cognium-ai 2.11.5 → 2.14.0

package/dist/cli/args.d.ts

@@ -67,10 +67,11 @@ export interface CliArgs {
     fileTimeout: number;
     maxFiles: number | null;
     pathB: string | null;
-    history: boolean;
-    maxCommits: number;
+    history: boolean | null;
+    maxCommits: number | null;
     includeCategory: string[];
     excludeCategory: string[];
+    llmVerifyBudget: number | null;
     includeTests: boolean;
     publicAsEntry: boolean;
     top: number | null;

package/dist/cli/args.d.ts.map

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+{"version":3,"file":"args.d.ts","sourceRoot":"","sources":["../../src/cli/args.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,SAAS,GAAG,OAAO,GAAG,UAAU,GAAG,KAAK,CAAC;AAC7E,MAAM,MAAM,OAAO,GAAG,SAAS,GAAG,WAAW,GAAG,MAAM,GAAG,QAAQ,GAAG,SAAS,GAAG,WAAW,GAAG,eAAe,GAAG,eAAe,GAAG,SAAS,GAAG,OAAO,GAAG,SAAS,GAAG,SAAS,GAAG,YAAY,GAAG,WAAW,GAAG,SAAS,CAAC;AACvN,MAAM,MAAM,QAAQ,GAAG,OAAO,GAAG,OAAO,GAAG,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,QAAQ,CAAC;AAEhF,MAAM,MAAM,UAAU,GAAG,QAAQ,GAAG,QAAQ,GAAG,WAAW,GAAG,iBAAiB,GAAG,aAAa,CAAC;AAE/F,MAAM,WAAW,OAAO;IACtB,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,MAAM,EAAE,YAAY,CAAC;IACrB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,EAAE,OAAO,CAAC;IAClB,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,OAAO,CAAC;IACd,OAAO,EAAE,OAAO,CAAC;IACjB,QAAQ,EAAE,QAAQ,GAAG,IAAI,CAAC;IAE1B,gBAAgB,EAAE,OAAO,CAAC;IAC1B,gBAAgB,EAAE,MAAM,CAAC;IAEzB,KAAK,EAAE,OAAO,CAAC;IACf,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,qEAAqE;IACrE,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B;;;;;OAKG;IACH,IAAI,EAAE,OAAO,CAAC;IAEd,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IAExB,OAAO,EAAE,MAAM,CAAC;IAEhB,MAAM,EAAE,UAAU,GAAG,IAAI,CAAC;IAE1B,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IAExB,KAAK,EAAE,OAAO,CAAC;IACf,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,UAAU,EAAE,OAAO,CAAC;IAEpB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,eAAe,EAAE,OAAO,CAAC;IAEzB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,aAAa,EAAE,OAAO,CAAC;IACvB,QAAQ,EAAE,OAAO,CAAC;IAClB,YAAY,EAAE,OAAO,CAAC;IACtB,UAAU,EAAE,OAAO,CAAC;IACpB,cAAc,EAAE,OAAO,CAAC;IACxB,SAAS,EAAE,OAAO,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IACvB,iBAAiB,EAAE,OAAO,CAAC;IAC3B,YAAY,EAAE,OAAO,CAAC;IAEtB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IAEvB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,WAAW,CAAC,EAAE,UAAU,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,MAAM,CAAC;IAE9D,QAAQ,EAAE,UAAU,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,IAAI,CAAC;IAExD,YAAY,EAAE,OAAO,CAAC;IAEtB,WAAW,EAAE,MAAM,EAAE,CAAC;IAEtB,WAAW,EAAE,MAAM,CAAC;IAEpB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IAExB,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IAKrB,OAAO,EAAE,OAAO,GAAG,IAAI,CAAC;IACxB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,eAAe,EAAE,MAAM,EAAE,CAAC;IAK1B,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAE/B,YAAY,EAAE,OAAO,CAAC;IACtB,aAAa,EAAE,OAAO,CAAC;IACvB,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,IAAI,EAAE,OAAO,CAAC;IAEd,cAAc,EAAE,MAAM,EAAE,CAAC;IAEzB,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,YAAY,EAAE,OAAO,CAAC;IAEtB,cAAc,EAAE,OAAO,CAAC;IACxB,aAAa,EAAE,OAAO,CAAC;IACvB,cAAc,EAAE,OAAO,CAAC;IACxB,aAAa,EAAE,OAAO,CAAC;IACvB,iBAAiB,EAAE,OAAO,CAAC;IAC3B,SAAS,EAAE,MAAM,CAAC;CACnB"}

