Yup, zhenning is correct, MPLAB IDE or MPLAB X IDE is just a IDE that allow you to edit code, call compilers to compile the code you wrote, integrate with ICD or program to load the hex produce after compiled to PIC microcontroller. All these process aiming to do 1 thing, prepare program for PIC Microcontroller. Same applied to Arduino IDE, write code, compile, load into Arduino board
Yes, you can use MPLAB X IDE on Linux (should be), but the aim never change, write code for PIC microcontroller.
From what I see, you have a long way to go, I am not familiar with Linux and ARM architecture/environment, cannot advise so much. Normally choosing a programming language will base on several factors:
1. Is the tools available for free? Like Arduino IDE and MPLAB IDE?
2. Is it user friendly? Or command base like a DOS? Which do you prefer?
3. Community support? When you get problem, where to get advice?
4. Of course, can it run on your platform? In this case the Linux on ARM.
5. Any particular limitations?
Looking at your system, you would really want to consider breaking down part to part. As advised by zhenning, is not possible to integrate subsystem once and hoping it would work like magic, it will not work So go and do more study.