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Update systematics tool

This MR may seem large but it's mostly lots of small changes affecting many lines after de-linting using flake8

  • fixes broken setupSystematicsTool.sh
  • delinting of the python (cleanup of conventions etc) after running flake8
  • sync with systematicsTool repo version hash feb8fabfa0e7a38d335bdf286f1fe66d1e33ad27

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