I recently also ran into this problem and tried to create a minimal project to reproduce the error: [project.zip](https://github.com/quarto-dev/quarto-cli/files/11614422/project.zip)

When rendering the document using `quarto render report/report.qmd -o alternate_name.html` I observed the following: 

- If `self-contained: false` the libs are not recognized by the final document
- If `self-contained: true` the above *could not fetch resource* warning comes up
- It only happens if the `qmd` file is in a subdirectory of the project, top-level documents seem fine

```
$ quarto --version
1.3.353
```

_Originally posted by @p-gw in https://github.com/quarto-dev/quarto-cli/discussions/4041#discussioncomment-6049811_
dragonstyle
2023-05-31T16:49:56Z
cderv
websites triaged-to
open
Rendering a document in subfolder with `-o` flag leads to libs not found
https://github.com/quarto-dev/quarto-cli/issues/5765