Documentation for JIRA 4.2. Documentation for other versions of JIRA is available too. 
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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.