diff --git a/src/cli/main.ts b/src/cli/main.ts
index 432739f..099e965 100644
--- a/src/cli/main.ts
+++ b/src/cli/main.ts
@@ -20,6 +20,7 @@ import {
   runSkillTasks,
   pluralize,
   writeJsonlReport,
+  getRunLogPath,
   type SkillTaskOptions,
 } from './output/index.js';
 import {
@@ -167,6 +168,11 @@ async function runSkills(
     reporter.success(`Wrote JSONL output to ${options.output}`);
   }
 
+  // Always write automatic run log for debugging
+  const runLogPath = getRunLogPath(cwd);
+  writeJsonlReport(runLogPath, reports, totalDuration);
+  reporter.debug(`Run log: ${runLogPath}`);
+
   // Output results
   reporter.blank();
   if (options.json) {
@@ -466,6 +472,11 @@ async function runConfigMode(options: CLIOptions, reporter: Reporter): Promise<n
     reporter.success(`Wrote JSONL output to ${options.output}`);
   }
 
+  // Always write automatic run log for debugging
+  const runLogPath = getRunLogPath(repoPath);
+  writeJsonlReport(runLogPath, reports, totalDuration);
+  reporter.debug(`Run log: ${runLogPath}`);
+
   // Output results
   reporter.blank();
   if (options.json) {
diff --git a/src/cli/output/index.ts b/src/cli/output/index.ts
index cc39d8d..261da67 100644
--- a/src/cli/output/index.ts
+++ b/src/cli/output/index.ts
@@ -29,4 +29,10 @@ export {
   type RunTasksOptions,
 } from './tasks.js';
 export { BoxRenderer, type BoxOptions } from './box.js';
-export { writeJsonlReport, type JsonlRecord, type JsonlRunMetadata } from './jsonl.js';
+export {
+  writeJsonlReport,
+  getRunLogsDir,
+  getRunLogPath,
+  type JsonlRecord,
+  type JsonlRunMetadata,
+} from './jsonl.js';
diff --git a/src/cli/output/jsonl.test.ts b/src/cli/output/jsonl.test.ts
index 929ca8a..974b767 100644
--- a/src/cli/output/jsonl.test.ts
+++ b/src/cli/output/jsonl.test.ts
@@ -1,8 +1,14 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
 import { existsSync, readFileSync, rmSync, mkdirSync } from 'node:fs';
 import { join } from 'node:path';
-import { tmpdir } from 'node:os';
-import { writeJsonlReport, type JsonlRecord } from './jsonl.js';
+import { homedir, tmpdir } from 'node:os';
+import {
+  writeJsonlReport,
+  getRunLogsDir,
+  generateRunLogFilename,
+  getRunLogPath,
+  type JsonlRecord,
+} from './jsonl.js';
 import type { SkillReport } from '../../types/index.js';
 
 describe('writeJsonlReport', () => {
@@ -174,3 +180,168 @@ describe('writeJsonlReport', () => {
     expect(summary.bySeverity.info).toBe(1);
   });
 });
+
+describe('getRunLogsDir', () => {
+  const originalEnv = process.env['WARDEN_STATE_DIR'];
+
+  afterEach(() => {
+    if (originalEnv === undefined) {
+      delete process.env['WARDEN_STATE_DIR'];
+    } else {
+      process.env['WARDEN_STATE_DIR'] = originalEnv;
+    }
+  });
+
+  it('returns default path when WARDEN_STATE_DIR is not set', () => {
+    delete process.env['WARDEN_STATE_DIR'];
+    const result = getRunLogsDir();
+    expect(result).toBe(join(homedir(), '.local', 'warden', 'runs'));
+  });
+
+  it('uses WARDEN_STATE_DIR when set', () => {
+    process.env['WARDEN_STATE_DIR'] = '/custom/state';
+    const result = getRunLogsDir();
+    expect(result).toBe('/custom/state/runs');
+  });
+});
+
+describe('generateRunLogFilename', () => {
