paperlint 9.0.1 → 10.1.0

package/CONTRIBUTING.md

@@ -132,13 +132,25 @@ site without `npx eslint . --prune-suppressions` fails lint, and #134 burns the
 New code is TypeScript (#78). The last block of [`eslint.config.mjs`](eslint.config.mjs) makes any
 `.js`, `.mjs` or `.cjs` file an error in the directories already converted (`TYPESCRIPT_ONLY`), so
 `npm run lint` fails on one; a directory that still mixes the two is not listed yet, and the change
-that converts it adds it. Code that only this repository runs (tests, `scripts/`, `test/e2e/`) is
+that converts it adds it. Everywhere else, a NEW `.js`, `.mjs` or `.cjs` file fails `local/js-needs-reason`
+unless its top comment says `JavaScript, not TypeScript: evidence|fixture|config-loader — <why>`;
+the files that predate the rule are bulk suppressions in `eslint-suppressions.json`, which only
+shrinks. Code that only this repository runs (tests, `scripts/`, `test/e2e/`) is
 run by `node` directly; code a consumer runs from `node_modules` needs a build first, because Node
 does not strip types there.
 
-`npm run build` is one `tsc` over two projects into one `dist/`: `tsconfig.json` builds `src/` to
-`dist/*.js`, and `tsconfig.pkg.json` builds `lib/` and `eslint-rules/` to `dist/lib/` and
-`dist/eslint-rules/`. Everything else imports those two through the package's subpath imports,
+`npm run build` is `tsc -b`: TypeScript's build mode over the project references in the root
+`tsconfig.json`, which is a solution file and compiles nothing itself. The three projects share
+`tsconfig.base.json`: `tsconfig.pkg.json` builds `lib/` and `eslint-rules/` to `dist/lib/` and
+`dist/eslint-rules/`; `tsconfig.src.json` builds `src/` to `dist/*.js` and references the first,
+whose declarations it reads; `tsconfig.skills.json` compiles a skill's scripts
+(`skills/*/scripts/*.ts`) to a `.js` BESIDE each, gitignored and shipped through `files` (their
+declarations go to `dist/skills/`): a skill names its script as `${CLAUDE_SKILL_DIR}/scripts/<name>.js`,
+and only a path inside the skill's own directory resolves the same through the consumer's
+`.claude/skills/<name>` link and in this checkout. A second `tsc -b` with nothing changed is a no-op;
+it decides that from `dist/.tsbuildinfo/`, so an output deleted by hand is rebuilt only by
+`npx tsc -b --force` (or by deleting `dist/` with it). `tsconfig.test.json` is not part of the build:
+it type-checks every `.ts` without emitting. Everything else imports `lib/` and `eslint-rules/` through the package's subpath imports,
 `#lib/<name>` and `#eslint-rules/<name>` (`"imports"` in `package.json`): the default target is the
 build, which is what an install runs; the `paperlint-source` condition points at the `.ts` instead,
 and `npm test` (so `npm run coverage` and `npm run check` too) and `tsconfig.test.json` set it so

package/README.md

@@ -6,6 +6,7 @@ README style — keep it scannable, not a wall of text:
 - Tables for comparisons (commands, venues, checks). Code blocks for every command and file.
 - A blank line between every block. Bold only for the one phrase a skimmer must see.
 - Mechanics and edge cases live in docs/, linked — not inline.
+- Budgets, held by test/readme-shape.test.ts: ≤ 300 lines, no ## section over 60, the install command in the first 90 lines. Over budget → move material to docs/ and link it; raising a budget is a decision, not a fix.
 - A reader must be able to answer "what is it, which venues, how do I start" from the first screen.
 - Sparse emoji are fine where they help rhythm and scanning (e.g. one per section heading or feature bullet); never decorative, never several in a row.
 - One name per thing, everywhere (lint, build, venue preset, kind, skill, papersDir), each explained once, before it is used.
@@ -37,37 +38,15 @@ before you submit.** It comes in two parts:
 
