Deprecate --file option

[speleo3]

The -f FILENAMES option is redundant with the input_pdb option, except that the former is optional and allows multiple files, and the latter is mandatory and only allows a single file.

I suggest to deprecate the -f and --file arguments and turn input_pdb into an nargs='+' option.

There is one more difference: input_pdb is only added if build_parser creates a new parser, but not if it creates a subparser. The --file option is always added. I don't know if this is relevant.