AtlasGeoModel: enable flake8 and fix/remove code

Enable flake8 and make code compliant. Delete all obsolete job option fragments in share/.

This merge request affects 35 files. Since this is a long list, I will not print it here.

Adding @nkoehler ,@rbianchi as watchers

added Geometry master review-pending-level-1 labels

CI Result SUCCESS (hash 3a1c70bd)

	Athena	AthSimulation	AthGeneration	AnalysisBase
externals
cmake
make
required tests
optional tests

Full details available on this CI monitor view
Athena: number of compilation errors 0, warnings 0
AthSimulation: number of compilation errors 0, warnings 0
AthGeneration: number of compilation errors 0, warnings 0
AnalysisBase: number of compilation errors 0, warnings 0
For experts only: Jenkins output [CI-MERGE-REQUEST-CC7 22793]

added review-approved label and removed review-pending-level-1 label

merged

mentioned in commit bfd1ede8

added sweep:ignore label

mentioned in merge request !37863 (merged)