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

@@ -3,7 +3,21 @@
  *
  * Scans for secrets in code and Git history.
  */
+import { type SecretScanResult, type DetectedSecret } from 'circle-ir-ai';
 import type { CliArgs } from '../args.js';
+/**
+ * Effective confidence for a finding: prefer the LLM verifier's score
+ * when it ran; otherwise fall back to the per-category default.
+ */
+export declare function effectiveConfidence(secret: DetectedSecret): number;
+/**
+ * Filter findings by minConfidence and recompute aggregate counts.
+ *
+ * SecretScanResult caches `bySeverity` / `byCategory` /
+ * `activeSecrets` / `historicalSecrets`; filtering only `secrets[]`
+ * would leave those stale, so we rebuild them off the filtered set.
+ */
+export declare function applyMinConfidence(result: SecretScanResult, minConfidence: number): SecretScanResult;
 /**
  * Execute secret scanning command.
  */

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

@@ -1 +1 @@
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+{"version":3,"file":"secrets.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/secrets.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAGH,OAAO,EAIL,KAAK,gBAAgB,EACrB,KAAK,cAAc,EAEpB,MAAM,cAAc,CAAC;AACtB,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAmB1C;;;GAGG;AACH,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,cAAc,GAAG,MAAM,CAElE;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAChC,MAAM,EAAE,gBAAgB,EACxB,aAAa,EAAE,MAAM,GACpB,gBAAgB,CA2BlB;AAED;;GAEG;AACH,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAuGnE"}

package/dist/cli/commands/secrets.js

@@ -6,6 +6,66 @@
 import * as fs from 'fs';
 import { scanForSecrets, formatSecretReport, } from 'circle-ir-ai';
 import { getEffectiveOptions } from '../effective-options.js';
+/**
+ * Confidence floor used when a finding hasn't been LLM-verified.
+ *
+ * Provider patterns (aws/github/stripe/openai/...) start at 0.95 — high
+ * regex specificity, expected low FPR. `jwt` sits at 0.85 because the
+ * built-in base64+JSON validator already filters most fixtures. The
+ * high-entropy bucket starts at 0.50 — these are the bucket the LLM
+ * verifier targets specifically, so an unverified high-entropy hit is
+ * by construction not-yet-trusted.
+ */
+function categoryConfidence(category) {
+    if (category === 'high-entropy')
+        return 0.5;
+    if (category === 'jwt')
+        return 0.85;
+    return 0.95;
+}
+/**
+ * Effective confidence for a finding: prefer the LLM verifier's score
+ * when it ran; otherwise fall back to the per-category default.
+ */
+export function effectiveConfidence(secret) {
+    return secret.llmConfidence ?? categoryConfidence(secret.category);
+}
+/**
+ * Filter findings by minConfidence and recompute aggregate counts.
+ *
+ * SecretScanResult caches `bySeverity` / `byCategory` /
+ * `activeSecrets` / `historicalSecrets`; filtering only `secrets[]`
+ * would leave those stale, so we rebuild them off the filtered set.
+ */
+export function applyMinConfidence(result, minConfidence) {
+    if (minConfidence <= 0)
+        return result;
+    const kept = result.secrets.filter((s) => effectiveConfidence(s) >= minConfidence);
+    if (kept.length === result.secrets.length)
+        return result;
+    const bySeverity = {
+        critical: 0, high: 0, medium: 0, low: 0,
+    };
+    const byCategory = {};
+    let activeSecrets = 0;
+    let historicalSecrets = 0;
+    for (const s of kept) {
+        bySeverity[s.severity] = (bySeverity[s.severity] ?? 0) + 1;
+        byCategory[s.category] = (byCategory[s.category] ?? 0) + 1;
+        if (s.presentInHead)
+            activeSecrets++;
+        else
+            historicalSecrets++;
+    }
+    return {
+        ...result,
+        secrets: kept,
+        bySeverity,
+        byCategory,
+        activeSecrets,
+        historicalSecrets,
+    };
+}
 /**
