circle-ir-ai 1.20.0 → 2.1.1

package/CHANGELOG.md

@@ -5,6 +5,238 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.1.1] - 2026-04-30
+
+### Fixed
+
+- **#16: scan hangs on JS projects when LLM endpoint is unreachable.**
+  Reproduced on 2.0.x — when `LLM_API_KEY` is set but the endpoint isn't
+  running, each `chatJSON` call waited the full 60s timeout, retried
+  once (another 60s), and we make many calls per file. With `MAX_
+  CONSECUTIVE_FAILURES = 5`, the circuit breaker eventually tripped but
+  only after minutes of hanging.
+
+  Now: connection-class errors (ECONNREFUSED, ENOTFOUND, EHOSTUNREACH,
+  ETIMEDOUT, ECONNRESET, "fetch failed") are detected on the first
+  failure and the breaker trips immediately. Subsequent calls
+  short-circuit (no fetch attempted). User sees one clear warning
+  on stderr:
+
+      LLM endpoint unreachable (http://localhost:4000/v1): fetch failed
+      Falling back to static analysis. Use --no-llm to silence,
+      or set LLM_BASE_URL/LLM_API_KEY.
+
+  Wall-clock impact on the issue's reproducer (NodeGoat scan with no
+  LLM endpoint): hung at >2:00 → completes in ~3s.
+
+  Regression test: `tests/llm/connection-failure.test.ts` (4 cases —
+  fast first-call failure, subsequent short-circuit, single warn,
+  `resetCircuitBreaker()` re-enables).
+
+## [2.1.0] - 2026-04-30
+
+LLM call observability. New env-gated JSONL logger that captures every
+LLM call's signature, model, phase, prompt/response size, duration,
+success, retry, and error — for offline analysis of slow signatures,
+high-failure prompts, and token waste.
+
+### Added
+
+- **`src/llm/call-logger.ts`** — singleton logger that writes one JSON
+  line per LLM call to the path in `LLM_LOG_JSONL`. No-op when the env
+  var is unset.
+- **`AxLLMClient.chatJSON`** wrapped: outer entrypoint records timing +
+  meta and emits a log entry for both top-level calls and recursive
+  retries (each retry logs separately so retry rate is computable).
+- **`AxLLMClient.getGenerator`** wrapped: monkey-patches the returned
+  `AxGen.forward` to log timing + size + success/failure for the
+  signature-driven LLM path (used by `analyzeCorrelatedPredicates`).
+- New `LLMCallEntry` interface exposed for downstream consumers.
+
+### Usage
+
+    LLM_LOG_JSONL=/tmp/llm.jsonl cognium-ai scan ./src
+    npx tsx cognium-ai/scripts/analyze-llm-log.ts /tmp/llm.jsonl
+
+The analyzer prints a per-signature table (count, success%, retry%,
+parse-error%, p50/p95 ms, avg prompt/response chars), top-10 slowest
+individual calls, error-type histogram, and per-run totals.
+
+### Performance
+
+- ~1ms per call overhead (sync appendFileSync).
+- Disabled entirely when `LLM_LOG_JSONL` is unset.
+
+## [2.0.1] - 2026-04-30
+
+Internal dependency refresh. No public-API changes; verified against
+the existing test suite (468 passing, 3 skipped).
+
+### Changed
+
+- **`@ax-llm/ax` 19.0.42 → 20.0.0** (major). The 20.0.0 line removes
+  MiPRO, drops `llmQuery` advanced mode, consolidates GEPA/RLM
+  templates, and modernizes devDeps. circle-ir-ai only uses
+  `AxAIOpenAI`, `AxGen`, `AxSignature`, `AxGenOut` — none of the
+  removed features — so the bump is mechanical.
+- **`@mastra/core` 1.23.0 → 1.30.0** (minor)
+- **`p-queue` 9.1.2 → 9.2.0** (minor)
+- **dev**: `@types/node` 25.5.2 → 25.6.0; `@vitest/coverage-v8` and
+  `vitest` 4.1.3 → 4.1.5; `typescript` 6.0.2 → 6.0.3.
+
+### Internal
+
+- `.claude/skills/ax*` skill metadata version footers refreshed to
+  20.0.0 (auto-tracked).
+
+## [2.0.0] - 2026-04-29
