Clean up nnpdfcpp/tools

Created by: Zaharid

Out of these

https://github.com/NNPDF/nnpdf/tree/master/nnpdfcpp/tools

I am pretty sure we have simpler solutions for theory manager, I don't know what the positive script is for.

While I was quite fond of the make-fit script, I don't believe anybody has used it in a while (maybe @siranipour wants to salvage it) and besides the main point was setting some naming convention that isn't used much.