Fixes "Check Answer" to previous state

[#39917671]
Note for TODOs
Getting expected behavior on "custom prompts" checkbox

[#39917671] The pseudo-attribute way of doing this was too cute and wasn't working properly (i.e. not persisting user changes across reloads) so here we'll do it the hard way.
Don't serialize custom MC prompts if they're off

[#39917671]
Making check-answer specs pass
Fixes Run#increment_run_count
Passing test for unique Run hashes (slow)