board: sama5d3xek: Update to support DM/DT

Update the configuration files to support the device tree and
driver model, so do SPL. The device clock and pins configuration
are handled by the clock and the pinctrl drivers respectively.

Signed-off-by: Wenyou Yang <wenyou.yang@atmel.com>
Add back CONFIG_PHY_MICREL to prevent a build error:
Signed-off-by: Simon Glass <sjg@chromium.org>