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This means the directories are not getting cleaned up properly from
previous runs before the next run. The extra patches are not, however,
being applied.

I am not sure where those files ( ie patch-2.6.8-rc4.bz2) came from, as
if they are patches, they should be named plm-*.patch (In PLM). Only
the base versions retain their original name.

This should not be this way and is confusing the output. PLM needs a
better clean-up routine.