setup: Fix path to extra patches in series file

Extra patches (typically contained in archives) end up in the working
directory, not the source directory where regular patches live. In
the most common case, it makes no difference because both directories
are the same. However, as soon as options -d or --sourcedir are used
in conjunction with extra patches, the working directory and the
source directory are different, and the paths to the extra patches in
the series file get wrong.

While we can't possible handle the case where the source and working
directories are completely different, we can easily handle the most
typical case where the working directory is a subdirectory of the
source directory.

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