Fixes required for 'clone' command

[pjbriggs]

The auto_process.py clone command needs some tweaks and fixes:

• The analysis_dir, primary_data_dir and sample_sheet parameters should be updated to point to the cloned directory
• The "custom" sample sheet should be copied
• It should be possible to specify the analysis version on the command line (and possibly other metadata, as with the setup command)
• Config files could also be copied from each project, if present