I'm afraid it's up to you to clean out the Tomcat work directory.
The Tomcat work directory, incidentally, is the same directory that webapps will be pointed at when they do a java.io.File get temp directory method call. I think you can therefore override it on the
java command line, but there should be a variable you can set in the catalina script.
Oh never mind. I'm not
that lazy today. It's CATALINA_TMPDIR, and its default value is CATALINA_BASE/temp.
You can add a CATALINA_BASE/bin/setenv script (.bat or .sh, depending on OS) and make the assignment there if it's convenient.