It is already in a separate folder. Offending files are in /usr/bin, namely pdsend and pdreceive that are essentially unchanged but still conflict nonetheless.
Why not remove pdsend and pdreceive and use the 'official' packages. I believe its called puredata-utils. Then the pd-l2ork package can Depend
or
Recommend puredata-utils to provide pdsend/pdreceive. This is how its done in Pd-extended.
This section of SVN should be useful for you: http://pure-data.svn.sourceforge.net/viewvc/pure-data/branches/pd- extended/0.43/debian/
.hc
Good point. I will need to investigate if they are truly identical and once that is done that certainly seems like a feasible way of doing things.