In regards to the CC recognising if u have manually un-installed an addon. Yes it can be done. With WAU and the WoWI updater, they both put a little file in each of the addons folders which handled revision numbers and such. I noticed, espescially with the WoWI updater if remove the little updater.wid file in the addons folder, the updater would no longer have it listed.
This is an approach that could be taken. I have mentioned this to Kaelten before and he had said that this is something they are looking into.
I personally think this would be a great idea, especially when it comes to updating addons and manuall uninstall of addons.
But on a seperate note, CC has been working great for me. It does tend to be a fiddely at times. i have noticed that if i dont have my computer on for a few days, boot it up, CC runs and only updates a couple of addons (addons which have been updated the day i turned my computer on), but other than that it works great. Just waiting on the Disembed support than i will be sweet.
In regards to the CC recognising if u have manually un-installed an addon. Yes it can be done.
The client already maintains a list of what you have installed. It knows when you manually install a new addon (if you have the scan option enabled). It just doesn't use that same logic in reverse to know when you manually uninstall an existing addon...
It means, whenever you install an addon for the "first" time with the curse client, it will install it over whatever version is on your computer. Period. Whether it's newer, or whether it's older. It's getting replaced.