KurtE: My solution is to have two directories, one that contains the common files, and the other that contains the non-teensy libraries that teensydunio provides, and I have a perl script that rebuilds ~/Arduino (under Linux) to include the libraries or not.
I also have separate directories for the ~/.arduino15 link as well, but right now, I have to manually change the symlink. One directory is arduino-1.6.5, which includes a-star/digistamp/squarewear support, one is the arduino-1.6.6 which does not include those support libraries (since they haven't been upgraded for 1.6.6) and a third for Teensy. At the moment, I use arduino-1.6.5 with Teensy.