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Projects are currently sorted to match how they are defined in the projects file. However, if you enable and then disable any filter, they will suddenly be sorted alphabetically (almost -- AEC is sorted before Aardvark for some reason).
The project list should be sorted upon load to be consistent with the post-filter sorting, and also to avoid errors where users do not define their projects in alphabetical order (such as C3 not being the first C project).