Allow marking things as something other than fully deobfuscated
It may be nice if it was possible to mark things as "could be named better" (yellow border) or "request changes" (orange border). That way we can map more things we're unsure about without worrying about them staying like that, and it allows others browsing the code to see names people are unsure about and see if they can provide better alternatives.
I suggest replacing the "mark as obfuscated" option with a "mark as" submenu that allows selecting from "deobfuscated", "improvable", "requesting changes" and "obfuscated".
This would break the format, by the way.
Couldn't it be stored in a separate file? Where would documentation eventually be stored?
Documentation would be adding a new type of "mark" into the format, which is notably less breaking. However, all our reading is done through Enigma anyway, so it's not a huge deal.