Mechanism for generating fileRef when adding new file

There is a problem when I'm using AppCode with git.
When adding file to project AppCode creates new file in ProjectName.xcodeproj/project.pbxproj. It generates fileRef to that class, something like this:

BDC2D308EB0CC957E64A5B41 /* NewClass.m in Sources */ = {isa = PBXBuildFile; fileRef = BDC2D308EB0CC957E64A5B40 /* NewClass.m */; };

The problem is that when I switch to another branch and create file there, AppCode uses same fileRef as in the first case:

BDC2D308EB0CC957E64A5B41 /* AnotherClass.m in Sources */ = {isa = PBXBuildFile; fileRef = BDC2D308EB0CC957E64A5B40 /* AnotherClass.m */; };

Due to this conflict, I can't merge two branches. So when I want to create new file I have to go to Xcode, because it uses unique fileRef every time.

Can the way AppCode generates fileRef be changed?