Fix Markdown code blocks in documentation.

[jonathancrabtree]

The Markdown code blocks in the documentation need fixing, specifically something needs to be done about the fact that many of the code lines run off the right hand side of the screen and the code block formatting (i.e. the grey background rectangle) doesn't expand to contain all of the text. One solution might be to modify the Circleator config file parser to allow explicit line breaks like the backslash character accepted by the shell to continue a command on a new line.

[jonathancrabtree]

For example, search for "Attempt to color-code hypothetical genes based on their length" on the following page:

http://jonathancrabtree.github.io/Circleator/configuration.html

The grey rectangle expands only to the width of the browser window.