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Refactoring #3

@howff

Description

@howff
  • better documentation overview targeted at specific user types
  • rewrite SRAnonTool to use less scripts or even integrate into a single application
  • tidy up all the different log locations and log files
  • rewrite semehr_anon.py as a single application instead of calling other scripts
  • rewrite semehr_annotate.sh as a single application semehr_annotate.py instead of calling other scripts
  • move the anon and annotate template config files into a better location
  • move all applications into a single folder instead of everything in tools
  • CI pipeline (copied from SmiServices?)

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