agentlint 0.1.0 → 0.2.0

package/CHANGELOG.md

@@ -7,6 +7,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.0] - 2026-01-11
+
+### Added
+
+- **Auto-fix**: Automatically fix simple issues with `--fix` and `--dry-run` flags
+  - OBS-002: Adds permission manifest comment
+- **Baseline support**: Suppress known findings with baseline files
+  - `--update-baseline`: Create/update baseline from current findings
+  - `--ignore-baseline`: Report all findings regardless of baseline
+  - `--prune-baseline`: Remove fixed findings from baseline
+  - `--baseline <path>`: Custom baseline file path
+- **Integrations**:
+  - [agentlint-action](https://github.com/akz4ol/agentlint-action): Native GitHub Action
+  - [agentlint-vscode](https://github.com/akz4ol/agentlint-vscode): VS Code extension
+  - Pre-commit hook support
+
+### Changed
+
+- CLI now respects `.agentlint-baseline.json` automatically when present
+
 ## [0.1.0] - 2025-01-11
 
 ### Added
@@ -28,5 +48,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Diff analysis**: Behavioral change detection between versions
 - **Permission manifest**: Recommended permissions generation
 
-[Unreleased]: https://github.com/akz4ol/agentlint/compare/v0.1.0...HEAD
+[Unreleased]: https://github.com/akz4ol/agentlint/compare/v0.2.0...HEAD
+[0.2.0]: https://github.com/akz4ol/agentlint/compare/v0.1.0...v0.2.0
 [0.1.0]: https://github.com/akz4ol/agentlint/releases/tag/v0.1.0

package/README.md

@@ -173,6 +173,43 @@ agentlint init
 agentlint init --ci github  # Include GitHub Actions workflow
 ```
 
+## Auto-Fix
+
+Automatically fix simple issues:
+
+```bash
+# Preview fixes without applying
+agentlint scan --dry-run --fix
+
+# Apply fixes
+agentlint scan --fix
+```
+
+Currently fixable rules:
+- `OBS-002`: Adds permission manifest comment
+
+## Baseline
+
+Suppress known findings to focus on new issues:
+
+```bash
+# Create/update baseline with current findings
+agentlint scan --update-baseline
+
+# Scan respects baseline automatically
+agentlint scan
+# Output: "Baseline: 15 known finding(s) suppressed"
+
+# Ignore baseline to see all findings
+agentlint scan --ignore-baseline
+
+# Remove fixed findings from baseline
+agentlint scan --prune-baseline
+
+# Use custom baseline path
+agentlint scan --baseline path/to/baseline.json
+```
+
 ## Diff Mode
 
 Detect behavioral changes between versions:
@@ -205,6 +242,14 @@ Status: FAIL (capability expansion detected)
 
 AgentLint is purpose-built for AI agent configs. General linters miss agent-specific risks.
 
+## Integrations
+
+| Tool | Link |
+|------|------|
+| **VS Code** | [agentlint-vscode](https://github.com/akz4ol/agentlint-vscode) |
+| **GitHub Action** | [agentlint-action](https://github.com/akz4ol/agentlint-action) |
+| **Pre-commit** | [docs/pre-commit.md](docs/pre-commit.md) |
+
 ## Roadmap
 
 - [x] Claude Code support (`.claude/`, `CLAUDE.md`)
@@ -212,8 +257,11 @@ AgentLint is purpose-built for AI agent configs. General linters miss agent-spec
 - [x] 20 security rules
 - [x] SARIF output for GitHub
 - [x] Diff mode
-- [ ] VS Code extension
-- [ ] GitHub Action (native)
+- [x] VS Code extension
+- [x] GitHub Action (native)
+- [x] Pre-commit hook
+- [x] Auto-fix for common issues
+- [x] Baseline support for suppressing known findings
 - [ ] Policy-as-code engine
 - [ ] Signed skill packs
 - [ ] Agent config registry
@@ -223,6 +271,7 @@ AgentLint is purpose-built for AI agent configs. General linters miss agent-spec
 - [CLI Reference](docs/cli.md)
 - [FAQ](docs/faq.md)
 - [Architecture](docs/design.md)
+- [Pre-commit Hook](docs/pre-commit.md)
 - [Contributing](CONTRIBUTING.md)
 - [Security Policy](SECURITY.md)
 

package/dist/baseline/index.d.ts

@@ -0,0 +1,61 @@
+/**
+ * Baseline manager for tracking and suppressing known findings
+ */
+import { Finding } from '../ir/types';
+import { Baseline, BaselineFilterResult } from './types';
+export * from './types';
+/**
+ * Baseline manager class
+ */
+export declare class BaselineManager {
+    private baselinePath;
+    private baseline;
+    constructor(rootDir: string, customPath?: string);
+    /**
