circle-ir-ai 1.13.0 → 1.15.0

package/CHANGELOG.md

@@ -5,6 +5,45 @@ 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).
 
+## [1.15.0] - 2026-03-30
+
+### Added
+
+- **cognium.config.json support**: Project-level configuration for pass disabling, options, and trust pass filtering
+  - `loadCogniumConfig()` — finds and parses `cognium.config.json` (walks up directories)
+  - `convertCogniumConfigToPassOptions()` — converts config to circle-ir `PassOptions` + `disabledPasses`
+  - Exported `CogniumConfig`, `Suppression` types from package index
+  - CLI `--disable-pass` flag for comma-separated pass disabling (e.g., `--disable-pass god-class,naming-convention`)
+  - Trust command: loads config, filters trust passes via `trust.disabledPasses`, forwards SAST pass options to `analyze()`
+- 24 new tests in `tests/config-cognium.test.ts`
+
+### Changed
+
+- **circle-ir dependency upgrade**: ^3.14.0 → ^3.16.0 (resolves to 3.16.3)
+  - 3.15.0: Enhanced null-deref, n-plus-one, sink-filter; 40 new tests
+  - 3.16.0: PassOptions API, disabledPasses runtime config, cognium.config.json project-level configuration
+  - 3.16.1-3.16.3: Bug fixes (infinite-loop for iterator-based loops, project-level pass filtering)
+
+## [1.14.0] - 2026-03-28
+
+### Added
+
+- **Phase 5: Semantic Understanding**
+  - **Effect Summarizer** (`src/understand/effect-summarizer.ts`): Extracts `FunctionEffect[]` from CircleIR per function — parameters, visibility, state reads/mutations (DFG), side effects (classified from calls + taint sinks), call targets
+  - **Module Summarizer** (`src/understand/module-summarizer.ts`): Aggregates function effects into `ModuleSummary` with role detection (annotations + class name suffixes), purpose generation, security surface counting
+  - **Spec-Gap Analyzer** (`src/spec-gap/analyzer.ts`): Compares Specifica spec requirements (REQ-NNN) against code behavior using token overlap matching. Identifies uncovered requirements and undocumented security behaviors
+  - **spec-gap-report** trust pass (`src/trust/passes/spec-gap-report.ts`): Trust pass wrapping spec-gap analyzer — medium findings for uncovered requirements, high findings for undocumented security behaviors
+  - CLI commands: `understand`, `spec-diff`, `cluster`
+  - 54+ new tests across 4 test files
+
+### Changed
+
+- Trust score now has 27 passes (26 → 27)
+- PASS_CATEGORY_MAP expanded from 31 to 32 entries
+- PASS_COMPONENT_MAP expanded from 27 to 28 entries
+- New CLI commands: `understand <path>`, `spec-diff <path> [--spec <dir>]`, `cluster <path>`
+- New `--spec` CLI flag for specifying .specifica/ directory path
+
 ## [1.13.0] - 2026-03-28
 
 ### Changed

package/dist/cli/args.d.ts

@@ -2,7 +2,7 @@
  * CLI Argument Parser
  */
 export type OutputFormat = 'json' | 'summary' | 'sarif' | 'markdown' | 'csv';
-export type Command = 'analyze' | 'benchmark' | 'scan' | 'health' | 'secrets' | 'dead-code' | 'generate-spec' | 'analyze-skill' | 'metrics' | 'trust' | 'compare' | 'quality';
+export type Command = 'analyze' | 'benchmark' | 'scan' | 'health' | 'secrets' | 'dead-code' | 'generate-spec' | 'analyze-skill' | 'metrics' | 'trust' | 'compare' | 'quality' | 'understand' | 'spec-diff' | 'cluster';
 export type LogLevel = 'trace' | 'debug' | 'info' | 'warn' | 'error' | 'silent';
 export type BundleType = 'jr-dev' | 'sr-dev' | 'architect' | 'security-review' | 'full-review';
 export interface CliArgs {
@@ -41,10 +41,12 @@ export interface CliArgs {
     specOverwrite: boolean;
     specSkip: boolean;
     specNoBackup: boolean;
+    specDir: string | null;
     crossArtifact?: boolean;
     verification?: boolean;
     minConfidence?: number;
     minSeverity?: 'critical' | 'high' | 'medium' | 'low' | 'info';
+    disablePass: string[];
 }
 /**
  * Parse command-line arguments.

