Allow java commands to use per-run temp folder.
Allow java commands to use per-run temp folder.

This is useful (at this point) mainly for the GATK IndelRealigner,
which creates a large number of files when a genome contains many
contigs. If multiple runs are carried out at the same time, extreme
numbers of files may be created in a single folder, causing performance
issues.

MikkelSchubert/paleomix,MikkelSchubert/paleomix,MikkelSchubert/paleomix