Fix variable name breakage (run_agent, hermes_constants, etc.) where
import rewriter changed 'import X' to 'import hermes_agent.Y' but
test code still referenced 'X' as a variable name.
Fix package-vs-module confusion (cli.auth, cli.models, cli.ui) where
single files became directories.
Fix hardcoded file paths in tests pointing to old locations.
Fix tool registry to discover tools in subpackage directories.
Fix stale import in hermes_agent/tools/__init__.py.
Part of #14182, #14183
Add timeout parameters to 4 subprocess.run() calls that could hang
indefinitely if the child process blocks (e.g., unresponsive docker
daemon, systemctl waiting for D-Bus):
- doctor.py: docker info (timeout=10), ssh check (timeout=15)
- status.py: systemctl is-active (timeout=5), launchctl list (timeout=5)
Each call site now catches subprocess.TimeoutExpired and treats it as
a failure, consistent with how non-zero return codes are already handled.
Add AST-based regression test that verifies every subprocess.run() call
in CLI modules specifies a timeout keyword argument.
Co-authored-by: dieutx <dangtc94@gmail.com>