+     * Load baseline from file
+     */
+    load(): boolean;
+    /**
+     * Check if a baseline exists
+     */
+    exists(): boolean;
+    /**
+     * Get the baseline path
+     */
+    getPath(): string;
+    /**
+     * Create a new baseline from findings
+     */
+    create(findings: Finding[], reason?: string): Baseline;
+    /**
+     * Update baseline with new findings (add to existing)
+     */
+    update(findings: Finding[], reason?: string): Baseline;
+    /**
+     * Save baseline to file
+     */
+    save(): void;
+    /**
+     * Filter findings against baseline, returning only new findings
+     */
+    filterFindings(findings: Finding[]): {
+        filtered: Finding[];
+        result: BaselineFilterResult;
+    };
+    /**
+     * Remove fixed findings from baseline
+     */
+    prune(currentFindings: Finding[]): number;
+    /**
+     * Get baseline stats
+     */
+    getStats(): {
+        total: number;
+        byRule: Record<string, number>;
+    };
+    /**
+     * Convert a Finding to a BaselinedFinding
+     */
+    private findingToBaseline;
+}
+//# sourceMappingURL=index.d.ts.map

package/dist/baseline/index.d.ts.map

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package/dist/baseline/index.js

@@ -0,0 +1,207 @@
+"use strict";
+/**
+ * Baseline manager for tracking and suppressing known findings
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.BaselineManager = void 0;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+__exportStar(require("./types"), exports);
+const BASELINE_FILENAME = '.agentlint-baseline.json';
+/**
+ * Baseline manager class
+ */
+class BaselineManager {
+    baselinePath;
+    baseline = null;
+    constructor(rootDir, customPath) {
+        this.baselinePath = customPath || path.join(rootDir, BASELINE_FILENAME);
+    }
+    /**
+     * Load baseline from file
+     */
+    load() {
+        if (!fs.existsSync(this.baselinePath)) {
+            return false;
+        }
+        try {
+            const content = fs.readFileSync(this.baselinePath, 'utf-8');
+            this.baseline = JSON.parse(content);
+            return true;
+        }
+        catch (err) {
+            console.error(`Failed to load baseline: ${err}`);
+            return false;
+        }
+    }
+    /**
+     * Check if a baseline exists
+     */
+    exists() {
+        return fs.existsSync(this.baselinePath);
+    }
+    /**
+     * Get the baseline path
+     */
+    getPath() {
+        return this.baselinePath;
+    }
+    /**
+     * Create a new baseline from findings
+     */
+    create(findings, reason) {
+        const now = new Date().toISOString();
+        this.baseline = {
+            version: 1,
+            created_at: now,
+            updated_at: now,
+            findings: findings.map(f => this.findingToBaseline(f, reason)),
+        };
+        return this.baseline;
+    }
+    /**
+     * Update baseline with new findings (add to existing)
+     */
+    update(findings, reason) {
+        if (!this.baseline) {
+            return this.create(findings, reason);
+        }
+        const now = new Date().toISOString();
+        const existingFingerprints = new Set(this.baseline.findings.map(f => f.fingerprint));
+        // Add new findings that aren't already baselined
+        for (const finding of findings) {
+            const fingerprint = finding.fingerprints.stable;
+            if (!existingFingerprints.has(fingerprint)) {
+                this.baseline.findings.push(this.findingToBaseline(finding, reason));
+            }
+        }
+        this.baseline.updated_at = now;
+        return this.baseline;
+    }
+    /**
+     * Save baseline to file
+     */
+    save() {
+        if (!this.baseline) {
+            throw new Error('No baseline to save');
+        }
+        fs.writeFileSync(this.baselinePath, JSON.stringify(this.baseline, null, 2), 'utf-8');
+    }
+    /**
+     * Filter findings against baseline, returning only new findings
+     */
+    filterFindings(findings) {
+        if (!this.baseline) {
+            return {
+                filtered: findings,
