Tomcat Server creating Directories in tmp
Unfortunately, both embedded and non-embedded Tomcat needs to have a directory to store temporary files. This is not configurable, however, you can specify the directory in which Tomcat stores these temporary files using setBaseDir.
This should be the first method called public void setBaseDir(String basedir) and if it is not specified in your code it will look for it in
system properties - catalina.base, catalina.home - $HOME/tomcat.$PORT
By knowing the location I recommend writing a simple scheduled script that checks every so often and removes the files under that directory.