Mupdf documentation shows me how to use the library as an application and deploy it. However, I want to suck it into an existing java project and build my application on top of it. Can this be done? If so, how do I bring just the pieces needed, into my project?
Take a look at jMuPdf. I never used it, but it seems to be active.
Otherwise you will need to create Java Native Bindings (JNA or JNI).