Bug 112534 was just reported and it seems this is caused by the stable version of patch and fixed in ~arch. 16 Nov 2004; Mike Frysinger <vapier@gentoo.org> +files/2.5.9-deb-cr.patch, +patch-2.5.9-r1.ebuild: Version bump with debian patch #49823 by JoWilly. This has certainly been out long enough and the only open bug I was able to find is bug 83632, which doesn't seem to have anything preventing from going stable. Just add arch teams to CC if you think it is ready of stable.
2.5.9-r1 is broken too with CRLFs, just in a different way
gnu-classpath is probably not going stable any time in the near future, but is a solution to this expected in the near future or do I just redo the patch?
not really ... your patch is broken