test.ts`.
+ */
+export declare const SWARM_AUTODETECT_LANGUAGES: readonly SupportedLanguage[];
+/** Scanned languages that need an explicit `--language` on the default action. */
+export declare const SWARM_EXPLICIT_ONLY_LANGUAGES: readonly SupportedLanguage[];
+export declare function resolveSwarmLanguages(language: string | null | undefined): SupportedLanguage[];
+/** Default exclude globs when the user passes none (pre-#348 behaviour, kept). */
+export declare const SWARM_DEFAULT_EXCLUDES: readonly string[];
 export interface SwarmOptions {
     directory: string;
     include: string[];
     exclude: string[];
+    /** cognium-ai#348 — `--language`: restricts discovery and is forwarded to the engine. */
+    language?: string;
     quiet: boolean;
     maxConcurrency: number;
     enableEnrichment: boolean;

package/dist/cli/commands/swarm.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"swarm.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/swarm.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,OAAO,EAML,KAAK,WAAW,EACjB,MAAM,cAAc,CAAC;AAKtB,MAAM,WAAW,YAAY;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,OAAO,CAAC;IACf,cAAc,EAAE,MAAM,CAAC;IACvB,gBAAgB,EAAE,OAAO,CAAC;IAC1B,kBAAkB,EAAE,OAAO,CAAC;IAE5B,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,OAAO,CAAC;IAErB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;IAE1B,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;CAC3B;AAED,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAuHlF"}
+{"version":3,"file":"swarm.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/swarm.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,OAAO,EAML,KAAK,WAAW,EACjB,MAAM,cAAc,CAAC;AACtB,OAAO,EAAgB,KAAK,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAK7E;;;;;;;;;;;;;;GAcG;AACH,eAAO,MAAM,0BAA0B,EAAE,SAAS,iBAAiB,EAElE,CAAC;AAEF,kFAAkF;AAClF,eAAO,MAAM,6BAA6B,EAAE,SAAS,iBAAiB,EAA+B,CAAC;AAEtG,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,iBAAiB,EAAE,CAG9F;AAED,kFAAkF;AAClF,eAAO,MAAM,sBAAsB,EAAE,SAAS,MAAM,EAGnD,CAAC;AAEF,MAAM,WAAW,YAAY;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,yFAAyF;IACzF,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,OAAO,CAAC;IACf,cAAc,EAAE,MAAM,CAAC;IACvB,gBAAgB,EAAE,OAAO,CAAC;IAC1B,kBAAkB,EAAE,OAAO,CAAC;IAE5B,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,OAAO,CAAC;IAErB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;IAE1B,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;CAC3B;AAED,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CA2HlF"}

