For separate(s) file(s), this "issue" comes also for others things, like project dependancy, debug config and so on.
At the time, I'm using C::B with 2 others peoples in a team. (among lot of others uses). Sources of products developped with C::B are commited in git repository. It's in embedded area, with about 15 custom library, 2 differents git repo (as codebase is shared among lot of projects). I've patched quite a few things in C::B, needed to be compatible with previous Eclipse system and handle problems that arised.
It's clear that some things should be separated in external file, outside of project files - that in general rules must ne be commited -, and other should be in project files, and must be commited.
So thanks for this patch repository, I will try to use the breakpoint one for my specific use