This article will show you how to find out exactly which layer is causing your FreeCAD file to balloon in size, by getting a granular list of all of the layers in your document tree, sorted by size.
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Ah, I see. I thought this was about an issue with FreeCAD, but it is actually a process problem. (Why wouldn't FreeCAD allow me to stuff arbitrarily complex meshes into a model, and of course that can lead to slow computation times.)
That said, analysis tools built into the software would probably be a useful thing to investigate what makes a file "slow."
Agreed. I also submitted a feature request to add this to the GUI: