Render only local docs

To avoid duplicating functionality in Toolhub, this change removes the links to user docs and focuses on the tools that use markdown files in a repository. I've tried for a grid with three columns on wide screens, reducing to two and then one on smaller screens. Here are some screenshots with all 500 tools to give you an idea of how it looks with more content:

This also removes the tool counter since there are significantly fewer docs. It also adds a small change to the contributing instructions since I keep forgetting to run composer update