Java for most startups won't be Java EE. My best experience with Java recently has been with Jetty as an application server. It's fast and it's lightweight.
I usually run Jetty behind nginx and don't generally need to configure Jetty to do anything.
The whole Tomcat and connectors for apache configuration from a few years ago is well and truly behind me.
I think one major difference/hurdle of java web development and deployment is the fact that you HAVE to setup something like nginx in front of the app server or else you're working on port 8080 for everything. Or you have to know how to configure the app server for port 80 directly and mitigate the security concerns of doing so. By comparison, apache defaults to port 80, no tricks required.
Apache forks a child process with lower rights than root. App servers that run on port 80 do not without a native JNI lancher. The solution is native launcher, a router rule or iptables.
I think the parent is talking about living in a chmod 777 world. Or maybe he is tired of crazy symlink hacks so that sftp becomes an option. Some appservers put class cache in WEB-INF by default, etc.
See my post below: a non-priv'd user can't start the java app server on a port sub-1024 unless you mess with the OS to allow it. I just double checked with my jetty install and I got a "java.net.SocketException: Permission denied".
Actually it isn't trivial for java webservers. Only root processes are allowed to use a port <=1024 by default, so you can't just change a config line in tomcat/jboss/jetty and have it work automatically. You would have to then start/run the app as root, which is a Bad Idea, or mess with getting the OS to allow you to use a lower port. The safest solution then is to have something in front that is allowed on port 80 and setup forwarding to 8080.