Adjust documentation to fit refinegems

[cb-Hades]

To allow better maintenance and development internally, it would be great to have the same documentation style in related project.

Goal: Adjust the documentation to the standard used in refinegems, since its already released and SPECIMEN is currently under development and being restructured.

Tasks (rewrite docs for):

• [x] core
  • [x] bidirectional_blast
  • [x] generate_draft_model
  • [x] refinement
    • [x] extension
    • [x] clean_up
    • [x] annotation
    • [x] smoothing
  • [x] validation
  • [x] analysis
• [x] util
  • [x] util
  • [x] set_up
  • [x] cmd_access
  • [x] workflow
  • [x] classes
  • [x] reports

[cb-Hades]

In-Code documentations have been converted to the refinegems standard and a mustache file with the basic format construct has been added to the dev folder.