There's "Tomcat in Eclipse" and then there's "TOMCAT in Eclipse". If you are like most people, you're using the WTP plugin that comes bundled with the
J2EE spin of Eclipse to run Tomcat.
One of the things I hate about WTP is that it doesn't simply use your Tomcat's config files, it makes copies of some (but NOT all of them!

) and puts them in an Eclipse workspace directory. When you change the master Tomcat configuration, you frequently have to whack WTP upside the head to get its attention; WTP won't automatically sense and apply those changes to its copy.
Which is why I use the sysdeo Tomcat plugin, myself. It doesn't play those games.