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

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package/dist/cli/args.js

@@ -41,6 +41,8 @@ export function parseArgs(argv) {
         specOverwrite: false,
         specSkip: false,
         specNoBackup: false,
+        specDir: null,
+        disablePass: [],
     };
     let i = 0;
     while (i < argv.length) {
@@ -79,6 +81,15 @@ export function parseArgs(argv) {
             case 'quality':
                 args.command = 'quality';
                 break;
+            case 'understand':
+                args.command = 'understand';
+                break;
+            case 'spec-diff':
+                args.command = 'spec-diff';
+                break;
+            case 'cluster':
+                args.command = 'cluster';
+                break;
             case '-h':
             case '--help':
                 args.help = true;
@@ -296,6 +307,20 @@ export function parseArgs(argv) {
             case '--spec-no-backup':
                 args.specNoBackup = true;
                 break;
+            case '--spec':
+                i++;
+                if (i >= argv.length) {
+                    throw new Error('Missing value for --spec');
+                }
+                args.specDir = argv[i];
+                break;
+            case '--disable-pass':
+                i++;
+                if (i >= argv.length) {
+                    throw new Error('Missing value for --disable-pass');
+                }
+                args.disablePass.push(...argv[i].split(',').map(s => s.trim()).filter(Boolean));
+                break;
             default:
                 // Check for --key=value style
                 if (arg.startsWith('--format=')) {
@@ -420,6 +445,12 @@ export function parseArgs(argv) {
                 else if (arg === '--spec-no-backup') {
                     args.specNoBackup = true;
                 }
+                else if (arg.startsWith('--spec=')) {
+                    args.specDir = arg.substring(7);
+                }
+                else if (arg.startsWith('--disable-pass=')) {
+                    args.disablePass.push(...arg.substring(15).split(',').map(s => s.trim()).filter(Boolean));
+                }
                 else if (arg.startsWith('-')) {
                     throw new Error(`Unknown option: ${arg}`);
                 }
@@ -440,7 +471,7 @@ export function parseArgs(argv) {
         i++;
     }
     // For directory-based commands, treat file as directory
-    if (['benchmark', 'scan', 'health', 'secrets', 'dead-code', 'analyze-skill', 'trust', 'compare', 'quality'].includes(args.command) && args.file) {
+    if (['benchmark', 'scan', 'health', 'secrets', 'dead-code', 'analyze-skill', 'trust', 'compare', 'quality', 'understand', 'spec-diff', 'cluster'].includes(args.command) && args.file) {
         args.directory = args.file;
         args.file = null;
     }

package/dist/cli/args.js.map

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

@@ -0,0 +1,12 @@
+/**
+ * Cluster Command
+ *
+ * Wires existing src/components/ analyzeComponents() to CLI.
+ * Performs two-phase component enrichment and clustering.
+ *
+ * Usage:
+ *   circle-ir cluster <path> [--format json] [--llm]
+ */
+import type { CliArgs } from '../args.js';
+export declare function executeCluster(args: CliArgs): Promise<number>;
+//# sourceMappingURL=cluster.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"cluster.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/cluster.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAoK1C,wBAAsB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA6EnE"}

