I have a Tomcat 7 running in Linux that I start via $CATALINA_HOME/bin/startup.sh and shutdown via $CATALINA_HOME/bin/shutdown.sh
Tomcat 7
$CATALINA_HOME/bin/startup.sh
$CATALINA_HOME/bin/shutdown.sh
In my case I had one rogue JPA EntityManager that wasn't being properly closed after use. Fixed that, and now I can Clean-and-Build again without killing the damn Java process everytime :)