Fix a merge case with files added in both heads but different

Since using git-merge-recursive instead of git-read-tree, the local
file is removed if it was added in both heads but different. We now
re-generated it in gitmergeonefile.merge. The patch also cleans the
working directory of extra files generated by git-merge-recursive
since our own merge re-generates them with nicer naming.

Signed-off-by: Catalin Marinas <catalin.marinas@gmail.com>