This is a somewhat involved question. It's a little hard to know which parts you don't know but here's the general outline.
You'll need to build the library. I assume this actually means you'll need to build the whole project. The "INSTALL" document lays out how to build:
https://github.com/v2k/poker-eval/blob/master/INSTALL
I haven't downloaded/installed it but it looks like it will build the C library and then also give you a jar file (or more than one jar file) containing a JNI wrapper for the C library. So the jar flle + the C library file will give you the ability to run the hand simulations from Java.
Presumably you know how to include jar files into your java project