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
Cherry-picked from PR #5136 by thakoreh.
setup_gateway() uses shutil.which('uv') at line 2126 but shutil was
never imported at module level, causing NameError during Matrix E2EE
auto-install. Adds top-level import and regression test.