Erik
For what its worth, I have my sketches in a seperate folder.
I generally just open a sketch, so the fact that a DS example might not be under the menu doesn't really matter.
Rather than try to reinvent the whole IDE and run the risk of future IDE versions crashing your party, you may wish to use a seperate folder to house them in.
Whether this will work with Mac's, I can't say as I don't own one.
Library handling is also something that needs some attention, as the user may have one optimised for DS and a similar one that works for normal Arduino.
Perhaps the Ardunion team are able to assist.
Up until now new boards have been added to boards.txt etc, without having to consider anything that isn't a full Arduino. The future is likely to include more part Arduino's and consideration to the proper handling of varying libraries and the like should be standardised to aid new users.
While not the most eligant or space saving (HD's are cheap) I have my Arduino IDE's in seperate directories, so that I avoid the issue's. (Digispark, 023 and 1.04)
Mark