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/libboard/common/resources/sam3s_ek_flash.gdb

@@ -0,0 +1,31 @@
+#*******************************************************
+#
+#  Connect to J-Link and debug application in flash.
+#
+
+# define 'reset' command
+define reset
+
+# Connect to the J-Link gdb server
+target remote localhost:2331
+# Reset the chip to get to a known state
+monitor reset
+
+# Select flash device
+monitor flash device = AT91SAM3S4C
+# Enable flash download and flash breakpoints
+monitor flash download = 1
+# Load the program
+load
+
+# Reset peripheral  (RSTC_CR)
+set *0x400e1400 = 0xA5000004
+
+# Initializing PC and stack pointer
+mon reg sp=(0x400000)
+set *0x400004 = *0x400004 & 0xFFFFFFFE
+mon reg pc=(0x400004)
+info reg
+
+# end of 'reset' command
+end