Currently when there are multiple copies of the same addon (such as one in master and one that was installed manually), an error is shown in the Addons tab of the user preferences stating "Multiple addons with the same name found! / likely a problem with the script search path. / (see console for details)". The user then has to open the console (or on linux/mac, restart blender from a terminal), read through the big mess of text and figure out where the duplicates are and then go delete one of them manually.
This patch attempts to improve the usability of how the user would solve this issue.
It lists the addons that have duplicates, and then lists the two duplicate files, providing a delete button to remove those files and resolve the issue directly in Blender.
I couldn't find an existing operator that could delete a file given only its path, so I wrote one at the top of space_userpref.py. I'm pretty sure that's not the right place for such an operator, but I don't know where is. The operator also removes the item in the addon_utils.error_duplicates list corresponding to the addon.
Finally, one limitation: if there are more than two duplicates of the same addon, it'll only show one pair in the list. When you delete one of the two, it'll appear as if the problem is solved, however when restarting blender next it'll show the error again, this time with a different pair of files. How it detects the duplicate modules confuses me a bit, so I couldn't think of a way to solve this.