File in subdirectory not found

Bug description

I recently updated to quarto version 1.5.57 from 1.5.35. After updating, quarto inspect is no longer able to find a document file in a subdirectory. Ironically, quarto render works fine. I could bisect that this problem appeard between v1.5.51 and v1.5.57. I assume this commit is the culprit.

Please see this MR as a reference where the issue appeared first.

Steps to reproduce

Create these files:

Main file:

---
title: main
format:
  html:
    default
---

{{< include "subdir/text2.qmd" >}}

Text 2 (in ./subdir/):

# Second File

Some text here.

{{< include "subdir/b/text3.qmd" >}}

Text 3 (in ./subdir/b/):

# Third File

Some text here.

Now, run quarto inspect.

Expected behavior

quarto inspect outputs the desired information.

Actual behavior

quarto inspect fails with the following message:

ERROR: NotFound: No such file or directory (os error 2): readfile '/home/***/tmp/tarche-test/subdir/subdir/b/text3.qmd'
Path: /home/***/tmp/tarche-test/subdir/subdir/b/text3.qmd

Stack trace:
Path: /home/***/tmp/tarche-test/subdir/subdir/b/text3.qmd
    at readTextFileSync (ext:deno_fs/30_fs.js:859:10)
    at Object.Deno.readTextFileSync (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:5047:25)
    at mappedStringFromFile (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:19592:24)
    at Object.markdownForFile (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:40863:32)
    at mdForFile (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:40283:29)
    at inner (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:40322:67)
    at inner (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:40322:23)
    at async projectResolveCodeCellsForFile (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:40342:5)
    at async inspectConfig (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:101478:13)
    at async Command.actionHandler (file:///tmp/.mount_quartodxyAMD/usr/bin/quarto.js:101515:20)

quarto render runs fine. Even after removing the subdir in the include of text3.qmd, the command fails.

Your environment

• OS: Linux

Quarto check output

Quarto 1.5.57
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.57
      Path: /tmp/.mount_quartoWCrNeu/usr/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /usr/bin
      Version: 2023

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.7
      Path: /usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.4.1
      Path: /usr/lib64/R
      LibPaths:
        - /home/***/.local/share/R/R.library
        - /usr/lib64/R/library
        - /usr/share/R/library
      knitr: 1.48
      rmarkdown: 2.26

[✓] Checking Knitr engine render......OK