+
+**BREAKING.** circle-ir-ai is now an engine-only package. The entire CLI
+surface has moved to `cognium-ai`, where it is the user-facing tool.
+
+### Removed (breaking)
+
+- **CLI re-exports from `circle-ir-ai/src/index.ts`**: `parseArgs`,
+  `CliArgs`, `OutputFormat`, `Command`, `LogLevel`, `BundleType`. These
+  now live in `cognium-ai`.
+- **`./commands` package export** is gone. `circle-ir-ai/commands` no
+  longer resolves. Wrappers that previously consumed `buildProgram`,
+  `executeXxx`, `getEffectiveOptions`, etc. should depend on
+  `cognium-ai` instead, or duplicate the logic.
+- **`commander`** dependency removed (CLI lives in cognium-ai).
+
+### Added
+
+- **9 trust passes** newly exposed at `circle-ir-ai`'s main entry:
+  `deprecatedUsagePass`, `throwsMismatchPass`, `inconsistentNamingPass`,
+  `deprecationNoReplacementPass`, `docCoveragePass`,
+  `inconsistentParamOrderPass`, `inconsistentErrorHandlingPass`,
+  `unnecessaryObjectHotspotPass`, `crossSkillInteractionPass`.
+- **9 utility/engine APIs** newly exposed: `isAnalyzerInitialized`,
+  `getDefaultLLMConfig`, `validateLLMConfig`, `logger`, `configureLogger`,
+  `registerSecurityAgents`, `runBundle`, `runBundleOnFiles`,
+  `globalPatternCache`, plus the `ProjectAnalysis` type.
+- **`src/config/cognium-config.ts`** — extracted CogniumConfig loader so
+  engine consumers can still import `loadCogniumConfig`,
+  `convertCogniumConfigToPassOptions`, `CogniumConfig`, `Suppression`
+  from circle-ir-ai's main entry.
+
+### Internal
+
+- All trust handler logic, command handlers, formatters, file walker,
+  Commander program, and related tests now live in cognium-ai.
+- 468 engine tests pass; 3 skipped.
+
+### Migration
+
+If you imported anything from `circle-ir-ai/commands` or
+`circle-ir-ai/cli/...`, switch to:
+- `cognium-ai/commands` (re-exported from cognium-ai's CLI subtree), or
+- run the `cognium-ai` binary directly.
+
+For programmatic engine access (security-scan, secret-scan, dead-code,
+trust passes, specifica, agents, understand, spec-gap, etc.), continue
+to import from `circle-ir-ai`.
+
+## [1.21.0] - 2026-04-29
+
+CLI polish pass on the eight commands that were hidden from
+`cognium-ai --help` in 1.20.0. Each command got purpose-fit flags and a
+clearer help footer; the commands remain hidden until the polish set has
+soaked, but every one is now respectable when called directly.
+
+### Added — per-command flags
+
+- **secrets**: `--no-history`, `--max-commits <n>` (default 100, surfaced
+  in help), `--include-category <cat>` (repeatable), `--exclude-category
+  <cat>` (repeatable). Global `--severity` now wires to engine
+  `minSeverity`. Help lists all 16 supported pattern categories. Status
+  line indicates "working tree only" vs "working tree + last N Git
+  commits" mode.
+- **dead-code**: `--include-tests`, `--public-as-entry`, `--top <n>`,
+  `--full`. The engine's `formatDeadCodeReport` now accepts truncation
+  options (\`FormatDeadCodeOptions\`). Truncation hint mentions the new
+  flags.
+- **metrics**: `--metric-category <cat>` (repeatable, filters to
+  size/complexity/coupling/inheritance/cohesion/documentation/composite/
+  performance), `--top <n>` (limits the per-file CK section + bug-hotspot
+  list, sorted by total CK weight). Section header reflects truncation.
+- **health**: `--no-security`, `--no-secrets`, `--no-dead-code`,
+  `--no-quality`, `--no-performance` (per-dimension toggles), and
+  `--threshold <n>` to override the previously-hardcoded 50 cutoff for
