echo and output options not working in manuscript companion notebooks

Hi there,

Very excited about the new manuscript project type. I think I may have encountered a bug, however. I have a companion.qmd file with R code sitting alongside index.qmd. When I render the project with knitr and view index.html, the companion notebook is automatically displayed in the "Notebooks" section of the sidebar of my rendered index.md. So far, so good.

The problem is that output: false not echo: false in companion.qmd don't appear to be working, either in the YAML header or within individual code blocks. I set them to false and both the code and the code output still appear in the rendered companion.html file. (Note that this file has a blue bar at the top that says "Back to Article", it isn't rendered separately.)

output and false options work just fine in the index.md article, however. I'm using quarto version 1.4.549, using the VSCode extension (though I doubt that matters).

Apologies is if this is posted in the wrong repo! Would love any help I can get.

Start by rendering the reported companion.qmd alongside index.qmd with knitr and compare how YAML and code-block options are handled in the generated companion.html versus index.html. The fix is complete when echo: false and output: false work in the companion notebook, both in its YAML header and individual code blocks.