Allow 'jvl' files to be processed via the jalview commandline tool

From a user's perspective there's little difference between downloading and opening a JVL file with the Jalview application and opening the same downloaded JVL file with the Jalview command line tool.

It would be great if we could have Jalview work out that it has been asked to *open* a JVL file and process the jalview.apparg it contains (within reason) - in the same way as if the file had been passed to it via the OS-specific mechanism for opening applications (ie 'open' on OSX, etc).