Upating to/from Milestones aren't really supported - its just luck if it works ;)
Note, there is no real god way to do what you want to do unless we get an "Uber" feature that includes all plugins, but then it will be harder to actually install subparts.
And we do try and put the same name prefix on our plugin/features but we can't do that for *all* projects for legacy or actually different naming reasons.