Circuit requirement for Arduino Due custom circuit without the ATMEGA16U2 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:
Since you have USB you just connect it to your computer. As long as the flash is blank (use the erase button) it will enter the BOSSA bootloader at powerup and you can use the Arduino IDE to upload the code as normal (or the bossac command line tool).

There are two ways of entering the bootloader: 


Wipe the flash with the ERASE button (or trigger from 16U2). 
Open the native port at 1200 baud. 


The latter is only possible if you have first programmed the board with a sketch with that ability in it. The most sure-fire way is to include the erase button.

You can either provide a physical button (as shown in the existing schematics) or a simple jumper that can be shorted when erasing is needed.