  * Execute secret scanning command.
  */
@@ -15,19 +75,39 @@ export async function executeSecrets(args) {
         console.error(`Error: Path not found: ${targetPath}`);
         return 1;
     }
+    // REFACTOR-012 (since 2.13.0): scanHistory / maxCommits /
+    // includeCategories / excludeCategories / minConfidence all resolve
+    // through `eff.secrets`. Precedence per field is **CLI > config >
+    // built-in default** — see effective-options.ts. Reading directly
+    // from `args` here would silently bypass cognium.config.json#secrets.
+    const eff = getEffectiveOptions(args, targetPath);
+    // REFACTOR-003 (since 2.14.0): LLM verify is ON by default for the
+    // secrets command (matches scan/trust/quality/health). Two opt-out
+    // paths:
+    //   - `--no-llm` (global LLM kill-switch — disables all LLM features)
+    //   - `--llm-verify-budget 0` (disables LLM verify only)
+    // Either pathway sends `llmVerify: false` to the engine, which
+    // skips `llmVerifySecrets` entirely.
+    const llmVerify = !args.noLlm && eff.secrets.verifyBudget > 0;
     if (!args.quiet) {
-        const histLabel = args.history ? `working tree + last ${args.maxCommits} Git commits` : 'working tree only';
-        console.error(`Scanning ${targetPath} for secrets (${histLabel})...`);
+        const histLabel = eff.secrets.scanHistory
+            ? `working tree + last ${eff.secrets.maxCommits} Git commits`
+            : 'working tree only';
+        const llmLabel = llmVerify
+            ? ` + LLM verify (budget ${eff.secrets.verifyBudget})`
+            : '';
+        console.error(`Scanning ${targetPath} for secrets (${histLabel}${llmLabel})...`);
     }
-    const eff = getEffectiveOptions(args, targetPath);
     const options = {
-        scanHistory: args.history,
-        maxCommits: args.maxCommits,
+        scanHistory: eff.secrets.scanHistory,
+        maxCommits: eff.secrets.maxCommits,
         minSeverity: eff.severity ?? undefined,
-        includeCategories: args.includeCategory.length > 0 ? args.includeCategory : undefined,
-        excludeCategories: args.excludeCategory.length > 0 ? args.excludeCategory : undefined,
+        includeCategories: eff.secrets.includeCategories.length > 0 ? eff.secrets.includeCategories : undefined,
+        excludeCategories: eff.secrets.excludeCategories.length > 0 ? eff.secrets.excludeCategories : undefined,
         includeFiles: eff.include.length > 0 ? eff.include : undefined,
         excludeFiles: eff.exclude.length > 0 ? eff.exclude : undefined,
+        llmVerify,
+        verifyBudget: eff.secrets.verifyBudget,
         onProgress: args.quiet ? undefined : (progress) => {
             if (progress.phase === 'scanning-files') {
                 console.error(`[${progress.filesScanned}/${progress.totalFiles}] ${progress.currentFile || ''}`);
@@ -38,7 +118,17 @@ export async function executeSecrets(args) {
         },
     };
     try {
-        const result = await scanForSecrets(targetPath, options);
+        const rawResult = await scanForSecrets(targetPath, options);
+        // 2.12.0: --min-confidence default 0.5 drops raw high-entropy findings.
+        // 2.13.0: also honors cognium.config.json#secrets.minConfidence.
+        // Users who want the legacy behavior should pass `--min-confidence 0`.
+        const minConfidence = eff.secrets.minConfidence;
+        const result = applyMinConfidence(rawResult, minConfidence);
+        if (!args.quiet && minConfidence > 0 && result.secrets.length !== rawResult.secrets.length) {
+            const dropped = rawResult.secrets.length - result.secrets.length;
+            console.error(`[min-confidence ${minConfidence}] dropped ${dropped} finding(s); ` +
+                `use --min-confidence 0 to disable.`);
+        }
         // Output results
         if (args.format === 'json') {
             const output = JSON.stringify(result, null, 2);

