PyJobTransformsCore: Enable flake8 checking and fix code

Tools/PyJobTransformsCore/CMakeLists.txt

Tools/PyJobTransformsCore/python/AtlasErrorCodes.py

Tools/PyJobTransformsCore/python/CVSutil.py

Tools/PyJobTransformsCore/python/CastorPreStager.py

Tools/PyJobTransformsCore/python/FakeAthena.py

Tools/PyJobTransformsCore/python/FilePreStager.py

Tools/PyJobTransformsCore/python/JobReport.py

Tools/PyJobTransformsCore/python/TransformConfig.py

Tools/PyJobTransformsCore/python/VTimer.py

Tools/PyJobTransformsCore/python/ValidateRootFile.py

Tools/PyJobTransformsCore/python/athena_wrapper.py

Tools/PyJobTransformsCore/python/basic_trfarg.py

Tools/PyJobTransformsCore/python/envutil.py

Tools/PyJobTransformsCore/python/extraMetadata.py

Tools/PyJobTransformsCore/python/fileutil.py

Tools/PyJobTransformsCore/python/full_trfarg.py

Tools/PyJobTransformsCore/python/pool.py

Tools/PyJobTransformsCore/python/runargs.py

Tools/PyJobTransformsCore/python/trf.py

Tools/PyJobTransformsCore/python/trfValidateRootFile.py