+  it('generates filename with directory name and timestamp', () => {
+    const timestamp = new Date('2026-01-29T14:32:15.123Z');
+    const result = generateRunLogFilename('/path/to/my-project', timestamp);
+    expect(result).toBe('my-project_2026-01-29T14-32-15.123Z.jsonl');
+  });
+
+  it('replaces colons in timestamp with hyphens', () => {
+    const timestamp = new Date('2026-01-29T10:05:30.000Z');
+    const result = generateRunLogFilename('/some/dir', timestamp);
+    expect(result).toMatch(/^\w+_2026-01-29T10-05-30\.000Z\.jsonl$/);
+  });
+
+  it('uses "unknown" for empty directory name', () => {
+    const timestamp = new Date('2026-01-29T12:00:00.000Z');
+    const result = generateRunLogFilename('/', timestamp);
+    expect(result).toBe('unknown_2026-01-29T12-00-00.000Z.jsonl');
+  });
+
+  it('handles directory paths with trailing slash', () => {
+    const timestamp = new Date('2026-01-29T12:00:00.000Z');
+    // basename handles trailing slashes, so /foo/bar/ becomes 'bar'
+    const result = generateRunLogFilename('/foo/bar', timestamp);
+    expect(result).toBe('bar_2026-01-29T12-00-00.000Z.jsonl');
+  });
+});
+
+describe('getRunLogPath', () => {
+  const originalEnv = process.env['WARDEN_STATE_DIR'];
+
+  afterEach(() => {
+    if (originalEnv === undefined) {
+      delete process.env['WARDEN_STATE_DIR'];
+    } else {
+      process.env['WARDEN_STATE_DIR'] = originalEnv;
+    }
+  });
+
+  it('returns full path combining logs dir and filename', () => {
+    delete process.env['WARDEN_STATE_DIR'];
+    const timestamp = new Date('2026-01-29T14:32:15.123Z');
+    const result = getRunLogPath('/path/to/warden', timestamp);
+    expect(result).toBe(
+      join(homedir(), '.local', 'warden', 'runs', 'warden_2026-01-29T14-32-15.123Z.jsonl')
+    );
+  });
+
+  it('respects WARDEN_STATE_DIR', () => {
+    process.env['WARDEN_STATE_DIR'] = '/custom/dir';
+    const timestamp = new Date('2026-01-29T14:32:15.123Z');
+    const result = getRunLogPath('/my/project', timestamp);
+    expect(result).toBe('/custom/dir/runs/project_2026-01-29T14-32-15.123Z.jsonl');
+  });
+});
+
+describe('automatic run logging integration', () => {
+  let testStateDir: string;
+  const originalEnv = process.env['WARDEN_STATE_DIR'];
+
+  beforeEach(() => {
+    testStateDir = join(tmpdir(), `warden-state-${Date.now()}`);
+    process.env['WARDEN_STATE_DIR'] = testStateDir;
+  });
+
+  afterEach(() => {
+    if (existsSync(testStateDir)) {
+      rmSync(testStateDir, { recursive: true });
+    }
+    if (originalEnv === undefined) {
+      delete process.env['WARDEN_STATE_DIR'];
+    } else {
+      process.env['WARDEN_STATE_DIR'] = originalEnv;
+    }
+  });
+
+  it('writes run log to auto-generated path', () => {
+    const reports: SkillReport[] = [
+      {
+        skill: 'test-skill',
+        summary: 'Test complete',
+        findings: [
+          { id: 'test-1', severity: 'low', title: 'Test', description: 'Test finding' },
+        ],
+        durationMs: 100,
+      },
+    ];
+
+    const timestamp = new Date('2026-01-29T14:32:15.123Z');
+    const runLogPath = getRunLogPath('/path/to/my-project', timestamp);
+
+    writeJsonlReport(runLogPath, reports, 500);
+
+    // Verify file was created at expected location
