En route for v2.2.0-rc4

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Polish the entry points.

Allow to specify the target file in the run method arguments.
Message the user if the file or an image cannot be found.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>