Improvements to documentation

[ramonawalls]

Brian, the documentation is very clear and thorough (at least for the parts documented!).

Here are a few suggestions based on reading of the current documentation. You may have thought of these already, but I included whatever I noticed, just in case.

-On the introductory page (Readme) mention that the default configurations are set to work well with OBO Foundry ontologies. This currently includes creating a BFO import file - you may want to remove that from the default config.

• On the installation page, provide instructions on how to update ontopilot (e.g. do a git pull if there has been an update).
• Add previous/next links a the bottom of each page.

Having the command line reference page is great!