The patch 2900_makefile-changes.patch should be removed and implemented in patch 1004_linux-2.6.31.5.patch as done by upstream in incremental patch.
Created attachment 213296 [details, diff] patch according to upstream with implemented 2900_makefile-changes.patch
Created attachment 213298 [details, diff] diff output of 1004_linux-2.6.31.5.patch
Please remove 2900_makefile-changes.patch and replace 1004_linux-2.6.31.5.patch with https://bugs.gentoo.org/attachment.cgi?id=213296
Makefile patches are removed from incremental patches since we tag our own accordingly. Therefore, when we have a makefile patch that has something other than the version, we implement the patch separate as we have done in 2900_makefile-changes.patch. So that patch stays as is.