USB init process violates datasheet recommendations

[abcminiuser]

As found by @NicoHood, the current core init code violates the best practice instructions in the datasheet for the U2 series (at a minimum). The PLL and pad regulators should be initialized before enabling the USB core.

[NicoHood]

This is how I handle the init process:
https://github.com/NicoHood/SecureLoader/blob/5ad74a64cdcf78b24e19940e90a780517122bd8c/SecureLoader/USB/USBController.h#L166

However this does not check if the Device is already running etc, what lufa does. And I totally removed those u4 interrupts which used a lot of space.

If you update this code It would be highly appreciated to have more comments with details about what is going on, in what order and why. That'd be really nice, as the usb stuff is very complex to understand and to do it right.