### Bug description

I was using quarto with a filter for pandoc, it was working great but it is not working anymore.
I am working on a custom filter developed with [panflute](https://github.com/sergiocorreia/panflute) to render plantuml diagram in image. A library used to develop pandoc filter with python.
A similar filter can be found [here](https://github.com/timofurrer/pandoc-plantuml-filter). I was trying to improve it.
I got the same error with this filter too.

I was using it with the `filters` parameter like this in a `index.qmd` file:
```yaml
    ---
    execute:
      echo: false
    pagination_next: null
    filters:
      - custom-filter
    editor:
      render-on-save: true
    ---
    
    # Welcome for fun
    
    ```plantuml
    @startuml
    actor "User" as user
    @enduml
    ```
```
_This file is in a quarto project to render it in a docusaurus website._


The code block was rendered into image by my custom filter. I assume the filter was passed to pandoc directly because the filter is working great with `--filter` of pandoc cli.

Now I got the following error:
```console
> quarto preview /home/user/project/template_docs/docs/index.qmd --no-browser --no-watch-inputs
pandoc 
  to: >-
    markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars+pipe_tables+tex_math_dollars+header_attributes+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links
  output-file: index.md
  standalone: true
  default-image-extension: png
  wrap: none
  html-math-method: webtex
  
metadata
  pagination_next: null
  editor:
    render-on-save: true
  
Error running filter /opt/quarto/share/filters/main.lua:
Error running filter /home/user/project/template_docs/docs/custom-filter:
Could not find executable /home/user/project/template_docs/docs/custom-filter
stack traceback:
        /opt/quarto/share/filters/main.lua:4026: in function </opt/quarto/share/filters/main.lua:4005>
        [C]: in ?
        [C]: in method 'walk'
        /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter'
        /opt/quarto/share/filters/main.lua:449: in local 'callback'
        /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain'
        /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476>
stack traceback:
        /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter'
        /opt/quarto/share/filters/main.lua:449: in local 'callback'
        /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain'
        /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476>
```


Operating system : WSL on Ubuntu 20.04.6 
Quarto check:
```
> 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: 1.3.340
      Path: /opt/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.11.3
      Path: /home/user/.pyenv/versions/3.11.3/bin/python3
      Jupyter: (None)

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

[✓] 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.
cscheid
2023-05-03T09:45:44Z
FabienSe
bug triaged-to
v1.5
open
Pandoc filters are not working anymore with quarto
https://github.com/quarto-dev/quarto-cli/issues/5392