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I had a situation recently where I had started out using made-up version numbers for a feature on which I was working. (7.x-1.0-beta1, …-beta2, etc…) When my project lead pointed out that we had the feature checked in a git repo containing all of the code for that particular site and that it didn’t make sense to version the feature, I set about removing it. But tried doing it in what I thought was the most obvious manner: recreating the feature without any values for “Version”, nothing changed.
I scratched my head for a bit, cleared cache a bunch of times, swapped out the value for “version” in my profile’s entry in the “System” table for NULL, all to no avail. It wasn’t till I asked that someone pointed out that it may have not removed the entry from the profile.info file. Sure enough, that was the case. (K.I.S.S.) I am not sure whether that is working as intended or not, but I thought I would file a bug report, in case it was not.