+                result: {
+                    newFindings: findings.length,
+                    suppressedFindings: 0,
+                    fixedFindings: 0,
+                },
+            };
+        }
+        const baselineFingerprints = new Set(this.baseline.findings.map(f => f.fingerprint));
+        const matchedFingerprints = new Set();
+        const filtered = findings.filter(finding => {
+            const fingerprint = finding.fingerprints.stable;
+            if (baselineFingerprints.has(fingerprint)) {
+                matchedFingerprints.add(fingerprint);
+                return false; // Suppress
+            }
+            return true; // New finding
+        });
+        // Count fixed findings (in baseline but not in current findings)
+        const fixedFindings = this.baseline.findings.filter(bf => !matchedFingerprints.has(bf.fingerprint)).length;
+        return {
+            filtered,
+            result: {
+                newFindings: filtered.length,
+                suppressedFindings: findings.length - filtered.length,
+                fixedFindings,
+            },
+        };
+    }
+    /**
+     * Remove fixed findings from baseline
+     */
+    prune(currentFindings) {
+        if (!this.baseline) {
+            return 0;
+        }
+        const currentFingerprints = new Set(currentFindings.map(f => f.fingerprints.stable));
+        const before = this.baseline.findings.length;
+        this.baseline.findings = this.baseline.findings.filter(bf => currentFingerprints.has(bf.fingerprint));
+        const removed = before - this.baseline.findings.length;
+        if (removed > 0) {
+            this.baseline.updated_at = new Date().toISOString();
+        }
+        return removed;
+    }
+    /**
+     * Get baseline stats
+     */
+    getStats() {
+        if (!this.baseline) {
+            return { total: 0, byRule: {} };
+        }
+        const byRule = {};
+        for (const f of this.baseline.findings) {
+            byRule[f.rule_id] = (byRule[f.rule_id] || 0) + 1;
+        }
+        return {
+            total: this.baseline.findings.length,
+            byRule,
+        };
+    }
+    /**
+     * Convert a Finding to a BaselinedFinding
+     */
+    findingToBaseline(finding, reason) {
+        return {
+            rule_id: finding.rule_id,
+            path: finding.location.path,
+            fingerprint: finding.fingerprints.stable,
+            baselined_at: new Date().toISOString(),
+            reason,
+        };
+    }
+}
+exports.BaselineManager = BaselineManager;
+//# sourceMappingURL=index.js.map

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package/dist/baseline/types.d.ts

@@ -0,0 +1,43 @@
+/**
+ * Baseline types for tracking known findings
+ */
+/**
+ * A baselined finding that should be suppressed
+ */
+export interface BaselinedFinding {
+    /** Rule ID */
+    rule_id: string;
+    /** File path */
+    path: string;
+    /** Stable fingerprint for matching */
+    fingerprint: string;
+    /** When the finding was baselined */
+    baselined_at: string;
+    /** Optional reason for baselining */
+    reason?: string;
+}
+/**
+ * Baseline file format
+ */
+export interface Baseline {
+    /** Baseline schema version */
+    version: 1;
+    /** When the baseline was created */
+    created_at: string;
+    /** When the baseline was last updated */
+    updated_at: string;
+    /** Baselined findings */
+    findings: BaselinedFinding[];
+}
+/**
+ * Result of filtering findings against baseline
+ */
+export interface BaselineFilterResult {
+    /** New findings not in baseline */
+    newFindings: number;
+    /** Findings that match baseline */
+    suppressedFindings: number;
+    /** Baseline entries that no longer match any finding (fixed) */
