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/cli/test_cli_user_message_preview.py

@@ -3,8 +3,6 @@ import os
 import sys
 from unittest.mock import MagicMock, patch
 
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
-
 
 _cli_mod = None
 
@@ -44,7 +42,7 @@ def _make_cli(user_message_preview=None):
         "prompt_toolkit.auto_suggest": MagicMock(),
     }
     with patch.dict(sys.modules, prompt_toolkit_stubs), patch.dict("os.environ", clean_env, clear=False):
-        import cli as mod
+        import hermes_agent.cli.repl as mod
 
         mod = importlib.reload(mod)
         _cli_mod = mod