board: sama5d3xek: Clean up code

Due to the introduction of the pinctrl and clk driver, and using
device tree files, remove the unneeded hardcoded pin configuration
and clock enabling code from the board file.

Signed-off-by: Wenyou Yang <wenyou.yang@atmel.com>
Remove CONFIG_PHY_MICREL as per previous patch:
Signed-off-by: Simon Glass <sjg@chromium.org>