Replace configure command's --jar option with properly handling --cp

[ktoso]

We should not be hardcoding some jar loading behaviors. We should be dealing with classpaths.

• Remove the --jar option entirely
• make the command work with --classpath
  • use an URLClassLoader to load classes that we then configure

[madsodgaard]

I removed the --jar in #449 and also added support for loading directory class paths by just iterating the files.