The way I use the UIBuilder, I make all my custom files read-only. Then, the one xml file I'm working on I switch to be writable. When saving in the UIBuilder it will give you a lot of errors because there are a lot of files it will try to save that are write-protected. After all that I sort all the UI files by date and delete all the new ones except the one file I was editing. Kind of a pain but it works for me.
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