+  `--exit-code`. Help footer surfaces the default weights.
+- **understand**: `--role <name>` (repeatable), `--security-only`,
+  `--top <n>`. Modules now sorted by public-API size; report opens with
+  a "Modules by role" breakdown line.
+- **analyze-skill**: `--no-cross-artifact`, `--min-confidence <0-1>`.
+  Global `--severity` wires to skill engine `minSeverity`.
+- **cluster**: argument tightened from \`[path]\` → \`<path>\`; help
+  footer explains static vs LLM-enhanced output. When `--no-llm` is given,
+  prints a clear note that feature clustering and architecture analysis
+  are skipped.
+- **compare**: discovery options (\`-x\`, \`-i\`, \`-l\`,
+  `--max-files`, `--file-timeout`, `--exclude-tests`) added — symmetric
+  application to both \`pathA\` and \`pathB\`. Help footer documents the
+  symmetric semantics + exit-code contract.
+- **benchmark**: discovery options added. Description recast to clarify
+  this is for research / regression use against OWASP-Benchmark-style
+  suites; help points everyday users to \`scan\`.
+
+### Added — CliArgs fields
+
+`history`, `maxCommits`, `includeCategory[]`, `excludeCategory[]`,
+`includeTests`, `publicAsEntry`, `top`, `full`, `metricCategory[]`,
+`role[]`, `securityOnly`, `healthSecurity`, `healthSecrets`,
+`healthDeadCode`, `healthQuality`, `healthPerformance`, `threshold`.
+The legacy `parseArgs` switch parser is unchanged; the new fields use
+their initial defaults when consumed by the legacy path.
+
+### Added — engine
+
+- **dead-code**: `formatDeadCodeReport(result, opts?)` — opts are
+  `{ topPerFile?, topEntryPoints?, full? }`. Defaults preserve previous
+  behaviour (top 20 / 10).
+- New export: `FormatDeadCodeOptions` from `circle-ir-ai/commands`.
+
+### Tests
+
+608 passing (was 593) — +15 new cases covering all flag plumbing across
+`secrets`, `dead-code`, `metrics`, `health` in `program-merge.test.ts`.
+
+## [1.20.1] - 2026-04-29
+
+Patch release wrapping up the gap list from the 1.20.0 critical review.
+
+### Added
+
+- **50 new unit tests** for the CLI infrastructure introduced in 1.20.0:
+  `file-collection.ts` (13 tests — minimatch glob behaviour, language
+  filtering, skip-list, maxFiles), `effective-options.ts` (16 tests —
+  CLI/cognium.config/.circle-ir.yaml precedence, disabled-passes union,
+  config search), and `program.ts` (21 tests — `merge()` priority logic,
+  LLM defaults, global flag positioning, repeatable flags, defaults).
+
+### Changed
+
+- **`generate-spec --no-llm` now errors out** with a clear message instead
+  of silently ignoring the flag. The engine is fundamentally LLM-driven, so
+  honoring `--no-llm` while still calling the LLM was misleading.
+- **Removed `compare.ts`'s legacy argv-scan fallback.** Compare now reads
+  both paths exclusively from `args.directory` + `args.pathB`. Programmatic
+  consumers must set both fields.
+- **Removed `src/cli/index.ts`** (the standalone dev CLI binary).
+  `cognium-ai` is now the single user-facing CLI for both production and
+  development. `src/cli/program.ts`, `args.ts`, `commands/`,
+  `effective-options.ts`, `file-collection.ts` remain exported via
+  `circle-ir-ai/commands` for wrapper CLIs.
+- **`circle-ir-ai/CLAUDE.md`** dev-workflow section rewritten to point at
+  cognium-ai with a local-link install (`npm install ../circle-ir-ai
+  --no-save`) instead of the deleted standalone CLI.
+
+### Internal
+
+- TODO.md: marked "Deprecate circle-ir-ai standalone CLI" as done.
+
 ## [1.20.0] - 2026-04-29
 
