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It looks like windows pays attention to the appId property in the electron builder config. It was set to "com.electron.brim" for Brim v30, Zui v1, and Zui-Insiders. This looks like the reason they were overwriting the folders.
Each one now has a unique app id.
It'd be good to check the auto-update behavior again before releasing Zui Stable. I expect it would be fine, but who knows.
Actually, since I've changed the appId for zui-insiders as well, we can see what happens when zui-insiders updates after this merges. If that works fine, then Zui will work fine as well.
fixes #2459