Make _flake8_noqa tighter

Only match '\s*# flake8[:=]\s*nqa' when it happens at the beginning of a
line. The previous version of this regex is incorrectly hitting the
following line:

        # Any "# flake8: noqa" line?

Causing flake8 to not be run on engine.py.
Also fix flake8 issues in engine.py.