Upgrade to Tomcat 7

- Remove logic in agent that uses a file to decide if an app is started
  (instead, we use Tomcat7's mechanism that doesn't bind to port until the
  app is started).

- Update server.xml such that the bindOnInit attribute is
  set to false (thus making it wait until the app is ready to bind to the port)
  and remove flags that no longer apply to Tomcat7