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Your solution seems very interesting  but it is complecated to. At final, we need to make a complex algorithm which can manage automatically :

Full Version 1

Full Version 2

Full Version 3

Update Version 1 -> 2 (calculating diffrence between 1 and 2)

Update Version 1 -> 3(calculating diffrence between 1 and 3)

Update Version 2 -> 3(calculating diffrence between 2 and 3)

Without speak of the place storage, i think it's complicated to implement un automatical systeme.

We can think that the creator make theses differents packages( he is the only person to know what need to change) . And the web site, propose the downlod off all package. The user can choose, maybe he prefers a complet reinstall.

And maybe the creator have completely, rebuild his plugin so it's a need a complet instalation.