Check references.bib for structural problems (brace balance, duplicate or empty keys).

Create a starter references.bib in a paper.

Resolve a DOI/arXiv id/title from the attached handoff to its BibTeX key. Use this before citing a record whose key you do not know.

Forget the session corpus and return to cwd/config discovery.

A compact context pack for writing one paper: front matter summary, outline, citation keys, current diagnostics and house style. This is the best first call; it is bounded by budget tokens.

Probe the render tools and render a minimal document; ok means a render actually succeeded, not just that quarto exists.

Initialise a paper corpus (config, _quarto.yml, papers/ directory).

Structural and style diagnostics: placeholders, heading hierarchy, missing sections, long paragraphs/sentences, abstract length, undefined citations, readability. Returns at most max_issues; the counts are always complete.

List the papers in the corpus with title, status, engine, render state and word count. Start here; it is much cheaper than reading any paper.

Read one front-matter key, or the whole front matter when key is omitted.

Set a front-matter key. The value is parsed as YAML, so 2026 becomes a number and '[a, b]' a list.

Scaffold a new paper from a template. Returns the entry path; then write it section by section with paper_write_section.

Pin a corpus for this MCP session (a corpus root or a papers/ directory). Use it when the server was launched outside the corpus.

The heading tree with per-section word counts, plus missing standard sections. Cheaper than reading the paper.

Read exactly one section (heading plus body), truncated to max_tokens. Use this instead of reading the whole file.

Render one paper (or the whole corpus with all=true) to PDF. Returns the output path, size and, on failure, a short stderr tail — not the full Quarto log.

Compact evidence brief for an imported paper: counts, screening, top core papers and citation keys. Bounded by budget; never returns the bundle.

Scaffold a paper from a researcher-python handoff bundle and wire its bibliographies. The manual references.bib is never overwritten.

Insert or replace a Quarto appendix that includes the generated PRISMA screening flow (research/prisma.md).

Refresh a paper's generated research/ files from a newer handoff bundle. Manuscript text and the manual references.bib are untouched.

List built-in and corpus-local paper templates.

Set the front-matter abstract. Keeps the abstract out of the section flow; returns its word count and any diagnostics.

Replace, append to, or insert a section. Content is markdown without the heading. Returns a small receipt and the updated outline — not the whole document.