I understand both provide different class (Nette\Callback and Nette\Utils\Callback) so no conflicts in class name, and when using composer.

So this is only a downstream issue, when merging all the components in a single tree, in system shared location (/usrs/share/php/Nette).

Proposal, as components rely on "classmap" autoloader, path have not a lot of importance, move this file to a "Deprecated" folder.

Other solution will be to try top match PSR-0 and so, move them in top directory to match namespace.

FYI Nette framework have been submitted for review for official Fedora / EPEL repository (used, at least by apigen), see https://bugzilla.redhat.com/showdependencytree.cgi?id=1277484&hide_resolved=0