Commit for the 111009 release.
Added User Application APIs to the CDC and DFU class bootloaders.
When automatic PLL management mode is enabled on the U4 series AVR8 chips, the PLL is now configured for 48MHz and not a divided 96MHz, to lower power consumption and to keep the system within the datasheet specs for 3.3V operation (thanks to Scott Vitale).
Added reliability patches to the AVRISP-MKII Clone project's PDI/TPI protocols (thanks to Justin Mattair).
Fixed ring buffer size limited to 255 elements, instead of the intended 65535 elements.
Fixed AVRISP-MKII Clone compile warning on AVR8 U4 targets even when NO_VTARGET_DETECT is enabled.
Rename the Doxygen page source directory from ManPages/ to DoxygenPages/ to prevent user confusion with the actual *nix Man tool.
Update XMEGA platform clock management example code to suit the currently released silicon.

Cleanups to the UC3 endpoint/pipe multi byte read code.
Fixed CDC class drivers not saving and sending all 16-bits of the control line states (thanks to Matthew Swabey).
Fix incorrect Android Accessory Host interface descriptor subclass value (thanks to Opendous Inc.).
XMEGA port improvements; connection and disconnection are now detected correctly. Fixed incorrect interrupt priority levels being set for XMEGA devices.
Minor documentation fixes.
Fix error in XMEGA clock platform driver for the DFLL calibration byte order.
Update XMEGA clock management so that the correct 16-bit calibration is used when requested. Fix endpoint descriptor table so that the frame number is stored into the correct location. Add compile time option to source the USB clock from the PLL rather than the internal 32MHz RC oscillator.
Namespace out the internal endpoint and pipe globals in the UC3 architecture.
Update ENDPOINT_EPNUM_MASK to be 0x0F, the maximum possible USB endpoint number within a device, rather than just the maximum number for the AVR8 and UC3 targets of 0x07.
Namespace out the internal endpoint globals in the XMEGA architecture.
Added INVERTED_ISP_MISO compile time option to the AVRISP-MKII clone project (thanks to Chuck Rohs).
Fix XMEGA core USB driver so that device mode enumerates correctly on the host PC.
Add support for the Atmel XMEGA A3BU Xplained board.

More XMEGA USB core fixes.