Include classpath entries in the resulting jar

A CLI application can load resources from the classpath. By default,
the classpath is "." but it can be set using the --classpath option. To
allow the application to run from the self-contained jar file, the
contents of the classpath need to be included in the jar. Rather than
including everything on the classpath in the jar, default includes
(public/**, static/**, resources/**, META-INF/**, *) and excludes
(.*, repository/**, build/**, target/**) are used for filtering. The
user can override these using the --includes and --excludes options.
Use JarWriter to create the CLI app's jar