docx-thesis

Word is a delivery format, not an authoring format. Author in plain text under git, convert at the end of each cycle, and treat the .docx as a build artifact you regenerate rather than edit. This keeps citation-verifier, humanize, and the whole pipeline working while the department gets what it asked for.

Pipeline

chapters/*.md  +  references.bib  +  template/reference.docx  +  style.csl
        │
        └── pandoc ──▶ build/thesis.docx

1. Author each chapter in Pandoc Markdown ([@key] citations, $math$, ![caption](figures/x.png){#fig:x}, Table: caption {#tbl:x}), or keep LaTeX and let pandoc read it (loses some packages; test early).
2. Reference document: open the department's template in Word, or create one with pandoc -o template/reference.docx --print-default-data-file reference.docx, then set the styles (Heading 1..3, Body Text, First Paragraph, Caption, Table, Source Code, Bibliography) to the required fonts and spacing. Pandoc copies styles from this file; it ignores its content.
3. Citation style: download the CSL for the required style (IEEE, APA 7, Harvard) from the Zotero style repository (https://www.zotero.org/styles/<name>) into style.csl.

4. Build:

   pandoc chapters/*.md \
     --reference-doc=template/reference.docx \
     --citeproc --bibliography=references.bib --csl=style.csl \
     --filter pandoc-crossref \
     --toc --number-sections \
     -o build/thesis.docx

   pandoc-crossref numbers figures, tables, and equations and resolves @fig:x. Install with pip install pandoc-crossref or the release binary.

5. Finish in Word only what pandoc cannot do: the title page from the template, the declaration page, updating the table of contents (right-click, Update field), page numbering sections. Keep a checklist so it is repeatable.

Zotero

The .bib remains the source of truth (bibtex-manager). Two ways to keep Zotero in step:

• Zotero as a view: import references.bib (File → Import), re-import after changes. Simple, one-way.
• Better BibTeX auto-export: install Better BibTeX, set its key format to auth.lower + year + shorttitle(1,1).lower so keys match the .bib, then right-click the thesis collection → Export → Better BibLaTeX with "Keep updated". Zotero becomes the editing UI and the file stays current. Use this when the supervisor shares a Zotero group.

If the supervisor insists on Zotero's Word plugin (live fields in the document), the .docx becomes the source for citations and the pipeline above stops applying to that document. Prefer the pandoc route; if the plugin is mandatory, export the bibliography from Zotero to references.bib weekly so citation-verifier still runs against the text.

Supervisor comments

Supervisors comment in Word. Extract them so the fixes go back into the Markdown source:

pandoc --track-changes=all reviewed.docx -t markdown -o reviewed.md

Comments appear as [comment text]{.comment-start} spans; tracked changes as {.insertion} / {.deletion}. Apply each to the source, then rebuild. Reply to the comments in the next RESEARCH_LOG.md entry so nothing is lost.

From LaTeX

pandoc main.tex --bibliography=references.bib --citeproc --csl=style.csl -o build/thesis.docx handles standard LaTeX. Things that need attention: \input (use --resource-path), custom macros (define in a macros.tex pandoc can read, or -f latex+raw_tex), TikZ figures (export to PDF/PNG first), booktabs tables (pandoc flattens them; check widths), \cref (becomes plain references; pandoc-crossref does not read cleveref).

Submission checks

• Styles: every heading uses a Heading style (the ToC depends on it); body is one style throughout.
• Captions above tables and below figures per the template; numbered per chapter if required (--number-sections and pandoc-crossref's chapters: true in the metadata).
• Page count and word count per the regulations (pandoc --lua-filter wordcount.lua or Word's count excluding references).
• No tracked changes or comments left: Review → Accept All, delete comments, then Inspect Document.
• PDF/A export if required: File → Save As → PDF → Options → PDF/A.
• Fonts embedded (Word does this for PDF export by default).

Run citation-verifier on the Markdown source, not the .docx, before every build.