 CLI rebuilt on Commander. New shared infrastructure for include/exclude

package/dist/agents/mastra/steps.d.ts

@@ -288,13 +288,13 @@ export declare const reportStep: import("@mastra/core/workflows").Step<"report",
         } | undefined;
     }[];
     stats: {
+        totalTimeMs: number;
         truePositives: number;
         falsePositives: number;
         uncertain: number;
         totalSources: number;
         totalSinks: number;
         verifiedVulnerabilities: number;
-        totalTimeMs: number;
     };
 }, unknown, unknown, import("@mastra/core/workflows").DefaultEngineType, unknown>;
 //# sourceMappingURL=steps.d.ts.map

package/dist/cli/args.d.ts

@@ -61,6 +61,23 @@ export interface CliArgs {
     fileTimeout: number;
     maxFiles: number | null;
     pathB: string | null;
+    history: boolean;
+    maxCommits: number;
+    includeCategory: string[];
+    excludeCategory: string[];
+    includeTests: boolean;
+    publicAsEntry: boolean;
+    top: number | null;
+    full: boolean;
+    metricCategory: string[];
+    role: string[];
+    securityOnly: boolean;
+    healthSecurity: boolean;
+    healthSecrets: boolean;
+    healthDeadCode: boolean;
+    healthQuality: boolean;
+    healthPerformance: boolean;
+    threshold: number;
 }
 /**
  * Parse command-line arguments.

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

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package/dist/cli/args.js

@@ -57,6 +57,23 @@ export function parseArgs(argv) {
         fileTimeout: 30,
         maxFiles: null,
         pathB: null,
+        history: true,
+        maxCommits: 100,
+        includeCategory: [],
+        excludeCategory: [],
+        includeTests: false,
+        publicAsEntry: false,
+        top: null,
+        full: false,
+        metricCategory: [],
+        role: [],
+        securityOnly: false,
+        healthSecurity: true,
+        healthSecrets: true,
+        healthDeadCode: true,
+        healthQuality: true,
+        healthPerformance: true,
+        threshold: 50,
     };
     let i = 0;
     while (i < argv.length) {

package/dist/cli/args.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"cluster.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/cluster.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAMH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AA+G1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAkFnE"}
+{"version":3,"file":"cluster.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/cluster.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAMH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AA+G1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAwFnE"}

package/dist/cli/commands/cluster.js

@@ -158,8 +158,14 @@ export async function executeCluster(args) {
         if (!args.quiet) {
             console.error(`  Extracted ${allComponents.length} components`);
         }
-        // Run component analysis (phase 1 needs LLM, skip if disabled)
+        // Run component analysis. The richer feature-clustering and
+        // architecture-pattern detection (Phase 1/2) needs LLM; without LLM we
+        // only get the static component list.
         const enableLLM = !args.noLlm && (args.llmEnrich || args.llmVerify);
+        if (!enableLLM && !args.quiet) {
+            console.error('  Note: --no-llm — feature clustering and architecture analysis are skipped.');
+            console.error('        Re-run without --no-llm for richer output.');
+        }
         const result = await analyzeComponents(allComponents, {
             enablePhase1: enableLLM,
             enablePhase2: enableLLM,

