Removed sym links, replaced them with actual folders
diff --git a/firmware/cmsis b/firmware/cmsis
deleted file mode 120000
index 895b677..0000000
--- a/firmware/cmsis
+++ /dev/null
@@ -1 +0,0 @@
-./atmel_softpack_libraries/libchip_sam3s/cmsis
\ No newline at end of file
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/CMSIS_Core.htm b/firmware/cmsis/CMSIS_Core.htm
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/CMSIS_Core.htm
rename to firmware/cmsis/CMSIS_Core.htm
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/core_cm3.c b/firmware/cmsis/core_cm3.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/core_cm3.c
rename to firmware/cmsis/core_cm3.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/core_cm3.h b/firmware/cmsis/core_cm3.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/cmsis/core_cm3.h
rename to firmware/cmsis/core_cm3.h
diff --git a/firmware/include/board_lowlevel.h b/firmware/include/board_lowlevel.h
deleted file mode 100644
index 5b58737..0000000
--- a/firmware/include/board_lowlevel.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/* ----------------------------------------------------------------------------
- * ATMEL Microcontroller Software Support
- * ----------------------------------------------------------------------------
- * Copyright (c) 2009, Atmel Corporation
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * - Redistributions of source code must retain the above copyright notice,
- * this list of conditions and the disclaimer below.
- *
- * Atmel's name may not be used to endorse or promote products derived from
- * this software without specific prior written permission.
- *
- * DISCLAIMER: THIS SOFTWARE IS PROVIDED BY ATMEL "AS IS" AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT ARE
- * DISCLAIMED. IN NO EVENT SHALL ATMEL BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
- * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
- * OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
- * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * ----------------------------------------------------------------------------
- */
-
-/**
- * \file
- *
- * Interface for the low-level initialization function.
- *
- */
-
-#ifndef BOARD_LOWLEVEL_H
-#define BOARD_LOWLEVEL_H
-
-/*----------------------------------------------------------------------------
- * Exported functions
- *----------------------------------------------------------------------------*/
-void LowLevelInit( void ) ;
-
-#endif /* BOARD_LOWLEVEL_H */
-
diff --git a/firmware/include/chip.h b/firmware/include/chip.h
deleted file mode 120000
index 2587804..0000000
--- a/firmware/include/chip.h
+++ /dev/null
@@ -1 +0,0 @@
-../atmel_softpack_libraries/libchip_sam3s/chip.h
\ No newline at end of file
diff --git a/firmware/include_board b/firmware/include_board
deleted file mode 120000
index 30cfb0f..0000000
--- a/firmware/include_board
+++ /dev/null
@@ -1 +0,0 @@
-./atmel_softpack_libraries/libboard_sam3s-ek/include/
\ No newline at end of file
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/bitbanding.h b/firmware/include_board/bitbanding.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/bitbanding.h
rename to firmware/include_board/bitbanding.h
diff --git a/firmware/include/board.h b/firmware/include_board/board.h
similarity index 100%
rename from firmware/include/board.h
rename to firmware/include_board/board.h
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/board_lowlevel.h b/firmware/include_board/board_lowlevel.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/board_lowlevel.h
rename to firmware/include_board/board_lowlevel.h
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/iso7816_4.h b/firmware/include_board/iso7816_4.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/iso7816_4.h
rename to firmware/include_board/iso7816_4.h
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/led.h b/firmware/include_board/led.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/led.h
rename to firmware/include_board/led.h
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/syscalls.h b/firmware/include_board/syscalls.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/syscalls.h
rename to firmware/include_board/syscalls.h
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/uart_console.h b/firmware/include_board/uart_console.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/include/uart_console.h
rename to firmware/include_board/uart_console.h
diff --git a/firmware/include_sam3s b/firmware/include_sam3s
deleted file mode 120000
index faa671a..0000000
--- a/firmware/include_sam3s
+++ /dev/null
@@ -1 +0,0 @@
-./atmel_softpack_libraries/libchip_sam3s/include
\ No newline at end of file
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/SAM3S.h b/firmware/include_sam3s/SAM3S.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/SAM3S.h
rename to firmware/include_sam3s/SAM3S.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/USBD_Config.h b/firmware/include_sam3s/USBD_Config.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/USBD_Config.h
rename to firmware/include_sam3s/USBD_Config.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/chip.h b/firmware/include_sam3s/chip.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/chip.h
rename to firmware/include_sam3s/chip.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/exceptions.h b/firmware/include_sam3s/exceptions.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/exceptions.h
