Formatting and consistency fixes to CLI and RUN references

* Removed double backticks.
* Reformatted paragraphs.
* Fixed consistent STDOUT/STDIN/STDERR references.
* Fixed several broken URLs.
* Fixed backtick mismatches.

Docker-DCO-1.1-Signed-off-by: James Turnbull <james@lovedthanlost.net> (github: jamtur01)