I didn't look into the details of the project, but to me it seems to like the following:
A JIT compiler is used in a virtual machine to run a function/method by compiling it from some sort of bytecode or intermediate representation to native code and then jumping to the generated code to execute it. So in this case this would be when the Common Language Runtime wants to run a CIL method for the first time: it generates LLVM intermediate representation from the CIL, then uses LLVM to compile that to native code.
So it would be: CIL --> LLVM data --> native code
This means that the CLR, and thus all code compiled for