If you copy a war file into Tomcat's webapps directory to deploy it (and that is only one of several very different ways to deploy), then by default Tomcat will explode the WAR file into a directory of the same name. Thereafter the WAR file is completely ignored. Including that deleting the WAR file will
not delete the exploded WAR directory. It also won't
update the exploded WAR directory if you replace the old WAR file with a new WAR file.
However, if you delete the WAR directory and
don't delete the WAR file, Tomcat will re-explode the WAR file and create a new exploded WAR directory, so
you should delete the file first and then the directory.