Brand new to JWowUpdater. Thanks for writing it. I was trying another updater but a friend turned me onto this one and talked me into switching. There's nearly 30 pages of messages here so forgive me if i ask a noob question that's already been answered elswhere.
When addons have multiple modules, like CT_MOD, Auctioneer, etc. the Non-WowAce "Not Monitored" page generates a nice long list of things it seems to think are separate addons. There doesn't seem to be a way to tell it that they belong to another addon. One nice thing about my previous updater is it seemed quite aware when an addon installed multiple folders and even aware when there was overlap between two addons (so that deleting one wouldn't delete shared folders). Maybe this is just a UI thing and JWowUpdater is handling all that correctly, but it would be great if this could be dealt with in the UI eventually.
Also, it might be worth considering unifying the addons lists. If, for example, someone is going through Curse website and finds an addon they want, and that happens to be a WowAce addon, they might try adding it to the Non-Wowace list not realizing all they needed to do was go to the other list and add it.
Or, at a minimum your users could submit a bunch of pre-configured non-wowace addons so that your application would have most of the popular ones already configured when they first try jWowUpdater.
Just some thoughts to consider.