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

@@ -1 +1 @@
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+{"version":3,"file":"cluster.js","sourceRoot":"","sources":["../../../src/cli/commands/cluster.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,EAAE,qBAAqB,EAAE,OAAO,EAAiB,MAAM,WAAW,CAAC;AAC1E,OAAO,EAAE,yBAAyB,EAAE,MAAM,8BAA8B,CAAC;AAEzE,OAAO,EAAE,iBAAiB,EAAkB,MAAM,2BAA2B,CAAC;AAC9E,OAAO,EAAE,YAAY,IAAI,kBAAkB,EAAE,MAAM,uBAAuB,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAE9D,8EAA8E;AAC9E,mCAAmC;AACnC,8EAA8E;AAE9E,SAAS,kBAAkB,CAAC,IAA+B;IACzD,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;IACrC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;IACzD,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CAAC;QAAE,OAAO,YAAY,CAAC;IACnG,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;QAAE,OAAO,SAAS,CAAC;IAC7D,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC;QAAE,OAAO,YAAY,CAAC;IACnE,IAAI,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QAAE,OAAO,YAAY,CAAC;IACjF,IAAI,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QAAE,OAAO,SAAS,CAAC;IAC3E,IAAI,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QAAE,OAAO,YAAY,CAAC;IAC7E,IAAI,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QAAE,OAAO,OAAO,CAAC;IAC9F,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,iBAAiB,CAAC,QAAgB,EAAE,EAAY;IACvD,MAAM,UAAU,GAAgB,EAAE,CAAC;IAEnC,KAAK,MAAM,IAAI,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;QAC5B,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QAE9C,UAAU,CAAC,IAAI,CAAC;YACd,EAAE,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,IAAI,CAAC,IAAI,EAAE;YAC7C,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,QAAQ;YACd,IAAI,EAAE,kBAAkB,CAAC,IAAI,CAAC;YAC9B,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,QAAQ,EAAE,IAAI,CAAC,QAAQ;YACvB,OAAO;YACP,WAAW,EAAE,IAAI,CAAC,WAAW;SAC9B,CAAC,CAAC;IACL,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC;AAED,8EAA8E;AAC9E,kBAAkB;AAClB,8EAA8E;AAE9E,SAAS,gBAAgB,CAAC,MAAqD;IAC7E,MAAM,KAAK,GAAa,EAAE,CAAC;IAE3B,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;IAC9E,KAAK,CAAC,IAAI,CAAC,8CAA8C,CAAC,CAAC;IAC3D,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;IAC9E,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAEf,aAAa;IACb,KAAK,CAAC,IAAI,CAAC,eAAe,MAAM,CAAC,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;IACtD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAEf,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;QACrC,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,EAAE,kBAAkB,IAAI,SAAS,CAAC;QAC5D,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,EAAE,gBAAgB,IAAI,EAAE,CAAC;QACtD,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,KAAK,IAAI,GAAG,CAAC,CAAC;QACvC,IAAI,OAAO;YAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,EAAE,CAAC,CAAC;IACrD,CAAC;IACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAEf,WAAW;IACX,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;QACtB,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;QAC9E,KAAK,CAAC,IAAI,CAAC,qBAAqB,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC;QACrE,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;QAE9E,KAAK,MAAM,OAAO,IAAI,MAAM,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC;YACjD,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,KAAK,OAAO,CAAC,UAAU,CAAC,MAAM,cAAc,CAAC,CAAC;YAC1E,KAAK,MAAM,IAAI,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC;gBACtC,KAAK,CAAC,IAAI,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAEf,IAAI,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACvC,KAAK,CAAC,IAAI,CAAC,UAAU,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;YACvD,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC;gBAC3C,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,OAAO,IAAI,CAAC,mBAAmB,CAAC,MAAM,aAAa,CAAC,CAAC;YAC9F,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,IAAI,MAAM,CAAC,UAAU,CAAC,YAAY,EAAE,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,cAAc,MAAM,CAAC,UAAU,CAAC,YAAY,CAAC,OAAO,EAAE,CAAC,CAAC;YACnE,IAAI,MAAM,CAAC,UAAU,CAAC,YAAY,CAAC,eAAe,EAAE,MAAM,EAAE,CAAC;gBAC3D,KAAK,CAAC,IAAI,CAAC,sBAAsB,MAAM,CAAC,UAAU,CAAC,YAAY,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAChG,CAAC;YACD,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,MAAM,CAAC,UAAU,CAAC,YAAY,CAAC,QAAQ,CAAC;YAC3F,IAAI,SAAS,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC1E,IAAI,UAAU,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC7E,IAAI,eAAe,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC9F,CAAC;IACH,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;IAC9E,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,8EAA8E;AAC9E,eAAe;AACf,8EAA8E;AAE9E,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAa;IAChD,MAAM,UAAU,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,IAAI,IAAI,OAAO,CAAC,GAAG,EAAE,CAAC;IAEhE,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,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,WAAW,EAAE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package/dist/cli/commands/compare.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"compare.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/compare.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAyF1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA0HnE"}
+{"version":3,"file":"compare.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/compare.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAY1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA2HnE"}

