It would be a great aid if the contents of RAM/ROMs would save with logic files. This could be implemented such that the circuit file either remembers the file location of the memory file, or that the memory contents itself is saved in the circuit file.
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We purposefully saved RAM/ROM data separately from the main file, so that people would be able to load different programs into their RAM in the same circuit. It would be nice if they could remember, though. I'm not sure how you can get the "best of both worlds" on this issue.