There appears to be a bug in the way the programming languages table is referenced in the example paper on the following lines:

using the label="proglangs" syntax appears to not generate a reference that is compatible with either the \ref{} nor \autoref{} commands used in

This is confirmed in the latest build log from the 1.1.5 release of Inara at https://github.com/openjournals/inara/actions/runs/12199377342/job/34033120544#step:4:5419. Despite this, it still builds the draft and production PDFs. The draft PDF is downloadable from https://github.com/openjournals/inara/actions/runs/12199377342 as it renders like:

Potential Solution

I think the correct syntax in the markdown file would be:

: Comparison of programming languages used in the publishing tool. 
   []{#proglangs}

This matches the syntax for assigning references to images, such as in

Trying the Solution

I haven't been able to test this locally since I'm on macOS and there's no usable docker builds from pandoc 3.2, which is the one used in Inara currently.

I opened a PR that triggered this workflow, but it created several other unrelated issues.