+    expect(existsSync(runLogPath)).toBe(true);
+    expect(runLogPath).toBe(join(testStateDir, 'runs', 'my-project_2026-01-29T14-32-15.123Z.jsonl'));
+
+    // Verify content
+    const content = readFileSync(runLogPath, 'utf-8');
+    const lines = content.trim().split('\n');
+    expect(lines.length).toBe(2); // 1 report + 1 summary
+
+    const record = JSON.parse(lines[0]!) as JsonlRecord;
+    expect(record.skill).toBe('test-skill');
+    expect(record.findings.length).toBe(1);
+  });
+
+  it('creates nested runs directory automatically', () => {
+    const runLogPath = getRunLogPath('/some/project', new Date());
+
+    // Directory shouldn't exist yet
+    expect(existsSync(join(testStateDir, 'runs'))).toBe(false);
+
+    writeJsonlReport(runLogPath, [], 100);
+
+    // Now it should exist with the file
+    expect(existsSync(runLogPath)).toBe(true);
+  });
+
+  it('handles multiple runs with unique timestamps', () => {
+    const timestamp1 = new Date('2026-01-29T14:00:00.000Z');
+    const timestamp2 = new Date('2026-01-29T14:01:00.000Z');
+
+    const path1 = getRunLogPath('/project', timestamp1);
+    const path2 = getRunLogPath('/project', timestamp2);
+
+    expect(path1).not.toBe(path2);
+
+    writeJsonlReport(path1, [], 100);
+    writeJsonlReport(path2, [], 200);
+
+    expect(existsSync(path1)).toBe(true);
+    expect(existsSync(path2)).toBe(true);
+
+    // Verify they have different durations
+    const content1 = JSON.parse(readFileSync(path1, 'utf-8').trim());
+    const content2 = JSON.parse(readFileSync(path2, 'utf-8').trim());
+    expect(content1.run.durationMs).toBe(100);
+    expect(content2.run.durationMs).toBe(200);
+  });
+});
diff --git a/src/cli/output/jsonl.ts b/src/cli/output/jsonl.ts
index 12a018b..082a302 100644
--- a/src/cli/output/jsonl.ts
+++ b/src/cli/output/jsonl.ts
@@ -1,8 +1,39 @@
 import { mkdirSync, writeFileSync } from 'node:fs';
-import { dirname, resolve } from 'node:path';
+import { homedir } from 'node:os';
+import { basename, dirname, join, resolve } from 'node:path';
 import type { SkillReport, UsageStats } from '../../types/index.js';
 import { countBySeverity } from './formatters.js';
 
+/**
+ * Get the default run logs directory.
+ * Uses WARDEN_STATE_DIR env var if set, otherwise ~/.local/warden/runs
+ */
+export function getRunLogsDir(): string {
+  const stateDir = process.env['WARDEN_STATE_DIR'];
+  if (stateDir) {
+    return join(stateDir, 'runs');
+  }
+  return join(homedir(), '.local', 'warden', 'runs');
+}
+
+/**
+ * Generate a run log filename from directory name and timestamp.
+ * Format: {dirname}_{timestamp}.jsonl
+ * Timestamp has colons replaced with hyphens for filesystem compatibility.
+ */
+export function generateRunLogFilename(cwd: string, timestamp: Date = new Date()): string {
+  const dirName = basename(cwd) || 'unknown';
+  const ts = timestamp.toISOString().replace(/:/g, '-');
+  return `${dirName}_${ts}.jsonl`;
+}
+
+/**
+ * Get the full path for an automatic run log.
+ */
+export function getRunLogPath(cwd: string, timestamp: Date = new Date()): string {
+  return join(getRunLogsDir(), generateRunLogFilename(cwd, timestamp));
+}
+
 /**
  * Metadata for a JSONL run record.
  */