Auto copy/paste changes in default preferences to user preferences

Any changes in the default preferences don't actually occur in that file, but are automatically pasted through to the user preferences. This saves on copy/paste time, helps new users deal with how the preference system works, and can automate copying comments through, too.

e.g. editing 

"font_size": 10, to "font_size": 12, in the defaults will actually add that change to user preferences, while leaving the default as it was. 

It would be helpful to have a small tooltip or something similar notifying the user of this.