Add gfm_auto_identifiers to reader for correct ids in TOC link

[cderv]

due to current limitation of Pandoc jgm/pandoc#8709

closes #4917

I used the tweak in resolveFormat() as we do it elsewhere, but we also do some tweaks like that in formatExtras() (see revealsj format) but it seemed to late to check pandoc[kToc]

This could be improved by making pandocFormat() not add an extension if already there.

cc @dragonstyle

For 1.3 or 1.4 - I just wanted to deal with it now. 😅

[cderv]

I rebased onto main which includes #4937 but the issue still remains 🤔

[cderv]

@cscheid your fix in #4957 for circular dependency solved the issue in the PR with bundling. Thanks !