circle-ir-ai 1.19.4 → 1.20.0

package/CHANGELOG.md

@@ -5,6 +5,67 @@ 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).
 
+## [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/cli/args.d.ts

@@ -60,6 +60,7 @@ export interface CliArgs {
     disablePass: string[];
     fileTimeout: number;
     maxFiles: number | null;
+    pathB: string | null;
 }
 /**
  * Parse command-line arguments.

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

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package/dist/cli/args.js

@@ -56,6 +56,7 @@ export function parseArgs(argv) {
         disablePass: [],
         fileTimeout: 30,
         maxFiles: null,
+        pathB: null,
     };
     let i = 0;
     while (i < argv.length) {

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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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+{"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;AAErE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAgB1C,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;AAyGD,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAuLnE"}

package/dist/cli/commands/analyze.js

@@ -1,31 +1,303 @@
 /**
- * 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 * as fs from 'fs';
 import * as path from 'path';
 import { analyze } from 'circle-ir';
 import { ensureAnalyzerInitialized } from '../../utils/analyzer-init.js';
-/**
- * Run analysis on a single file.
- */
+import { loadCogniumConfig, convertCogniumConfigToPassOptions } from '../config.js';
+import { analyzeFile } from '../../agents/mastra/workflow.js';
+import { runBundle, runBundleOnFiles, registerSecurityAgents, } from '../../agents/multi/index.js';
+import { runSwarmAnalysis } from './swarm.js';
+import { formatOutput } from '../formatters/index.js';
 export async function runAnalysis(filePath, options = {}) {
-    // Initialize analyzer with correct WASM paths
     await ensureAnalyzerInitialized();
-    // Read file content
     const code = fs.readFileSync(filePath, 'utf-8');
-    // Detect language from extension
     const ext = path.extname(filePath).toLowerCase();
     let language = 'java';
-    if (ext === '.c' || ext === '.h') {
+    if (ext === '.c' || ext === '.h')
         language = 'c';
-    }
-    else if (['.cpp', '.cc', '.cxx', '.hpp'].includes(ext)) {
+    else if (['.cpp', '.cc', '.cxx', '.hpp'].includes(ext))
         language = 'cpp';
+    return analyze(code, filePath, language, { taintConfig: options.taintConfig });
+}
+// ---------------------------------------------------------------------------
+// executeAnalyze — CLI entry for `cognium-ai <path>` (no subcommand)
+// ---------------------------------------------------------------------------
+function detectLanguageFromFile(filePath) {
+    const ext = path.extname(filePath).toLowerCase();
+    switch (ext) {
+        case '.java': return 'java';
+        case '.js':
+        case '.jsx':
+        case '.mjs':
+        case '.cjs': return 'javascript';
+        case '.ts':
+        case '.tsx':
+        case '.mts':
+        case '.cts': return 'typescript';
+        case '.py': return 'python';
+        case '.rs': return 'rust';
+        case '.c':
+        case '.h': return 'c';
+        case '.cpp':
+        case '.cc':
+        case '.cxx':
+        case '.hpp':
+        case '.hxx': return 'cpp';
+        default: return 'java';
+    }
+}
+function collectJavaFiles(dir, include, exclude) {
+    const files = [];
+    const walk = (d) => {
+        for (const entry of fs.readdirSync(d, { withFileTypes: true })) {
+            const fullPath = path.join(d, entry.name);
+            if (entry.isDirectory()) {
+                const relPath = path.relative(dir, fullPath);
+                if (exclude.some(p => relPath.includes(p) || entry.name === p))
+                    continue;
+                walk(fullPath);
+            }
+            else if (entry.name.endsWith('.java')) {
+                const relPath = path.relative(dir, fullPath);
+                if (include.length > 0 && !include.some(p => relPath.includes(p) || entry.name.includes(p)))
+                    continue;
+                if (exclude.some(p => relPath.includes(p) || entry.name === p))
+                    continue;
+                files.push(fullPath);
+            }
+        }
+    };
+    walk(dir);
+    return files;
+}
+function getSeverityIcon(severity) {
+    switch (severity) {
+        case 'CRITICAL': return '🔴';
+        case 'HIGH': return '🟠';
+        case 'MEDIUM': return '🟡';
+        case 'LOW': return '🟢';
+        default: return 'ℹ️';
+    }
+}
+function formatBundleResult(result) {
+    const lines = [];
+    lines.push('═══════════════════════════════════════════════════════════════');
+    lines.push('                    MULTI-AGENT ANALYSIS RESULTS');
+    lines.push('═══════════════════════════════════════════════════════════════');
+    lines.push('');
+    lines.push(`Files analyzed: ${result.summary.totalFiles}`);
+    lines.push(`Total findings: ${result.summary.totalFindings}`);
