taking 10m to help with triage, confirming this with MWE

: Comparison of programming languages. []{label="proglangs"}

| Language | Typing          | Garbage Collected | Evaluation | Created |
|----------|:---------------:|:-----------------:|------------|---------|
| Haskell  | static, strong  | yes               | non-strict | 1990    |
| Lua      | dynamic, strong | yes               | strict     | 1993    |
| C        | static, weak    | no                | strict     | 1972    |


autoref: \autoref{proglangs}
ref: \ref{proglangs}

and building PDF with the docker command

yields

but the latex version works

: Comparison of programming languages. \label{proglangs}

| Language | Typing          | Garbage Collected | Evaluation | Created |
|----------|:---------------:|:-----------------:|------------|---------|
| Haskell  | static, strong  | yes               | non-strict | 1990    |
| Lua      | dynamic, strong | yes               | strict     | 1993    |
| C        | static, weak    | no                | strict     | 1972    |


autoref: \autoref{proglangs}
ref: \ref{proglangs}

the intermediate LaTeX for the caption in the first case is

\caption{Comparison of programming languages. {}}\tabularnewline

and for the second case is

\caption{Comparison of programming languages.
\label{proglangs}}\tabularnewline

so i don't know exactly when the markdown gets latex'd but ya something not working.

I thought that it might have been that we didn't have bracketed_spans enabled, but if i instead just put in an HTML span like <span label="proglangs"></span> that also doesn't work.

If i look at the JATS output, the references are at least correctly created by autoref and ref commands, though proglangs is not added as the table's id property, which is what i see the latex style figure label doing.

  <p>autoref: <xref alt="Table 1" rid="proglangs">Table 1</xref> ref:
  <xref alt="1" rid="proglangs">1</xref></p>

so i think the problem maybe, might be that the lua code for handling references bails if the format is latex? but it also seems like the markdown span isn't being converted into the latex command in the initial pandoc translation stage before the lua filters are applied.
https://github.com/openjournals/inara/blob/b259a53005804d260208e8a30c9a09347169ea83/data/filters/resolve-references.lua#L2-L4

with the big caveat that i don't know how to read lua ;)