There's been a lot of discussion on Discord on how to handle versioning and dependencies, most of which is above my pay grade. From the end-user side of things, my biggest concern is trying to avoid having two or three versions of the same multi-GB content pack installed at the same time for the sake of maintaining compatibility. (FS2 is one of the few games I have installed on my SSD, and while I'm not exactly hurting for room I like to keep it as clean as possible.) Right now I have three separate versions of the MediaVPs, and two each of the FSPort and its MediaVPs, and Knossos won't allow me to delete any of the older versions because certain other mods I have installed have them listed as a specific dependency. I know the overall modding environment is much more complex now than it was in the bad old days, when you could plop a new MediaVPs release into your FS2 folder and other mods would (mostly) handle it without issue, but I also feel like that some of these smaller classic mods (the likes of Derelict and Warzone) still stuck on the old versions could probably be bumped up to the new ones without issue.
I'm not sure what the best solution is here. Having some way to manually override the version dependencies (with a hefty warning attached to it) would be good, though I think jr2's idea of a reset function would be a necessity for it, since we're just asking for support headaches otherwise. If there's any way you have of being able to automatically detect potential conflicts with an updated dependency, that'd be fantastic, but I can't imagine that's an easy problem to solve. Maybe the best solution is a human one, i.e. making sure there are enough people who have permissions on these mods to test them out when a new MediavPs version drops and verify them for it in a timely manner. That's especially important for the more classic community mods that may have had just one person upload them to Knossos in the first place.