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.
Recently in Server Hardware/OS Category
Upgraded the underlying SWI-Prolog to the most recent stable release, 5.2.10. Checked speeds and generation seems the same, but parsing a tiny bit slower, not enough to worry, change has been made permanent.
Finally got the new hard drive in the server and got everything back online.