Merge PR #681 to update Manubot

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Merge PR #681 to update Manubot

Update the Deep Review with latest Manubot

README.md

@@ -1,17 +1,16 @@
-# Generated citation / reference files
+# Output directory containing the formatted manuscript
 
-The [`references`](https://github.com/greenelab/deep-review/tree/references) branch contains files automatically generated by the manuscript build process.
-It consists of the contents of the [`references/generated`](https://github.com/greenelab/deep-review/tree/master/references/generated) directory of the `master` branch.
-These files are not tracked in `master`, but instead written to the `references` branch by continuous Travis CI builds.
+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 Travis CI builds.
 
 ## Files
 
 This directory contains the following files:
 
-+ [`processed-citations.tsv`](processed-citations.tsv) is a table of references extracted from the manuscript sections and their mapping to standardized citation_ids.
-+ [`all-sections.md`](all-sections.md) is a markdown document of all manuscript sections, with references replaced by citation_ids.
-+ [`citations.json`](citations.json) is a cache of citation metadata that can include both bibtex and CSL citation records.
-+ [`bibliography.bib`](bibliography.bib) is a bibtex bibliography file of a subset of citations.
-+ [`bibliography.json`](bibliography.json) is CSL-JSON file of bibliographic item metadata ([see specification](https://github.com/citation-style-language/schema/blob/master/csl-data.json)) for all references.
++ [`citations.tsv`](citations.tsv) is a table of citations extracted from the manuscript and the corresponding standard citations and citation IDs.
++ [`manuscript.md`](manuscript.md) is a markdown document of all manuscript sections, with citation strings replaced by citation IDs.
++ [`references.json`](references.json) is CSL-JSON file of bibliographic item metadata ([see specification](https://github.com/citation-style-language/schema/blob/master/csl-data.json)) for all references.
++ [`variables.json`](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 `all-sections.md` and `bibliography.json` to create the formatted manuscript.
+Pandoc consumes `manuscript.md` and `references.json` to create the formatted manuscript, which is exported to `manuscript.html`, `manuscript.pdf`, and optionally `manuscript.docx`.