You can use the System Studio with the Intel Quark D2000. Intel® System Studio for Microcontrollers: Getting Started Guide. The System Studio has C compilers (GCC 5.2.1) and is supported on:
Windows* versions 7, 8.1 (64bit), 10.
Linux Ubuntu (64bit, version 14.04 LTS)
You can also use the Command Line: Developing in the Command Line | Intel® Developer Zone
What software does the Quark D2000 support? The most complete answer is any software that can run on the x86 architecture of Quark D2000, but the ISSM tool for this kit has a GCC compiler for C/C++ only. GCC, which stands for the GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go. But ISSM has only the C/C++ version at this point. It’s entirely possible that another GCC could be bolted in some day, or that other tools for this architecture exist or will be created, but that is beyond the scope here.