I was a little worried at first because DoxyFilt uses Doxygen::Perl::Filter, Doxygen::POD::Filter, Doxygen::Script::Filter, etc.
Your namespace Doxygen::Filter::Perl doesn't look like it would cause much of a conflict. Mark Adkins (of doorways.org) wrote DoxyFilt and he uses Filter.pm in each of his subdirectories (Perl, POD, etc.) as a generalized method of calling the parser for each type of entity. I wish you luck in your new project. Let me know when you have your repository setup.
