The /webapps/ folder in ${jetty.home} is just remnant kept for backwards compatibility.
It really has no place anymore, as you shouldn't be running, editing, or changing anything in ${jetty.home} anymore.
In a proper setup and configuration, you unpack jetty-distribution, and treat that entire directory as read-only.
Then you create your own directory somewhere, anywhere outside of the jetty-distribution (ideally), and that becomes your ${jetty.base}.
In your ${jetty.base} you configure your environment for running your own web applications.
Everything from the startup of Jetty itself, the connectors, ssl/tls, do extra libraries, and even your war files.
This is all done via the ${jetty.base}/start.ini - its declared modules and configured properties.
By default, the use of the 'deploy' module will create the ${jetty.base}/webapps/ if it doesn't exist.
You can configure a different directory, like you have, with jetty.deploy.monitoredDir, but its probably easier to just setup a ${jetty.base} in your alternate directory tree instead.
