Tooling: resolve mypy duplicate module in molecule tests

[miciav]

Problem

Mypy reports duplicate module names in molecule/controller-stop.

Evidence

• arch_report/mypy.txt:1

Plan

1. Decide whether to exclude molecule/ from mypy or convert it into a package with __init__.py.
2. Update mypy config accordingly.
3. Re-run mypy.

Validation

• uv run mypy .