fix: exclude Python virtual environments from skill scanner

- Add .venv, venv, env to ignored patterns
- Add __pycache__, .pytest_cache, .tox, .egg-info to ignored patterns
- Prevents FD exhaustion when skills contain Python virtual environments
- Fixes #3708: spawn EBADF errors from file descriptor leak

The skill scanner was opening thousands of files in Python virtual
environments without closing them, causing immediate FD exhaustion
(~11,000 open FDs). This change adds common Python dependency
directories to the ignore list, similar to how node_modules and
.git are already ignored.

Added comprehensive test cases to verify all Python-related directories
are properly ignored.

src/agents/skills/refresh.test.ts

@@ -28,4 +28,32 @@ describe("ensureSkillsWatcher", () => {
     expect(ignored.some((re) => re.test("/tmp/workspace/skills/.git/config"))).toBe(true);
     expect(ignored.some((re) => re.test("/tmp/.hidden/skills/index.md"))).toBe(false);
   });
+
+  it("ignores Python virtual environments and cache directories", async () => {
+    const mod = await import("./refresh.js");
+    const ignored = mod.DEFAULT_SKILLS_WATCH_IGNORED;
+
+    // Python virtual environments
+    expect(
+      ignored.some((re) => re.test("/tmp/workspace/skills/.venv/lib/python3.9/site-packages/")),
+    ).toBe(true);
+    expect(
+      ignored.some((re) => re.test("/tmp/workspace/skills/venv/lib/python3.9/site-packages/")),
+    ).toBe(true);
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/env/bin/python"))).toBe(true);
+
+    // Python cache directories
+    expect(
+      ignored.some((re) => re.test("/tmp/workspace/skills/__pycache__/module.cpython-39.pyc")),
+    ).toBe(true);
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/.pytest_cache/"))).toBe(true);
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/.tox/py39/lib/"))).toBe(true);
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/package.egg-info/PKG-INFO"))).toBe(
+      true,
+    );
+
+    // Should not ignore files that just contain these names
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/my_venv_config.json"))).toBe(false);
+    expect(ignored.some((re) => re.test("/tmp/workspace/skills/pytest.ini"))).toBe(false);
+  });
 });

src/agents/skills/refresh.ts

@@ -31,6 +31,15 @@ export const DEFAULT_SKILLS_WATCH_IGNORED: RegExp[] = [
   /(^|[\\/])\.git([\\/]|$)/,
   /(^|[\\/])node_modules([\\/]|$)/,
   /(^|[\\/])dist([\\/]|$)/,
+  // Python virtual environments
+  /(^|[\\/])\.venv([\\/]|$)/,
+  /(^|[\\/])venv([\\/]|$)/,
+  /(^|[\\/])env([\\/]|$)/,
+  // Python cache directories
+  /(^|[\\/])__pycache__([\\/]|$)/,
+  /(^|[\\/])\.pytest_cache([\\/]|$)/,
+  /(^|[\\/])\.tox([\\/]|$)/,
+  /(^|[\\/])[^/\\]*\.egg-info([\\/]|$)/,
 ];
 
 function bumpVersion(current: number): number {