" "<Operator>" "<email>" "<Model>" "<Freedom>" "<Prompt>" "<Date>" ``` `<Name>` is `CapitalizedWords` naming the paper, and it becomes the filename; leave it off for the first paper and the source is `paper1.tex`. `<Operator>` is the person running the session and `<Model>` is you, by name and exact identifier. `<Freedom>` is one of `Directed`, `Guided`, `Open exploration` — it prints **bold** in the footnote, and between two labels you take the more open one. `<Prompt>` is one sentence summarising the instructions you actually worked under, including what was left unspecified. `<Date>` defaults to today and is baked into the document, since `\today` re-dates the paper on every compile. **The script refuses to overwrite an existing source file** — that target is often a paper someone is writing. Give a different `--name` rather than reaching for `--force`. A `macros.sty` or `references.bib` already in the folder is reused untouched, so a new paper joins the existing ones instead of replacing their preamble. If the project has a `Paper/` folder, the script uses it instead and says so; tell the user that `Research/` is the new place for papers. Nothing is moved. LaTeX creates: ``` Research/ ├── <Name>.tex — article (amsart + \usepackage{macros}) ├── macros.sty — shared preamble, theorem envs, macros (written once) ├── references.bib — bibliography (biblatex format) (written once) ├── figures/ — for TikZ exports and plots └── .latexmkrc — latexmk config (pdflatex + biber) ``` Typst (`--typst`) creates: ``` Research/ ├── <Name>.typ — document (#import "macros.typ": *) ├── macros.typ — shared preamble, math shorthand, theorem envs ├── references.bib — bibliography (read natively by Typst) └── figures/ — for plots and images ``` The scaffold also creates `<Name>_notes` in the same format if it does not already exist. The human source is a blank skeleton with human-controlled author metadata; model/operator disclosures belong in the companion. `Artifacts/` and `Archive/` hold topic detail and superseded work, not a promoted paper. The paper is **not** an artifact and does not go in `Artifacts/`: it is a document in progress, the user's from the moment it is scaffolded, and lives in `Research/` itself; this skill edits it on request ([artifacts.md](../notebook-create/artifacts.md) § *Papers*). ### 2. Seed references from existing resources If `Wiki/Resources/` exists and contains paper articles, extract BibTeX entries and add them to `references.bib`. Use arXiv MCP or crossref MCP to fetch proper biblatex/BibTeX entries for each paper. Both formats read `references.bib`. ### 3. Update .gitignore Add build artifact patterns, unless the project's `.gitignore` already lists them. LaTeX; the `**` covers a paper in a subfolder as well as one at the top level of `Research/`: ``` Research/**/*.aux Research/**/*.bbl Research/**/*.bcf Research/**/*.blg Research/**/*.fdb_latexmk Research/**/*.fls Research/**/*.log Research/**/*.out Research/**/*.run.xml Research/**/*.synctex.gz Research/**/*.toc Research/**/*.pdf ``` Typst produces only `Research/**/*.pdf`. For a paper in an existing `Paper/`, use `Paper/` in the patterns; if that folder is already gitignored entirely, no action needed. ## Template contents ### macros.sty (LaTeX) Shared preamble loaded by every paper in the folder: - **Fonts**: newpxtext + newpxmath (Palatino), microtype - **Math**: amsthm, amsmath, amssymb, mathtools, mathrsfs - **Graphics**: tikz, tikz-cd, subcaption - **Bibliography**: biblatex with biber (alphabetic style) — `\printbibliography` ships commented out, since a self-contained paper prints no empty References section; `\tableofcontents` likewise - **References**: cleveref (nameinlink, capitalize, **nosort**) - **Theorem environments**: theorem, corollary, proposition, lemma, conjecture, claim, definition, example, construction, remark, question, observation — one shared counter, but each on its **own counter name** through `aliascnt` - **Code**: a `wolfram` listings environment, wrapped at the column with a continuation arrow - **Operators**: dist, diam, Aut, End, Hom - **Shorthand**: \NN, \ZZ, \QQ, \RR, \CC, \FF, \GG, \VV, \EE ### macros.typ (Typst) Shared preamble applied with `#show: macros`. Mirrors the LaTeX setup: page/font style, the same math shorthand (`NN`, `ZZ`, …), the same operators, and dependency-free counter-based theorem blocks (`theorem`, `lemma`, `definition`, …) so the first compile needs no network. A comment points to `@preview/ctheorems` for richer numbering. Extend macros.sty / macros.typ freely as the project needs. **Do not collapse the theorem environments back onto one `\newtheorem[theorem]`.