package/dist/cli/commands/swarm.js

@@ -4,29 +4,60 @@
 import * as fs from 'fs';
 import * as path from 'path';
 import { analyzeFilesSwarm, FileCache, logger, } from 'circle-ir-ai';
-import { discoverFiles } from '../discovery.js';
+import { collectFiles } from '../file-collection.js';
+import { expandScanLanguages } from './scan.js';
 import { colors } from '../colors.js';
 const { cyan, green, yellow, red, dim, bold } = colors;
+/**
+ * cognium-ai#348 — languages the default `cognium-ai <path>` walk collects.
+ *
+ * The engine's `analyzeFilesSwarm` detects a file's language from its
+ * extension and only takes a *request-level* `language` override (no per-file
+ * field), and its detector knows java/js/ts/tsx/py/rs/go/c/cpp — any other
+ * extension falls back to `java`. So the default walk is restricted to the
+ * scanned languages the swarm can route on its own; `csharp` / `bash` / `html`
+ * are collected only when `--language` names one of them (the request-level
+ * override then routes them correctly). `c` / `cpp` are not walked at all:
+ * `scan` already rejects them (#312 — no tree-sitter-c/cpp WASM shipped) and
+ * the old default include list produced PARSER_FAIL on every `.c`/`.h`.
+ *
+ * Pinned against DEFAULT_SCAN_LANGUAGES by `autofix-348-default-action.test.ts`.
+ */
+export const SWARM_AUTODETECT_LANGUAGES = [
+    'java', 'javascript', 'typescript', 'tsx', 'python', 'rust', 'go',
+];
+/** Scanned languages that need an explicit `--language` on the default action. */
+export const SWARM_EXPLICIT_ONLY_LANGUAGES = ['csharp', 'bash', 'html'];
+export function resolveSwarmLanguages(language) {
+    if (language)
+        return expandScanLanguages(language);
+    return [...SWARM_AUTODETECT_LANGUAGES];
+}
+/** Default exclude globs when the user passes none (pre-#348 behaviour, kept). */
+export const SWARM_DEFAULT_EXCLUDES = [
+    '**/test/**', '**/tests/**', '**/*Test.java', '**/*_test.rs',
+    '**/node_modules/**', '**/target/**', '**/build/**',
+];
 export async function runSwarmAnalysis(options) {
     const startTime = Date.now();
     // Discover files
     if (!options.quiet) {
         console.error(cyan(`Discovering files in ${options.directory}...`));
     }
-    const discoveryOpts = {
-        include: options.include.length > 0 ? options.include : [
-            '**/*.java',
-            '**/*.js', '**/*.ts', '**/*.jsx', '**/*.tsx',
-            '**/*.py',
-            '**/*.rs',
-            '**/*.c', '**/*.cpp', '**/*.h', '**/*.hpp',
-        ],
-        exclude: options.exclude.length > 0 ? options.exclude : [
-            '**/test/**', '**/tests/**', '**/*Test.java', '**/*_test.rs',
-            '**/node_modules/**', '**/target/**', '**/build/**',
-        ],
-    };
-    const discoveredFiles = discoverFiles(options.directory, discoveryOpts);
+    // cognium-ai#348 — discover through the same minimatch-based collector
+    // `scan` uses (file-collection.ts) instead of a stale parallel walker with
+    // a hand-rolled glob translator (`**/*.py` → `.*/[^/]*\.py` never matched a
+    // root-level file) and a C/C++ include the engine cannot parse.
+    const languages = resolveSwarmLanguages(options.language);
+    const discoveredFiles = collectFiles(options.directory, {
+        include: options.include.length > 0 ? options.include : undefined,
+        exclude: options.exclude.length > 0 ? options.exclude : [...SWARM_DEFAULT_EXCLUDES],
+        languages,
+    });
+    if (!options.quiet && !options.language) {
+        console.error(dim(`Languages: ${languages.join(', ')} (pass --language <${SWARM_EXPLICIT_ONLY_LANGUAGES.join('|')}> ` +
+            'to analyze those, or use `cognium-ai scan`)'));
+    }
     if (discoveredFiles.length === 0) {
         console.error(yellow('No files found to analyze.'));
         return {
@@ -79,8 +110,11 @@ export async function runSwarmAnalysis(options) {
         process.stderr.write(`\r${cyan(`Progress: ${completed}/${files.length} (${percent}%)`)}`);
     }, 500);
     try {
-        // Run swarm analysis (language auto-detected per file from extension)
+        // Run swarm analysis (language auto-detected per file from extension;
+        // cognium-ai#348 — an explicit --language is forwarded as the engine's
+        // request-level override so csharp/bash/html files route correctly)
         const result = await analyzeFilesSwarm(files, {
+            language: options.language,
             enableEnrichment: options.enableEnrichment,
             enableVerification: options.enableVerification,
             maxConcurrency: options.maxConcurrency,

