Enable `flake8` and make code compliant. Delete unused `JetTileD3PD.py`
and `ModJetD3PD.py`. Also remove a lot of commented code.

Also remove some deprecated truth-related modules and adjust last
remaining references to them in JetD3PDMaker.

Adjust for components moved from TrackD3PDMaker to InDetD3PDMaker.



Former-commit-id: 7af59274