Add user documentation

[glesica]

It would be nice to add some documentation around how to actually use the tool. Presumably most of the users will be familiar with the major concepts, but it might be good to provide a very lightweight intro there as well for those who are less familiar (e.g. students). Additionally, documenting the command line flags should be table stakes here.

• Usage instructions
• Explanation of command line options / flags
• Description of the algorithm (very basic) with a link to more information
• Example usages using the example input files

Note that there is some existing documentation in the README file (in the NINJA subdirectory) but it appears to be somewhat outdated.

Put a separate README in the examples directory that explains what they are and how to run them and what the output should look like (in general terms)