msysgit path issues

I've got one problem regarding msysgit.

My git work dir is say, at C:\sw\work.git. My source is at "C:\sw\work.git\src\myfile.h".

I've used both command prompt and bash prompt from msysgit. Somehow, I have ended up with this issue (I cannot开发者_高级运维 recall how): both "C:/sw/work.git/src/myfile.h" and "src/myfile.h" are in my repository. The first path is not my intention at all. Whenever I made changes to myfile.h, I've got mysterious modification notices in both files since essentially they are the same file with two different name.

Any merging, update or rebase operation becomes entangled with these paths and stopped half-way.

Is there any way to resolve this issue? At least removing hardcoded path out of my repository and leaving relative path only?

Try cloning again your C:\sw\work.git (git clone --no-hardlinks C:\sw\work.git C:\anotherPath), and see if the issue persists with that new repo.
(The '--no-hardlinks' option shouldn't matter with Windows, but it is just to be on the safe side)