circle-ir-ai 1.19.5 → 2.0.0

package/CHANGELOG.md

@@ -5,6 +5,215 @@ 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).
 
+## [2.0.0] - 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
+filtering, config-file resolution, and per-command help. The Commander
+program is now exported so wrapper CLIs (cognium-ai) can build on it
+directly.
+
+### Added
+
+- **`buildProgram(handlers, options?)`** exported from `circle-ir-ai/commands`.
+  Builds the full Commander program with all 14 subcommands wired up.
+  Wrappers can layer additional subcommands on top before calling
+  `parseAsync`. `BuildProgramOptions` lets callers override `name` /
+  `version` / `description`.
+- **`getEffectiveOptions(args, target)`** — merges CLI flags with
+  `cognium.config.json` and `.circle-ir.yaml` into a single resolved
+  options object. Every command now uses it.
+- **`collectFiles(root, options)`** — minimatch-based directory walker with
+  language filtering, `include`/`exclude` globs, max-files cap, and a
+  default skip-list. Replaces five hand-coded walkers across commands.
+- **Specifica engine** gained `includePatterns` / `excludePatterns` /
+  `maxFiles` on `SpecificaOptions`.
+- **`analyze-skill`** subcommand has a `skill` alias.
+- **Per-command `--help`** for every subcommand (usage, options, examples).
+- **`pathB`** field on `CliArgs` for the `compare` command (replaces an
+  env-var tunnel).
+
+### Changed
+
+- **LLM is on by default** across all commands. `--no-llm` opts out.
+  Granular `--no-llm-discovery` / `--no-llm-enrich` / `--no-llm-verify`
+  available everywhere.
+- **`scan`**: validation failure for LLM config now warns and falls back
+  to static analysis instead of hard-erroring.
+- **`compare`**: forwards analyzer options + include/exclude to both runs
+  so the comparison is symmetric.
+- **`trust`**, **`metrics`**, **`understand`**, **`spec-diff`**,
+  **`cluster`** — replaced hand-coded directory walkers with the shared
+  `collectFiles` (now honors `--include`/`--exclude` and config).
+- **`scan`**, **`secrets`**, **`dead-code`**, **`health`** — pipe
+  `include`/`exclude` into the engine's filter (was previously dropped).
+- All user-facing strings in the CLI now say `cognium-ai`, not
+  `circle-ir`.
+
+### Fixed
+
+- **Commander option-precedence bug** — discovered during review that
+  `optsWithGlobals()` lets parent defaults override subcommand-explicit
+  values. Replaced with custom merge using `getOptionValueSource()` so
+  the more specific user input always wins.
+
+### Internal
+
+- New files: `src/cli/program.ts`, `src/cli/file-collection.ts`,
+  `src/cli/effective-options.ts`.
+- `src/cli/index.ts` is now a thin Commander wiring (~70 lines, was 700).
+- Legacy `parseArgs` switch parser preserved for backwards compatibility
+  but no longer the active path.
+- TODO.md: added "Deprecate circle-ir-ai standalone CLI" and "CLI Commands
+  Review Backlog" sections.
+
 ## [1.18.10] - 2026-04-14
 
 ### Changed

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

@@ -60,6 +60,24 @@ export interface CliArgs {
     disablePass: string[];
     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

@@ -56,6 +56,24 @@ export function parseArgs(argv) {
         disablePass: [],
         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/analyze-skill.d.ts

@@ -4,11 +4,11 @@
  * Analyzes AI skill bundles for security issues.
  *
  * Usage:
- *   circle-ir analyze-skill <skill-path>
- *   circle-ir analyze-skill <skill-path> --format json
- *   circle-ir analyze-skill <skill-path> --format json -o report.json
- *   circle-ir analyze-skill <skill-path> --no-cross-artifact
- *   circle-ir analyze-skill <skill-path> --min-confidence 0.8
+ *   cognium-ai analyze-skill <skill-path>
+ *   cognium-ai analyze-skill <skill-path> --format json
+ *   cognium-ai analyze-skill <skill-path> --format json -o report.json
+ *   cognium-ai analyze-skill <skill-path> --no-cross-artifact
+ *   cognium-ai analyze-skill <skill-path> --min-confidence 0.8
  */
 export interface AnalyzeSkillOptions {
     /** Output format */

package/dist/cli/commands/analyze-skill.js

@@ -4,11 +4,11 @@
  * Analyzes AI skill bundles for security issues.
  *
  * Usage:
- *   circle-ir analyze-skill <skill-path>
- *   circle-ir analyze-skill <skill-path> --format json
- *   circle-ir analyze-skill <skill-path> --format json -o report.json
- *   circle-ir analyze-skill <skill-path> --no-cross-artifact
- *   circle-ir analyze-skill <skill-path> --min-confidence 0.8
+ *   cognium-ai analyze-skill <skill-path>
+ *   cognium-ai analyze-skill <skill-path> --format json
+ *   cognium-ai analyze-skill <skill-path> --format json -o report.json
+ *   cognium-ai analyze-skill <skill-path> --no-cross-artifact
+ *   cognium-ai analyze-skill <skill-path> --min-confidence 0.8
  */
 import * as fs from 'fs/promises';
 import { analyzeSkillBundle, } from '../../skills/index.js';

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

@@ -1,7 +1,10 @@
 /**
- * Single file analysis command
+ * Analyze command — single-file, directory swarm, or multi-agent bundle.
+ *
+ * Also exports the lower-level runAnalysis() helper used by other code.
  */
 import { type CircleIR, type TaintConfig } from 'circle-ir';
+import type { CliArgs } from '../args.js';
 export interface AnalysisOptions {
     taintConfig?: TaintConfig;
     discoverPatterns?: boolean;
@@ -11,8 +14,6 @@ export interface AnalysisOptions {
     llmBaseUrl?: string;
     llmApiKey?: string;
 }
-/**
- * Run analysis on a single file.
- */
 export declare function runAnalysis(filePath: string, options?: AnalysisOptions): Promise<CircleIR>;
+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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