In that case (i.e. stage2/01-sys-tweaks and stage2/02-net-tweaks) a
directory with a same name (00-pc) is getting created for both quilt
patch sets. This might yield a situation when second patch set is not
applied.
The fix is to come up with a more sophisticated naming convention for intermediate
patchset directory (which .pc symlinks to) and create separate
directories for each patchset.