Fix user guide to reflect new version

[dwysocki]

This is a generalization of #65. We have a number of changes since v0.2.5, which need to be reflected in the documentation. This should really be a requirement of any new release.

Here I'll list new/changed behavior that needs to be documented still. Feel free to update this as more changes arise, or are completed.

• The replacement of --periods FILE with --parameters FILE, and its behavior
• The multiple new output types, and how to use them.
• The changes to the output table