These are the relevant instructions for building the library from the Interfaces Guide:
7.6.3 Creating the Native Library On Linux
Launch the Terminal application (as described in section 7.2). Set the directory to the CLIPSJNI/ library-src directory (using the cd command).
To create a native library, enter the following command (where <distribution> is either ubuntu, fedora, debian, mint, or centos):make -f makefile.lnx <distribution>
Once you have create the shared library, copy the libCLIPSJNI.so file from the CLIPSJNI/library-src to the top-level CLIPSJNI directory.
So you need to be in the CLIPSJNI/library-src directory to build libCLIPSJNI.so, not in CLIPSJNI. Issuing the make command in CLIPSJNI will build the jar files.