The output branch contains files automatically generated by the manuscript build process. It consists of the contents of the output directory of the master branch. These files are not tracked in master, but instead written to the output branch by continuous integration builds.

This directory contains the following files:

• citations.tsv is a table of citations extracted from the manuscript and the corresponding standard citations and citation IDs.
• manuscript.md is a markdown document of all manuscript sections, with citation strings replaced by citation IDs.
• references.json is CSL-JSON file of bibliographic item metadata (see specification) for all references.
• variables.json contains variables that were passed to the jinja2 templater. These variables contain those automatically generated by the manubot as well as those provided by the user via the --template-variables-path option.

Pandoc consumes manuscript.md and references.json to create the formatted manuscript, which is exported to manuscript.html, manuscript.pdf, and optionally manuscript.docx.