Good news! Testing with a plain FemtoUSB (ARM Cortex M0+ ATSAMD21E18A), the Arduino IDE 1.6.5 appears to load sketches just fine when selecting the "Arduino Zero (native port)" option. Since the FemtoBeacon ATSAMR21E18A is essentially the same chip with an AT86RF233 RF chip, and since Arduino libraries for this RF chip exist, we *may* have the groundwork already in place to be 100% Arduino Compatible in the next release of the IDE (1.6.6). We submitted a merge request (accepted) a few days ago to have the BOSSA utility recognize the ATSAMR21E18A, so if the next IDE release also updates the version of BOSSA, the FemtoBeacon should just work. I'll test with the nightly IDE builds and report back. Stay tuned! :-)

Sincerely,
Alex Albino
CTO - Femto.io