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

@@ -1 +1 @@
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+{"version":3,"file":"secrets.js","sourceRoot":"","sources":["../../../src/cli/commands/secrets.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,EACL,cAAc,EACd,kBAAkB,GAKnB,MAAM,cAAc,CAAC;AAEtB,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAE9D;;;;;;;;;GASG;AACH,SAAS,kBAAkB,CAAC,QAAgB;IAC1C,IAAI,QAAQ,KAAK,cAAc;QAAE,OAAO,GAAG,CAAC;IAC5C,IAAI,QAAQ,KAAK,KAAK;QAAE,OAAO,IAAI,CAAC;IACpC,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CAAC,MAAsB;IACxD,OAAO,MAAM,CAAC,aAAa,IAAI,kBAAkB,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;AACrE,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAwB,EACxB,aAAqB;IAErB,IAAI,aAAa,IAAI,CAAC;QAAE,OAAO,MAAM,CAAC;IAEtC,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,aAAa,CAAC,CAAC;IACnF,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM,CAAC,OAAO,CAAC,MAAM;QAAE,OAAO,MAAM,CAAC;IAEzD,MAAM,UAAU,GAAmC;QACjD,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC;KACxC,CAAC;IACF,MAAM,UAAU,GAA2B,EAAE,CAAC;IAC9C,IAAI,aAAa,GAAG,CAAC,CAAC;IACtB,IAAI,iBAAiB,GAAG,CAAC,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;QACrB,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC;QAC3D,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC;QAC3D,IAAI,CAAC,CAAC,aAAa;YAAE,aAAa,EAAE,CAAC;;YAChC,iBAAiB,EAAE,CAAC;IAC3B,CAAC;IAED,OAAO;QACL,GAAG,MAAM;QACT,OAAO,EAAE,IAAI;QACb,UAAU;QACV,UAAU;QACV,aAAa;QACb,iBAAiB;KAClB,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAa;IAChD,MAAM,UAAU,GAAG,IAAI,CAAC,SAAS,IAAI,OAAO,CAAC,GAAG,EAAE,CAAC;IAEnD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,0BAA0B,UAAU,EAAE,CAAC,CAAC;QACtD,OAAO,CAAC,CAAC;IACX,CAAC;IAED,0DAA0D;IAC1D,oEAAoE;IACpE,kEAAkE;IAClE,kEAAkE;IAClE,sEAAsE;IACtE,MAAM,GAAG,GAAG,mBAAmB,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC;IAElD,mEAAmE;IACnE,mEAAmE;IACnE,SAAS;IACT,sEAAsE;IACtE,yDAAyD;IACzD,+DAA+D;IAC/D,qCAAqC;IACrC,MAAM,SAAS,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,GAAG,CAAC,OAAO,CAAC,YAAY,GAAG,CAAC,CAAC;IAE9D,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;QAChB,MAAM,SAAS,GAAG,GAAG,CAAC,OAAO,CAAC,WAAW;YACvC,CAAC,CAAC,uBAAuB,GAAG,CAAC,OAAO,CAAC,UAAU,cAAc;YAC7D,CAAC,CAAC,mBAAmB,CAAC;QACxB,MAAM,QAAQ,GAAG,SAAS;YACxB,CAAC,CAAC,yBAAyB,GAAG,CAAC,OAAO,CAAC,YAAY,GAAG;YACtD,CAAC,CAAC,EAAE,CAAC;QACP,OAAO,CAAC,KAAK,CAAC,YAAY,UAAU,iBAAiB,SAAS,GAAG,QAAQ,MAAM,CAAC,CAAC;IACnF,CAAC;IAED,MAAM,OAAO,GAAsB;QACjC,WAAW,EAAE,GAAG,CAAC,OAAO,CAAC,WAAW;QACpC,UAAU,EAAE,GAAG,CAAC,OAAO,CAAC,UAAU;QAClC,WAAW,EAAE,GAAG,CAAC,QAAQ,IAAI,SAAS;QACtC,iBAAiB,EAAE,GAAG,CAAC,OAAO,CAAC,iBAAiB,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAC,CAAC,SAAS;QACvG,iBAAiB,EAAE,GAAG,CAAC,OAAO,CAAC,iBAAiB,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAC,CAAC,SAAS;QACvG,YAAY,EAAE,GAAG,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS;QAC9D,YAAY,EAAE,GAAG,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS;QAC9D,SAAS;QACT,YAAY,EAAE,GAAG,CAAC,OAAO,CAAC,YAAY;QACtC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE;YAChD,IAAI,QAAQ,CAAC,KAAK,KAAK,gBAAgB,EAAE,CAAC;gBACxC,OAAO,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC,YAAY,IAAI,QAAQ,CAAC,UAAU,KAAK,QAAQ,CAAC,WAAW,IAAI,EAAE,EAAE,CAAC,CAAC;YACnG,CAAC;iBAAM,IAAI,QAAQ,CAAC,KAAK,KAAK,kBAAkB,EAAE,CAAC;gBACjD,OAAO,CAAC,KAAK,CAAC,aAAa,QAAQ,CAAC,cAAc,IAAI,CAAC,IAAI,QAAQ,CAAC,YAAY,IAAI,CAAC,UAAU,CAAC,CAAC;YACnG,CAAC;QACH,CAAC;KACF,CAAC;IAEF,IAAI,CAAC;QACH,MAAM,SAAS,GAAG,MAAM,cAAc,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;QAC5D,wEAAwE;QACxE,iEAAiE;QACjE,uEAAuE;QACvE,MAAM,aAAa,GAAG,GAAG,CAAC,OAAO,CAAC,aAAa,CAAC;QAChD,MAAM,MAAM,GAAG,kBAAkB,CAAC,SAAS,EAAE,aAAa,CAAC,CAAC;QAE5D,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,aAAa,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,SAAS,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YAC3F,MAAM,OAAO,GAAG,SAAS,CAAC,OAAO,CAAC,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC;YACjE,OAAO,CAAC,KAAK,CACX,mBAAmB,aAAa,aAAa,OAAO,eAAe;gBACnE,oCAAoC,CACrC,CAAC;QACJ,CAAC;QAED,iBAAiB;QACjB,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;YAC/C,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;gBAChB,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;gBACtC,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;oBAChB,OAAO,CAAC,KAAK,CAAC,qBAAqB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;gBACpD,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;YACtB,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,MAAM,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAC;YAC1C,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;gBAChB,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;gBACtC,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;oBAChB,OAAO,CAAC,KAAK,CAAC,qBAAqB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;gBACpD,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;YACtB,CAAC;QACH,CAAC;QAED,wCAAwC;QACxC,IAAI,IAAI,CAAC,QAAQ,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC/C,OAAO,CAAC,CAAC;QACX,CAAC;QAED,OAAO,CAAC,CAAC;IACX,CAAC;IAAC,OAAO,KAAK,EAAE,C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package/dist/cli/config.d.ts