 ## Contents
 
-- [The pipeline](#-the-pipeline)
 - [Supported venues](#-supported-venues)
 - [Getting started](#-getting-started)
-  - [A new paper](#a-new-paper)
-  - [A paper you already have](#a-paper-you-already-have)
+- [The pipeline](#-the-pipeline)
 - [Commands](#-commands)
 - [Skills](#-skills)
 - [Lint and build](#-lint-and-build)
-- [Configuration](#-configuration)
-  - [Add a venue that isn't listed](#-add-a-venue-that-isnt-listed)
+- [Configuration](#-configuration) · [add a venue](#-add-a-venue-that-isnt-listed)
 - [Run it in CI](#-run-it-in-ci)
-- [FAQ](#-faq)
-- [Docs](#-docs)
-
-## 🧭 The pipeline
-
-```text
-stage           what you get                          skills  linter
-1 idea          a go / no-go, with the reason         yes
-2 venue         venues ranked, deadlines planned      yes
-3 study         a study design, honest statistics     yes
-4 draft         a first draft, then a tighter one     yes     lint
-5 review        the objections, before the reviewers  yes     lint
-6 submit        a PDF within the limit, recorded      yes     build, lint
-7 camera-ready  the final, de-anonymised PDF          yes     build, lint
-8 extend        a plan for the next paper             yes
-
-skills: optional, with Claude Code
-lint:   every edit and every CI run, once the paper exists (paperlint new)
-build:  compiles and measures the PDF; lint then checks pages, fonts, references
-```
+- [FAQ](#-faq) · [Docs](#-docs)
 
 ## 🎯 Supported venues
 
@@ -94,24 +73,18 @@ REALM.
 
 <!-- `vigiles:symbol src/init.ts#init` — `npm run check` fails if this function is renamed or removed. -->
 
-1. Install (Node 22.13 or newer):
+1. Install (Node 22.13 or newer) and set up. `init` asks where your papers live (default
+   `papers/`), whether to install TeX Live now, and whether to add a CI workflow; with Claude Code
+   it also installs the skills and four hooks ([what they do](docs/install.md)).
 
    ```sh
    npm i -D paperlint
-   ```
-
-2. Set up. `init` asks three questions: where your papers live (default `papers/`), whether to
-   install TeX Live now, and whether to add a CI workflow. With Claude Code it also installs the
-   skills and three hooks ([what they do](docs/install.md)).
-
-   ```sh
    npx paperlint init
    ```
 
-3. Create a paper. `--venue` names its venue preset from the table above, `--kind` which of its page
-   limits applies. Name the folder after the work, not the venue: a rejected paper moves to another
-   venue and keeps its folder, so `new` refuses a name like `aisec-2026` (`--allow-venue-name` when
-   the word really is the work's):
+2. Create a paper. `--venue` names its venue preset from the table above, `--kind` which of its page
+   limits applies. Name the folder after the work, not the venue: a rejected paper moves on and keeps
+   its folder, so `new` refuses a name like `aisec-2026`.
 
    <!-- `vigiles:symbol src/new-paper.ts#newPaper` — `npm run check` fails if this function is renamed or removed. -->
    <!-- `vigiles:symbol src/new-paper.ts#ALLOW_VENUE_NAME` — the flag's one spelling; `npm run check` fails if it is renamed or removed. -->
@@ -120,25 +93,19 @@ REALM.
    npx paperlint new my-paper --venue agenticdev --kind short
    ```
 
-   It writes `papers/my-paper/` (in the folder you gave `init`) with three files:
-   - `paper.tex` — your paper;
-   - `paperlint.json` — its venue preset and kind;
-   - `PIPELINE-STATUS.md` — which stage the paper is at; the skills read and update it.
+   It writes `papers/my-paper/` with `paper.tex`, `paperlint.json` (venue and kind),
+   `PIPELINE-STATUS.md` (the stage the paper is at) and the empty folders of the
+   [layout](docs/layout.md#the-map).
 
-4. Build the PDF. **This needs TeX Live, a ~270 MB download (~3 min, once).** If you said no in
-   `init`, run `npx paperlint toolchain` first.
+3. Build the PDF. **This needs TeX Live, a ~270 MB download (~3 min, once)**; if you said no in
+   `init`, run `npx paperlint toolchain` first. Then check it:
 
    ```sh
    npx paperlint build papers/my-paper
-   ```
-
-5. Check it:
-
-   ```sh
    npx paperlint lint
    ```
 
-   On the stub from step 3 the first run already catches something (output shortened):
+   On the stub from step 2 the first run already catches something (output shortened):
 
    ```text
    papers/my-paper/paper.tex
@@ -152,13 +119,34 @@ REALM.
 
