I *thought* I fixed this, but libpd/Makefile in the pure-data repo (not the separate libpd repo), still does not correctly clear the object files out of the extra subdirectories, ie. extra/bob~/bob~.o, etc. In any case, I pushed a small commit to the develop branch adding a note about this to readme.

I don't feel like figuring out the VPATH trickery to properly fix this. In the separate libpd repo Makefile, we use full paths. ;)