X-to-Y steps should remove old configs even in full output mode

[colinschmidt]

For example: when par-to-sim sets sim.inputs.all_regs from par.outputs.all_regs we should drop par.outputs.all_regs from the data structure.

[colinschmidt]

This would help alleviate #574 as well.

[colinschmidt]

This would be good to do but we will probably have to do some cleanup if any actions/tools have been looking at keys that won't be defined now.