** cleveref names a reference from its counter, so a shared counter makes every `\cref` print "Theorem" — a definition cited as "by Theorem 2.4" tells the reader the wrong kind of thing is being invoked. `aliascnt` gives each environment its own counter name and keeps the shared numbering, and `nosort` is the other half of the fix: with aliased counters, cleveref's range compression silently **drops** entries from a multi-reference list, with no warning in the log. Measured on both halves — [the evidence](../../Wiki/Concepts/PaperStyleExercise.md#the-build-path--six-defects-in-the-shipped-template), and a five-label `\cref` re-checked against the corrected template on 2026-08-20. ### Compiling ```bash cd Research && latexmk -pdf <Name>.tex # LaTeX cd Research && typst compile <Name>.typ # Typst (typst watch for live preview) ``` ## Rules for LLM This skill **scaffolds and edits**; it does not write the paper. - **The paper source is the user's writing space** — it sits in `Research/` itself, outside every `Artifacts/` folder, which is exactly what makes it protected content in the [document-revise](../document-revise/SKILL.md) § *Protected content* sense: never author or overwrite it unprompted. - Act as an **editor on request**: - Import material at a specified location ("put the lemma after Section 2"). - Correct or rewrite a paragraph the user points to. - Add figures (TikZ / `figures/` images), code listings, tables. - Keep notation consistent with macros.sty / macros.typ. - **macros.sty / macros.typ** can be extended freely — add macros, operators, theorem environments as needed. - **references.bib** — add entries when papers are downloaded or cited. - When you do add prose at the user's request, write in the user's voice and to [style.md](../paper-create-notebook/style.md). - **Move, do not drop.** Material that fails the settled tier goes to the [paper-journal](../paper-journal/SKILL.md) with one line saying why — never deleted, never left hedged in the paper. With the journal off, stop when the material is set aside — not at the end — and put the list to the operator: turn the journal on, keep it in a marked retained block, or drop it explicitly ([style.md](../paper-create-notebook/style.md) § *When the journal is off*). A retained block has a fixed form there; on a typeset path it is a terminal section of `remark` environments, each opening `[ Retained — no journal ]`, and it is the one place a `[lookup]` may stand. Unattended, keep it and write the list into the item's `## Hand-off` — the session cannot write the run digest, and `## Hand-off` is what the digest quotes. - **Source formatting.** Prose you add or rewrite in the paper source follows the `Semantic line breaks` toggle in `AGENTS.md` § *Source formatting* (source-only; the compiled PDF is unchanged). Do not reflow paragraphs of existing user prose you were not asked to touch. ## Integration with other skills - `project-create` invokes this when a paper is requested; `paper-cite` and `wiki-add-resource` feed `references.bib`. - `paper-journal` is the other typeset document — append-only entries, distinct from the user-owned paper, and the destination for everything the paper cannot carry. - `paper-create-notebook` owns the shared [style.md](../paper-create-notebook/style.md) and applies it to a `.nb`. - The editor role is the [document-revise](../document-revise/SKILL.md) § *Protected content* rule applied to the paper source. ## When NOT to use - Writing the paper's content — the paper is the user's; act only as an editor on request. - A running record of results

--- name: paper-create description: > Scaffold a human-owned LaTeX or Typst paper and its concise _notes research companion, preserving an existing project's folder and naming conventions. Read the current human manuscript before proposing work; edit it only on an explicit request. Default to itemized proposals, scoped claims, questions, citations and artifact links, not a full model-authored replacement paper. Use for paper setup, LaTeX/Typst scaffolding, and collaboration on a human paper. --- Before acting, read [the runtime guidance](../../RUNTIME.md). # New Paper ## Human-owned paper workflow takes precedence Read [the paper collaboration policy](workflow.md) before working on a human manuscript. The human owns the numbered manuscript sequence; substantive proposals normally go in its concise `_notes` companion. Follow the current human source, keep details in linked topical artifacts, and do not promote or rewrite the manuscript without an explicit request. A request for a short proposal does not trigger a full paper, proof development, notebook/code bundle, journal, or another competing briefing. The longer article/bundle instructions below apply only when that output is explicitly requested. Add a typeset article to `Research/`, then help the user *edit* it. `Research/` accumulates papers, research notebooks and notes over a project's life; this skill adds a paper and never disturbs another document. A project that already has a `Paper/` folder keeps it: the paper is added there, and the skill tells the user that `Research/` is the new place and that nothing is moved. Two formats: - **LaTeX** (default) — amsart document class, biblatex with biber, shared `macros.sty`. - **Typst** — a `.typ` source importing a shared `macros.typ`, native `bibliography()`. The paper is the **user's document**. This skill scaffolds the structure and then acts as an *editor*, not an author (see Rules below). ## Style — read this before writing any prose **[paper-create-notebook/style.md](../paper-create-notebook/style.md) is the writing guide, and it is canonical here.