Refactoring

[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?)