Correctly unset citeproc meta if set by user as we use filter

[cderv]

Deactivating citeproc should happen in allDefaults options that will be used for default files

fixes #5585

As mentioned there in #5585 (comment)

The regression was a side effect of this change I made as resolvedFilters() which happens now on a cloned version of options

quarto-cli/src/command/render/defaults.ts

Lines 43 to 53 in 8781ac3

	allDefaults = (options.format.pandoc
	? ld.cloneDeep(options.format.pandoc)
	: {}) as FormatPandoc;
	// resolve filters
	const resolvedFilters = await resolveFilters(
	[
	...(allDefaults[kFilters] || []),
	],
	options,
	);

This change was done in #4348 to fix #4260 after a discussion with @dragonstyle

I added a regression test so that we don't mess with this again.

This is happening with 1.3 and 1.4. This should probably be a hot fix in 1.3. I don't know how you handle that usually. This PR is again main, and I supposed you cherry-pick for a new 1.3 release ? Where should the bullet news be in that case ?

@dragonstyle @jjallaire I let you check this change, and do the right thing for the patch if needed.

[dragonstyle]

This seems like a reasonable fix to me (not ideal that we're continuing to mutate the FormatPandoc all the way in filters, but not sure I see an easy way around that).

• Agree about hot fixing. We just need to cherry pick the commit(s) onto the v1.3 branch once merged.
• On the v1.3, we should edit the changelog-1.3.qmd file to move the items currently in the ## New In This Patch Release section into a new section below it titled ## Fixed In Previous Patch Releases and add a new item to the New In.. section with the bug description and link...

[cderv]

Thank you Charles !