### Bug description

I'm not sure if this is an RStudio issue or a Quarto issue (it doesn't happen when using VS Code, so it might be an RStudio thing; but there also might be some setting in Quarto that I'm missing that could fix it).

*(This is all with Quarto 1.3.49 in RStudio 2022.12.0+353 on macOS Ventura 13.1)*

An RStudio Project in a subfolder in a Quarto project inherits the Quarto-ness of the parent directory, so that .Rmd files in the child directory are rendered with Quarto instead of `rmarkdown::render()`. 

As a reproducible example, consider a Quarto project folder structured like this:

```
.
├── _quarto.yml
├── child-project
│   ├── child-project.Rproj
│   └── rmd_document.Rmd
├── index.qmd
└── quarto-parent.Rproj
```

<img width="220" alt="image" src="https://user-images.githubusercontent.com/73663/212736802-4449b763-a712-4cbb-9edc-1a0f16624e1b.png">

**index.qmd**

```markdown
---
title: "Parent project"
---

This is a Quarto file in the overarching project. It gets rendered with Quarto.

```

**child-project/rmd_document.Rmd**

```markdown
---
title: "R Markdown document"
---

This is an R Markdown document. It should get rendered with `rmarkdown::render()`, but sometimes 
it gets rendered with Quarto
```

### Main problem

When the `child-project` folder is placed inside the `quarto-parent` folder, it inherits the fact that it's part of a larger Quarto project and when it is knit, it goes through Quarto instead of `rmarkdown::render()`. 

<img width="629" alt="image" src="https://user-images.githubusercontent.com/73663/212737680-f860317e-2530-46fd-a82f-eda4ceb75142.png">

The "Knit" button in RStudio is replaced with the "Render" button that appears with .qmd files

<img width="405" alt="image" src="https://user-images.githubusercontent.com/73663/212737707-1154603a-f7a0-498a-a5fe-182c353833bd.png">

When the `child-project` folder is placed elsewhere (i.e. if I move it to not be inside a Quarto folder), the document is built with `rmarkdown::render()` as expected…

<img width="630" alt="image" src="https://user-images.githubusercontent.com/73663/212738037-e67332f3-c2f5-4e61-8346-5d888f5cdec9.png">

…and RStudio shows a "Knit" button.

<img width="392" alt="image" src="https://user-images.githubusercontent.com/73663/212737980-ade1e199-f89f-4482-b456-220ba18bb5d5.png">

### Why it's a problem

Often R Markdown files use specific output format options that aren't directly compatible with Quarto. For instance, in [this Quarto project](https://github.com/andrewheiss/evalsp23.classes.andrewheiss.com) I use Quarto to build a website, but the slides for the course are built using {{xaringan}} and are still .Rmd files. Those .Rmd files all live in a [slides subdirectory](https://github.com/andrewheiss/evalsp23.classes.andrewheiss.com/tree/main/slides), and each contains extra metadata in their YAML headers specifying that they should be rendered using {{xaringan}}:

```yaml
output:
  xaringan::moon_reader:
    ...
```

If I open `slides/evalsp23-slides.Rproj` and edit slide files there and then knit the document, Quarto takes over and tries to render the .Rmd file (and can't, since {{xaringan}} isn't one of Quarto's outputs). 

Right now, my workaround is to move that `slides` child directory outside of the main Quarto project folder (like to the Desktop), work on edits and knit documents there (so that R Markdown handles the knitting instead of Quarto), and then move the child directory back into the main Quarto project folder to build the website and upload it. It's a hassle, but it works.

It would be nice if child project directories didn't inherit the Quarto rendering properties of their parent folders so that .Rmd files in those child projects can be build with `rmarkdown::render()` instead of Quarto.

### Checklist

- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
2023-01-16T17:52:22Z
andrewheiss
bug
closed
Projects stored in subfolders inherit the rendering settings from the parent directory
https://github.com/quarto-dev/quarto-cli/issues/3985