Arduino LLC have released their latest IDE - version 1.6.5.

The Arduino Zero is based on the SAM D21G18 processor, a 48-pin variant from the D20/D1 series. It should be possible to use the Arduino interface to upload the Arduino Zero bootloader to other SAMD21G18 micro controllers - however, an Arduino Zero may be required to do this. Alternatively, it should be possible to upload the bootloader by using a dedicated programmer (such as an Atmel ICE), though this method may not be supported within the Arduino IDE, and may require other software, such as Atmel Studio.

The Arduino Zero boot loader is based on Atmel's SAM BA Bootloader, though I believe it has been slightly modified by Arduino for use in the Zero. This may mean that the Zero bootloader will only work for the SAMD21G18, however the SAM BA bootloader will work for the full D20/D21 range.