+    fixedFindings: number;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/baseline/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/baseline/types.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,cAAc;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,gBAAgB;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,sCAAsC;IACtC,WAAW,EAAE,MAAM,CAAC;IACpB,qCAAqC;IACrC,YAAY,EAAE,MAAM,CAAC;IACrB,qCAAqC;IACrC,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,QAAQ;IACvB,8BAA8B;IAC9B,OAAO,EAAE,CAAC,CAAC;IACX,oCAAoC;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,yCAAyC;IACzC,UAAU,EAAE,MAAM,CAAC;IACnB,yBAAyB;IACzB,QAAQ,EAAE,gBAAgB,EAAE,CAAC;CAC9B;AAED;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,mCAAmC;IACnC,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,kBAAkB,EAAE,MAAM,CAAC;IAC3B,gEAAgE;IAChE,aAAa,EAAE,MAAM,CAAC;CACvB"}

package/dist/baseline/types.js

@@ -0,0 +1,6 @@
+"use strict";
+/**
+ * Baseline types for tracking known findings
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=types.js.map

package/dist/baseline/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/baseline/types.ts"],"names":[],"mappings":";AAAA;;GAEG"}

package/dist/cli/index.js

@@ -46,7 +46,9 @@ const loader_1 = require("../policy/loader");
 const engine_1 = require("../rules/engine");
 const reports_1 = require("../reports");
 const diff_1 = require("../diff");
-const VERSION = '0.1.0';
+const fixer_1 = require("../fixer");
+const baseline_1 = require("../baseline");
+const VERSION = '0.2.0';
 const program = new commander_1.Command();
 program
     .name('agentlint')
@@ -73,6 +75,12 @@ program
     .option('--tool <tool>', 'Tool mode: claude|cursor|auto', 'auto')
     .option('--emit-ir', 'Include IR in JSON output')
     .option('--permissions-only', 'Output only recommended permission manifest')
+    .option('--fix', 'Auto-fix fixable issues')
+    .option('--dry-run', 'Show what would be fixed without making changes')
+    .option('--baseline <path>', 'Path to baseline file for suppressing known findings')
+    .option('--update-baseline', 'Update baseline with current findings')
+    .option('--ignore-baseline', 'Ignore baseline and report all findings')
+    .option('--prune-baseline', 'Remove fixed findings from baseline')
     .action(async (scanPath, options) => {
     const globalOpts = program.opts();
     const targetPath = scanPath || process.cwd();
@@ -120,6 +128,98 @@ program
     });
     try {
         const result = await scanner.scan();
+        // Handle fix mode
+        if (options.fix || options.dryRun) {
+            const fixer = new fixer_1.Fixer({
+                rootDir: path.resolve(targetPath),
+                dryRun: options.dryRun || false,
+            });
+            const fixResult = await fixer.fixAll(result.findings, result.capabilitySummary);
+            if (options.dryRun) {
+                console.log('Dry run - no changes made\n');
+            }
+            if (fixResult.applied > 0) {
+                console.log(`Fixed ${fixResult.applied} issue(s) in ${fixResult.modifiedFiles.length} file(s):`);
+                for (const fix of fixResult.fixes.filter(f => f.success)) {
+                    console.log(`  [${fix.ruleId}] ${fix.path}: ${fix.description}`);
+                }
+                console.log();
+            }
+            if (fixResult.skipped > 0) {
+                console.log(`Skipped ${fixResult.skipped} issue(s) (not auto-fixable)`);
+                console.log();
+            }
+            if (fixResult.errors.length > 0) {
+                console.error('Errors:');
+                fixResult.errors.forEach(e => console.error(`  ${e}`));
+            }
+            // Re-scan after fixes if not dry run
+            if (!options.dryRun && fixResult.applied > 0) {
+                const newResult = await scanner.scan();
+                result.findings = newResult.findings;
+                result.exitCode = newResult.exitCode;
+                result.status = newResult.status;
+            }
+        }
+        // Handle baseline
+        const baselineManager = new baseline_1.BaselineManager(path.resolve(targetPath), options.baseline);
+        if (options.updateBaseline) {
+            // Update baseline with current findings
+            const existed = baselineManager.exists();
+            if (existed) {
+                baselineManager.load();