package/dist/cli/commands/swarm.js.map

@@ -1 +1 @@
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+{"version":3,"file":"swarm.js","sourceRoot":"","sources":["../../../src/cli/commands/swarm.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,EACL,iBAAiB,EACjB,SAAS,EACT,MAAM,GAIP,MAAM,cAAc,CAAC;AACtB,OAAO,EAAE,YAAY,EAA0B,MAAM,uBAAuB,CAAC;AAC7E,OAAO,EAA0B,mBAAmB,EAAE,MAAM,WAAW,CAAC;AACxE,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AACtC,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,MAAM,CAAC;AAEvD;;;;;;;;;;;;;;GAcG;AACH,MAAM,CAAC,MAAM,0BAA0B,GAAiC;IACtE,MAAM,EAAE,YAAY,EAAE,YAAY,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI;CAClE,CAAC;AAEF,kFAAkF;AAClF,MAAM,CAAC,MAAM,6BAA6B,GAAiC,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;AAEtG,MAAM,UAAU,qBAAqB,CAAC,QAAmC;IACvE,IAAI,QAAQ;QAAE,OAAO,mBAAmB,CAAC,QAAQ,CAAmC,CAAC;IACrF,OAAO,CAAC,GAAG,0BAA0B,CAAC,CAAC;AACzC,CAAC;AAED,kFAAkF;AAClF,MAAM,CAAC,MAAM,sBAAsB,GAAsB;IACvD,YAAY,EAAE,aAAa,EAAE,eAAe,EAAE,cAAc;IAC5D,oBAAoB,EAAE,cAAc,EAAE,aAAa;CACpD,CAAC;AAuBF,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,OAAqB;IAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;IAE7B,iBAAiB;IACjB,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;QACnB,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,wBAAwB,OAAO,CAAC,SAAS,KAAK,CAAC,CAAC,CAAC;IACtE,CAAC;IAED,uEAAuE;IACvE,2EAA2E;IAC3E,4EAA4E;IAC5E,gEAAgE;IAChE,MAAM,SAAS,GAAG,qBAAqB,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC1D,MAAM,eAAe,GAAG,YAAY,CAAC,OAAO,CAAC,SAAS,EAAE;QACtD,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS;QACjE,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,sBAAsB,CAAC;QACnF,SAAS;KACV,CAAC,CAAC;IACH,IAAI,CAAC,OAAO,CAAC,KAAK,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QACxC,OAAO,CAAC,KAAK,CAAC,GAAG,CACf,cAAc,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,sBAAsB,6BAA6B,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI;YACnG,6CAA6C,CAC9C,CAAC,CAAC;IACL,CAAC;IAED,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACjC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,4BAA4B,CAAC,CAAC,CAAC;QACpD,OAAO;YACL,OAAO,EAAE,EAAE;YACX,OAAO,EAAE;gBACP,UAAU,EAAE,CAAC;gBACb,oBAAoB,EAAE,CAAC;gBACvB,YAAY,EAAE,CAAC;gBACf,UAAU,EAAE,CAAC;gBACb,wBAAwB,EAAE,CAAC;gBAC3B,WAAW,EAAE,CAAC;gBACd,cAAc,EAAE,CAAC;aAClB;SACF,CAAC;IACJ,CAAC;IAED,8BAA8B;IAC9B,MAAM,YAAY,GAAG,OAAO,CAAC,YAAY,KAAK,KAAK,CAAC;IACpD,IAAI,KAAwC,CAAC;IAE7C,IAAI,YAAY,EAAE,CAAC;QACjB,KAAK,GAAG,IAAI,SAAS,CAAa;YAChC,QAAQ,EAAE,OAAO,CAAC,QAAQ,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,kBAAkB,CAAC;YAC5F,OAAO,EAAE,IAAI;SACd,CAAC,CAAC;QAEH,2BAA2B;QAC3B,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC;YACvB,KAAK,CAAC,KAAK,EAAE,CAAC;YACd,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;gBACnB,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC;YACvC,CAAC;QACH,CAAC;QAED,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACnB,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC;QACvC,CAAC;IACH,CAAC;IAED,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;QACnB,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,eAAe,CAAC,MAAM,mBAAmB,CAAC,CAAC,CAAC;QACxE,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,OAAO,CAAC,cAAc,mBAAmB,CAAC,CAAC,CAAC;QACxE,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACpB,CAAC;IAED,oDAAoD;IACpD,8DAA8D;IAC9D,MAAM,KAAK,GAAgB,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACtD,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,UAAU,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC;KACtD,CAAC,CAAC,CAAC;IAEJ,oBAAoB;IACpB,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,MAAM,gBAAgB,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE;QAC/D,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,CAAC,CAAC;QAC7D,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,aAAa,SAAS,IAAI,KAAK,CAAC,MAAM,KAAK,OAAO,IAAI,CAAC,EAAE,CAAC,CAAC;IAC5F,CAAC,EAAE,GAAG,CAAC,CAAC;IAER,IAAI,CAAC;QACH,sEAAsE;QACtE,uEAAuE;QACvE,oEAAoE;QACpE,MAAM,MAAM,GAAG,MAAM,iBAAiB,CAAC,KAAK,EAAE;YAC5C,QAAQ,EAAE,OAAO,CAAC,QAAQ;YAC1B,gBAAgB,EAAE,OAAO,CAAC,gBAAgB;YAC1C,kBAAkB,EAAE,OAAO,CAAC,kBAAkB;YAC9C,cAAc,EAAE,OAAO,CAAC,cAAc;YACtC,KAAK;YACL,YAAY;YACZ,YAAY,EAAE,OAAO,CAAC,YAAY;YAClC,eAAe,EAAE,OAAO,CAAC,eAAe;YACxC,cAAc,EAAE,OAAO,CAAC,cAAc;YACtC,cAAc,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,EAAE;gBACrC,SAAS,GAAG,KAAK,GAAG,CAAC,CAAC;gBACtB,MAAM,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;YACtD,CAAC;YACD,eAAe,EAAE,OAAO,CAAC,YAAY,IAAI,CAAC,OAAO,CAAC,KAAK;gBACrD,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,uBAAuB,IAAI,EAAE,CAAC;gBAC9D,CAAC,CAAC,SAAS;SACd,CAAC,CAAC;QAEH,IAAI,gBAAgB,EAAE,CAAC;YACrB,aAAa,CAAC,gBAAgB,CAAC,CAAC;YAChC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC;QACrD,CAAC;QAED,gBAAgB;QAChB,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACnB,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,CAAC,CAAC;QACtD,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;YAAS,CAAC;QACT,IAAI,gBAAgB,EAAE,CAAC;YACrB,aAAa,CAAC,gBAAgB,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,YAAY,CAAC,MAAmB,EAAE,WAAmB,EAAE,KAA6B;IAC3F,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IAClB,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC,CAAC;IACvF,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,kEAAkE,CAAC,CAAC,CAAC;IACxF,OAAO,CAAC,KA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package/dist/cli/inner-scan-options.d.ts

