.quarto directory should have quarto's version information in it to remove stale crossref index and prevent unexplicit errors

Bug description

Quarto produces an error when attempting to render or preview a document with a thm- cross reference.
Other cross references suggest as rem- and .proof cross references do not cause this error.

Steps to reproduce

Render or preview this Quarto file:

---
title: Theorems don't work here
format:
  html:
    code-fold: true
---

::: {#thm-line}

## Line

The equation of any straight line, called a linear equation, can be written as:

$$
y = mx + b
$$
:::

See @thm-line.

Expected behavior

No error and document renders.

Actual behavior

Quarto produces the indicated error and the document does not render.

Error running filter /opt/quarto/share/filters/main.lua:
/opt/quarto/share/filters/main.lua:12347: attempt to index a nil value (local 'order')
stack traceback:
/opt/quarto/share/filters/main.lua:11793: in function 'captionPrefix'
/opt/quarto/share/filters/main.lua:20686: in field 'render'
/opt/quarto/share/filters/main.lua:835: in local 'filter_fn'
/opt/quarto/share/filters/main.lua:302: in function </opt/quarto/share/filters/main.lua:292>
(...tail calls...)
[C]: in ?
[C]: in method 'walk'
/opt/quarto/share/filters/main.lua:224: in function </opt/quarto/share/filters/main.lua:214>
(...tail calls...)
/opt/quarto/share/filters/main.lua:936: in local 'callback'
/opt/quarto/share/filters/main.lua:951: in upvalue 'run_emulated_filter_chain'
/opt/quarto/share/filters/main.lua:987: in function </opt/quarto/share/filters/main.lua:984>
stack traceback:
/opt/quarto/share/filters/main.lua:224: in function </opt/quarto/share/filters/main.lua:214>
(...tail calls...)
/opt/quarto/share/filters/main.lua:936: in local 'callback'
/opt/quarto/share/filters/main.lua:951: in upvalue 'run_emulated_filter_chain'
/opt/quarto/share/filters/main.lua:987: in function </opt/quarto/share/filters/main.lua:984>

Your environment

• IDE: VS Code V
  Version: 1.86.0
  Commit: 05047486b6df5eb8d44b2ecd70ea3bdf775fd937
  Date: 2024-01-31T10:27:46.147Z
  Electron: 27.2.3
  ElectronBuildId: 26495564
  Chromium: 118.0.5993.159
  Node.js: 18.17.1
  V8: 11.8.172.18-electron.0
  OS: Linux x64 6.6.10-76060610-generic
• Quarto Version: 1.4.529
• OS: Pop!_OS 22.04 LTS
  GNOME Version 42.9
  Windowing System X11

Quarto check output

Quarto 1.4.529
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.69.5: OK
      Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.529
      Path: /opt/quarto/bin

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

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/robert/.TinyTeX/bin/x86_64-linux
      Version: 2023

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

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      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: 4.3.2
      Path: /usr/lib/R
      LibPaths:
        - /home/robert/R/x86_64-pc-linux-gnu-library/4.3
        - /usr/local/lib/R/site-library
        - /usr/lib/R/site-library
        - /usr/lib/R/library
      knitr: 1.44
      rmarkdown: 2.23

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

Reproduce the failure with the Quarto document in the issue, then inspect the project’s .quarto directory and the filter path reported in /opt/quarto/share/filters/main.lua. Determine how stale cross-reference index data is identified and how Quarto version information should be recorded. Done means the example renders without the nil-value error and existing cross-reference behavior remains intact.