I am running Ubuntu 16.04 and want to use Eclipse Oxygen with a large Tomcat application. Should I just use the standard Tomcat that came with the Ubuntu distro? I have seen a lot of posts about changing file permissions and it seems pretty messy.
It is much simpler to get Eclipse working with Tomcat on Ubuntu 16.04 (and earlier releases) by simply downloading the compressed Tomcat tar file and installing it in a local directory (ie. your home directory).
This avoids the file permission and soft link problems that occur on the Ubuntu Tomcat distro since the files are not all under the CATALINA_HOME directory (such as /etc/tomcat8 and /var/log/tomcat8). I run multiple versions of Tomcat servers for Eclipse testing purposes while still leaving the distro server installed. They can be run in parallel by changing the ports they run on, or one at a time if you want to leave them all on the standard 8080 port. Just be sure to stop the distro Tomcat when running Eclipse so it can start the servers it is using on 8080.