@@ -114,6 +114,39 @@ export interface Suppression {
     /** Reason for suppression (for documentation) */
     reason?: string;
 }
+/**
+ * `secrets` block in cognium.config.json — covers all knobs the `secrets`
+ * CLI command exposes. Every field is optional; resolution order is
+ * **CLI flag → cognium.config.json → built-in default** (see
+ * `getEffectiveOptions` for the actual merge logic).
+ *
+ * Shape locked in
+ * `.specifica/hardcoded-secrets/implementation-plan.md` §"Resolved
+ * design decisions (2026-06-18)" item 3.
+ */
+export interface SecretsConfig {
+    /** Mirror of `--max-commits`. Built-in default is 100. */
+    maxCommits?: number;
+    /** Mirror of `--include-category`. Built-in default is [] (no filter). */
+    includeCategories?: string[];
+    /** Mirror of `--exclude-category`. Built-in default is [] (no filter). */
+    excludeCategories?: string[];
+    /** Mirror of `--no-history` inverted. Built-in default is `true`. */
+    scanHistory?: boolean;
+    /**
+     * Mirror of `--min-confidence`. Built-in default is `0.5` (drops raw
+     * high-entropy findings — see CHANGELOG 2.12.0 BREAKING note).
+     */
+    minConfidence?: number;
+    /**
+     * Mirror of `--llm-verify-budget` (since 2.14.0). Max findings the
+     * secrets command sends to the LLM verifier per scan. Built-in
+     * default is `100` (the engine's `DEFAULT_VERIFY_BUDGET`, ~$0.005 on
+     * gpt-4o-mini batched 10-per-call). Set to `0` to disable LLM
+     * verification entirely while keeping other LLM features on.
+     */
+    verifyBudget?: number;
+}
 /**
  * cognium.config.json schema — shared with cognium and cognium-ai CLIs.
  */
@@ -139,6 +172,8 @@ export interface CogniumConfig {
         /** Trust passes to skip (e.g., 'god-class', 'naming-convention') */
         disabledPasses?: string[];
     };
+    /** Secrets-specific configuration (REFACTOR-012, since 2.13.0). */
+    secrets?: SecretsConfig;
     /** Findings to suppress */
     suppressions?: Suppression[];
     /** Minimum severity filter */

package/dist/cli/config.d.ts.map

@@ -1 +1 @@
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package/dist/cli/config.js.map

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package/dist/cli/effective-options.d.ts

@@ -11,6 +11,28 @@
 import type { AnalyzerOptions } from 'circle-ir';
 import type { CliArgs } from './args.js';
 import { type CogniumConfig, type ResolvedConfig } from './config.js';
+/**
+ * Resolved secrets-command knobs (REFACTOR-012, since 2.13.0).
+ *
+ * Each field is the result of merging
+ *   CLI flag → cognium.config.json#secrets.* → built-in default
+ * with CLI flag always winning. Built-in defaults match what the
+ * Commander option used to ship: history=true, maxCommits=100,
+ * includes/excludes empty, minConfidence=0.5.
+ */
+export interface EffectiveSecretsOptions {
+    scanHistory: boolean;
+    maxCommits: number;
+    includeCategories: string[];
+    excludeCategories: string[];
+    minConfidence: number;
+    /**
+     * REFACTOR-003 (since 2.14.0). Resolved LLM verify budget. Built-in
+     * default is the engine's `DEFAULT_VERIFY_BUDGET = 100`. Set to `0`
+     * to disable LLM verification entirely.
+     */
+    verifyBudget: number;
+}
 export interface EffectiveOptions {
     /** Glob patterns to include. */
     include: string[];
@@ -24,6 +46,8 @@ export interface EffectiveOptions {
     categories: string[];
     /** Trust-specific disabled passes (subset of disabledPasses, source-tracked). */
     trustDisabledPasses: string[];
+    /** Secrets-command knobs (CLI > cognium.config.json#secrets > built-in default). */
+    secrets: EffectiveSecretsOptions;
     /** AnalyzerOptions for circle-ir analyze() — passOptions + disabledPasses. */
     analyzerOptions: AnalyzerOptions | undefined;
     /** The loaded cognium.config.json (or null). */