 ### A paper you already have
 
-paperlint finds a paper by its folder: `<papersDir>/<name>/`, with the main file named `paper.tex`.
+Put it at `papers/my-paper/paper.tex` (or [set `papersDir`](#-configuration) to where your papers
+live), then run the same `new` command: on a folder that holds anything it only adds the missing
+`paperlint.json` and `PIPELINE-STATUS.md`, and never touches `paper.tex`. Build and lint as above.
+
+## 🧭 The pipeline
+
+A paper goes through eight stages. The skills help at each one; lint checks the folder from the
+moment it exists.
+
+```text
+stage           what you get                          where it goes
+1 idea          a go / no-go, with the reason         siblings/
+2 venue         venues ranked, deadlines planned      paperlint.json, the venue's corpus
+3 study         a study design, honest statistics     repro/<study>/
+4 draft         a first draft, then a tighter one     paper.tex, sections/, figures/
+5 review        the objections, before the reviewers  reviews/, PIPELINE-STATUS.md
+6 submit        a PDF within the limit, recorded      paper.pdf, versions/, submission/
+7 camera-ready  the final, de-anonymised PDF          versions/, talk/
+8 extend        a plan for the next paper             a new paper folder
+
+skills: every stage; optional, with Claude Code
+lint:   any stage once the paper folder exists (paperlint new) — when you run it, and in CI
+build:  stages 6–7; compiles and measures the PDF, and lint then checks pages, fonts, references
+hook:   with Claude Code, refuses a new file in the wrong place before it is written
+```
 
-1. Put the paper there — for example `papers/my-paper/paper.tex`, the rest of its files beside it. If
-   your paper folders already live elsewhere, say `thesis/`, [set `papersDir`](#-configuration) instead.
-2. Run `npx paperlint new my-paper --venue <preset> --kind <kind>`. On an existing folder it only
-   adds the missing `paperlint.json` and `PIPELINE-STATUS.md`; it never touches `paper.tex`.
-3. Build and lint, as above.
+Each stage's skills, what it writes and what checks it, drawn as one flow, with the folder layout:
+[`docs/layout.md`](docs/layout.md).
 
 ## 🧰 Commands
 
@@ -182,6 +170,7 @@ what it does — "is this idea worth a paper?", "find me a venue for this". `ini
 
 - **A go / no-go on your idea, with the reason.** `research-ideate`
 - **A ranked list of venues that fit** — deadline, page limit, indexing. `find-venue`
+- **A page to label the study's items on your phone**, blind, with the answers exported into the paper's folder. `build-label-page`
 - **A first draft from your results.** `draft-paper`
 - **A hostile review before the real one.** `paper-adversarial-review`
 - **A ready / not ready verdict before you submit**, worst problem first. `harden-paper`
@@ -192,52 +181,34 @@ Every skill, by stage: [`docs/skills.md`](docs/skills.md).
 
 ## 🔍 Lint and build
 
-|        | `paperlint build`                                                                                       | `paperlint lint`                                                                                      |
-| ------ | ------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
-| needs  | Node, TeX Live, the network                                                                             | Node                                                                                                  |
-| does   | compiles `paper.tex`, measures the PDF, checks each reference online (exists, right authors)            | checks the source, and judges what build recorded: page limit, fonts, the reference results — offline |
-| writes | `paper.pdf`, in `_build/` the measurements and the reference results, and `repro/references-cache.json` | nothing (`--fix`: the three fixable slips)                                                            |
+|        | `paperlint build`                                                                            | `paperlint lint`                                                                          |
+| ------ | -------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------- |
+| needs  | Node, TeX Live, the network                                                                  | Node                                                                                      |
+| does   | compiles `paper.tex`, measures the PDF, checks each reference online (exists, right authors) | checks the source, and judges what build recorded: page limit, fonts, references; offline |
+| writes | `paper.pdf`, `_build/`, `repro/data/references-cache.json` (commit it)                       | nothing (`--fix`: the three fixable slips)                                                |
 
