A Quarto Question (or Six)

I am converting the notes for “Managing Research Software Projects” from McCole to Quarto. Most of the changes have gone smoothly, but I’m stuck on a few things and would appreciate guidance. For reference, the materials are in this repository and you can view the rendered version here. The landing page shows the contents of index.qmd (which is good) but that page shows up as entry #1 in the table of contents (which is bad). I have tried using a # Title heading in index.qmd instead of a title field in the YAML frontmatter, and/or adding.unnumbered, .toc-ignore, and other classes to that H1 heading, but those don’t achieve what I want. Each page that has bibliographic citations lists references at the bottom of that page (see for example the Project Health page). I don’t want this: I want all citations to link to the appropriate entry in the bibliography page (e.g., this page in the example project). Each chapter in the tutorial is in a subdirectory of the root, e.g., ./intro/index.qmd…