upgrading add-on

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Hi all,

I want to upgrade one of the add-ons I have in the market place. Originally it had js files in the js folders so they would load automatically.
I modified the add-on and now I have the js files out of the js folder so they don't load automatically and my code can control the way they load.

My question is how do I make sure users who update the add-on don't end up with the js file still in the js folder and the other one as well?

Does C5 takes care of deleting files automatically to match the new version or do I have to specify it in the upgrade routine. If I have to specify it, how do I do that?

Thank you

mnakalay