 - If `paper.pdf` or the bibliography changed since the last build, lint fails and tells you to rebuild.
-- Commit `repro/references-cache.json`: it keeps what the citation services answered, so a build
-  asks only about new or edited entries (and answers older than 30 days), so an unchanged
-  bibliography usually builds without the network ([`docs/references.md`](docs/references.md)).
-- A paper whose body is in other files (`\input{sections/intro}`) is linted file by file: a finding
-  lands at the file and line it is in, and `--fix` edits that file. The files are the ones TeX read
-  after `\begin{document}` in the last build (`_build/sources.json`) — not every `.tex` beside it,
-  and not an included `.bbl` (a tool's output, read only as part of the whole paper). A paper that
-  was not built, or changed since, is linted as `paper.tex` alone, and `paper/sources-fresh` says so.
-- Lint also checks the pipeline's own records: `PIPELINE-STATUS.md`, reviews, notes on related
-  papers ([`docs/rules.md`](docs/rules.md)).
-- The rules run on ESLint, so a deliberate exception is a comment on the line above:
+- Lint also checks the pipeline's own records (`PIPELINE-STATUS.md`, reviews, notes on related
+  papers) and the paper folder's layout.
+- A deliberate exception is a comment on the line above:
   `% eslint-disable-next-line paper/leading-zero -- quoted from the reviewer`.
-- Errors fail the run; warnings only print, unless you pass `--max-warnings <n>`.
 
 Every check: [`docs/rules.md`](docs/rules.md). How build compiles:
 [`docs/configuration.md`](docs/configuration.md#how-paperlint-build-compiles-a-paper).
 
 ## 🧩 Configuration
 
-Two levels, one file name, both optional:
+Two levels, one file name, both optional; a paper's file overrides the project's key by key, and
+**an unknown key is an error**, so a typo cannot silently turn a setting off.
 
 ```
-paperlint.json                   the project: papersDir, rules, defaults for every paper
+paperlint.json                   the project: papersDir (default papers), rules, defaults for every paper
 papers/my-paper/paperlint.json   one paper: its venue preset ("extends"), its kind, its own rules
 ```
 
-- `papersDir` is the folder that holds your paper folders; it defaults to `papers`.
-- The paper's venue preset is its `"extends"` key — the one `new --venue` writes.
-- A paper's `paperlint.json` overrides the project's, key by key.
-- **An unknown key is an error**, so a typo cannot silently turn a setting off.
-- A paper that moves between venues keeps a list of attempts, `cycles`, instead of `"extends"`; each
-  records its deadlines as read from the portal and the call, plus any override the chairs granted,
-  and the earlier reading binds ([`docs/configuration.md`](docs/configuration.md#deadlines)).
-- **Deadlines of a shipped venue preset stay current on their own:** paperlint's repository re-reads
-  each preset's portal daily and releases a patch when a date moves, so your normal dependency update
-  (Dependabot, Renovate) brings it. `paperlint lint` itself never reads the clock or the network.
-
-Every key: [`docs/configuration.md`](docs/configuration.md). Already use ESLint for other files? See
-[`docs/configuration.md`](docs/configuration.md#using-the-rules-from-an-existing-eslint-config).
+Shipped venue presets keep their deadlines current: a date that moves is released as a patch, so your
+normal dependency update brings it. Every key, a paper that moves between venues (`cycles`), and
+using the rules from your own ESLint config: [`docs/configuration.md`](docs/configuration.md).
 
 ### ➕ Add a venue that isn't listed
 
@@ -267,51 +238,17 @@ Give the path from where you run the command; `new` rewrites it relative to the
 
 ## 🤖 Run it in CI
 
-Two options:
-
-| job                        | time                          | checks                                     |
-| -------------------------- | ----------------------------- | ------------------------------------------ |
-| build, then lint           | ~3 min first run, then cached | everything                                 |
-| lint only (`init` adds it) | seconds                       | the source; not pages, fonts or references |
-
-Lint judges pages, fonts and references from what build measured, so the full job builds first:
-
-```yaml
-name: papers
-on: [push, pull_request]
-jobs:
-  papers:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
-        with:
-          node-version: 22
-      - run: npm ci
-      - uses: actions/cache@v4
-        with:
-          path: ~/.cache/paperlint/texlive
-          key: texlive-${{ runner.os }}-${{ hashFiles('package-lock.json') }}
-      - run: npx paperlint toolchain
-      - run: npx paperlint build --all
-      - run: npx paperlint lint
-```
-
-Lint only — each paper then gets one warning that it was not built. Call the action from the
-installed package, after `npm ci`: the action and the CLI it runs are then one revision, pinned by
-your lockfile.
+`init` offers a lint-only workflow (seconds; skips pages, fonts and references). The full job builds
+first (~3 min, then cached) and checks everything:
 
 ```yaml
-steps:
-  - uses: actions/checkout@v4
-  - uses: actions/setup-node@v4
-    with:
-      node-version: 22
-  - run: npm ci
-  - uses: ./node_modules/paperlint
+- run: npm ci
+- run: npx paperlint toolchain
+- run: npx paperlint build --all
+- run: npx paperlint lint
 ```
 
-With no `paths` it lints the `papersDir` of your `paperlint.json`; pass `paths:` only to lint less.
+Both workflows in full, with the TeX Live cache: [`docs/ci.md`](docs/ci.md).
 
