I would like to create a custom Arduino board based on the Arduino Due. Upon looking at the Due's schematics under the documentation tab there are some stuff that i do not need and removed them. the last thing that i want removed is the ATMEGA16U2. This part just takes so many components that i want it removed.
I would like to build my code using the arduino IDE and with the 16u2 gone i do not know a way how to upload my codes.
This seems to be possible since under the documentations there is a native usb port of the due that is directly connected to the SAM3X8E,
from here on out im lost what how do i upload my code to the same sam3x8E
Special tools that i have that might be usefull:
J-link EDU Mini
USB to UART
My Current draft schematics: