#70: update doc

[ccarouge]

The changes to the documentation include:

• change options descriptions
• use of sub-commands instead of command line options.
• add expected stdout
• modify some formatting in the user guide
• move the default science configurations to their own page to improve visibility

The documentation still needs some documentation to use me.org but it is better to move that to its own ticket I think.

[SeanBryan51]

I've added a few minor suggestions which might be a bit cosmetic (feel free to ignore some suggestions).

I think we should have options in the configuration file as subsubsubheadings (with three subs), for example for science_configurations we replace

+### `science_configurations`
-`science_configurations`

And to reference the section:

This is [a link to `science_configurations`](#`science_configurations`)

Lastly, can we have permalinks for headings? This can enabled by adding the following to mkdocs.yml:

markdown_extensions:
    - toc:
        permalink: True