package/dist/cli/commands/cluster.js

@@ -0,0 +1,246 @@
+/**
+ * Cluster Command
+ *
+ * Wires existing src/components/ analyzeComponents() to CLI.
+ * Performs two-phase component enrichment and clustering.
+ *
+ * Usage:
+ *   circle-ir cluster <path> [--format json] [--llm]
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+import { initAnalyzer, isAnalyzerInitialized, analyze } from 'circle-ir';
+import { analyzeComponents } from '../../components/index.js';
+// ---------------------------------------------------------------------------
+// File collection
+// ---------------------------------------------------------------------------
+const LANG_EXTENSIONS = {
+    '.java': 'java',
+    '.js': 'javascript',
+    '.mjs': 'javascript',
+    '.ts': 'typescript',
+    '.tsx': 'typescript',
+    '.py': 'python',
+    '.rs': 'rust',
+    '.sh': 'bash',
+    '.bash': 'bash',
+};
+const SKIP_DIRS = new Set([
+    'node_modules', 'dist', 'build', '.git', '.next', '__pycache__',
+    'target', 'vendor', 'coverage', '.tsbuildinfo',
+]);
+function collectFiles(dir) {
+    const results = [];
+    function walk(currentDir, depth) {
+        if (depth > 20 || results.length >= 500)
+            return;
+        let entries;
+        try {
+            entries = fs.readdirSync(currentDir, { withFileTypes: true });
+        }
+        catch {
+            return;
+        }
+        for (const entry of entries) {
+            if (results.length >= 500)
+                break;
+            if (entry.name.startsWith('.') && entry.isDirectory())
+                continue;
+            const fullPath = path.join(currentDir, entry.name);
+            if (entry.isDirectory()) {
+                if (!SKIP_DIRS.has(entry.name))
+                    walk(fullPath, depth + 1);
+            }
+            else if (entry.isFile()) {
+                const ext = path.extname(entry.name).toLowerCase();
+                const lang = LANG_EXTENSIONS[ext];
+                if (lang)
+                    results.push({ path: fullPath, language: lang });
+            }
+        }
+    }
+    const stat = fs.statSync(dir);
+    if (stat.isDirectory()) {
+        walk(dir, 0);
+    }
+    else {
+        console.error('Error: cluster command requires a directory path');
+    }
+    return results;
+}
+// ---------------------------------------------------------------------------
+// Extract components from CircleIR
+// ---------------------------------------------------------------------------
+function inferComponentType(type) {
+    const name = type.name.toLowerCase();
+    const annos = type.annotations.map(a => a.toLowerCase());
+    if (annos.some(a => a.includes('controller') || a.includes('restcontroller')))
+        return 'controller';
+    if (annos.some(a => a.includes('service')))
+        return 'service';
+    if (annos.some(a => a.includes('repository')))
+        return 'repository';
+    if (name.endsWith('controller') || name.endsWith('handler'))
+        return 'controller';
+    if (name.endsWith('service') || name.endsWith('manager'))
+        return 'service';
+    if (name.endsWith('repository') || name.endsWith('dao'))
+        return 'repository';
+    if (name.endsWith('model') || name.endsWith('entity') || name.endsWith('dto'))
+        return 'model';
+    return 'utility';
+}
+function extractComponents(filePath, ir) {
+    const components = [];
+    for (const type of ir.types) {
+        const methods = type.methods.map(m => m.name);
+        components.push({
+            id: `${path.basename(filePath)}:${type.name}`,
+            name: type.name,
+            file: filePath,
+            type: inferComponentType(type),
+            line_start: type.start_line,
+            line_end: type.end_line,
+            methods,
+            annotations: type.annotations,
+        });
+    }
+    return components;
+}
+// ---------------------------------------------------------------------------
+// Text formatting
+// ---------------------------------------------------------------------------
+function formatTextReport(result) {
+    const lines = [];
+    lines.push('===============================================================');
+    lines.push('                    COMPONENT CLUSTER REPORT');
+    lines.push('===============================================================');
+    lines.push('');
+    // Components
+    lines.push(`Components: ${result.components.length}`);
+    lines.push('');
+    for (const comp of result.components) {
+        const role = comp.semantic?.architectural_role ?? 'unknown';
+        const purpose = comp.semantic?.business_purpose ?? '';
+        lines.push(`  ${comp.name} [${role}]`);
+        if (purpose)
+            lines.push(`    Purpose: ${purpose}`);
+    }
+    lines.push('');
+    // Clusters