+    lines.push(`Total time: ${(result.totalTimeMs / 1000).toFixed(2)}s`);
+    lines.push('');
+    lines.push('Findings by category:');
+    for (const [cat, count] of Object.entries(result.summary.byCategory)) {
+        if (count > 0)
+            lines.push(`  ${cat}: ${count}`);
+    }
+    lines.push('');
+    const filesWithFindings = result.results.filter(r => r.summary.totalFindings > 0);
+    if (filesWithFindings.length > 0) {
+        lines.push('───────────────────────────────────────────────────────────────');
+        lines.push('FILES WITH FINDINGS');
+        lines.push('───────────────────────────────────────────────────────────────');
+        for (const fileResult of filesWithFindings) {
+            lines.push('');
+            lines.push(`📁 ${fileResult.filePath}`);
+            for (const agentResult of fileResult.results) {
+                for (const f of agentResult.findings) {
+                    const sev = (f.severity ?? 'INFO').toUpperCase();
+                    const loc = f.location;
+                    const line = loc?.line ?? '?';
+                    const msg = f.message ?? f.type;
+                    const cwe = f.cwe ? ` [${f.cwe}]` : '';
+                    lines.push(`  ${getSeverityIcon(sev)} Line ${line}: ${msg}${cwe}`);
+                }
+            }
+        }
+    }
+    lines.push('');
+    lines.push('═══════════════════════════════════════════════════════════════');
+    return lines.join('\n');
+}
+export async function executeAnalyze(args) {
+    const targetPath = args.file || args.directory;
+    if (!targetPath) {
+        console.error('Error: No file or directory specified');
+        console.error('Usage: cognium-ai <file|directory> [options]');
+        return 1;
+    }
+    if (!fs.existsSync(targetPath)) {
+        console.error(`Error: Path not found: ${targetPath}`);
+        return 1;
+    }
+    const isDirectory = fs.statSync(targetPath).isDirectory();
+    // Merge cognium.config.json into pass-disable list
+    const cogniumConfig = loadCogniumConfig(args.config || undefined, targetPath);
+    let configDisabledPasses = [];
+    if (cogniumConfig) {
+        const { disabledPasses } = convertCogniumConfigToPassOptions(cogniumConfig);
+        configDisabledPasses = disabledPasses;
+    }
+    const mergedDisabledPasses = [...new Set([...configDisabledPasses, ...args.disablePass])];
+    // 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 ?? []);
+    try {
+        if (args.bundle) {
+            registerSecurityAgents();
+            if (isDirectory) {
+                const files = collectJavaFiles(targetPath, include, exclude);
+                const fileInputs = files.map(f => ({
+                    path: f,
+                    content: fs.readFileSync(f, 'utf-8'),
+                    language: 'java',
+                }));
+                if (!args.quiet) {
+                    console.error(`Running ${args.bundle} bundle on ${fileInputs.length} files...`);
+                }
+                const bundleResult = await runBundleOnFiles(args.bundle, fileInputs, {
+                    maxConcurrency: args.threads,
+                    onFileComplete: args.quiet ? undefined : (file, i, total) => {
+                        console.error(`[${i}/${total}] ${path.basename(file)}`);
+                    },
+                });
+                const output = args.format === 'json'
+                    ? JSON.stringify(bundleResult, null, 2)
+                    : formatBundleResult(bundleResult);
+                if (args.output) {
+                    fs.writeFileSync(args.output, output);
+                    if (!args.quiet)
+                        console.error(`Output written to ${args.output}`);
+                }
+                else {
+                    console.log(output);
+                }
+                if (args.exitCode && bundleResult.summary.totalFindings > 0)
+                    return 1;
+            }
+            else {
+                const sourceCode = fs.readFileSync(targetPath, 'utf-8');
+                const detectedLang = detectLanguageFromFile(targetPath);
+                const bundleLang = (['java', 'c', 'cpp'].includes(detectedLang) ? detectedLang : 'java');
+                const bundleResult = await runBundle(args.bundle, sourceCode, targetPath, {
+                    language: bundleLang,
+                });
+                const output = args.format === 'json'
+                    ? JSON.stringify(bundleResult, null, 2)
+                    : formatBundleResult({
+                        results: [bundleResult],
+                        totalTimeMs: bundleResult.totalTimeMs,
+                        summary: { totalFiles: 1, ...bundleResult.summary },
+                    });
+                if (args.output) {
+                    fs.writeFileSync(args.output, output);
+                    if (!args.quiet)
+                        console.error(`Output written to ${args.output}`);
+                }
+                else {
+                    console.log(output);
+                }