 ## ❓ FAQ
 
@@ -329,6 +266,9 @@ Only `paperlint lint --fix`, and only three rules: `paper/section-word` (`§`
 ## 📚 Docs
 
 - [`docs/skills.md`](docs/skills.md) — every skill, by stage
+- [`docs/layout.md`](docs/layout.md) — the pipeline's flow, where each stage writes, and what checks it when
+- [`docs/venues.md`](docs/venues.md) — a venue's corpus of accepted papers, presets and cards: three places, three jobs
+- [`docs/ci.md`](docs/ci.md) — the two CI workflows, in full
 - [`docs/install.md`](docs/install.md) — what `init` does, the hooks, package managers, troubleshooting
 - [`docs/configuration.md`](docs/configuration.md) — every setting, how `build` compiles, using your own ESLint
 - [`docs/rules.md`](docs/rules.md) — every check, venue presets, recording a submitted PDF

package/dist/build.d.ts

@@ -133,7 +133,7 @@ export declare const measureStep: BuildStep;
  * `_build/references.json` for the offline lint rules (`reference-rules.ts`). OPTIONAL and NEVER
  * FAILING: without network the PDF is still built, and the record says `not-checked`.
  *
- * What the services answered is read from and added to `<paper>/repro/references-cache.json`
+ * What the services answered is read from and added to `<paper>/repro/data/references-cache.json`
  * (`references.ts`, `domain/lookup-cache.ts`), committed with the paper, so only a new or edited
  * entry is asked, and an unchanged bibliography is checked with no network at all (#107).
  */

package/dist/build.js

@@ -420,7 +420,7 @@ export const measureStep = {
  * `_build/references.json` for the offline lint rules (`reference-rules.ts`). OPTIONAL and NEVER
  * FAILING: without network the PDF is still built, and the record says `not-checked`.
  *
- * What the services answered is read from and added to `<paper>/repro/references-cache.json`
+ * What the services answered is read from and added to `<paper>/repro/data/references-cache.json`
  * (`references.ts`, `domain/lookup-cache.ts`), committed with the paper, so only a new or edited
  * entry is asked, and an unchanged bibliography is checked with no network at all (#107).
  */

package/dist/cli.d.ts

@@ -146,7 +146,7 @@ export declare function toPaths(papers: unknown): string[];
  * real verdict (2 included) passes through. Silent degradation is worse than explicit degradation,
  * but blocking everything is worse than both.
  */
-export declare function runHook(name: string | undefined, { err, run, resolve, }?: {
+export declare function runHook(name: string | undefined, { err, run, resolve, stdin, out, }?: {
     err?: typeof console.error;
     /** Runs the hook with the terminal's streams: `spawnSync` is one, and only its status is read. */
     run?: (file: string, args: readonly string[], options: {
@@ -155,6 +155,10 @@ export declare function runHook(name: string | undefined, { err, run, resolve, }
         readonly status: number | null;
     };
     resolve?: (spec: string) => string;
+    /** The hook's payload, as Claude Code sends it on stdin. */
+    stdin?: () => string;
+    /** Where an in-process hook's output goes: stdout, which Claude Code reads. */
+    out?: (text: string) => void;
 }): number;
 /**
  * Create one paper and lint it — shared by `paperlint new` and `paperlint init --paper`, so the two cannot

package/dist/cli.d.ts.map

@@ -1 +1 @@
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package/dist/cli.js

