Make Tool OS independent

[cb-Hades]

Re-Check OS-independency of the tool.

E.g. some of the paths have a hard-coded '/', which is likely to cause problems under Windows.

Additionally, tools has not been tested on Windows for a long time - make sure it does run as expected.

Currently known issues:

• use of temporary files in current implementation can cause issues on Windows
  • gapfill.GapFiller

[cb-Hades]

most of the problems in the "newly" added functions have been fixed.
-> re-check, to make sure, everything else is fine, too