There are 2 (or more) ways to run Tomcat from Eclipse. Plus a third option where you run Tomcat separately but have Eclipse talk to it.
Fundamentally, they're all the same thing, just differences in the way that Tomcat gets started.
The most common way to run Tomcat is to install the Eclipse
J2EE spin and use its server controller. This is actually a very horrible thing to do.
Why? Because the built-in Tomcat plugin (WTP) doesn't run a clean Tomcat. Instead it selectively clones only some of the config files, leaving others behind. This causes 2 problems. First, for just about anyone, getting the run configuration to match what you
think the run configuration is is not trivial. Not everything syncs up automatically. The second problem has to to with the incomplete cloning of the Tomcat config. Some of us - like me - require customizations to the files that get left behind.
Which leads to the second way to run Tomcat. Get the mongrel plugin developed by sysdeo and install it. Mongrel will co-exist happily with the built-in Tomcat plugin. In fact, they totally ignore each other, so it's simply a matter of which menu/toolbar options you use to launch Tomcat. Unlike the WTP plugin, Mongrel uses the original installed Tomcat configuration without cloning or modification. Much cleaner.
The third option is to go Tim Moores' route. Launch Tomcat stand-alone with the remote debug options switched on and have Tomcat connect to it. Actually, all 3 options do remote debug connections - it's merely a matter of who starts what and how. Note that also you can do a stand-alone launch of Tomcat on any server, not just the local host. Doing that from within Eclipse is a bit trickier.
Oh. And by the way. Neither mongrel nor stand-alone Tomcat should be copying the catalina policy file, so they shouldn't have your problem.
Most of the time, I use mongrel. It has the advantage that I can stop and restart Tomcat from Eclipse and the catalina.out log gets directed to an Eclipse console window so there's no annoying flipping back and forth in and out of Eclipse to get things going. However, stand-alone Tomcat is the ultimate proof. When the apps go into production, no sane IT shop is going to have a development IDE controlling them. It's going to be Tomcat all the way.
I'm going to try and mirror this
thread into the Tomcat forum, since it's Tomcat-specific and probably of general interest to anyone using Tomcat.