@@ -71,7 +71,7 @@ import { paperPreset, settingsProblemLine, presetProblemText, resolvePreset, shi
 import { mergeRequirements, declaredUnion, requirementsFor, NO_REQUIREMENTS, } from "./tex-requirements.js";
 import { doctor } from "./doctor.js";
 import { askOnTerminal, askOrDefault, init, processInteractivity, } from "./init.js";
-import { newPaper, reportNewPaper } from "./new-paper.js";
+import { newPaper, reportNewPaper, STATUS_FILE, } from "./new-paper.js";
 // The one source for the consumer's config key lives in lib/ (the ESLint rules and the skill scripts
 // import it too). It is imported compiled, from dist/, the one path that resolves the same from src/
 // and from dist/ — see CONTRIBUTING.md.
@@ -80,9 +80,13 @@ import { parseRuleBlocks, parseRuleEntries, shippedRuleIds, unknownKeys, } from
 export { init };
 export { nextSteps } from "./init.js";
 import paperStages from "#eslint-rules/paper-stages";
+import preregCoverage from "#eslint-rules/prereg-coverage";
 import cycleStage from "#eslint-rules/cycle-stage";
 import { CYCLE_RULE_LEVELS, cycleRules } from "./cycle-rules.js";
 import { FOLDER_VENUE_RULE_LEVELS, folderVenueRules, } from "./folder-venue-rule.js";
+import { FOLDER_LAYOUT_RULE_LEVELS, folderLayoutRules, } from "./folder-layout-rule.js";
+import { folderLayoutHook } from "./folder-layout-hook.js";
+import { REPRO_LAYOUT_RULE_LEVELS, reproLayoutRules, } from "./repro-layout-rule.js";
 import typography from "#eslint-rules/paper-typography";
 import texBuild from "#eslint-rules/tex-build";
 import reviewFrontmatter from "#eslint-rules/review-frontmatter";
@@ -90,6 +94,7 @@ import siblingFrontmatter from "#eslint-rules/sibling-frontmatter";
 import pdfRules from "#eslint-rules/pdf-last-page-balance";
 import { messageOf } from "./domain/text.js";
 import { isRecord } from "./domain/record.js";
+import { ESCAPE_HATCH } from "./domain/paper-layout.js";
 /** The shipped venue presets, read from the package's venues directory — the one list. */
 const SHIPPED_VENUES = () => shippedPresets(presetsDir());
 const USAGE = `paperlint — machine-checkable gates for a paper kept in git
@@ -251,6 +256,8 @@ const FRAGMENT_RULES = {
     "future-promise": texBuild["future-promise"],
     "heading-case": REGISTER_AND_CASE_RULES["heading-case"],
 };
+/** What the two layout rules read with: the disk and its directory listings. */
+const LAYOUT_RULE_DEPS = { files: nodeFiles, listDir: nodeListDir };
 /** What the talk rules read with: the disk, the shipped presets, and the three media readers. */
 const TALK_RULE_DEPS = {
     files: nodeFiles,
@@ -278,7 +285,9 @@ export function buildConfig(opts = {}, texLanguage) {
         // its files carry every marker a paper does. Flat config does NOT ignore dot-directories by
         // default (only `node_modules/` and `.git/`), so without this block `paperlint lint` would lint the
         // template as a paper — and a richer template with placeholder stages would fail the run.
-        { ignores: ["**/.template/"] },
+        // The same for a paper's `extra/`: the layout promises it is never judged, and an archived
+        // snapshot there carries a paper's markers too, so its folder read as a paper root with strays.
+        { ignores: ["**/.template/", `**/${ESCAPE_HATCH}/`] },
         // The `pdf` plugin is registered for EVERY file. A consumer's block (`rules`, appended below)
         // may name its rules for a glob that also matches markdown files; with the plugin defined only
         // beside `paper.tex`, ESLint would refuse those files with "could not find plugin". Every rule
@@ -307,8 +316,12 @@ export function buildConfig(opts = {}, texLanguage) {
                     rules: {
                         ...paperStages.rules,
                         ...folderVenueRules({ files: nodeFiles, venuesDir: presetsDir() }),
+                        ...folderLayoutRules(LAYOUT_RULE_DEPS),
                     },
                 },
+                repro: { rules: reproLayoutRules(LAYOUT_RULE_DEPS) },
+                // Registered, on for no paper: `"study/declare-sample": "error"` in paperlint.json turns it on.
+                study: { rules: preregCoverage.rules },
                 cycle: { rules: CYCLE_STATUS_RULES },
             },
             ...md,
@@ -316,6 +329,8 @@ export function buildConfig(opts = {}, texLanguage) {
