Bug: Changing the theme through the graphical menu overwrites the user settings so that the formatting and comments are lost. (note the settings are still correct, just formatting is lost)
I had the idea that it would be nice to always be able to diff my User/Base File.sublime-settings with the global one to remember what I had changed and refer to my comments to remember why.
With the benefit that if a new global setting was introduced I could see it in the diff after an upgrade and decide if I liked the default or wanted to customize it in my user settings.
However this workflow isn't really possible because even if I attempt to keep my user settings nice and documented, my formatting and comments get overwritten when I change the theme through the graphical menu (I guess other places that automatically update the user settings file will do this as-well).
I guess I could just be careful not to touch the theme menu, but I'd much rather the system replace the setting value while leaving the formatting alone.