+                if (args.exitCode && bundleResult.summary.totalFindings > 0)
+                    return 1;
+            }
+            return 0;
+        }
+        if (isDirectory) {
+            const result = await runSwarmAnalysis({
+                directory: targetPath,
+                include,
+                exclude,
+                quiet: args.quiet,
+                maxConcurrency: args.threads,
+                enableEnrichment: args.llmEnrich,
+                enableVerification: args.llmVerify,
+                cacheEnabled: args.cache,
+                cacheDir: args.cacheDir ?? undefined,
+                clearCache: args.clearCache,
+                streamOutput: args.streamOutput ?? undefined,
+                memoryEfficient: args.memoryEfficient,
+                disabledPasses: mergedDisabledPasses.length > 0 ? mergedDisabledPasses : undefined,
+            });
+            if (args.output) {
+                fs.writeFileSync(args.output, JSON.stringify(result, null, 2));
+                if (!args.quiet)
+                    console.error(`Output written to ${args.output}`);
+            }
+            else if (args.format === 'json') {
+                console.log(JSON.stringify(result, null, 2));
+            }
+            if (args.exitCode && result.summary.totalVulnerabilities > 0)
+                return 1;
+            return 0;
+        }
+        // Single-file path
+        const sourceCode = fs.readFileSync(targetPath, 'utf-8');
+        const detectedLang = detectLanguageFromFile(targetPath);
+        const mastraResult = await analyzeFile(targetPath, sourceCode, {
+            language: detectedLang,
+            enableEnrichment: args.llmEnrich,
+            enableVerification: args.llmVerify,
+            disabledPasses: mergedDisabledPasses.length > 0 ? mergedDisabledPasses : undefined,
+        });
+        const result = {
+            meta: {
+                file_path: targetPath,
+                language: detectedLang,
+                loc: sourceCode.split('\n').length,
+                parse_time_ms: 0,
+                analysis_time_ms: mastraResult.stats.totalTimeMs || 0,
+            },
+            types: [],
+            imports: [],
+            exports: [],
+            calls: [],
+            cfg: { blocks: [], edges: [] },
+            dfg: { definitions: [], uses: [] },
+            taint: {
+                sources: mastraResult.vulnerabilities.map((v) => {
+                    const src = v.source;
+                    return {
+                        line: src?.line ?? 0,
+                        type: src?.type ?? 'unknown',
+                        location: `Line ${src?.line ?? 0}`,
+                        severity: v.severity ?? 'medium',
+                    };
+                }),
+                sinks: mastraResult.vulnerabilities.map((v) => {
+                    const sink = v.sink;
+                    return {
+                        line: sink?.line ?? 0,
+                        type: sink?.type ?? 'unknown',
+                        cwe: v.cwe ?? 'CWE-Unknown',
+                        location: `Line ${sink?.line ?? 0}`,
+                    };
+                }),
+                sanitizers: [],
+                flows: [],
+            },
+            unresolved: [],
+            enriched: { llm_sources: [], llm_sinks: [], llm_verified: [] },
+        };
+        const output = formatOutput(result, args.format, targetPath);
+        if (args.output) {
+            fs.writeFileSync(args.output, output);
+            if (!args.quiet)
+                console.error(`Output written to ${args.output}`);
+        }
+        else {
+            console.log(output);
+        }
+        if (args.exitCode && result.taint.sinks.length > 0)
+            return 1;
+        return 0;
+    }
+    catch (error) {
+        console.error('Error:', error instanceof Error ? error.message : error);
+        return 1;
     }
-    // Run analysis
-    const result = await analyze(code, filePath, language, {
-        taintConfig: options.taintConfig,
-    });
-    return result;
 }
 //# sourceMappingURL=analyze.js.map

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

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package/dist/cli/commands/benchmark.js

@@ -13,7 +13,7 @@ export async function executeBenchmark(args) {
     const expectedFile = args.expectedResults;
     if (!testDir) {
         console.error('Error: No test directory specified');
-        console.error('Usage: circle-ir benchmark <directory> --expected <file>');
+        console.error('Usage: cognium-ai benchmark <directory> --expected <file>');
         return 1;
     }
     if (!fs.existsSync(testDir)) {
@@ -22,7 +22,7 @@ export async function executeBenchmark(args) {
     }
     if (!expectedFile) {
         console.error('Error: No expected results file specified');
-        console.error('Usage: circle-ir benchmark <directory> --expected <file>');
+        console.error('Usage: cognium-ai benchmark <directory> --expected <file>');
         return 1;
     }
     if (!fs.existsSync(expectedFile)) {