If you have a file foo/bar.txt and try to remove it, by default in git that will remove the foo/ folder as well (since in git directories are not tracked, only files are). webkit-patch upload/land-cowboy/etc will then die because they attempt to determine the version control system by looking at the enclosing directory of modified files. The workaround is easy (just mkdir foo and re-run the command) but definitely non-obvious. This shows up for me quite a bit when doing rebaselines since the optimize step can often remove the last baseline from some platform-specific directory.
I might need some help fixing this because my git foo is somewhat... light. :)