+    if (result.clustering) {
+        lines.push('---------------------------------------------------------------');
+        lines.push(`Feature Clusters: ${result.clustering.features.length}`);
+        lines.push('---------------------------------------------------------------');
+        for (const feature of result.clustering.features) {
+            lines.push(`  ${feature.name} (${feature.components.length} components)`);
+            for (const comp of feature.components) {
+                lines.push(`    - ${comp}`);
+            }
+        }
+        lines.push('');
+        if (result.clustering.flows.length > 0) {
+            lines.push(`Flows: ${result.clustering.flows.length}`);
+            for (const flow of result.clustering.flows) {
+                lines.push(`  ${flow.name} [${flow.type}] — ${flow.components_involved.length} components`);
+            }
+            lines.push('');
+        }
+        if (result.clustering.architecture) {
+            lines.push('Architecture Insights:');
+            lines.push(`  Pattern: ${result.clustering.architecture.pattern}`);
+            if (result.clustering.architecture.design_patterns?.length) {
+                lines.push(`  Design Patterns: ${result.clustering.architecture.design_patterns.join(', ')}`);
+            }
+            const { strengths, weaknesses, recommendations } = result.clustering.architecture.insights;
+            if (strengths?.length)
+                lines.push(`  Strengths: ${strengths.join(', ')}`);
+            if (weaknesses?.length)
+                lines.push(`  Weaknesses: ${weaknesses.join(', ')}`);
+            if (recommendations?.length)
+                lines.push(`  Recommendations: ${recommendations.join(', ')}`);
+        }
+    }
+    lines.push('');
+    lines.push('===============================================================');
+    return lines.join('\n');
+}
+// ---------------------------------------------------------------------------
+// Main command
+// ---------------------------------------------------------------------------
+export async function executeCluster(args) {
+    const targetPath = args.directory || args.file || process.cwd();
+    if (!fs.existsSync(targetPath)) {
+        console.error(`Error: Path not found: ${targetPath}`);
+        return 1;
+    }
+    if (!fs.statSync(targetPath).isDirectory()) {
+        console.error('Error: cluster command requires a directory path');
+        return 1;
+    }
+    if (!args.quiet) {
+        console.error(`Running component clustering on ${targetPath}...`);
+    }
+    try {
+        // Initialize analyzer
+        if (!isAnalyzerInitialized()) {
+            if (!args.quiet)
+                console.error('  Initializing circle-ir analyzer...');
+            await initAnalyzer();
+        }
+        // Collect and analyze files
+        const files = collectFiles(targetPath);
+        if (!args.quiet) {
+            console.error(`  Found ${files.length} source file(s)`);
+        }
+        const allComponents = [];
+        for (const file of files) {
+            try {
+                const content = fs.readFileSync(file.path, 'utf-8');
+                const ir = await analyze(content, path.basename(file.path), file.language);
+                allComponents.push(...extractComponents(file.path, ir));
+            }
+            catch {
+                // Skip files that fail analysis
+            }
+        }
+        if (!args.quiet) {
+            console.error(`  Extracted ${allComponents.length} components`);
+        }
+        // Run component analysis (phase 1 needs LLM, skip if not enabled)
+        const enableLLM = args.llmEnrich || args.llmVerify;
+        const result = await analyzeComponents(allComponents, {
+            enablePhase1: enableLLM,
+            enablePhase2: enableLLM,
+        });
+        // Output
+        if (args.format === 'json') {
+            const output = JSON.stringify(result, null, 2);
+            if (args.output) {
+                fs.writeFileSync(args.output, output);
+                if (!args.quiet)
+                    console.error(`Output written to ${args.output}`);
+            }
+            else {
+                console.log(output);
+            }
+        }
+        else {
+            const report = formatTextReport(result);
+            if (args.output) {
+                fs.writeFileSync(args.output, report);
+                if (!args.quiet)
+                    console.error(`Output written to ${args.output}`);
+            }
+            else {
+                console.log(report);
+            }
+        }
+        return 0;
+    }
+    catch (error) {
+        console.error('Error:', error instanceof Error ? error.message : error);
+        return 1;
+    }
+}
+//# sourceMappingURL=cluster.js.map

