Change directory structure to align with Atmel softpack

This way we can easily check with 'diff' for differences in our code and
Atmel softpack.  Also, this layout is more suitable for building various
different firmware images (e.g. factory-test, dfu-loader, main
application) for a variety of different boards (simtrace, owhw, qmod).

firmware/atmel_softpack_libraries/libchip_sam3s/chip.h

@@ -0,0 +1,59 @@
+#ifndef _LIB_SAM3S_
+#define _LIB_SAM3S_
+
+/*
+ * Peripherals registers definitions
+ */
+#if defined sam3s4
+#elif defined sam3s2
+#elif defined sam3s1
+#else
+    #warning Library does not support the specified chip, specifying sam3s4.
+    #define sam3s4
+#endif
+#include "SAM3S.h"
+
+
+/* Define attribute */
+#if defined   ( __CC_ARM   ) /* Keil µVision 4 */
+    #define WEAK __attribute__ ((weak))
+#elif defined ( __ICCARM__ ) /* IAR Ewarm 5.41+ */
+    #define WEAK __weak
+#elif defined (  __GNUC__  ) /* GCC CS3 2009q3-68 */
+    #define WEAK __attribute__ ((weak))
+#endif
+
+/* Define NO_INIT attribute */
+#if defined   ( __CC_ARM   )
+    #define NO_INIT
+#elif defined ( __ICCARM__ )
+    #define NO_INIT __no_init
+#elif defined (  __GNUC__  )
+    #define NO_INIT
+#endif
+
+
+/*
+ * Core
+ */
+
+#include "exceptions.h"
+
+/*
+ * Peripherals
+ */
+#include "pio.h"
+#include "pio_it.h"
+#include "pio_capture.h"
+#include "pmc.h"
+#include "tc.h"
+#include "usart.h"
+//#include "USBD_Config.h"
+
+#include "trace.h"
+#include "wdt.h"
+#include "unique_id.h"
+#include "efc.h"
+#include "flashd.h"
+
+#endif /* _LIB_SAM3S_ */