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Here is the ebuild I've created to successfully compile and install eclipse-3.2.1 some patches were removed as their upstream bugs are solved/closed {P}-helpindexbuilder.patch ${P}-swt-rm-ON_TOP.patch some others needed to be revised as source code has changed but upstream bugs are still open. you find them attached. all the other patches are ok
Created an attachment (id=98413) [details] diff from old ebuild to new one diff from old ebuild to new one
Created an attachment (id=98414) [details] eclipse-sdk-3.2.1-build.patch updated patch
Created an attachment (id=98415) [details] eclipse-sdk-3.2.1-build.patch
Created an attachment (id=98416) [details] eclipse-sdk-3.2.1-disable-junit4-apt.patch updated ebuild
Created an attachment (id=98417) [details] eclipse-sdk-3.2.1-updatehomedir.patch updated patch
Added to portage. Thanks for the help!