fix(restructure): fix test regressions from import rewrite

Fix variable name breakage (run_agent, hermes_constants, etc.) where
import rewriter changed 'import X' to 'import hermes_agent.Y' but
test code still referenced 'X' as a variable name.

Fix package-vs-module confusion (cli.auth, cli.models, cli.ui) where
single files became directories.

Fix hardcoded file paths in tests pointing to old locations.
Fix tool registry to discover tools in subpackage directories.
Fix stale import in hermes_agent/tools/__init__.py.

Part of #14182, #14183

tests/hermes_cli/test_web_server_host_header.py

@@ -14,9 +14,6 @@ from pathlib import Path
 
 import pytest
 
-_repo = str(Path(__file__).resolve().parents[1])
-if _repo not in sys.path:
-
 class TestHostHeaderValidator:
     """Unit test the _is_accepted_host helper directly — cheaper and
     more thorough than spinning up the full FastAPI app."""