Hi! Foam author here. We generate markdown references to bridge [[wiki-link]]s to work with Markdown tools. For the time being this is optimised for a) the editing experience in VS Code and b) the GitHub pages publishing pipeline, so it's more convenient to generate markdown links without the `.md` suffix.
I think the problem is that you're including these links in the README. New visitors expect all the links there to work, but they are broken.
If the README only included basic information and a link to the github pages, it would be easier to follow.
P.S. since I'm already typing, have you considered supporting semantic links, in addition to the regular ones? It will make the relationships between the pages clearer at a glance, and allow for better automation in the future. It might also help in visualization, for example you could toggle only specific relationships, to get a simpler graph of the information you care about.