How to program Due on Raspberry Pi?

I am doing a project by combining the Arduino Due and Raspberry Pi together now.

The Due is responsible for stepper motor controlling, A/D module, and so on.
The data collected by the Due need to be transferred to the Raspberry Pi.

Currently, I met two issues as follows:

(1) The Arduino IDE installed on Raspberry Pi is V1.0.1, can not program Due. Although it can detect the serial port of Due. Is there any way to install the Arduino IDE 1.6.4 on Raspberry Pi. Because there is Linux version of Arduino IDE 1.6.4. Can I install it on Raspberry Pi?

(2) When I connect the programmable USB port of Due to the RasPi, the python program on Pi can communicate with the Due at serial mode. But When I connect the native USB port of Due to the Raspberry Pi, the Pi can also detect the port, but the communication is out of work. Because the native USB port of Due can work well at high data transfer speed, therefore I wish I can use this port to connect the Due and Pi. Is that possible?

Could any one give me some suggestions for the above issues?

Thanks a lot!

You might want to take a look at this: piupdue

Someone's written a python script that will upload the hex file from Arduino onto the due through the native port.

pls see Arduino-ide-1.6.0 + due on the Raspberry Pi - #3 by kllsamui - Arduino Due - Arduino Forum

I was needing information on a way to use raspberry pi to sense the top LED bulb on Christmas Tree in drag racing. I need it to sense the first amber as tree comes down & send a signal to activate trans brake & start delay box timer. If this is possible can any on give me a schematics or overview on how to make this project work. Thanks!