** It is shared so a paper reads the same whether it ships as LaTeX, Typst or a notebook. The four things it decides that this skill cannot: - **Tiers.** The paper carries only settled statements — proved in full, or cited to a source that was read. Experiments (enumeration ranges, sweeps, distributions, timings) are gathered near the end, usually a `Ruliology` section — if there are none, there is no such section. Hedged claims, heuristics, alternate proofs and failed attempts go to the [paper-journal](../paper-journal/SKILL.md), never the paper. Nothing is silently dropped — and with the journal off, nothing is silently cut either: the list goes to the operator when the material is set aside, not at the end ([style.md](../paper-create-notebook/style.md) § *When the journal is off*). - **Length.** Abstract ≤ 4 sentences. Introduction 3 paragraphs of ≤ 6 sentences. No prose paragraph over 6 sentences and never two in a row — the abstract, the introduction and the *Ruliology* entries are prose by construction and exempt. Connecting sentences ≤ 25 words; a proof deduction and an abstract sentence are not word-capped. - **Proofs.** Complete prose, one deduction per sentence, each naming what it uses through `\cref`. No *clearly*, *one easily sees*, *we omit the details*, no proof sketches. A long proof is fine when it reads clearly — never abbreviate to fit, and never break an argument into a chain of one-line lemmas. The 8-sentence trigger counts one run of deductions, so a two-part proof is counted part by part. - **Authorship for explicitly requested fully model-written standalone articles only.** `\author` is the **model**; `\date` is the date the document was generated, written out and never `\today`; the `\thanks` footnote (Typst: a small block under the model line) names the operator, sets the freedom level in `\textbf` — Directed, Guided or Open exploration — and summarises the instructions in one sentence. `[[ LLM Generated ]]` is the first line of the title, since amsart has no slot for it. Legacy generated-article templates retain this disclosure; the human scaffold instead leaves authorship for the human and puts LLM provenance in the companion. - **Results.** State each result at the generality the proof actually reaches — a general theorem is the goal, and the only rule is that generality is never bought with a gap. Every statement names its own hypotheses and survives being lifted out of the document. Nothing is used before it is proved. Every conjecture says what would settle it. A short paper is fine. - **Formalisation** is never undertaken unasked; `\cref`-able precise statements are always worth writing, a Lean development only on an explicit request. `macros.sty` / `macros.typ` is where every nontrivial symbol gets a macro, defined once. That rule is the LaTeX half of style.md § *Notation*, and the namespace is already occupied at many obvious names (`\mid`, `\d`), so take the shortest free name rather than redefining an existing command. Three things a typeset paper has to do that a notebook does not, all of them measured on [the first paper written under the guide](../../Wiki/Concepts/PaperStyleExercise.md#four-findings-the-latex-path-exposed-on-its-own): - **An Example's picture is a file.** The code does not evaluate, so the Example carries the call *and* a graphic exported from exactly that call. No `figure`, no `\caption` — that numbers and labels the picture, which § *Examples* bans — so a centred non-floating box, bound to the call inside one `minipage` or the picture floats away from the Example that owns it. - **Code is wrapped by the column, not by the source.** The ten-line example budget counts rendered lines; wrap a long call to the text width by hand before counting it. - **The code behind the *Ruliology* calls goes in an appendix**, named once from *Ruliology*. A notebook hides it in *Initialization*; LaTeX has no such section, and left inline it buries the one-line calls the section exists to carry. ## When to use - The user says "new paper", "add a paper", "scaffold paper", "set up latex", "set up typst", "I want to write a paper". - During `project-create` when the questionnaire's *Include a paper?