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

@@ -0,0 +1 @@
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package/dist/cli/commands/generate-spec.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"generate-spec.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/generate-spec.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AASH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C;;GAEG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CA8DxE"}
+{"version":3,"file":"generate-spec.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/generate-spec.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C;;GAEG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAiFxE"}

package/dist/cli/commands/generate-spec.js

@@ -4,15 +4,16 @@
  * Generate Specifica-format specifications from existing code.
  */
 import * as fs from 'fs';
-import { generateSpecifica, } from '../../specifica/index.js';
+import { initAnalyzer } from 'circle-ir';
+import { generateSpecifica, generateSpecificaForDirectory, } from '../../specifica/index.js';
 /**
  * Execute Specifica generation command.
  */
 export async function executeGenerateSpec(args) {
     const targetPath = args.file || args.directory;
     if (!targetPath) {
-        console.error('Error: No file specified');
-        console.error('Usage: circle-ir generate-spec <file> [options]');
+        console.error('Error: No path specified');
+        console.error('Usage: circle-ir generate-spec <file|directory> [options]');
         return 1;
     }
     if (!fs.existsSync(targetPath)) {
@@ -20,41 +21,61 @@ export async function executeGenerateSpec(args) {
         return 1;
     }
     const isDirectory = fs.statSync(targetPath).isDirectory();
-    if (isDirectory) {
-        console.error('Error: Directory analysis not yet supported (Phase 2)');
-        console.error('Please specify a single file for now.');
-        return 1;
-    }
     if (!args.quiet) {
         console.error(`Generating Specifica specification for ${targetPath}...`);
     }
     const options = {
         specModel: args.specModel || 'cognium/gpt-oss-120b',
         overwrite: args.specOverwrite,
+        quiet: args.quiet,
     };
+    // Initialize WASM analyzer
+    await initAnalyzer();
     try {
-        const result = await generateSpecifica(targetPath, options);
-        if (!args.quiet) {
-            console.error('');
-            console.error('✓ Specification generated successfully!');
-            console.error('');
-            console.error(`Feature:  ${result.featureName}`);
-            console.error(`Output:   ${result.outputPath}/spec.md`);
-            console.error('');
-            console.error('⚠️  Review required: This specification was automatically generated.');
-            console.error('Please review and refine before using.');
-        }
-        // Output JSON if requested
-        if (args.format === 'json') {
-            const output = JSON.stringify(result, null, 2);
-            if (args.output) {
-                fs.writeFileSync(args.output, output);
-                if (!args.quiet) {
-                    console.error(`JSON output written to ${args.output}`);
+        if (isDirectory) {
+            const results = await generateSpecificaForDirectory(targetPath, options);
+            if (!args.quiet) {
+                console.error('');
+                console.error(`✓ Generated ${results.length} specification(s)`);
+                for (const result of results) {
+                    console.error(`  - ${result.featureName}: ${result.outputPath}/spec.md`);
+                }
+                console.error('');
+                console.error('Review required: specifications were automatically generated.');
+            }
+            if (args.format === 'json') {
+                const output = JSON.stringify(results, null, 2);
+                if (args.output) {
+                    fs.writeFileSync(args.output, output);
+                    if (!args.quiet)
+                        console.error(`JSON output written to ${args.output}`);
                 }
+                else {
+                    console.log(output);
+                }
+            }
+        }
+        else {
+            const result = await generateSpecifica(targetPath, options);
+            if (!args.quiet) {
+                console.error('');
+                console.error('✓ Specification generated successfully!');
+                console.error('');
+                console.error(`Feature:  ${result.featureName}`);
+                console.error(`Output:   ${result.outputPath}/spec.md`);
+                console.error('');
+                console.error('Review required: This specification was automatically generated.');
             }
-            else {
-                console.log(output);
+            if (args.format === 'json') {
+                const output = JSON.stringify(result, null, 2);
+                if (args.output) {
+                    fs.writeFileSync(args.output, output);
+                    if (!args.quiet)
+                        console.error(`JSON output written to ${args.output}`);
+                }
+                else {
+                    console.log(output);
+                }
             }
         }
         return 0;

package/dist/cli/commands/generate-spec.js.map

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

@@ -0,0 +1,12 @@
+/**
+ * Spec-Diff Command
+ *
+ * Compares code behavior against Specifica spec requirements.
+ * Identifies uncovered requirements and undocumented behaviors.
+ *
+ * Usage:
+ *   circle-ir spec-diff <path> [--spec <dir>] [--format json]
+ */
+import type { CliArgs } from '../args.js';
+export declare function executeSpecDiff(args: CliArgs): Promise<number>;
+//# sourceMappingURL=spec-diff.d.ts.map