I see drh just made a fix to prevent adding a file which difference only in case from a file in the repo.  OS/X users will I think need a similar treatment.

What happens when the repo is shared between Linux and Windows users, and the Linux users add two files, say "makefile" and "Makefile"?  When the Windows user does an 'update', she will get one of the files, since Windows doesn't distinguish case (neither does OS/X).  So one file will be missing on Windows.

Perhaps it makes sense to issue a notice to the Windows user in that case?