I've not used CLion but have no doubt it will work if ...
You can tell it the name and location of the cross compiler.
You can tell it where to find the WPI library to link against.
You can tell it where to find the WPI headers to compile against.
CMake is just another rules engine. Teach it how to generate a .o file from a .c file, a .out file from a C++ file and an ELF executable file with the linker. It should work.
CLion supports gcc and gdb. Check this out ...
https://youtrack.jetbrains.com/issue/CPP-871
https://dev.widemeadows.de/2015/02/1...ap-on-windows/