Pardon me, it's been awhile since I used pd.
$ file /usr/lib/puredata/extra/bob~/output~.pd /usr/lib/puredata/extra/bob~/output~.pd: ASCII text
I added "/usr/lib/puredata/extra" into Preferences > Path. Then I created an [output~] and... "Couldn't create."
So I added "/usr/lib/puredata/extra/bob~" and... then it worked.
Is that expected behavior? I'd have imagined pd would search subdirectories, but it seems it doesn't. (Or it chokes on the fact that it's "bob~" rather than "bob.")