I’ve just been encountering a very similar issue in Ubuntu while trying to get Eclipse Mars and Tomcat7 integrated because Eclipse was expecting the tomcat configuration files etc to be all in the same location, and with the necessary permissions to be able to change those files.
The following instructions from this blog article helped me in the end:
cd /usr/share/tomcat7
sudo ln -s /var/lib/tomcat7/conf conf
sudo ln -s /var/log/tomcat7 log
sudo ln -s /etc/tomcat7/policy.d/03catalina.policy conf/catalina.policy
sudo chmod -R a+rwx /usr/share/tomcat7/conf