package/dist/cli/commands/compare.js

@@ -13,81 +13,19 @@ import { runTrustAnalysis } from './trust.js';
 import { getEffectiveOptions } from '../effective-options.js';
 import { compareTrustResults, formatComparisonReport, } from '../../trust/compare.js';
 // ---------------------------------------------------------------------------
-// Path extraction
-// ---------------------------------------------------------------------------
-/**
- * Extract the two comparison paths.
- *
- * The Commander-driven path passes both as args.directory + args.pathB.
- * For backwards compatibility with the legacy parseArgs (which only captured
- * a single positional), we fall back to scanning process.argv.
- */
-function extractComparisonPaths(args) {
-    if (args.directory && args.pathB) {
-        return { pathA: args.directory, pathB: args.pathB };
-    }
-    const argv = process.argv.slice(2);
-    const positional = [];
-    let foundCommand = false;
-    let skipNext = false;
-    for (const arg of argv) {
-        if (skipNext) {
-            skipNext = false;
-            continue;
-        }
-        // Flags that consume a following value
-        if ([
-            '-f', '--format',
-            '-o', '--output',
-            '-c', '--config',
-            '-i', '--include',
-            '-x', '--exclude',
-            '-t', '--threads',
-            '-b', '--bundle',
-            '--log-level',
-            '--expected', '--expected-results',
-            '--limit',
-            '--category',
-            '--parallel',
-            '--cache-dir',
-            '--stream-output',
-            '--spec-model',
-            '--llm-base-url',
-            '--llm-api-key',
-            '--llm-model',
-            '--pattern-threshold',
-        ].includes(arg)) {
-            skipNext = true;
-            continue;
-        }
-        // Skip --key=value style flags and boolean flags
-        if (arg.startsWith('-')) {
-            continue;
-        }
-        // Skip the 'compare' command word itself
-        if (!foundCommand && arg === 'compare') {
-            foundCommand = true;
-            continue;
-        }
-        positional.push(arg);
-    }
-    if (positional.length < 2) {
-        return null;
-    }
-    return { pathA: positional[0], pathB: positional[1] };
-}
-// ---------------------------------------------------------------------------
 // Main command
 // ---------------------------------------------------------------------------
 export async function executeCompare(args) {
-    // Extract both paths (CliArgs first, argv fallback for legacy parser)
-    const paths = extractComparisonPaths(args);
-    if (!paths) {
+    // Both paths must be set explicitly on CliArgs. The Commander program
+    // (cli/program.ts) populates them from `<pathA> <pathB>` positional args.
+    // Programmatic consumers must set both `args.directory` and `args.pathB`.
+    if (!args.directory || !args.pathB) {
         console.error('Error: compare requires two paths');
         console.error('Usage: cognium-ai compare <pathA> <pathB>');
         return 1;
     }
-    const { pathA, pathB } = paths;
+    const pathA = args.directory;
+    const pathB = args.pathB;
     // Validate both paths exist
     if (!fs.existsSync(pathA)) {
         console.error(`Error: Path A not found: ${pathA}`);