@@ -0,0 +1,41 @@
+/**
+ * cognium-ai#348 — shared inner-scan option builder.
+ *
+ * `health` and `quality` register the same discovery / LLM / budget flags as
+ * `scan` (via `addCommonOptions`) and both delegate their security dimension to
+ * the engine's `scanDirectory()` through `scanOptions`. Until #348 those two
+ * handlers forwarded only `{ enableLLM, projectProfile }`, so every other
+ * advertised flag — `--no-llm-verify`, `--language`, `--file-timeout`,
+ * `--max-scan-time`, `--isolate-parse`, `-t` — was a silent no-op on the inner
+ * scan. `trust` got the same wiring under #321/#322/#324; this module lifts that
+ * block into one place so the three commands cannot drift apart again.
+ */
+import type { ScanOptions } from 'circle-ir-ai';
+import type { CliArgs } from './args.js';
+import type { EffectiveOptions } from './effective-options.js';
+/**
+ * #252 — `--isolate-parse` is communicated to the engine via env (same shape
+ * as the LLM knobs) so every engine entry point picks it up. Mirrors scan.ts /
+ * trust.ts; call before the first engine invocation.
+ */
+export declare function applyIsolateParseEnv(args: Pick<CliArgs, 'isolateParse'>): void;
+/**
+ * Resolve the language list the inner scan should walk — the same rule as
+ * `scan` / `trust`: an explicit `--language` (with the #311 typescript→tsx
+ * expansion), otherwise the full default scanned set.
+ */
+export declare function resolveInnerScanLanguages(language: string | null | undefined): ScanOptions['languages'];
+/**
+ * Build the `scanOptions` forwarded to the engine's inner security scan by
+ * `health` / `quality`. Field-for-field the contract `scan` and post-#324
+ * `trust` already honor:
+ *
+ * - `enableLLMVerify` follows `--llm-verify` / `--no-llm-verify` (#124/#324),
+ *   gated on `--llm` so `--no-llm --llm-verify` is unambiguous.
+ * - `fileTimeoutMs` / `maxScanMs` / `maxConcurrency` follow `--file-timeout` /
+ *   `--max-scan-time` / `-t` (#321).
+ * - `languages` follows `--language` (#322).
+ * - `includePatterns` / `excludePatterns` follow the effective include/exclude.
+ */
+export declare function buildInnerScanOptions(args: Pick<CliArgs, 'noLlm' | 'fileTimeout' | 'maxScanTime' | 'threads' | 'language'>, eff: Pick<EffectiveOptions, 'llm' | 'include' | 'exclude'>, projectProfile: ScanOptions['projectProfile'] | undefined): Partial<ScanOptions>;
+//# sourceMappingURL=inner-scan-options.d.ts.map

package/dist/cli/inner-scan-options.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/inner-scan-options.js

