YAML includes - unintended behavior

[nithinmkp]

Description

I am trying to create a manuscript project with a main.qmd and other sections as using include. For example

my 01-intro.qmd might look something like this

---
bibligropahy: ref.bib
---
Lorem Ipsum

I have tried to include this YAML in all stand alone qmd files which form the part of main.qmd

I have my main.qmd as follows

---
author: bla bla
title: bleh
---

# Intro
{{< include 01-intro.qmd >}}

This results in something like

This is not intended. This was not the case working with quarto 1.6.43.

Also Since that version I have two more issues

One is in inclusion of some custom tables.

Please note the unintended behavior.

Second issue is more critical

The cross ref doesnt seem to realise "_" in labels. I have verified this using tex file.

The crossref style (@fig-mean_educ) doesnt work because of "_" it seems. This again was not an issue in earlier version of quarto.

Github

[mcanouil]

@nithinmkp

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[nithinmkp]

sorry. I have edited the post

[mcanouil]

You broke the markdown syntax with your edits.

[nithinmkp]

I am sorry. I tried hard but somehow not working.

[cderv]

This is not intended. This was not the case working with quarto 1.6.43.

Just add spaces.

❯ git diff .\main.qmd
diff --git a/main.qmd b/main.qmd
index 229ec52..817a849 100644
--- a/main.qmd
+++ b/main.qmd
@@ -18,15 +18,19 @@ linestretch: 1.1
 ---

 # Introduction
+
 {{< include 01-intro.qmd >}}

 # Tables
+
 {{< include 02-tables.qmd >}}

 # Model
+
 {{< include 03-model.qmd >}}

 # Figures
+
 {{< include 04-figures.qmd >}}

 # References {.unnumbered}

You currenly get this results because you are missing spaces after your headers, and also in some files after your YAML block.

Check for spaces around block in your source, and re-render again.

[mcanouil]

To complete the reply from Christophe, the required empty lines surrounding the include shortcode is explicitly documented in an important (red) call-out at the very beginning of the documentation for that shortcode: https://quarto.org/docs/authoring/includes.html

[mcanouil]

Note that the use of underscores in cross-reference can lead to issues in LaTeX and that is also documented in a callout at https://quarto.org/docs/authoring/cross-references.html#overview

(This is not a new addition by the way)

[mcanouil]

Regarding the "need" to have multiple bibliographies defines in each documents (see end of #13616).
The autocomplete does work with one single bibliography defined in _quarto.yml.

[nithinmkp]

The first issue is sorted. adding space solves the problem. Also the solution of adding bib file in _quarto.yml was brilliant. However the issue of tables as mentioned is still not settled

here is the original table as produced using quarto on 6th of July 2025 (using code in 02-tables.qmd)

I have updated my main.qmd. It now includes only the problem causing element (02-tables.qmd). The actual expected output is given above.

[mcanouil]

Could you simplify your example code to only focus on this? There are too many unrelated elements.
Simplifying your project is also likely to help you figure out the issue yourself.

[nithinmkp]

sorted. Thanks for all the help