package/dist/cli/effective-options.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"effective-options.d.ts","sourceRoot":"","sources":["../../src/cli/effective-options.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,WAAW,CAAC;AACjD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAIL,KAAK,aAAa,EAClB,KAAK,cAAc,EACpB,MAAM,aAAa,CAAC;AAErB,MAAM,WAAW,gBAAgB;IAC/B,gCAAgC;IAChC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,gCAAgC;IAChC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,gFAAgF;IAChF,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,qDAAqD;IACrD,QAAQ,EAAE,UAAU,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,SAAS,CAAC;IAC7D,6CAA6C;IAC7C,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,iFAAiF;IACjF,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,8EAA8E;IAC9E,eAAe,EAAE,eAAe,GAAG,SAAS,CAAC;IAC7C,gDAAgD;IAChD,OAAO,EAAE,aAAa,GAAG,IAAI,CAAC;IAC9B,2EAA2E;IAC3E,QAAQ,EAAE,cAAc,CAAC;CAC1B;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,gBAAgB,CAmEnF;AAED;;;;;;;;GAQG;AACH,wBAAgB,mCAAmC,CACjD,YAAY,EAAE,OAAO,GAAG,QAAQ,GAAG,SAAS,EAC5C,KAAK,EAAE,OAAO,GACb,IAAI,CAEN;AAkCD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,OAAO,GAAG,IAAI,CAoCxD;AAED;;;;GAIG;AACH,wBAAgB,8BAA8B,IAAI,IAAI,CAErD;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,OAAO,GAAG,IAAI,CAuBtD"}
+{"version":3,"file":"effective-options.d.ts","sourceRoot":"","sources":["../../src/cli/effective-options.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,WAAW,CAAC;AACjD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAIL,KAAK,aAAa,EAClB,KAAK,cAAc,EACpB,MAAM,aAAa,CAAC;AAErB;;;;;;;;GAQG;AACH,MAAM,WAAW,uBAAuB;IACtC,WAAW,EAAE,OAAO,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB;;;;OAIG;IACH,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,gBAAgB;IAC/B,gCAAgC;IAChC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,gCAAgC;IAChC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,gFAAgF;IAChF,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,qDAAqD;IACrD,QAAQ,EAAE,UAAU,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,SAAS,CAAC;IAC7D,6CAA6C;IAC7C,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,iFAAiF;IACjF,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,oFAAoF;IACpF,OAAO,EAAE,uBAAuB,CAAC;IACjC,8EAA8E;IAC9E,eAAe,EAAE,eAAe,GAAG,SAAS,CAAC;IAC7C,gDAAgD;IAChD,OAAO,EAAE,aAAa,GAAG,IAAI,CAAC;IAC9B,2EAA2E;IAC3E,QAAQ,EAAE,cAAc,CAAC;CAC1B;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,gBAAgB,CAwFnF;AAED;;;;;;;;GAQG;AACH,wBAAgB,mCAAmC,CACjD,YAAY,EAAE,OAAO,GAAG,QAAQ,GAAG,SAAS,EAC5C,KAAK,EAAE,OAAO,GACb,IAAI,CAEN;AAkCD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,OAAO,GAAG,IAAI,CAoCxD;AAED;;;;GAIG;AACH,wBAAgB,8BAA8B,IAAI,IAAI,CAErD;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,OAAO,GAAG,IAAI,CAuBtD"}

package/dist/cli/effective-options.js

@@ -65,6 +65,23 @@ export function getEffectiveOptions(args, target) {
             disabledPasses: disabledPasses.length > 0 ? disabledPasses : undefined,
         }
         : undefined;
+    // Secrets command knobs (REFACTOR-012). Precedence per field: CLI > config > built-in.
+    // CLI fields are null when the user didn't pass the flag (see args.ts comment).
+    // includeCategory/excludeCategory use empty-array as the "no CLI override" signal
+    // — consistent with how `include` / `exclude` are resolved above.
+    const cfgSecrets = cognium?.secrets;
+    const secrets = {
+        scanHistory: args.history ?? cfgSecrets?.scanHistory ?? true,
+        maxCommits: args.maxCommits ?? cfgSecrets?.maxCommits ?? 100,
+        includeCategories: args.includeCategory.length > 0
+            ? args.includeCategory
+            : (cfgSecrets?.includeCategories ?? []),
+        excludeCategories: args.excludeCategory.length > 0
+            ? args.excludeCategory
+            : (cfgSecrets?.excludeCategories ?? []),
+        minConfidence: args.minConfidence ?? cfgSecrets?.minConfidence ?? 0.5,
+        verifyBudget: args.llmVerifyBudget ?? cfgSecrets?.verifyBudget ?? 100,
+    };
     return {
         include,
         exclude,
@@ -72,6 +89,7 @@ export function getEffectiveOptions(args, target) {
         severity,
         categories,
         trustDisabledPasses: [...new Set([...args.disablePass, ...trustDisabled])],
+        secrets,
         analyzerOptions,
         cognium,
         circleIr,

package/dist/cli/effective-options.js.map

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package/dist/cli/program.d.ts