@@ -0,0 +1,60 @@
+/**
+ * cognium-ai#348 — shared inner-scan option builder.
+ *
+ * `health` and `quality` register the same discovery / LLM / budget flags as
+ * `scan` (via `addCommonOptions`) and both delegate their security dimension to
+ * the engine's `scanDirectory()` through `scanOptions`. Until #348 those two
+ * handlers forwarded only `{ enableLLM, projectProfile }`, so every other
+ * advertised flag — `--no-llm-verify`, `--language`, `--file-timeout`,
+ * `--max-scan-time`, `--isolate-parse`, `-t` — was a silent no-op on the inner
+ * scan. `trust` got the same wiring under #321/#322/#324; this module lifts that
+ * block into one place so the three commands cannot drift apart again.
+ */
+import { DEFAULT_SCAN_LANGUAGES, expandScanLanguages } from './commands/scan.js';
+/**
+ * #252 — `--isolate-parse` is communicated to the engine via env (same shape
+ * as the LLM knobs) so every engine entry point picks it up. Mirrors scan.ts /
+ * trust.ts; call before the first engine invocation.
+ */
+export function applyIsolateParseEnv(args) {
+    if (args.isolateParse) {
+        process.env.SCAN_PARSE_ISOLATION = '1';
+    }
+}
+/**
+ * Resolve the language list the inner scan should walk — the same rule as
+ * `scan` / `trust`: an explicit `--language` (with the #311 typescript→tsx
+ * expansion), otherwise the full default scanned set.
+ */
+export function resolveInnerScanLanguages(language) {
+    return (language
+        ? expandScanLanguages(language)
+        : [...DEFAULT_SCAN_LANGUAGES]);
+}
+/**
+ * Build the `scanOptions` forwarded to the engine's inner security scan by
+ * `health` / `quality`. Field-for-field the contract `scan` and post-#324
+ * `trust` already honor:
+ *
+ * - `enableLLMVerify` follows `--llm-verify` / `--no-llm-verify` (#124/#324),
+ *   gated on `--llm` so `--no-llm --llm-verify` is unambiguous.
+ * - `fileTimeoutMs` / `maxScanMs` / `maxConcurrency` follow `--file-timeout` /
+ *   `--max-scan-time` / `-t` (#321).
+ * - `languages` follows `--language` (#322).
+ * - `includePatterns` / `excludePatterns` follow the effective include/exclude.
+ */
+export function buildInnerScanOptions(args, eff, projectProfile) {
+    const llmEnabled = !args.noLlm;
+    return {
+        enableLLM: llmEnabled,
+        enableLLMVerify: llmEnabled ? eff.llm.verify : false,
+        fileTimeoutMs: args.fileTimeout * 1000,
+        maxScanMs: args.maxScanTime ? args.maxScanTime * 1000 : undefined,
+        maxConcurrency: args.threads,
+        languages: resolveInnerScanLanguages(args.language),
+        includePatterns: eff.include.length > 0 ? eff.include : undefined,
+        excludePatterns: eff.exclude.length > 0 ? eff.exclude : undefined,
+        projectProfile,
+    };
+}
+//# sourceMappingURL=inner-scan-options.js.map

package/dist/cli/inner-scan-options.js.map

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package/dist/cli/scan-watchdog.d.ts

