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/cli-watch-stale-running.test.js

@@ -0,0 +1,131 @@
+/**
+ * ccw cli watch - stale running fallback tests
+ */
+
+import { after, afterEach, before, describe, it, mock } from 'node:test';
+import assert from 'node:assert/strict';
+import http from 'node:http';
+import { mkdtempSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+
+const TEST_CCW_HOME = mkdtempSync(join(tmpdir(), 'ccw-cli-watch-home-'));
+process.env.CCW_DATA_DIR = TEST_CCW_HOME;
+
+const cliCommandPath = new URL('../dist/commands/cli.js', import.meta.url).href;
+const historyStorePath = new URL('../dist/tools/cli-history-store.js', import.meta.url).href;
+
+describe('ccw cli watch stale running fallback', async () => {
+  let cliModule;
+  let historyStoreModule;
+
+  before(async () => {
+    cliModule = await import(cliCommandPath);
+    historyStoreModule = await import(historyStorePath);
+  });
+
+  afterEach(() => {
+    mock.restoreAll();
+    try {
+      historyStoreModule?.closeAllStores?.();
+    } catch {
+      // ignore
+    }
+  });
+
+  after(() => {
+    try {
+      historyStoreModule?.closeAllStores?.();
+    } catch {
+      // ignore
+    }
+    rmSync(TEST_CCW_HOME, { recursive: true, force: true });
+  });
+
+  it('treats stale active running state as completed when saved conversation is newer', async () => {
+    const projectRoot = mkdtempSync(join(tmpdir(), 'ccw-cli-watch-project-'));
+    const previousCwd = process.cwd();
+    const now = Date.now();
+    const executionId = `EXEC-WATCH-STALE-${now}`;
+
+    try {
+      process.chdir(projectRoot);
+      const store = new historyStoreModule.CliHistoryStore(projectRoot);
+      store.saveConversation({
+        id: executionId,
+        created_at: new Date(now - 10_000).toISOString(),
+        updated_at: new Date(now - 5_000).toISOString(),
+        tool: 'codex',
+        model: 'default',
+        mode: 'analysis',
+        category: 'user',
+        total_duration_ms: 2100,
+        turn_count: 1,
+        latest_status: 'success',
+        turns: [{
+          turn: 1,
+          timestamp: new Date(now - 5_000).toISOString(),
+          prompt: 'saved prompt',
+          duration_ms: 2100,
+          status: 'success',
+          exit_code: 0,
+          output: {
+            stdout: 'saved output',
+            stderr: '',
+            truncated: false,
+            cached: false,
+          }
+        }]
+      });
+      store.close();
+
+      mock.method(http, 'request', (_options, callback) => {
+        const payload = JSON.stringify({
+          executions: [{
+            id: executionId,
+            tool: 'codex',
+            mode: 'analysis',
+            status: 'running',
+            prompt: 'stale active prompt',
+            startTime: now - 60_000,
+            output: ''
+          }]
+        });
+        const res = {
+          on(event, handler) {
+            if (event === 'data') handler(Buffer.from(payload, 'utf8'));
+            if (event === 'end') handler();
+            return res;
+          }
+        };
+        if (callback) callback(res);
+        const req = {
+          on() { return req; },
+          end() {},
+          destroy() {},
+        };
+        return req;
+      });
+
+      const stderrWrites = [];
+      const exitCodes = [];
+      mock.method(process.stderr, 'write', (chunk) => {
+        stderrWrites.push(String(chunk));
+        return true;
+      });
+      mock.method(process, 'exit', (code) => {
+        exitCodes.push(code);
+      });
+
+      await cliModule.cliCommand('watch', [executionId], { timeout: '1' });
+
+      const rendered = stderrWrites.join('');
+      assert.match(rendered, /Execution already completed/);
+      assert.match(rendered, new RegExp(`Use: ccw cli output ${executionId}`));
+      assert.deepEqual(exitCodes, [0]);
+    } finally {
+      process.chdir(previousCwd);
+      rmSync(projectRoot, { recursive: true, force: true });
+    }
+  });
+});