Add ability to read input from file instead of STDIN

Use CommandLineOptions in a similar way to the java MetaTagger, so
that data-did isn’t hard-coded, and at the same time, add in an option
to allow, instead of “input.xml -> output.xml” pairs to stream in via
STDIN, to get them from a file specified in the command line options
(i.e. support for “—input /path/to/file_with_in_and_out_pairs.txt”)