+            }
+            baselineManager.update(result.findings, 'Baselined via --update-baseline');
+            baselineManager.save();
+            const stats = baselineManager.getStats();
+            console.log(`Baseline ${existed ? 'updated' : 'created'}: ${baselineManager.getPath()}`);
+            console.log(`  Total baselined findings: ${stats.total}`);
+            for (const [rule, count] of Object.entries(stats.byRule)) {
+                console.log(`    ${rule}: ${count}`);
+            }
+            console.log();
+        }
+        else if (options.pruneBaseline) {
+            // Remove fixed findings from baseline
+            if (!baselineManager.exists()) {
+                console.error('No baseline file found to prune');
+                process.exit(2);
+            }
+            baselineManager.load();
+            const removed = baselineManager.prune(result.findings);
+            baselineManager.save();
+            console.log(`Pruned ${removed} fixed finding(s) from baseline`);
+            console.log();
+        }
+        else if (!options.ignoreBaseline && baselineManager.exists()) {
+            // Filter findings against baseline
+            baselineManager.load();
+            const { filtered, result: baselineResult } = baselineManager.filterFindings(result.findings);
+            if (baselineResult.suppressedFindings > 0) {
+                console.log(`Baseline: ${baselineResult.suppressedFindings} known finding(s) suppressed`);
+                if (baselineResult.fixedFindings > 0) {
+                    console.log(`  ${baselineResult.fixedFindings} baselined finding(s) appear to be fixed`);
+                }
+                console.log();
+            }
+            // Update result with filtered findings
+            result.findings = filtered;
+            // Recalculate exit code based on filtered findings
+            const highCount = filtered.filter(f => f.severity === 'high').length;
+            const mediumCount = filtered.filter(f => f.severity === 'medium').length;
+            if (highCount > 0 && ['high'].includes(policy.policy.fail_on)) {
+                result.exitCode = 1;
+                result.status = 'fail';
+            }
+            else if (mediumCount > 0 && ['medium', 'high'].includes(policy.policy.fail_on)) {
+                result.exitCode = 1;
+                result.status = 'fail';
+            }
+            else if (filtered.length === 0) {
+                result.exitCode = 0;
+                result.status = 'pass';
+            }
+        }
         // Handle permissions-only mode
         if (options.permissionsOnly) {
             const output = JSON.stringify(result.recommendedPermissions, null, 2);

package/dist/cli/index.js.map

@@ -1 +1 @@
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package/dist/fixer/index.d.ts

@@ -0,0 +1,46 @@
+/**
+ * Auto-fixer for AgentLint findings
+ */
+import { Finding, CapabilitySummary } from '../ir/types';
+import { FixResult } from './types';
+export * from './types';
+/**
+ * Fixer class for auto-fixing findings
+ */
+export declare class Fixer {
+    private rootDir;
+    private dryRun;
+    constructor(options: {
+        rootDir: string;
+        dryRun?: boolean;
+    });
+    /**
+     * Check if a finding is auto-fixable
+     */
+    isFixable(finding: Finding): boolean;
+    /**
+     * Get list of fixable rule IDs
+     */
+    getFixableRules(): string[];
+    /**
+     * Fix all fixable findings
+     */
+    fixAll(findings: Finding[], capabilitySummary: CapabilitySummary): Promise<FixResult>;
+    /**
+     * Generate fixes for findings in a file
+     */
+    private generateFixes;
+    /**
+     * Generate fix for adding permission manifest (OBS-002)
+     */
+    private generateManifestFix;
+    /**
+     * Generate permission manifest comment
+     */
+    private generatePermissionManifest;
+    /**
+     * Apply fixes to a file
+     */
+    private applyFixes;
+}
+//# sourceMappingURL=index.d.ts.map

