Moving the codebase from RH 7.2, JPL 1.0.1 and SWIPL 5.2.10 to Fedora C3, and SWIPL 5.4.7 broke everything. The code was eventually rewritten, removing the cgi parsing stuff in java, and moving it to some AWK in the shell script. The goal was to use JPL3, but that broke oddly.
