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See bug 341036 comment 6
http://egit.eclipse.org/r/#change,4980 could be the first step for adding "workspace patches" support. It would be implemented as another "header format".
Initial version of the patch has been pushed to Gerrit, see https://git.eclipse.org/r/#/c/5046/ Comments are most welcome. Please note, that you will need to apply patches from blocking bugs first.
Fixed with 624ec10bd93e6ec14dc2cbdc59c6843bd4fec940
Verified in 2.0.0.201204191915. It works but is a bit hard to use because one has to manually select the 'Workspace' format and because the user's choice is not remembered. For those coming from CVS this is even more confusing because there, 'Workspace' is the default. I filed bug 377390 for remembering the selection.