SAMA54D-EK:  Don't disable any features in the NSH configuration.  Comments updated in several files

SAM3/4: Important bugfix.  Values read from PIO input pins do not change unless clocking to the PIO block is enabled

SAMA5D3/4: Fix some logic in conversion of physical and virtal DRAM addresses when running out of DRAM

 Unconfigure GPIO pins when closing a serial port to prevent back effects from back-powering on the TX pin. From Kosma Moczek

Add support for a network device IOCTL to access PHY registers.  Ioctls only implemented for STM32.  From Lazlo

Move the remaining files from include/nuttx/net/uip to include/nuttx/net; Rename *_internal.h header files in net/ to just *.h