I've prepaered a blinky project for the Arduino Due/SAM3X8E that can be used as a project template.
The code is tailored for the SAM3X8E, would it be better to support the whole SAM3X family? That would require some extra file; if instead you think it's better to support only the SAM3X8E I'll have to remove some #ifdef and prune the unnecessary parts.
I also had to define th symbol SAM3X8E to make it build (see system/include/CMSIS/sam3xa.h), I'm still looking into it.
Here below is the license for ATMEL files, it seems alright to me, as long as the files are used only for ATMEL MCUs.
/ Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. The name of Atmel may not be used to endorse or promote products derived
* from this software without specific prior written permission.
* 4. This software may only be redistributed and used in connection with an
* Atmel microcontroller product.
* 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
* EXPRESSLY AND SPECIFICALLY 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.