@@ -0,0 +1,68 @@
+export interface WatchdogInfo {
+    target: string;
+    maxScanMs: number;
+    graceMs: number;
+    startedAt: number;
+    firedAt: number;
+}
+/** The PARTIAL result the watchdog emits — the scan JSON's top-level shape, empty. */
+export declare function buildWatchdogPartialResult(info: WatchdogInfo): {
+    meta: {
+        target: string;
+        timestamp: string;
+        durationMs: number;
+        degraded: boolean;
+        degradedReason: string;
+        degradedDetail: string;
+        maxScanMs: number;
+        filesAnalyzed: number;
+    };
+    findings: never[];
+    byOWASP: {};
+    summary: {
+        totalFiles: number;
+        totalLOC: number;
+        totalFindings: number;
+        bySeverity: {
+            critical: number;
+            high: number;
+            medium: number;
+            low: number;
+        };
+        byType: {};
+    };
+    files: never[];
+    parseFailures: never[];
+    totalFindings: number;
+    tier: string;
+    tiers: {
+        static_high_confidence: never[];
+        llm_enriched: never[];
+    };
+    degraded: string;
+};
+export interface ArmOptions {
+    target: string;
+    maxScanMs: number;
+    /** Output file (`-o`); `null` writes to stdout (fd 1). */
+    outputPath: string | null;
+    /** Only JSON is emitted by the watchdog; other formats get the `[DEGRADED]` line + exit. */
+    format: string;
+    graceMs?: number;
+    /** Signal to send (default SIGKILL — the only signal a wedged main thread cannot swallow). */
+    signal?: NodeJS.Signals;
+}
+export interface ArmedWatchdog {
+    disarm(): Promise<void>;
+    readonly graceMs: number;
+}
+export declare function watchdogGraceMs(): number;
+export declare function watchdogEnabled(): boolean;
+/**
+ * Arm the watchdog. Resolves once the worker is actually running (`online`), bounded
+ * to 2 s: a worker only starts executing after the main loop yields once, so arming
+ * synchronously and then wedging immediately would leave it never started. The
+ * returned handle's `disarm()` must be awaited when the scan returns.
+ */
+export declare function armScanWatchdog(opts: ArmOptions): Promise<ArmedWatchdog>;
+//# sourceMappingURL=scan-watchdog.d.ts.map

package/dist/cli/scan-watchdog.d.ts.map

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package/dist/cli/scan-watchdog.js

