Many of the link texts don't make it obvious what you're going to get before you click on it.
In terms of content, I'd actually switch "project" and "pantograph". I think you can just rename them
Go through each link and ask if it's clear what on the other side from the text - reword and clarify
maybe parens like "Specification (gdoc)" would help
remove redundant links with different text on the same page. i.e. multiple pointers to graph-genome/Projects/ that makes it look like different pages will be there.
Many of the link texts don't make it obvious what you're going to get before you click on it.