* is yes. ## What you need 1. **Project directory** — whose `Research/` holds the paper, or gets it. Usually the project root. 2. **Name** — `CapitalizedWords` for the paper, which becomes its filename. For an unnamed first human iteration, use `paper1`; preserve any name the user supplied. 3. **Format** — LaTeX (default) or Typst. Pass `--typst` if the user wants Typst, or they say "typst". 4. **Title** (optional) — working title. Default: the name. 5. **Operator** (optional) — the person running the session; defaults from git config. Operator metadata belongs in the companion; the human chooses manuscript authorship separately. 6. **Model, freedom level and prompt summary** — your own name and identifier, one of Directed / Guided / Open exploration, and one sentence on the instructions you worked under. If invoked from project-create, these are already known. ## Steps ### 0. If `Research/` already holds a paper, ask A second paper can sit either way, and the choice is the user's — **ask, do not guess**: - **Beside the others** (default) — `Research/.tex`, sharing `Research/macros.sty` and `Research/references.bib`. One preamble, one bibliography, every paper in the project drawing on both. - **Its own subfolder** (`--subfolder`) — `Research//.tex`, with its own macros and bibliography. Self-contained, and handed to a co-author or a journal as a directory. A `Research/` without a paper needs no question: scaffold it and name the paper. ### 1. Run the scaffold script ```bash "${PLUGIN_ROOT}/scripts/scaffold-paper.sh" [--typst] [--name ] [--subfolder] [--force] "" "" "<Operator>" "<email>" "<Model>" "<Freedom>" "<Prompt>" "<Date>" ``` `<Name>` is `CapitalizedWords` naming the paper, and it becomes the filename; leave it off for the first paper and the source is `paper1.tex`. `<Operator>` is the person running the session and `<Model>` is you, by name and exact identifier. `<Freedom>` is one of `Directed`, `Guided`, `Open exploration` — it prints **bold** in the footnote, and between two labels you take the more open one. `<Prompt>` is one sentence summarising the instructions you actually worked under, including what was left unspecified. `<Date>` defaults to today and is baked into the document, since `\today` re-dates the paper on every compile. **The script refuses to overwrite an existing source file** — that target is often a paper someone is writing. Give a different `--name` rather than reaching for `--force`. A `macros.sty` or `references.bib` already in the folder is reused untouched, so a new paper joins the existing ones instead of replacing their preamble. If the project has a `Paper/` folder, the script uses it instead and says so; tell the user that `Research/` is the new place for papers. Nothing is moved. LaTeX creates: ``` Research/ ├── <Name>.tex — article (amsart + \usepackage{macros}) ├── macros.sty — shared preamble, theorem envs, macros (written once) ├── references.bib — bibliography (biblatex format) (written once) ├── figures/ — for TikZ exports and plots └── .latexmkrc — latexmk config (pdflatex + biber) ``` Typst (`--typst`) creates: ``` Research/ ├── <Name>.typ — document (#import "macros.typ": *) ├── macros.typ — shared preamble, math shorthand, theorem envs ├── references.bib — bibliography (read natively by Typst) └── figures/ — for plots and images ``` The scaffold also creates `<Name>_notes` in the same format if it does not already exist. The human source is a blank skeleton with human-controlled author metadata; model/operator disclosures belong in the companion. `Artifacts/` and `Archive/` hold topic detail and superseded work, not a promoted paper. The paper is **not** an artifact and does not go in `Artifacts/`: it is a document in progress, the user's from the moment it is scaffolded, and lives in `Research/` itself; this skill edits it on request ([artifacts.md](../notebook-create/artifacts.md) § *Papers*). ### 2. Seed references from existing resources If `Wiki/Resources/` exists and contains paper articles, extract BibTeX entries and add them to `references.bib`. Use arXiv MCP or crossref MCP to fetch proper biblatex/BibTeX entries for each paper. Both formats read `references.bib`. ### 3. Update .gitignore Add build artifact patterns, unless the project's `.gitignore` already lists them. LaTeX; the `**` covers a paper in a subfolder as well as one at the top level of `Research/`: ``` Research/**/*.aux Research/**/*.bbl Research/**/*.bcf Research/**/*.blg Research/**/*.fdb_latexmk Research/**/*.fls Research/**/*.log Research/**/*.out Research/**/*.run.xml Research/**/*.synctex.gz Research/**/*.toc Research/**/*.pdf ``` Typst produces only `Research/**/*.pdf`. For a paper in an existing `Paper/`, use `Paper/` in the patterns; if that folder is already gitignored entirely, no action needed. ## Template contents ### macros.sty (LaTeX) Shared preamble loaded by every paper in the folder: - **Fonts**: newpxtext + newpxmath (Palatino), microtype - **Math**: