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

hermes_agent/tools/code_execution.py

@@ -317,7 +317,7 @@ def _rpc_server_loop(
     Accept one client connection and dispatch tool-call requests until
     the client disconnects or the call limit is reached.
     """
-    from model_tools import handle_function_call
+    from hermes_agent.tools.dispatch import handle_function_call
 
     conn = None
     try:
@@ -436,7 +436,7 @@ def _get_or_create_env(task_id: str):
     terminal and file tools use, creating one if it doesn't exist yet.
     Returns ``(env, env_type)`` tuple.
     """
-    from tools.terminal_tool import (
+    from hermes_agent.tools.terminal import (
         _active_environments, _env_lock, _create_environment,
         _get_env_config, _last_activity, _start_cleanup_thread,
         _creation_locks, _creation_locks_lock, _task_env_overrides,
@@ -578,7 +578,7 @@ def _rpc_poll_loop(
     independent process, so these calls run safely concurrent with the
     script-execution thread.
     """
-    from model_tools import handle_function_call
+    from hermes_agent.tools.dispatch import handle_function_call
 
     poll_interval = 0.1  # 100 ms
 
@@ -856,11 +856,11 @@ def _execute_remote(
         )
 
     # Strip ANSI escape sequences
-    from tools.ansi_strip import strip_ansi
+    from hermes_agent.tools.ansi_strip import strip_ansi
     stdout_text = strip_ansi(stdout_text)
 
     # Redact secrets
-    from agent.redact import redact_sensitive_text
+    from hermes_agent.agent.redact import redact_sensitive_text
     stdout_text = redact_sensitive_text(stdout_text)
 
     # Build response
@@ -929,7 +929,7 @@ def execute_code(
         return tool_error("No code provided.")
 
     # Dispatch: remote backends use file-based RPC, local uses UDS
-    from tools.terminal_tool import _get_env_config
+    from hermes_agent.tools.terminal import _get_env_config
     env_type = _get_env_config()["env_type"]
     if env_type != "local":
         return _execute_remote(code, task_id, enabled_tools)
@@ -937,7 +937,7 @@ def execute_code(
     # --- Local execution path (UDS) --- below this line is unchanged ---
 
     # Import per-thread interrupt check (cooperative cancellation)
-    from tools.interrupt import is_interrupted as _is_interrupted
+    from hermes_agent.tools.interrupt import is_interrupted as _is_interrupted
 
     # Resolve config
     _cfg = _load_config()
@@ -1005,7 +1005,7 @@ def execute_code(
         _SECRET_SUBSTRINGS = ("KEY", "TOKEN", "SECRET", "PASSWORD", "CREDENTIAL",
                               "PASSWD", "AUTH")
         try:
-            from tools.env_passthrough import is_env_passthrough as _is_passthrough
+            from hermes_agent.tools.env_passthrough import is_env_passthrough as _is_passthrough
         except Exception:
             _is_passthrough = lambda _: False  # noqa: E731
         child_env = {}
@@ -1043,7 +1043,7 @@ def execute_code(
 
         # Per-profile HOME isolation: redirect system tool configs into
         # {HERMES_HOME}/home/ when that directory exists.
-        from hermes_constants import get_subprocess_home
+        from hermes_agent.constants import get_subprocess_home
         _profile_home = get_subprocess_home()
         if _profile_home:
             child_env["HOME"] = _profile_home
@@ -1160,7 +1160,7 @@ def execute_code(
             # Periodic activity touch so the gateway's inactivity timeout
             # doesn't kill the agent during long code execution (#10807).
             try:
-                from tools.environments.base import touch_activity_if_due
+                from hermes_agent.backends.base import touch_activity_if_due
                 touch_activity_if_due(_activity_state, "execute_code running")
             except Exception:
                 pass
@@ -1196,7 +1196,7 @@ def execute_code(
 
         # Strip ANSI escape sequences so the model never sees terminal
         # formatting — prevents it from copying escapes into file writes.
-        from tools.ansi_strip import strip_ansi
+        from hermes_agent.tools.ansi_strip import strip_ansi
         stdout_text = strip_ansi(stdout_text)
         stderr_text = strip_ansi(stderr_text)
 
@@ -1204,7 +1204,7 @@ def execute_code(
         # The sandbox env-var filter (lines 434-454) blocks os.environ access,
         # but scripts can still read secrets from disk (e.g. open('~/.hermes/.env')).
         # This ensures leaked secrets never enter the model context.
-        from agent.redact import redact_sensitive_text
+        from hermes_agent.agent.redact import redact_sensitive_text
         stdout_text = redact_sensitive_text(stdout_text)
         stderr_text = redact_sensitive_text(stderr_text)
 
@@ -1309,7 +1309,7 @@ def _kill_process_group(proc, escalate: bool = False):
 def _load_config() -> dict:
     """Load code_execution config from CLI_CONFIG if available."""
     try:
-        from cli import CLI_CONFIG
+        from hermes_agent.cli.repl import CLI_CONFIG
         return CLI_CONFIG.get("code_execution", {})
     except Exception:
         return {}
@@ -1562,7 +1562,7 @@ EXECUTE_CODE_SCHEMA = build_execute_code_schema()
 
 
 # --- Registry ---
-from tools.registry import registry, tool_error
+from hermes_agent.tools.registry import registry, tool_error
 
 registry.register(
     name="execute_code",