Add comprehensive tests for CLI functionality and CodexLens compatibility

- Introduced tests for stale running fallback in CLI watch functionality to ensure proper handling of saved conversations.
- Added compatibility tests for CodexLens CLI to verify index initialization despite compatibility conflicts.
- Implemented tests for Smart Search MCP usage to validate default settings and path handling.
- Created tests for UV Manager to ensure Python preference handling works as expected.
- Added a detailed guide for CCW/Codex commands and skills, covering core commands, execution modes, and templates.

ccw/tests/codex-lens-cli-compat.test.js

@@ -0,0 +1,35 @@
+import { after, describe, it } from 'node:test';
+import assert from 'node:assert/strict';
+import { mkdtempSync, rmSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+
+const tempDirs = [];
+
+after(() => {
+  for (const dir of tempDirs) {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
+
+describe('CodexLens CLI compatibility retries', () => {
+  it('initializes a tiny index even when CLI emits compatibility conflicts first', async () => {
+    const moduleUrl = new URL(`../dist/tools/codex-lens.js?compat=${Date.now()}`, import.meta.url).href;
+    const { checkVenvStatus, executeCodexLens } = await import(moduleUrl);
+
+    const ready = await checkVenvStatus(true);
+    if (!ready.ready) {
+      console.log('Skipping: CodexLens not ready');
+      return;
+    }
+
+    const projectDir = mkdtempSync(join(tmpdir(), 'codexlens-init-'));
+    tempDirs.push(projectDir);
+    writeFileSync(join(projectDir, 'sample.ts'), 'export const sample = 1;\n');
+
+    const result = await executeCodexLens(['index', 'init', projectDir, '--force'], { timeout: 600000 });
+
+    assert.equal(result.success, true, result.error ?? 'Expected init to succeed');
+    assert.ok((result.output ?? '').length > 0 || (result.warning ?? '').length > 0, 'Expected init output or compatibility warning');
+  });
+});