Update pandoc docker image from 3.2 to 3.6.3

[cthoyt]

This PR does the following:

• Updates the dockerfile from 3.2 (2024-05-11) to 3.6.3 (2025-02-10)
• Updates the LaTeX outputs with minor changes due to pandoc version bump, see explanation below
• Debug issues in the example paper build workflow
• [ ]

The new version of pandoc causes the following minor changes in latex output:

1. Tables - tables are now sized with \linewidth instead of \columnwidth. This affects the tables captioned Basic inline markup and examples and Comparison of programming languages used in the publishing tool

2. Inline Images - the width of the nyan-cat image and sylt images are now determined by the \linewidth instead of \textwidth. Inline images now get the keepaspectratio flag

3. Free-standing Images - the mandrill image is now wrapped with\pandocbounded{}. Free-standing images now get the keepaspectratio flag.

   This command was introduced in Pandoc in jgm/pandoc@26b25a4 and lives in https://github.com/jgm/pandoc/blob/786356ace43d622866041f021b09452441ced009/data/templates/common.latex#L99-L108 in Pandoc 3.6.3. This requires adding the corresponding command to Inara's latex template

Blockers

It appears that two pre-existing issues that were suppressed by pandoc 3.2 are now causing failures for pandoc 3.6 (or at least, obscuring other errors that are happening with 3.6), so it would be nice to address these first in isolation:

• Issue with reference to fermat equation in example.md #104
• Issue with reference to programming languages table in example.md #102 / Fix table reference in example.md #103

[cthoyt]

@xuanxu do you think you could take a look at this? It's strange that the compilation the test job works but the example PDF workflow does not

[cthoyt]

I think the issue is that latex needs to run twice, and it is erroring the first time when it hasn't taken a pass that it makes the citations https://github.com/openjournals/inara/actions/runs/13244251628/job/36966750145?pr=100#step:4:5417