@@ -61,6 +61,7 @@ interface CommanderOpts {
     maxCommits?: number;
     includeCategory?: string[];
     excludeCategory?: string[];
+    llmVerifyBudget?: number;
     includeTests?: boolean;
     publicAsEntry?: boolean;
     top?: number;

package/dist/cli/program.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"program.d.ts","sourceRoot":"","sources":["../../src/cli/program.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,OAAO,EAAwB,MAAM,WAAW,CAAC;AAI1D,OAAO,KAAK,EACV,UAAU,EACV,OAAO,EACP,OAAO,IAAI,WAAW,EACtB,QAAQ,EACR,YAAY,EACb,MAAM,WAAW,CAAC;AA2OnB,UAAU,aAAa;IAErB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,YAAY,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,YAAY,CAAC,EAAE,OAAO,CAAC;IAEvB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IAEf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,OAAO,CAAC;IAErB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IAEvB,OAAO,CAAC,EAAE,MAAM,CAAC;IAEjB,QAAQ,CAAC,EAAE,UAAU,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,CAAC;IAClD,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IAEpB,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;IAE1B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAElB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAE1B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,eAAe,CAAC,EAAE,MAAM,CAAC;IAEzB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,OAAO,CAAC;IAEf,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAE1B,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,YAAY,CAAC,EAAE,OAAO,CAAC;IAEvB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,SAAS,CAAC,EAAE,MAAM,CAAC;IAEnB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,UAAU,cAAc;IACtB,OAAO,EAAE,WAAW,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,IAAI,EAAE,aAAa,CAAC;CACrB;AAyBD,iBAAS,YAAY,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,cAAc,GAAG,OAAO,CAyHlG;AAkBD,MAAM,MAAM,YAAY,GAAG,CAAC,IAAI,EAAE,OAAO,KAAK,OAAO,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;AAE9E,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,YAAY,CAAC;IACtB,IAAI,EAAE,YAAY,CAAC;IACnB,MAAM,EAAE,YAAY,CAAC;IACrB,OAAO,EAAE,YAAY,CAAC;IACtB,QAAQ,EAAE,YAAY,CAAC;IACvB,YAAY,EAAE,YAAY,CAAC;IAC3B,YAAY,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IAC7D,OAAO,EAAE,YAAY,CAAC;IACtB,KAAK,EAAE,YAAY,CAAC;IACpB,OAAO,EAAE,YAAY,CAAC;IACtB,OAAO,EAAE,YAAY,CAAC;IACtB,UAAU,EAAE,YAAY,CAAC;IACzB,QAAQ,EAAE,YAAY,CAAC;IACvB,OAAO,EAAE,YAAY,CAAC;IACtB,SAAS,EAAE,YAAY,CAAC;CACzB;AAED,MAAM,WAAW,mBAAmB;IAClC,2DAA2D;IAC3D,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,uFAAuF;IACvF,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,0CAA0C;IAC1C,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,wBAAgB,YAAY,CAAC,QAAQ,EAAE,eAAe,EAAE,OAAO,GAAE,mBAAwB,GAAG,OAAO,CAmiBlG;AAED,OAAO,EAAE,YAAY,IAAI,cAAc,EAAE,CAAC"}