                 "paper/stages": "error",
                 "paper/source": "error",
                 ...FOLDER_VENUE_RULE_LEVELS,
+                ...FOLDER_LAYOUT_RULE_LEVELS,
+                ...REPRO_LAYOUT_RULE_LEVELS,
                 ...CYCLE_RULE_LEVELS,
             },
         },
@@ -516,7 +531,7 @@ export const OPTIONAL_RULES = new Set([...SHIPPED_RULES].filter((id) => !buildCo
  * 🔴 AN OPTIONAL RULE THAT IS ON AND REACHES NO PAPER IS A GREEN ZERO. A `files` glob that matches
  * nothing — a typo, a path relative to the wrong directory — leaves the rule never invoked, and a
  * rule that never runs reports exactly like a rule that passed. So for every optional rule the
- * consumer turned on, some `paper.tex` must actually have it enabled; the ones none has are
+ * consumer turned on, some paper's `paper.tex` or `PIPELINE-STATUS.md` must actually have it enabled; the ones none has are
  * returned, for the caller to refuse.
  *
  * `files` is every `paper.tex` the guard may count: the ones this run linted AND every paper of the
@@ -533,9 +548,14 @@ export async function silentOptionalRules(eslint, files, opts) {
         .filter(([id, e]) => OPTIONAL_RULES.has(id) && isOn(e))
         .map(([id]) => id)));
     const reached = new Set();
-    for (const f of new Set(files.filter((p) => basename(p) === MAIN))) {
+    // A paper's rules reach it through two files: `paper.tex` and the `PIPELINE-STATUS.md` beside it,
+    // where the rules about the paper folder itself run.
+    const probes = [
+        ...new Set(files.filter((p) => basename(p) === MAIN)),
+    ].flatMap((f) => [f, join(dirname(f), STATUS_FILE)]);
+    for (const probe of probes) {
         // Undefined for a file outside ESLint's cwd or scope: it reaches nothing.
-        const cfg = ComputedConfig.parse(await eslint.calculateConfigForFile(f));
+        const cfg = ComputedConfig.parse(await eslint.calculateConfigForFile(probe));
         // Reached is "some block names the rule for this paper", on OR off: a paper that turns off what
         // its venue preset turned on is the documented way out, and reads the same as a glob that missed
         // only if "off" is counted as "not there" — which refused every such paper.
@@ -877,6 +897,27 @@ export function toPaths(papers) {
         return papers.filter((x) => typeof x === "string" && x.trim() !== "");
     return [];
 }
+/**
+ * Hooks that run inside this process instead of as a vigiles program, each because it must call the
+ * package's own code (`src/folder-layout-hook.ts` says why for its one). Advisory: whatever goes
+ * wrong, the tool call has already happened, so it says so on stderr and exits 0.
+ */
+const IN_PROCESS_HOOKS = {
+    "paper-folder-layout": ({ err, stdin, out }) => {
+        try {
+            const said = folderLayoutHook(JSON.parse(stdin()), {
+                files: nodeFiles,
+                listDir: nodeListDir,
+            });
+            if (said !== null)
+                out(`${JSON.stringify(said)}\n`);
+        }
+        catch (e) {
+            err(`paperlint: the paper-folder-layout hook did not run: ${messageOf(e)}`);
+        }
+        return 0;
+    },
+};
 /**
  * `paperlint hook <name>` — run an editor hook. It exists for ONE thing: so that the wiring does not
  * address the runtime from the project root.
@@ -912,11 +953,16 @@ export function runHook(name, { err = console.error, run = spawnSync,
 // This is neither our oversight nor their bug: a closed export map is normal practice. So we
 // resolve the root entry ("." → dist/test.js), take its directory and put `cli.js` next to it —
 // the very file the package itself declares as its `bin`.
-resolve = (spec) => createRequire(import.meta.url).resolve(spec), } = {}) {
+resolve = (spec) => createRequire(import.meta.url).resolve(spec), stdin = () => readFileSync(0, "utf8"), out = (text) => {
+    process.stdout.write(text);
+}, } = {}) {
     if (!name) {
         err(`\`hook\` needs a name, e.g. \`paperlint hook paper-edit-guard\``);
         return 2;
     }
+    const inProcess = IN_PROCESS_HOOKS[name];
+    if (inProcess !== undefined)
+        return inProcess({ err, stdin, out });
     const program = fileURLToPath(new URL(`../hooks/${name}.hook.mjs`, import.meta.url));
     if (!existsSync(program)) {
         err(`unknown hook \`${name}\` — no such program at ${program}`);