It is more convenient to have this data outside of any directory that contains source code that is being edited. If Bundles end up being inside the vendor/ directory keeping pyrus in vendor/pyrus is no longer an option since pyrus would back itself up prior to an installation and thus never mark any packages as installed. This is caused by the way its atomic file operations work. Unfortunately the php files cannot be stored anywhere other than /pear2/php/ then, so an addition to the autoloader is necessary to use PEAR2 dependencies.
… install. Added a custom role for bundle files which is automatically installed on setup.