It seems to me like a precausion:
in the server.xml you can define the documentroot
Check server.xml for this entry and make sure it does not point to e.g.
<Context path="/tomcat" docBase="c:/tomcat" />
<Context path="/system" docBase="c:/" />
then you could get access to the system directory by calling
http://localhost/system
and access with
http://localhost/tomcat/conf/tomcat-users.xml the user password file.