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Is there a quick way to remove all output from a sagews file?

Yes. Select all, then hit the delete output button (just right of the "in" and "out" toggles - it looks like a white "x" in a black circle). If you use vim editor mode, which I do, you need to be in input mode when doing this.

Is there a quick way to split a sagews into two sagewses?

The quickest way I can think of is to duplicate the file (there is a button for this in the Files tab), then delete the bottom half from one file and the top half from the other. A sage worksheet is one big edit buffer, so you can easily select large stretches of the file and delete. Again, if you use vim editor mode, you need to be in input mode to do this.