Merging second

### Minor changes:
* add *.root files to git ignore
* edited the user/.. files

### Root merging:
Allow to merge multiple plots of multiple spaces into a single plot for each space

### Cuts
Allow to make cuts based on the vars, before passing to be considered to update spaces.
(Note: "file" means: src/file.cpp and include/file.h)
* introduce Cut class in "Cut"
* introduce Cut Manager in "CutManager" 
* introducd CutFunctions in "CutFunctions"
* update "RootMakePlots" 
* update make_plots.py routine
* update "CtypesWrappers"
* update py_modules/CtypesWrappers.py