I am using Eclipse for Java web development. I have WTP and Tomcat installed. I run Tomcat via Eclipse (which is a pretty standard configuration).
What I want to unders
Clean: Purges all webapps and redeploys them (don't do this while the Tomcat instance is running)
Clean working dir: Cleans out Tomcat's work dir, e.g., where compiled JSPs go. See here.