package/dist/fixer/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/fixer/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,OAAO,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACzD,OAAO,EAAO,SAAS,EAA6B,MAAM,SAAS,CAAC;AAEpE,cAAc,SAAS,CAAC;AAExB;;GAEG;AACH,qBAAa,KAAK;IAChB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,MAAM,CAAU;gBAEZ,OAAO,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE,OAAO,CAAA;KAAE;IAK1D;;OAEG;IACH,SAAS,CAAC,OAAO,EAAE,OAAO,GAAG,OAAO;IAIpC;;OAEG;IACH,eAAe,IAAI,MAAM,EAAE;IAI3B;;OAEG;IACG,MAAM,CACV,QAAQ,EAAE,OAAO,EAAE,EACnB,iBAAiB,EAAE,iBAAiB,GACnC,OAAO,CAAC,SAAS,CAAC;IA2CrB;;OAEG;IACH,OAAO,CAAC,aAAa;IAuBrB;;OAEG;IACH,OAAO,CAAC,mBAAmB;IAgB3B;;OAEG;IACH,OAAO,CAAC,0BAA0B;IAmClC;;OAEG;YACW,UAAU;CA4FzB"}

package/dist/fixer/index.js

@@ -0,0 +1,257 @@
+"use strict";
+/**
+ * Auto-fixer for AgentLint findings
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Fixer = void 0;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const types_1 = require("./types");
+__exportStar(require("./types"), exports);
+/**
+ * Fixer class for auto-fixing findings
+ */
+class Fixer {
+    rootDir;
+    dryRun;
+    constructor(options) {
+        this.rootDir = options.rootDir;
+        this.dryRun = options.dryRun ?? false;
+    }
+    /**
+     * Check if a finding is auto-fixable
+     */
+    isFixable(finding) {
+        return finding.rule_id in types_1.FIXABLE_RULES && types_1.FIXABLE_RULES[finding.rule_id].canFix;
+    }
+    /**
+     * Get list of fixable rule IDs
+     */
+    getFixableRules() {
+        return Object.keys(types_1.FIXABLE_RULES);
+    }
+    /**
+     * Fix all fixable findings
+     */
+    async fixAll(findings, capabilitySummary) {
+        const result = {
+            applied: 0,
+            skipped: 0,
+            modifiedFiles: [],
+            fixes: [],
+            errors: [],
+        };
+        // Group findings by file
+        const findingsByFile = new Map();
+        for (const finding of findings) {
+            const filePath = finding.location.path;
+            if (!findingsByFile.has(filePath)) {
+                findingsByFile.set(filePath, []);
+            }
+            findingsByFile.get(filePath).push(finding);
+        }
+        // Process each file
+        for (const [filePath, fileFindings] of findingsByFile) {
+            const fixes = this.generateFixes(fileFindings, capabilitySummary);
+            if (fixes.length === 0) {
+                result.skipped += fileFindings.length;
+                continue;
+            }
+            const applyResult = await this.applyFixes(filePath, fixes);
+            result.fixes.push(...applyResult.fixes);
+            result.applied += applyResult.applied;
+            result.skipped += fileFindings.length - applyResult.applied;
+            result.errors.push(...applyResult.errors);
+            if (applyResult.applied > 0) {
+                result.modifiedFiles.push(filePath);
+            }
+        }
+        return result;
+    }
+    /**
+     * Generate fixes for findings in a file
+     */
+    generateFixes(findings, capabilitySummary) {
+        const fixes = [];
+        for (const finding of findings) {
+            if (!this.isFixable(finding)) {
+                continue;
+            }
+            const strategy = types_1.FIXABLE_RULES[finding.rule_id];
+            switch (strategy.strategy) {
+                case 'add-manifest':
+                    fixes.push(this.generateManifestFix(finding, capabilitySummary));
+                    break;
+            }
+        }
+        return fixes.filter((f) => f !== null);
+    }
+    /**
+     * Generate fix for adding permission manifest (OBS-002)
+     */
+    generateManifestFix(finding, capabilitySummary) {
+        const manifest = this.generatePermissionManifest(capabilitySummary);
+        return {
+            path: finding.location.path,
+            description: 'Add permission manifest comment',
+            ruleId: finding.rule_id,
+            type: 'insert',
+            line: 1,
+            replacement: manifest + '\n\n',
+        };
+    }
+    /**
+     * Generate permission manifest comment
+     */
