Track-changes PDFs from two versions of a Quarto paper — the copy journals ask for on resubmission, which quarto has no output for.

qdiff OLD [NEW] [options]

OLD and NEW are directories (taken as they sit, uncommitted changes included) or git refs (commit, branch, tag). NEW defaults to the current directory.

1. Stage both sides in scratch space: a directory is cloned (APFS copy-on-write on macOS, so large data trees cost nothing), a ref is checked out as a detached worktree. qdiff never renders in, writes to, or deletes from the author's tree.
2. Render each side to bare typst with the same quarto (quarto render --to typst -M keep-typ:true), so toolchain churn cancels and the diff shows what changed in the paper.
3. Prepare each .typ as a standalone diff input (see below).
4. Diff with typst-diff, which evaluates both documents — show rules, includes, citations, cross-references — and diffs what typst actually typesets, word by word, with figures, tables, lists and equations diffed as units. Insertions are green, deletions red and struck.

Staged sides and worktrees are removed when qdiff exits, including on failure (--keep keeps them for inspection).

cargo install --locked --git https://github.com/alexanderkoller/typst-diff typst-diff
pip install -e .            # provides the `qdiff` command

Requires quarto on PATH. typst-diff embeds its own typst (0.14.2 as of 2026-09) and finds system fonts only; a font the paper's template names must be installed on the system to appear in the diff.

qdiff 10fde27 . --entry paper/index.qmd       # ref vs working tree
qdiff submitted/ revised/ -o changes.pdf      # dir vs dir
qdiff v1 v2 --profile blind --open            # two tags, blind profile

Next to the PDF: <name>-changes.txt (typst-diff's log of every insertion, deletion and modification) and old.typ / new.typ (the prepared diff inputs).

• Citations: pandoc's typst writer emits @key; typst label syntax extends over -, so [@key]---because glues into an unknown label. Bib-key refs become #cite(<key>); @key[supp] becomes the named supplement: form typst 0.13+ requires. Cross-references pass through.
• CSL path: quarto escapes a leading . in the csl: path, which typst rejects; the escapes are stripped.
• Document metadata: set document(...) rules are removed — typst-diff lays content out inside a container, where typst rejects them. They carry PDF metadata only.
• Title block: title, subtitle, date, abstract, keywords and acknowledgments move out of the template's article(...) call into the body. typst-diff treats the title block as one opaque unit and mangles an edited title; as body paragraphs they diff word by word.
• Line numbers: #set par.line(numbering: "1") is prepended.

• Raw LaTeX is dropped. Quarto's typst writer drops {=latex} blocks, so tables written as raw LaTeX are missing from both sides and from the diff; qdiff warns and names the files. Write tables in a form that renders to typst too (pipe or grid tables, or a generator that emits both).
• Footnotes can break typst-diff. On some documents with footnotes it renders old-side content live and fails ("page configuration is not allowed inside of containers"). qdiff then retries with footnotes set inline as small parenthetical notes, and says so.
• Deleted figures show their caption struck, numbered from the new side's counters ("Figure 0"), since old-side counters do not run.
• The bibliography is shown as a whole old block and a whole new block.

pip install -e ".[test]"
pytest

The end-to-end tests run real quarto and typst-diff (skipped when either is missing) and cover the defects of the earlier typdiff-based qdiff: the author's tree untouched, sized and deleted figures, math edits, deleted citations and em-dash glue, and worktree cleanup for git-ref sides.