clang doesn't support creation of dependency files, which makes it hard to use it as a GCC replacement. The proposed fix can be found at: http://lists.cs.uiuc.edu/pipermail/cfe-dev/2008-July/002398.html
Patch review sent out to cfe-dev
Kovarththanan: ping?
Follow up was here: http://lists.cs.uiuc.edu/pipermail/cfe-dev/2008-August/002513.html
Patch applied here: http://llvm.org/viewvc/llvm-project?view=rev&revision=58122