Fix the handling of bibliography sections in R Markdown notebooks

[mwouts]

Will close #1161

[github-actions]

Thank you for making this pull request.

Did you know? You can try it on Binder: or .

Also, the version of Jupytext developed in this PR can be installed with pip:

pip install git+https://github.com/mwouts/jupytext.git@fix_bibliography_in_rmarkdown

(this requires nodejs, see more at Developing Jupytext)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (4a133b5) 96.81% compared to head (aa55b9d) 97.73%.
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1180      +/-   ##
==========================================
+ Coverage   96.81%   97.73%   +0.92%     
==========================================
  Files          29       29              
  Lines        4452     4456       +4     
==========================================
+ Hits         4310     4355      +45     
+ Misses        142      101      -41     

Flag	Coverage Δ
external	75.17% <40.00%> (+0.06%)	⬆️
functional	88.56% <100.00%> (+0.01%)	⬆️
integration	77.31% <40.00%> (-0.05%)	⬇️
unit	66.56% <20.00%> (-0.07%)	⬇️

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