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
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