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

@@ -1 +1 @@
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+{"version":3,"file":"compare.js","sourceRoot":"","sources":["../../../src/cli/commands/compare.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AAEzB,OAAO,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAC9C,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAC9D,OAAO,EACL,mBAAmB,EACnB,sBAAsB,GACvB,MAAM,wBAAwB,CAAC;AAEhC,8EAA8E;AAC9E,eAAe;AACf,8EAA8E;AAE9E,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAa;IAChD,sEAAsE;IACtE,0EAA0E;IAC1E,0EAA0E;IAC1E,IAAI,CAAC,IAAI,CAAC,SAAS,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;QACnC,OAAO,CAAC,KAAK,CAAC,mCAAmC,CAAC,CAAC;QACnD,OAAO,CAAC,KAAK,CAAC,2CAA2C,CAAC,CAAC;QAC3D,OAAO,CAAC,CAAC;IACX,CAAC;IAED,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;IAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;IAEzB,4BAA4B;IAC5B,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,KAAK,CAAC,4BAA4B,KAAK,EAAE,CAAC,CAAC;QACnD,OAAO,CAAC,CAAC;IACX,CAAC;IACD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,KAAK,CAAC,4BAA4B,KAAK,EAAE,CAAC,CAAC;QACnD,OAAO,CAAC,CAAC;IACX,CAAC;IAED,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;QAChB,OAAO,CAAC,KAAK,CAAC,yBAAyB,CAAC,CAAC;QACzC,OAAO,CAAC,KAAK,CAAC,mBAAmB,KAAK,EAAE,CAAC,CAAC;QAC1C,OAAO,CAAC,KAAK,CAAC,mBAAmB,KAAK,EAAE,CAAC,CAAC;QAC1C,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACpB,CAAC;IAED,IAAI,CAAC;QACH,0EAA0E;QAC1E,gDAAgD;QAChD,MAAM,IAAI,GAAG,mBAAmB,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;QAC9C,MAAM,IAAI,GAAG,mBAAmB,CAAC,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,EAAE,KAAK,CAAC,CAAC;QAE1E,+BAA+B;QAC/B,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;QAC5C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,gBAAgB,CACpC,KAAK,EACL,IAAI,EACJ,IAAI,CAAC,eAAe,EACpB,IAAI,CAAC,mBAAmB,EACxB,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,QAAQ,IAAI,IAAI,CACtB,CAAC;QAEF,+BAA+B;QAC/B,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;QAC5C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,gBAAgB,CACpC,KAAK,EACL,IAAI,EACJ,IAAI,CAAC,eAAe,EACpB,IAAI,CAAC,mBAAmB,EACxB,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,QAAQ,IAAI,IAAI,CACtB,CAAC;QAEF,UAAU;QACV,MAAM,UAAU,GAAG,mBAAmB,CACpC,OAAO,CAAC,WAAW,EACnB,OAAO,CAAC,WAAW,CACpB,CAAC;QAEF,SAAS;QACT,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC3B,MAAM,UAAU,GAAG,IAAI,CAAC,SAAS,CAC/B;gBACE,UAAU,EAAE,UAAU,CAAC,UAAU;gBACjC,KAAK,EAAE,UAAU,CAAC,KAAK;gBACvB,KAAK,EAAE,UAAU,CAAC,KAAK;gBACvB,WAAW,EAAE,UAAU,CAAC,WAAW;gBACnC,KAAK,EAAE,UAAU,CAAC,KAAK;gBACvB,MAAM,EAAE,UAAU,CAAC,OAAO,CAAC,KAAK;gBAChC,MAAM,EAAE,UAAU,CAAC,OAAO,CAAC,KAAK;gBAChC,UAAU,EAAE,UAAU,CAAC,UAAU;gBACjC,gBAAgB,EAAE,UAAU,CAAC,WAAW,CAAC,MAAM;gBAC/C,kBAAkB,EAAE,UAAU,CAAC,aAAa,CAAC,MAAM;gBACnD,WAAW,EAAE,UAAU,CAAC,WAAW;gBACnC,aAAa,EAAE,UAAU,CAAC,aAAa;gBACvC,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;aACpC,EACD,IAAI,EACJ,CAAC,CACF,CAAC;YAEF,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;gBAChB,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;gBAC1C,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,UAAU,CAAC,CAAC;YAC1B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,wBAAwB;YACxB,MAAM,MAAM,GAAG,sBAAsB,CAAC,UAAU,CAAC,CAAC;YAElD,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,iDAAiD;QACjD,OAAO,UAAU,CAAC,KAAK,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACjD,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CACX,QAAQ,EACR,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAC/C,CAAC;QACF,OAAO,CAAC,CAAC;IACX,CAAC;AACH,CAAC"}

package/dist/cli/commands/dead-code.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dead-code.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/dead-code.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAG1C;;GAEG;AACH,wBAAsB,eAAe,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA2DpE"}
+{"version":3,"file":"dead-code.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/dead-code.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAG1C;;GAEG;AACH,wBAAsB,eAAe,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAiEpE"}

package/dist/cli/commands/dead-code.js

@@ -23,6 +23,8 @@ export async function executeDeadCode(args) {
         target: targetPath,
         includePatterns: eff.include.length > 0 ? eff.include : undefined,
         excludePatterns: eff.exclude.length > 0 ? eff.exclude : undefined,
+        includeTests: args.includeTests,
+        publicMethodsAsEntryPoints: args.publicAsEntry,
         onProgress: args.quiet ? undefined : (progress) => {
             console.error(`[${progress.phase}] ${progress.message || ''}`);
         },
@@ -43,8 +45,12 @@ export async function executeDeadCode(args) {
             }
         }
         else {
-            // Summary format
-            const report = formatDeadCodeReport(result);
+            // Summary format — honor --full / --top <n> for truncation
+            const report = formatDeadCodeReport(result, {
+                full: args.full,
+                topPerFile: args.top ?? undefined,
+                topEntryPoints: args.top ?? undefined,
+            });
             if (args.output) {
                 fs.writeFileSync(args.output, report);
                 if (!args.quiet) {

package/dist/cli/commands/dead-code.js.map

@@ -1 +1 @@
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