package/dist/cli/program.js

@@ -29,6 +29,12 @@ function toPosInt(value) {
         throw new InvalidArgumentError('must be a positive integer');
     return n;
 }
+function toNonNegInt(value) {
+    const n = toInt(value);
+    if (n < 0)
+        throw new InvalidArgumentError('must be a non-negative integer');
+    return n;
+}
 function toFloat01(value) {
     const n = parseFloat(value);
     if (Number.isNaN(n) || n < 0 || n > 1) {
@@ -111,10 +117,13 @@ function makeDefaultCliArgs(command) {
         fileTimeout: 30,
         maxFiles: null,
         pathB: null,
-        history: true,
-        maxCommits: 100,
+        // null = "user did not pass the CLI flag". Effective-options merges
+        // cognium.config.json#secrets.* then the built-in default (true / 100).
+        history: null,
+        maxCommits: null,
         includeCategory: [],
         excludeCategory: [],
+        llmVerifyBudget: null,
         includeTests: false,
         publicAsEntry: false,
         top: null,
@@ -315,15 +324,21 @@ function buildCliArgs({ command, target, targetIsDirectory, pathB, opts }) {
         args.discoverPatterns = true;
     if (opts.patternThreshold !== undefined)
         args.patternThreshold = opts.patternThreshold;
-    // Secrets
-    if (opts.history !== undefined)
-        args.history = opts.history;
+    // Secrets — REFACTOR-012 (since 2.13.0): null = "user did not pass the
+    // CLI flag". Commander's `--no-history` synthesizes `opts.history=true`
+    // by default, so the only signal that the user **explicitly** opted out
+    // is `opts.history === false`. Anything else (true or missing) falls
+    // through to effective-options' cognium.config.json#secrets.* merge.
+    if (opts.history === false)
+        args.history = false;
     if (opts.maxCommits !== undefined)
         args.maxCommits = opts.maxCommits;
     if (opts.includeCategory && opts.includeCategory.length > 0)
         args.includeCategory = opts.includeCategory;
     if (opts.excludeCategory && opts.excludeCategory.length > 0)
         args.excludeCategory = opts.excludeCategory;
+    if (opts.llmVerifyBudget !== undefined)
+        args.llmVerifyBudget = opts.llmVerifyBudget;
     // Dead-code
     if (opts.includeTests)
         args.includeTests = true;
@@ -518,22 +533,58 @@ Examples:
         .command('secrets')
         .description('Scan for hardcoded secrets in code and Git history (last 100 commits by default)')
         .argument('[path]', 'Directory to scan', '.')
-        .option('--no-history', 'Skip Git history scan (only scan working tree)')
-        .option('--max-commits <n>', 'Maximum Git commits to scan', toPosInt, 100)
-        .option('--include-category <cat>', 'Limit to pattern categories (repeatable: aws, github, stripe, jwt, private-key, ...)', appendArray, [])
-        .option('--exclude-category <cat>', 'Skip pattern categories (repeatable)', appendArray, [])
+        // Commander defaults are deliberately omitted on the secrets-specific
+        // flags (REFACTOR-012, since 2.13.0). When the user doesn't pass the
+        // flag, Commander leaves the field as `undefined`; effective-options
+        // then falls back to cognium.config.json#secrets.* and finally to the
+        // built-in default. The previous defaults are documented inline so
+        // `--help` still tells the user what happens absent any flag.
+        .option('--no-history', 'Skip Git history scan (working tree only). Default: scan history.')
+        .option('--max-commits <n>', 'Maximum Git commits to scan. Default 100 (config: secrets.maxCommits).', toPosInt)
+        .option('--include-category <cat>', 'Limit to pattern categories (repeatable: aws, github, stripe, jwt, private-key, ...; config: secrets.includeCategories)', appendArray, [])
+        .option('--exclude-category <cat>', 'Skip pattern categories (repeatable; config: secrets.excludeCategories)', appendArray, [])
+        .option('--min-confidence <n>', 'Drop findings below this confidence threshold (0.0-1.0). Default 0.5 drops raw high-entropy findings. Set 0 to disable. Config: secrets.minConfidence.', toFloat01)
+        .option('--llm-verify-budget <n>', 'Max findings sent to LLM verifier per scan. Default 100 (~$0.005 on gpt-4o-mini). Set 0 to disable LLM verify. Config: secrets.verifyBudget.', toNonNegInt)
         .addHelpText('after', `
 Pattern categories:
   aws, azure, gcp, github, slack, stripe, twilio, sendgrid, paypal,
   square, discord, jwt, private-key, database, api-key, high-entropy
 
+Confidence defaults by category (used when LLM verifier hasn't scored a finding):
+  provider patterns (aws, github, stripe, openai, ...): 0.95
+  jwt:                                                  0.85
+  high-entropy:                                         0.50
+
+LLM verification (since 2.14.0):
+  ON by default when LLM is configured. Pass --no-llm to disable.
+  Verifies high-entropy + jwt + provider-pattern-on-fixture-path
+  findings (production provider hits skip LLM per PRIN-004).
+  Capped by --llm-verify-budget (default 100). Set budget 0 to
+  disable LLM verify only (other LLM features stay on).
+
 Examples:
   $ cognium-ai secrets ./src
   $ cognium-ai secrets ./src --no-history             # working-tree only
   $ cognium-ai secrets ./src --max-commits 500        # deeper Git scan
   $ cognium-ai secrets ./src --include-category aws --include-category github
   $ cognium-ai secrets ./src --exclude-category high-entropy --severity high
+  $ cognium-ai secrets ./src --min-confidence 0       # legacy: keep all findings
+  $ cognium-ai secrets ./src --min-confidence 0.9     # only highly-confident findings
+  $ cognium-ai secrets ./src --llm-verify-budget 0    # static only (no LLM verify)
+  $ cognium-ai secrets ./src --llm-verify-budget 500  # generous LLM budget
   $ cognium-ai secrets ./src --format json -o secrets.json
+
+Config file (cognium.config.json, since 2.13.0) — CLI flags always win:
+  {
+    "secrets": {
+      "maxCommits": 500,
+      "scanHistory": true,
+      "includeCategories": ["aws", "github"],
+      "excludeCategories": ["high-entropy"],
+      "minConfidence": 0.85,
+      "verifyBudget": 200
+    }
+  }
 `)
         .action(async (target, _opts, cmd) => {
         const args = buildCliArgs({ command: 'secrets', target, targetIsDirectory: true, opts: merge(cmd) });

package/dist/cli/program.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "cognium-ai",
-  "version": "2.11.5",
+  "version": "2.14.0",
   "description": "AI-powered static analysis CLI with LLM-enhanced vulnerability detection",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -42,7 +42,7 @@
   ],
   "dependencies": {
     "circle-ir": "3.74.0",
-    "circle-ir-ai": "^2.11.5",
+    "circle-ir-ai": "^2.12.0",
     "commander": "^14.0.3",
     "minimatch": "^10.2.5"
   },