### Bug description

Hi

I am writing a large document using quarto book.
When organizing my files in folders. Quarto is no longer able to solve cross-references.
Not sure if I am doing something wrong or if it is a bug.

I put a sample here: https://github.com/andlekbra/minimal-sample-quarto-cross-ref-issue

I am using VS code on windows:

```
Version: 1.77.3 (user setup)
Commit: 704ed70d4fd1c6bd6342c436f1ede30d1cff4710
Date: 2023-04-12T09:16:02.548Z
Electron: 19.1.11
Chromium: 102.0.5005.196
Node.js: 16.14.2
V8: 10.2.154.26-electron.0
OS: Windows_NT x64 10.0.19044
Sandboxed: Yes
```

Result from `quarto check`

```
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.3.299
      Path: C:\Users\ALB\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
      Version: 3.11.2
      Path: C:/Users/ALB/AppData/Local/Programs/Python/Python311/python.exe
      Jupyter: 5.3.0
      Kernels: python3

(-) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[>] Checking Jupyter engine render....OK

[>] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/
```


### 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.
- [ ] 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.
- [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.
dragonstyle
2023-04-25T06:20:35Z
andlekbra
v1.4
closed
Not resolving cross reference to subfolder
https://github.com/quarto-dev/quarto-cli/issues/5298