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_interrupt_subagent.py

@@ -18,7 +18,7 @@ import time
 import unittest
 from unittest.mock import MagicMock, patch, PropertyMock
 
-from tools.interrupt import set_interrupt, is_interrupted
+from hermes_agent.tools.interrupt import set_interrupt, is_interrupted
 
 
 class TestCLISubagentInterrupt(unittest.TestCase):
@@ -32,7 +32,7 @@ class TestCLISubagentInterrupt(unittest.TestCase):
 
     def test_full_delegate_interrupt_flow(self):
         """Full integration: parent runs delegate_task, main thread interrupts."""
-        from run_agent import AIAgent
+        from hermes_agent.agent.loop import AIAgent
 
         interrupt_detected = threading.Event()
         child_started = threading.Event()
@@ -98,8 +98,8 @@ class TestCLISubagentInterrupt(unittest.TestCase):
             }
 
         # Patch AIAgent to use our mock
-        from tools.delegate_tool import _run_single_child
-        from run_agent import IterationBudget
+        from hermes_agent.tools.delegate import _run_single_child
+        from hermes_agent.agent.loop import IterationBudget
 
         parent.iteration_budget = IterationBudget(max_total=100)
 
@@ -109,7 +109,7 @@ class TestCLISubagentInterrupt(unittest.TestCase):
 
         def run_delegate():
             try:
-                with patch('run_agent.AIAgent') as MockAgent:
+                with patch('hermes_agent.agent.loop.AIAgent') as MockAgent:
                     mock_instance = MagicMock()
                     mock_instance._interrupt_requested = False
                     mock_instance._interrupt_message = None