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

pyproject.toml

@@ -54,6 +54,9 @@ dev = [
     "pytest>=9.0.0,<10.0.0",
     "pytest-asyncio>=1.3.0,<2.0.0",
     "ruff>=0.1.0",
+    "matrix-nio[e2e]>=0.25.2",
+    "mistune>=3.0.0,<4.0.0",
+    "nh3>=0.2.17,<1.0.0",
 ]
 
 [project.scripts]