I am not completely sure what your problem is, so let me give you two answers (pick your favorite or let me know if that’s not what you were asking for):
– I would recommend you to create an own copy of the Arepo repository somewhere (github, bitbucket etc…) and change it there. It might be helpful e.g. to have the master branch identical to the gitlab branch which you can update in case of bug-fixes, and a second branch in which you do your development.
– In the makefile, the “OBJS” variable contains all the source files that are compiled (with *.o instead of *.c), theoretically, you can replace one by your own (with a different name), provided it contains all the same functions. The “INCL” variable contains the headers. I would not recommend replacing these, since they are also included in various source files. Overall, I am not sure you want to use this as a long-term solution, though.