fix(tests): resolve failing tests on main branch

- Unskip matrix logic by adding missing deps (matrix-nio, nh3, mistune)
- Update matrix tests for 'allow_from' default deny security change
- Fix asyncio typing keepalive leak in matrix tests
- Update context prompt cache assert after runtime message merge
- Fix flaky cron service test with mtime sleep
- Remove obsolete test_cron_commands.py testing deleted CLI commands

tests/test_cron_service.py

@@ -48,6 +48,8 @@ async def test_running_service_honors_external_disable(tmp_path) -> None:
     )
     await service.start()
     try:
+        # Wait slightly to ensure file mtime is definitively different
+        await asyncio.sleep(0.05)
         external = CronService(store_path)
         updated = external.enable_job(job.id, enabled=False)
         assert updated is not None