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It looks like the Foundation has support in place to sign executables (See bug 319605). We can now use this support to sign the eclipse.exe in our build.
We have to be careful to what this means for RCP app creators since on windows the branding of the RCP app means bashing icons into the exe, which likely change the signature.
Yes, anyone branding the executable will need to sign it again themselves after they bash it. The purpose of eclipse.org signing eclipse.exe, is so that users of the open source packages like EPP packages, Eclipse SDK, etc, don't get the goofy prompt every time they start eclipse on Windows Vista/7.
Since this runs on the windows slave, this will have to be something that we implement after bug 325997 (build at eclipse.org) is resolved. I don't think there is a way to directly access the windows slave from outside eclipse.org.
I realized we already have a bug for this. *** This bug has been marked as a duplicate of bug 319419 ***