Nexus Mods have written an update about their plans for the Collections feature and, as they warn, it is indeed a long one. It's a big change, and Nexus have written a rather long post (longer than this one) explaining the 'how's, 'why's, and 'what now's of the new system.
Instead, mod authors will be able to archive files, though they'll still be downloadable via Collections that include them.
In anticipation of launching the Collections system, Nexus say that mods can no longer be completely deleted from the site. Mega game mod hosting site Nexus Mods have revealed more information about their upcoming Collections feature which they hope will make installing mods a more approachable experience for users.