I see that the xaduino IDE was reported as having a file identified as malware back in 2013(Atxmega Series development - #9 by Coding_Badly - Microcontrollers - Arduino Forum) which may be related to the current security warning.
A possible alternative is GitHub - Xmegaduino/Xmegaduino: Xmegaduino fork of Arduino. The Apitronics Bee board is ATXmega128a3.
I'm not aware of any xmega support packages that take advantage of the Arduino IDE 1.5+'s improved support for 3rd party hardware. The old way of releasing a modified IDE is problematic since it quickly becomes outdated if the developer isn't actively keeping up with the standard IDE developments.