+    generatePermissionManifest(capabilitySummary) {
+        const lines = [
+            '<!-- agentlint:permissions',
+            '  filesystem:',
+        ];
+        if (capabilitySummary.filesystem.read.length > 0) {
+            lines.push(`    read: ${JSON.stringify(capabilitySummary.filesystem.read)}`);
+        }
+        else {
+            lines.push('    read: ["**/*"]');
+        }
+        if (capabilitySummary.filesystem.write.length > 0) {
+            lines.push(`    write: ${JSON.stringify(capabilitySummary.filesystem.write)}`);
+        }
+        lines.push('  shell_exec:');
+        lines.push(`    enabled: ${capabilitySummary.shell_exec.enabled}`);
+        if (capabilitySummary.shell_exec.examples.length > 0) {
+            lines.push(`    allowed_commands: ${JSON.stringify(capabilitySummary.shell_exec.examples.slice(0, 5))}`);
+        }
+        lines.push('  network:');
+        lines.push(`    outbound: ${capabilitySummary.network.outbound}`);
+        if (capabilitySummary.network.allowed_domains.length > 0) {
+            lines.push(`    allowed_domains: ${JSON.stringify(capabilitySummary.network.allowed_domains)}`);
+        }
+        lines.push('-->');
+        return lines.join('\n');
+    }
+    /**
+     * Apply fixes to a file
+     */
+    async applyFixes(filePath, fixes) {
+        const result = {
+            fixes: [],
+            applied: 0,
+            errors: [],
+        };
+        const fullPath = path.join(this.rootDir, filePath);
+        let content;
+        try {
+            content = fs.readFileSync(fullPath, 'utf-8');
+        }
+        catch (err) {
+            result.errors.push(`Failed to read ${filePath}: ${err}`);
+            return result;
+        }
+        // Sort fixes by line number descending so we can apply from bottom up
+        const sortedFixes = [...fixes].sort((a, b) => b.line - a.line);
+        let modified = content;
+        const lines = modified.split('\n');
+        for (const fix of sortedFixes) {
+            try {
+                switch (fix.type) {
+                    case 'insert':
+                        // Insert at beginning of specified line
+                        lines.splice(fix.line - 1, 0, ...(fix.replacement || '').split('\n'));
+                        result.fixes.push({
+                            path: filePath,
+                            ruleId: fix.ruleId,
+                            description: fix.description,
+                            success: true,
+                        });
+                        result.applied++;
+                        break;
+                    case 'replace':
+                        if (fix.original && fix.replacement) {
+                            const lineContent = lines[fix.line - 1];
+                            if (lineContent.includes(fix.original)) {
+                                lines[fix.line - 1] = lineContent.replace(fix.original, fix.replacement);
+                                result.fixes.push({
+                                    path: filePath,
+                                    ruleId: fix.ruleId,
+                                    description: fix.description,
+                                    success: true,
+                                });
+                                result.applied++;
+                            }
+                        }
+                        break;
+                    case 'delete':
+                        lines.splice(fix.line - 1, 1);
+                        result.fixes.push({
+                            path: filePath,
+                            ruleId: fix.ruleId,
+                            description: fix.description,
+                            success: true,
+                        });
+                        result.applied++;
+                        break;
+                }
+            }
+            catch (err) {
+                result.fixes.push({
+                    path: filePath,
+                    ruleId: fix.ruleId,
+                    description: fix.description,
