Make it so that plugins can be added to upgrades without being modified

Is there a way that I could add some code to the upgrades-plugins folder that would make it so that I could ad a plugin to the upgrades packages, but can update the plugin without having it to modify it everytime there is an update for it?

For example if I add marketpress, I have to modify the plugin and everytime there is an update for it, I have to modify it again. Is there a better way?