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/plugins/test_retaindb_plugin.py

@@ -58,8 +58,6 @@ def _cap_retaindb_sleeps(monkeypatch):
 
 # We need the repo root on sys.path so the plugin can import agent.memory_provider
 import sys
-_repo_root = str(Path(__file__).resolve().parents[2])
-if _repo_root not in sys.path:
 from hermes_agent.plugins.memory.retaindb import (
     _Client,
     _WriteQueue,