Hey Ico,
I'm just trying out the latest pd-l2ork. I noticed that the executable is now 'pd-l2ork' and it installs into /usr/local/lib/pd-l2ork. That's great, that makes installing in parallel much easier. But there are still a few things that conflict with other packages, including things that have also been removed from the big Pd-extended all-in-one package:
bin/cyclist 'cyclist' is now its own package included in Debian and Ubuntu/oneiric and up, or available from my Launchpad PPA for older distros: https://launchpad.net/~eighthave/+archive/libdirs
bin/pdreceive share/man/man1/pdreceive.1.gz bin/pdsend share/man/man1/pdsend.1.gz 'puredata' or 'puredata-utils' have provided these for a long time
include/Base/ These are the Gem headers, they should be in the 'gem' package, but I don't think they are. They are still included in the 'pd-extended' package. I think you'd only need to include them in pd-l2ork if there are changes to Gem in pd-l2ork.
.hc