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_skill_size_limits.py

@@ -12,7 +12,7 @@ from unittest.mock import patch
 
 import pytest
 
-from tools.skill_manager_tool import (
+from hermes_agent.tools.skills.manager import (
     MAX_SKILL_CONTENT_CHARS,
     MAX_SKILL_FILE_BYTES,
     _validate_content_size,
@@ -25,8 +25,8 @@ def isolate_skills(tmp_path, monkeypatch):
     """Redirect SKILLS_DIR to a temp directory."""
     skills_dir = tmp_path / "skills"
     skills_dir.mkdir()
-    monkeypatch.setattr("tools.skill_manager_tool.SKILLS_DIR", skills_dir)
-    monkeypatch.setattr("tools.skills_tool.SKILLS_DIR", skills_dir)
+    monkeypatch.setattr("hermes_agent.tools.skills.manager.SKILLS_DIR", skills_dir)
+    monkeypatch.setattr("hermes_agent.tools.skills.tool.SKILLS_DIR", skills_dir)
     monkeypatch.setenv("HERMES_HOME", str(tmp_path))
     return skills_dir
 
@@ -201,7 +201,7 @@ class TestHandPlacedSkillsNoLimit:
 
     def test_oversized_handplaced_skill_loads(self, isolate_skills, tmp_path):
         """A hand-placed 200k skill can still be read via skill_view."""
-        from tools.skills_tool import skill_view
+        from hermes_agent.tools.skills.tool import skill_view
 
         skill_dir = tmp_path / "skills" / "manual-giant"
         skill_dir.mkdir(parents=True)