Migrate to pandoc-crossref and add short captions filters for figures and tables

[prakaa]

This PR:

1. Migrates cross-referencing to pandoc-crossref
2. Adds Lua filters that enable short captions for figures and tables (i.e. shorter captions for use in TeX/PDF List of Figures/Tables)
3. Updates source/*.md files to match pandoc-crossref + short-caption syntax
4. Provides examples of pandoc-crossref customisation in source/metadata.yaml]
5. Updates README to reflect changes above (plus some other opinionated changes, happy for those to be changed)

Provisos:

1. The table-short-captions filter must be listed as a flag (i.e. run) before pandoc-crossref
2. pandoc-crossref uses the --include-in-header option. That is, specifying this overwrites definitions created by pandoc-crossref. To navigate this, the definitions have been manually added into style/preamble.tex.

• Changing xnos flags to crossref in Makefile
• Adding working figure-short-captions and table-short-captions Lua filters, and calling these in Makefile
• Changing referencing in the sample text to conform with crossref style
• Updating README
  • Require pandoc 3.1+

closes #53, closes #68, closes #91, closes #107, closes #116, closes #117

[prakaa]

I think I have changed all the relevant files, but have not changed the fabfile @tompollard

[tompollard]

I appreciate you doing this @prakaa, many thanks!