Documentation for JIRA 5.0. Documentation for other versions of JIRA is available too.

To move the temp directory, edit <JIRA>/bin/catalina.sh:

if [ -z "$CATALINA_TMPDIR" ] ; then
  # Define the java.io.tmpdir to use for Catalina
  CATALINA_TMPDIR="$CATALINA_BASE"/temp
fi

Replace the "$CATALINA_BASE"/temp with your temporary file directory.