amsthm, amsmath, amssymb, mathtools, mathrsfs - **Graphics**: tikz, tikz-cd, subcaption - **Bibliography**: biblatex with biber (alphabetic style) — `\printbibliography` ships commented out, since a self-contained paper prints no empty References section; `\tableofcontents` likewise - **References**: cleveref (nameinlink, capitalize, **nosort**) - **Theorem environments**: theorem, corollary, proposition, lemma, conjecture, claim, definition, example, construction, remark, question, observation — one shared counter, but each on its **own counter name** through `aliascnt` - **Code**: a `wolfram` listings environment, wrapped at the column with a continuation arrow - **Operators**: dist, diam, Aut, End, Hom - **Shorthand**: \NN, \ZZ, \QQ, \RR, \CC, \FF, \GG, \VV, \EE ### macros.typ (Typst) Shared preamble applied with `#show: macros`. Mirrors the LaTeX setup: page/font style, the same math shorthand (`NN`, `ZZ`, …), the same operators, and dependency-free counter-based theorem blocks (`theorem`, `lemma`, `definition`, …) so the first compile needs no network. A comment points to `@preview/ctheorems` for richer numbering. Extend macros.sty / macros.typ freely as the project needs. **Do not collapse the theorem environments back onto one `\newtheorem[theorem]`.** cleveref names a reference from its counter, so a shared counter makes every `\cref` print "Theorem" — a definition cited as "by Theorem 2.4" tells the reader the wrong kind of thing is being invoked. `aliascnt` gives each environment its own counter name and keeps the shared numbering, and `nosort` is the other half of the fix: with aliased counters, cleveref's range compression silently **drops** entries from a multi-reference list, with no warning in the log. Measured on both halves — [the evidence](../../Wiki/Concepts/PaperStyleExercise.md#the-build-path--six-defects-in-the-shipped-template), and a five-label `\cref` re-checked against the corrected template on 2026-08-20. ### Compiling ```bash cd Research && latexmk -pdf <Name>.tex # LaTeX cd Research && typst compile <Name>.typ # Typst (typst watch for live preview) ``` ## Rules for LLM This skill **scaffolds and edits**; it does not write the paper. - **The paper source is the user's writing space** — it sits in `Research/` itself, outside every `Artifacts/` folder, which is exactly what makes it protected content in the [document-revise](../document-revise/SKILL.md) § *Protected content* sense: never author or overwrite it unprompted. - Act as an **editor on request**: - Import material at a specified location ("put the lemma after Section 2"). - Correct or rewrite a paragraph the user points to. - Add figures (TikZ / `figures/` images), code listings, tables. - Keep notation consistent with macros.sty / macros.typ. - **macros.sty / macros.typ** can be extended freely — add macros, operators, theorem environments as needed. - **references.bib** — add entries when papers are downloaded or cited. - When you do add prose at the user's request, write in the user's voice and to [style.md](../paper-create-notebook/style.md). - **Move, do not drop.** Material that fails the settled tier goes to the [paper-journal](../paper-journal/SKILL.md) with one line saying why — never deleted, never left hedged in the paper. With the journal off, stop when the material is set aside — not at the end — and put the list to the operator: turn the journal on, keep it in a marked retained block, or drop it explicitly ([style.md](../paper-create-notebook/style.md) § *When the journal is off*). A retained block has a fixed form there; on a typeset path it is a terminal section of `remark` environments, each opening `[ Retained — no journal ]`, and it is the one place a `[lookup]` may stand. Unattended, keep it and write the list into the item's `## Hand-off` — the session cannot write the run digest, and `## Hand-off` is what the digest quotes. - **Source formatting.** Prose you add or rewrite in the paper source follows the `Semantic line breaks` toggle in `AGENTS.md` § *Source formatting* (source-only; the compiled PDF is unchanged). Do not reflow paragraphs of existing user prose you were not asked to touch. ## Integration with other skills - `project-create` invokes this when a paper is requested; `paper-cite` and `wiki-add-resource` feed `references.bib`. - `paper-journal` is the other typeset document — append-only entries, distinct from the user-owned paper, and the destination for everything the paper cannot carry. - `paper-create-notebook` owns the shared [style.md](../paper-create-notebook/style.md) and applies it to a `.nb`. - The editor role is the [document-revise](../document-revise/SKILL.md) § *Protected content* rule applied to the paper source. ## When NOT to use - Writing the paper's content — the paper is the user's; act only as an editor on request. - A running record of results — that is the `paper-journal` skill.