Write basic user guide.

A basic user guide showing how and why the end user should use this program.

There is already a start in the man file, but even that is half written.

What we want is:

• A README.md in the repo, introducing the program, gives basic examples, and provides installation instruction. It should link to the usage documentation, and the API documentation.
• The usage documentation, which can be the man page. It should also include good example uses, but also all command line flags.
• The API documentation, which should primarily be generated from the Python code.