Hi,
I added a section in the existing software page which I called "Bootstrapping the Java Software".
https://confluence.slac.stanford.edu/display/hpsg/Installing+HPS+Software#InstallingHPSSoftware-BootstraptheJavaSoftware
It covers installing lcsim and hps-java, as well as JAS.
This is based on some emails to hps-software that covered how to "reset" the Java environment or build from scratch.
--Jeremy
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