You are right it's already documented here in pjrc datasheet page:
Atmel's Official Page
The Official Atmel Page provides this datasheet and other information. However, most of their code is NOT compatible with GCC (it only works with expensive commercial compilers).
Atmel uses a different bootloader called "DFU", which is different from HalfKay on the Teensy. DFU takes 4K of the 16K flash memory, whereas HalfKay uses only 0.5K! Atmel's FLIP tool only works with DFU. You need to use the Teensy Loader with Teensy boards that have HalfKay
What can we do about that?