@@ -0,0 +1,127 @@
+/**
+ * cognium-ai#315 — hard scan-deadline watchdog.
+ *
+ * `--max-scan-time` (#252) is enforced cooperatively: the engine checks the
+ * budget between files and `awaitWorkersWithDeadline` arms a `setTimeout`. Both
+ * live on the main event loop, so a synchronous wedge (a pathological parse, a
+ * sync read, a tight loop under 429 back-off) blocks the deadline itself and the
+ * process runs until the orchestrator SIGKILLs it — with **no JSON and no
+ * `[DEGRADED]` line** (markdown-preview.nvim, #315).
+ *
+ * A worker thread has its own event loop and is not blocked by the main thread.
+ * At `maxScanMs + graceMs` it writes a schema-compatible PARTIAL result straight
+ * to the output descriptor with `fs.writeSync` (an OS-level write — a worker's
+ * `process.stdout` would route through the wedged main thread, so it is not
+ * used), prints the `[DEGRADED]` line to fd 2, and terminates the process with
+ * SIGTERM. The contract "hitting the budget always yields PARTIAL JSON and
+ * exits" therefore holds even when the main loop cannot run.
+ *
+ * Disarmed (worker terminated) the moment the scan returns normally, so a
+ * healthy run never sees it. Kill switch: `SCAN_WATCHDOG=0`.
+ *
+ * Known non-case: under `node -e` (an eval'd main script) worker timers never
+ * fire while the main thread is wedged; the CLI always runs from a file
+ * (dist/cli.js), where they do — the integration test spawns a file for that reason.
+ * Grace: `SCAN_WATCHDOG_GRACE_MS` (default 30 000 ms) — the cooperative path
+ * gets that long to finish its own partial emit before the watchdog fires.
+ */
+import { Worker } from 'node:worker_threads';
+/** The PARTIAL result the watchdog emits — the scan JSON's top-level shape, empty. */
+export function buildWatchdogPartialResult(info) {
+    return {
+        meta: {
+            target: info.target,
+            timestamp: new Date(info.firedAt).toISOString(),
+            durationMs: info.firedAt - info.startedAt,
+            degraded: true,
+            degradedReason: 'watchdog',
+            degradedDetail: `cognium-ai#315: scan budget (${info.maxScanMs}ms) exceeded by more than the ${info.graceMs}ms grace and the main thread did not yield; watchdog emitted this partial result and terminated the process. Findings gathered before the wedge are not available.`,
+            maxScanMs: info.maxScanMs,
+            filesAnalyzed: 0,
+        },
+        findings: [],
+        byOWASP: {},
+        summary: { totalFiles: 0, totalLOC: 0, totalFindings: 0, bySeverity: { critical: 0, high: 0, medium: 0, low: 0 }, byType: {} },
+        files: [],
+        parseFailures: [],
+        totalFindings: 0,
+        tier: 'static',
+        tiers: { static_high_confidence: [], llm_enriched: [] },
+        degraded: 'watchdog',
+    };
+}
+export function watchdogGraceMs() {
+    const v = Number(process.env.SCAN_WATCHDOG_GRACE_MS);
+    return Number.isFinite(v) && v >= 0 ? v : 30_000;
+}
+export function watchdogEnabled() {
+    return process.env.SCAN_WATCHDOG !== '0';
+}
+// Runs inside the worker (CommonJS eval context). Kept as a string so it needs no
+// separate file to resolve in dev (tsx) and dist (compiled) alike.
+const WORKER_SOURCE = `
+const { workerData } = require('node:worker_threads');
+const fs = require('node:fs');
+const { maxScanMs, graceMs, outputPath, format, target, startedAt, signal, partialBuilder } = workerData;
+const build = new Function('info', partialBuilder);
+setTimeout(() => {
+  const firedAt = Date.now();
+  const info = { target, maxScanMs, graceMs, startedAt, firedAt };
+  let wrote = 'nothing';
+  try {
+    if (format === 'json') {
+      const json = JSON.stringify(build(info), null, 2) + '\\n';
+      if (outputPath) { fs.writeFileSync(outputPath, json); wrote = outputPath; }
+      else { fs.writeSync(1, json); wrote = 'stdout'; }
+    }
+  } catch (e) { wrote = 'FAILED: ' + (e && e.message ? e.message : String(e)); }
+  try {
+    fs.writeSync(2, '[DEGRADED] cognium-ai#315: scan budget (' + maxScanMs + 'ms) exceeded by >' + graceMs + 'ms grace with the main thread wedged; watchdog wrote PARTIAL result (' + wrote + ') and is terminating the process (' + signal + ').\\n');
+  } catch {}
+  try { process.kill(process.pid, signal); } catch {}
+}, Math.max(0, maxScanMs + graceMs - (Date.now() - startedAt)));
+`;
+/**
+ * Arm the watchdog. Resolves once the worker is actually running (`online`), bounded
+ * to 2 s: a worker only starts executing after the main loop yields once, so arming
+ * synchronously and then wedging immediately would leave it never started. The
+ * returned handle's `disarm()` must be awaited when the scan returns.
+ */
+export async function armScanWatchdog(opts) {
+    const graceMs = opts.graceMs ?? watchdogGraceMs();
+    const startedAt = Date.now();
+    // Ship the builder's body so the worker produces exactly `buildWatchdogPartialResult`.
+    const src = buildWatchdogPartialResult.toString();
+    const body = src.slice(src.indexOf('{') + 1, src.lastIndexOf('}'));
+    const worker = new Worker(WORKER_SOURCE, {
+        eval: true,
+        workerData: {
+            maxScanMs: opts.maxScanMs,
+            graceMs,
+            outputPath: opts.outputPath,
+            format: opts.format,
+            target: opts.target,
+            startedAt,
+            signal: opts.signal ?? 'SIGKILL',
+            partialBuilder: body,
+        },
+    });
+    worker.unref(); // never keeps a finished scan alive
+    worker.on('error', () => { });
+    await new Promise((resolve) => {
+        // The timer is deliberately ref'd: the worker is unref'd, so this bounded wait
+        // is the only thing keeping the loop alive until `online` (or the 2 s cap).
+        const t = setTimeout(resolve, 2_000);
+        worker.once('online', () => { clearTimeout(t); resolve(); });
+    });
+    return {
+        graceMs,
+        async disarm() {
+            try {
+                await worker.terminate();
+            }
+            catch { /* already gone */ }
+        },
+    };
+}
+//# sourceMappingURL=scan-watchdog.js.map

package/dist/cli/scan-watchdog.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cognium-ai",
-  "version": "4.10.0",
+  "version": "4.11.0",
   "description": "AI-powered static analysis CLI with LLM-enhanced vulnerability detection",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -42,8 +42,8 @@
   ],
   "dependencies": {
     "@cognium/project-profile-detect": "^1.1.0",
-    "circle-ir": "4.9.9",
-    "circle-ir-ai": "^4.10.0",
+    "circle-ir": "4.9.10",
+    "circle-ir-ai": "^4.11.0",
     "commander": "^14.0.3",
     "minimatch": "^10.2.5"
   },