Multiple fixes to the cli.md document.

*. Fixed headings so the side menu will now be consistent. Some sections
had H3s that were displaying and others did not leaving the left menu
very mismatched.

* Fixed several spelling errors.

* Re-formatted several long lines and badly laid out paragraphs.

* Fixed several double backticks.

* Added backticks to several outputs and variables.

* Removed two issues that are no longer valid.

* Removed several double spaces and extra lines.

Docker-DCO-1.1-Signed-off-by: James Turnbull <james@lovedthanlost.net> (github: jamtur01)