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I'm sure one of you brilliant people know how to do this, but I don't. It would make stuff easier to find. :)
Safari Menus: Bookmarks > Edit Bookmarks. For any folders (including Favorites), right click and choose Sort by > Name.

This sorting is per folder, so you will need to repeat that for all subfolders.

I prefer to sort by hand (if I get around to it). Use drag and drop to move folders and bookmarks.
 
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