rename to firmware/include_sam3s/exceptions.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/hsmci.h b/firmware/include_sam3s/hsmci.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/hsmci.h
rename to firmware/include_sam3s/hsmci.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/pio.h b/firmware/include_sam3s/pio.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/pio.h
rename to firmware/include_sam3s/pio.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/pio_capture.h b/firmware/include_sam3s/pio_capture.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/pio_capture.h
rename to firmware/include_sam3s/pio_capture.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/pio_it.h b/firmware/include_sam3s/pio_it.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/pio_it.h
rename to firmware/include_sam3s/pio_it.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/pmc.h b/firmware/include_sam3s/pmc.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/pmc.h
rename to firmware/include_sam3s/pmc.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/spi.h b/firmware/include_sam3s/spi.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/spi.h
rename to firmware/include_sam3s/spi.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/tc.h b/firmware/include_sam3s/tc.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/tc.h
rename to firmware/include_sam3s/tc.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/trace.h b/firmware/include_sam3s/trace.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/trace.h
rename to firmware/include_sam3s/trace.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/usart.h b/firmware/include_sam3s/usart.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/usart.h
rename to firmware/include_sam3s/usart.h
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/include/wdt.h b/firmware/include_sam3s/wdt.h
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/include/wdt.h
rename to firmware/include_sam3s/wdt.h
diff --git a/firmware/src_board b/firmware/src_board
deleted file mode 120000
index 5ce1bf4..0000000
--- a/firmware/src_board
+++ /dev/null
@@ -1 +0,0 @@
-./atmel_softpack_libraries/libboard_sam3s-ek/source
\ No newline at end of file
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/board_cstartup_gnu.c b/firmware/src_board/board_cstartup_gnu.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/board_cstartup_gnu.c
rename to firmware/src_board/board_cstartup_gnu.c
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/board_lowlevel.c b/firmware/src_board/board_lowlevel.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/board_lowlevel.c
rename to firmware/src_board/board_lowlevel.c
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/iso7816_4.c b/firmware/src_board/iso7816_4.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/iso7816_4.c
rename to firmware/src_board/iso7816_4.c
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/led.c b/firmware/src_board/led.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/led.c
rename to firmware/src_board/led.c
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/syscalls.c b/firmware/src_board/syscalls.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/syscalls.c
rename to firmware/src_board/syscalls.c
diff --git a/firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/uart_console.c b/firmware/src_board/uart_console.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libboard_sam3s-ek/source/uart_console.c
rename to firmware/src_board/uart_console.c
diff --git a/firmware/src_sam3s b/firmware/src_sam3s
deleted file mode 120000
index 6355c88..0000000
--- a/firmware/src_sam3s
+++ /dev/null
@@ -1 +0,0 @@
-./atmel_softpack_libraries/libchip_sam3s/source
\ No newline at end of file
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/USBD_HAL.c b/firmware/src_sam3s/USBD_HAL.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/USBD_HAL.c
rename to firmware/src_sam3s/USBD_HAL.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/exceptions.c b/firmware/src_sam3s/exceptions.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/exceptions.c
rename to firmware/src_sam3s/exceptions.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/pio.c b/firmware/src_sam3s/pio.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/pio.c
rename to firmware/src_sam3s/pio.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/pio_capture.c b/firmware/src_sam3s/pio_capture.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/pio_capture.c
rename to firmware/src_sam3s/pio_capture.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/pio_it.c b/firmware/src_sam3s/pio_it.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/pio_it.c
rename to firmware/src_sam3s/pio_it.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/pmc.c b/firmware/src_sam3s/pmc.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/pmc.c
rename to firmware/src_sam3s/pmc.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/spi.c b/firmware/src_sam3s/spi.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/spi.c
rename to firmware/src_sam3s/spi.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/tc.c b/firmware/src_sam3s/tc.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/tc.c
rename to firmware/src_sam3s/tc.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/usart.c b/firmware/src_sam3s/usart.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/usart.c
rename to firmware/src_sam3s/usart.c
diff --git a/firmware/atmel_softpack_libraries/libchip_sam3s/source/wdt.c b/firmware/src_sam3s/wdt.c
similarity index 100%
rename from firmware/atmel_softpack_libraries/libchip_sam3s/source/wdt.c
rename to firmware/src_sam3s/wdt.c