I've tried to resolve this manually by extracting this piece with a Lua filter, converting it into a new document and running Pandoc plus Citeproc on this temporary document with `pandoc.utils.run_json_filter`, retrieving the processed citation and putting it back as codeblock caption in the original document. However, this approach seems not to be working.
To narrow this down further, I wrote a short document (`test.md`, see attachment) and a Lua filter (`codecite.lua`, see attachment). (To make it even shorter, in the Lua filter I simply replace the text block of the document with a similar new block).
But this does not seem to work. The call `pandoc -L codecite.lua test.md -t json` returns only
```json
{"pandoc-api-version":[1,22],"meta":{"references":{"t":"MetaList","c":[{"t":"MetaMap","c":{"author":{"t":"MetaList","c":[{"t":"MetaMap","c":{"family":{"t":"MetaInlines","c":[{"t":"Str","c":"Wuppie"}]}}}]},"id":{"t":"MetaInlines","c":[{"t":"Str","c":"FOO"}]},"title":{"t":"MetaInlines","c":[{"t":"Str","c":"Lorem"},{"t":"Space"},{"t":"Str","c":"Ipsum"}]}}}]}},"blocks":[{"t":"Para","c":[{"t":"Str","c":"see [@FOO]"}]}]}
```
i.e. the citation is not resolved.
However, if I run Pandoc directly on this document, i.e `pandoc -t json --citeproc test.md`, the result is as expected:
```json
{"pandoc-api-version":[1,22],"meta":{"references":{"t":"MetaList","c":[{"t":"MetaMap","c":{"author":{"t":"MetaList","c":[{"t":"MetaMap","c":{"family":{"t":"MetaInlines","c":[{"t":"Str","c":"Wuppie"}]}}}]},"id":{"t":"MetaInlines","c":[{"t":"Str","c":"FOO"}]},"title":{"t":"MetaInlines","c":[{"t":"Str","c":"Lorem"},{"t":"Space"},{"t":"Str","c":"Ipsum"}]}}}]}},"blocks":[{"t":"Para","c":[{"t":"Str","c":"see"},{"t":"Space"},{"t":"Cite","c":[[{"citationId":"FOO","citationPrefix":[],"citationSuffix":[],"citationMode":{"t":"NormalCitation"},"citationNoteNum":1,"citationHash":0}],[{"t":"Str","c":"(Wuppie,"},{"t":"Space"},{"t":"Str","c":"n.d.)"}]]}]},{"t":"Div","c":[["refs",["references","csl-bib-body","hanging-indent"],[]],[{"t":"Div","c":[["ref-FOO",["csl-entry"],[]],[{"t":"Para","c":[{"t":"Str","c":"Wuppie."},{"t":"Space"},{"t":"Str","c":"n.d."},{"t":"Space"},{"t":"Span","c":[["",[],[]],[{"t":"Str","c":"“"},{"t":"Str","c":"Lorem"},{"t":"Space"},{"t":"Str","c":"Ipsum"},{"t":"Str","c":"."},{"t":"Str","c":"”"}]]}]}]]}]]}]}
```
Clearly I'm missing something here. But what is it? Can you please advise?