You have separate directories.
One for ${jetty.home} (sometimes referred to as $JETTY_HOME) - this is your unpacked `jetty-home` archive/tarball (or the older `jetty-distribution` archive/tarball) - leave this directory alone, don't edit it, don't change it, don't add things, don't delete things. Generally speaking treat this directory as read-only.
Then you have the ${jetty.base} directory, this is your specific instance configuration.
The ${jetty.base} directory is not the same directory as ${jetty.home}.
The ${jetty.base} directory is not contained within the ${jetty.home} directory.
The ${jetty.base} directory does not contain the ${jetty.home} directory.
But a general/quick example (in shell speak) is ...
$ mkdir /path/to/myjettybase
$ cd /path/to/myjettybase
# Configure it
$ java -jar /path/to/jetty-home/start.jar --add-to-start=http,deploy,annotations
$ cp /tmp/myapp.war /path/to/myjettybase/webapps/
# Show what the configuration looks like
$ cd /path/to/myjettybase
$ java -jar /path/to/jetty-home/start.jar --list-config
# Start Jetty
$ cd /path/to/myjettybase
$ java -jar /path/to/jetty-home/start.jar
