Allow site-specific configuration to change command line defaults

This can be very useful, e.g. if a site wants to specify local repository mirrors or so.
E.g.:
```
        parser.set_defaults(casim="/local/casim/mirror", jules="/local/jules/mirror")
```
While this can already be done using the `handle_command_line_options` callback, this is too late to update the help message with the new default values.
