Allow me to repeat. Serious 
Especially considering they put it in the web editor.
I don't know what is in the *.ino file. But I can't see that it is that big of a change. On load, read the *.ino, extract the selection set the menu bar. On save, store the menu selection in the *.ino file.
Can the *.ino file be used for any other purpose than for the Arduino IDE? (ie., is there another application or compiler that can use it)