+                    success: false,
+                    error: String(err),
+                });
+                result.errors.push(`Failed to apply fix ${fix.ruleId} to ${filePath}: ${err}`);
+            }
+        }
+        // Write back if not dry run and we made changes
+        if (!this.dryRun && result.applied > 0) {
+            try {
+                modified = lines.join('\n');
+                fs.writeFileSync(fullPath, modified, 'utf-8');
+            }
+            catch (err) {
+                result.errors.push(`Failed to write ${filePath}: ${err}`);
+            }
+        }
+        return result;
+    }
+}
+exports.Fixer = Fixer;
+//# sourceMappingURL=index.js.map

package/dist/fixer/index.js.map

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package/dist/fixer/types.d.ts

@@ -0,0 +1,59 @@
+/**
+ * Fixer types and interfaces
+ */
+/**
+ * A fix that can be applied to a file
+ */
+export interface Fix {
+    /** The file path to modify */
+    path: string;
+    /** Description of the fix */
+    description: string;
+    /** The rule ID this fix addresses */
+    ruleId: string;
+    /** Type of fix operation */
+    type: 'insert' | 'replace' | 'delete';
+    /** Line number to apply fix (1-indexed) */
+    line: number;
+    /** Column number (for replace/delete) */
+    column?: number;
+    /** Original text (for replace/delete) */
+    original?: string;
+    /** New text (for insert/replace) */
+    replacement?: string;
+}
+/**
+ * Result of attempting to fix findings
+ */
+export interface FixResult {
+    /** Number of fixes applied */
+    applied: number;
+    /** Number of fixes skipped (not auto-fixable) */
+    skipped: number;
+    /** Files that were modified */
+    modifiedFiles: string[];
+    /** Details of each fix */
+    fixes: AppliedFix[];
+    /** Errors encountered */
+    errors: string[];
+}
+/**
+ * A fix that was applied
+ */
+export interface AppliedFix {
+    path: string;
+    ruleId: string;
+    description: string;
+    success: boolean;
+    error?: string;
+}
+/**
+ * Rules that support auto-fix
+ */
+export declare const FIXABLE_RULES: Record<string, FixStrategy>;
+export interface FixStrategy {
+    description: string;
+    canFix: boolean;
+    strategy: string;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/fixer/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/fixer/types.js

@@ -0,0 +1,17 @@
+"use strict";
+/**
+ * Fixer types and interfaces
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FIXABLE_RULES = void 0;
+/**
+ * Rules that support auto-fix
+ */
+exports.FIXABLE_RULES = {
+    'OBS-002': {
+        description: 'Add permission manifest comment',
+        canFix: true,
+        strategy: 'add-manifest',
+    },
+};
+//# sourceMappingURL=types.js.map

package/dist/fixer/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/fixer/types.ts"],"names":[],"mappings":";AAAA;;GAEG;;;AAqDH;;GAEG;AACU,QAAA,aAAa,GAAgC;IACxD,SAAS,EAAE;QACT,WAAW,EAAE,iCAAiC;QAC9C,MAAM,EAAE,IAAI;QACZ,QAAQ,EAAE,cAAc;KACzB;CACF,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentlint",
-  "version": "0.1.0",
+  "version": "0.2.0",
   "description": "Static analysis and security scanner for AI agent configuration files",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -54,23 +54,23 @@
     "CHANGELOG.md"
   ],
   "dependencies": {
-    "commander": "^12.0.0",
     "chalk": "^4.1.2",
+    "commander": "^12.0.0",
+    "crypto-js": "^4.2.0",
     "glob": "^10.3.10",
-    "yaml": "^2.3.4",
-    "crypto-js": "^4.2.0"
+    "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@types/node": "^20.10.0",
     "@types/crypto-js": "^4.2.0",
-    "typescript": "^5.3.0",
-    "ts-node": "^10.9.2",
-    "jest": "^29.7.0",
     "@types/jest": "^29.5.0",
-    "ts-jest": "^29.1.0",
+    "@types/node": "^20.10.0",
     "@typescript-eslint/eslint-plugin": "^6.0.0",
     "@typescript-eslint/parser": "^6.0.0",
     "eslint": "^8.56.0",
-    "prettier": "^3.2.0"
+    "jest": "^29.7.0",
+    "prettier": "^3.2.0",
+    "ts-jest": "^29.1.0",
+    "ts-node": "^10.9.2",
+    "typescript": "^5.3.0"
   }
 }