Docs/reference removal

[DidierRLopes]

• Remove auto-generated markdown files
• Add these same files to .gitignore

@piiq maybe the generate_markdown files should all be under a folder and we can have a script that goes through all of them called generate_docs_markdown? food for thought.

@tehcoderer even though there's a bot generate_index I believe that it's not currently being used and was just used to "bootstrap" the work of doing it for each command. But please confirm. If so not sure if it's not best to remove that file as it's confusing.

Please test on your side that this works!