I would like to know if the compiled sketches for DUE can be uploaded to a SAM3X chip which is not on a DUE board ?
In other words can I use skteches created initially for DUE and upload them directly on "custom board" based on SAM3X ?
Since there is another ATMEL (ATmega16U2) chip on the Due board i was wondering if ARduino IDE is also creating some special files for the ATmega chip when compiling
If yes, what tools would be required ? ATMEL Studio I guess?
That sounds like an interesting idea. We can do this with the Uno chip (328P) and the AtTiny chips, so why not the ARM chip right?
The custom boards would be harder to make though, but if you have gotten past that then it would be good to be able to program them using the IDE.
Maybe someone here has looked into this already.
I upload Arduino sketches to custom boards all of the time. The SAM3X processor has its own bootloader which works over either the first serial port (Serial in arduino) or the built-in USB port. The native port works perfectly fine for programming the Due and it is much faster too. So, if you forget the silly ATMEGA to serial pathway on the Due and go straight native you can use any board with a SAM3X where the USB port on the chip is properly exposed to the outside world. Don't even bother with the programming port. If you need an example of how to create a custom board that works with Arduino then look at the GEVCU project I'm involved with. Or, just grab the Arduino PCB files and modify them.
If you do make a custom board you really are best off to modify the official Due board files. The reason is that the Arduino core files expect certain pins to be used for certain things and you're best off keeping that scheme.
Look at the Teensy while you are searching. That's a much better alternative in my opinion. It has much more useable capability, other than having fewer pins. It can be programmed with the Arduino IDE although the real Teensy experts don't use Arduino.