refactor(restructure): rewrite all imports for hermes_agent package

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

tests/tools/test_managed_server_tool_support.py

@@ -16,8 +16,6 @@ from pathlib import Path
 
 import pytest
 
-sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
-
 try:
     import atroposlib  # noqa: F401
 except ImportError: