Rewrite all import statements, patch() targets, sys.modules keys,
importlib.import_module() strings, and subprocess -m references to use
hermes_agent.* paths.
Strip sys.path.insert hacks from production code (rely on editable install).
Update COMPONENT_PREFIXES for logger filtering.
Fix 3 hardcoded getLogger() calls to use __name__.
Update transport and tool registry discovery paths.
Update plugin module path strings.
Add legacy process-name patterns for gateway PID detection.
Add main() to skills_sync for console_script entry point.
Fix _get_bundled_dir() path traversal after move.
Part of #14182, #14183
When a command timed out, all captured output was discarded — the agent
only saw 'Command timed out after Xs' with zero context. Now returns
the buffered output followed by a timeout marker, matching the existing
interrupt path behavior.
Salvaged from PR #3286 by @binhnt92.
Co-authored-by: nguyen binh <binhnt92@users.noreply.github.com>
