I am running a multi level maven project. It has webapps packaged as WAR, which depend on components packaged as JAR files
Most of the code changes that i do belong
I use the eclipse webtools plugin, and run my Tomcat from it. It has a republish method that publishes the jars as well (if not, you just clean the directory and republish).
In the pom file, you should have the following lines so that the webtools will be supported automatically
...
maven-eclipse-plugin
1.5
...
...
...