paperlint 10.4.0 → 10.4.1

package/dist/study-modes.js

@@ -1,70 +1,59 @@
 /**
  * Reading a paper's studies with their modes: each registered study whose `plan.json` parses with a
- * `mode`, and the files under a study's folder. What `repro/outputs-before-decision`, `studies gate`
+ * `mode`, and how a decision's path stands. What `repro/outputs-before-decision`, `studies gate`
  * and the index's mode columns read with (docs/design/study-modes.md). A row whose folder is not one
  * folder inside `repro/` is never read through.
  */
-import { basename, dirname, join } from "node:path";
-import { callerPath } from "./caller-path.js";
-import { REPRO_DIR } from "./domain/repro-layout.js";
-import { isInside, } from "./domain/study-registry.js";
-import { readableFolders, registryOf, textAt } from "./study-registry-rule.js";
-const ON_DISK = {
-    file: "file",
-    dir: "directory",
-    symlink: "symbolic link",
-};
+import { posix } from "node:path";
+import { filter, map, pipe } from "remeda";
+import { studiesOf, } from "./domain/study-registry.js";
 /**
- * What `p` is on disk, read from its directory's entries without following a link: a decision must
- * be a regular file — git answers for a directory with the commits of anything under it, and for a
- * link with the link, not the file it points to.
+ * What the decision file `file` (relative to the paper) is, read through `folder` without following
+ * a link: a decision must be a regular file in real directories — git answers for a directory with
+ * the commits of anything under it, for a link with the link and not the file it points to, and for a
+ * path through a linked directory with what lies behind the link.
  */
-export const onDisk = (p, deps) => {
-    const e = deps
-        .entries(callerPath(dirname(p)))
-        .find((x) => x.name === basename(p));
-    return e === undefined ? "absent" : ON_DISK[e.kind];
+export const decisionEntry = (folder, file) => {
+    const at = folder.entryAt(file);
+    if (at.kind === "dir")
+        return { kind: "not-a-file", what: "directory" };
+    if (at.kind === "other")
+        return { kind: "not-a-file", what: "special file" };
+    if (at.kind !== "linked")
+        return { kind: "ok" };
+    return at.link === posix.normalize(file)
+        ? { kind: "not-a-file", what: "symbolic link" }
+        : at;
 };
 /**
- * Every file under `dir`, relative to it, `/`-separated; none when it is not a directory. A symbolic
- * link is listed as a file — git stores it as one — and never followed: a link to the folder itself
- * would recurse forever, and one to a tree outside would bring its files into the study.
- */
-export const filesUnder = (dir, deps, prefix = "") => deps.entries(callerPath(dir)).flatMap(({ name, kind }) => {
-    const rel = prefix === "" ? name : `${prefix}/${name}`;
-    return kind === "dir" ? filesUnder(join(dir, name), deps, rel) : [rel];
-});
-/**
- * The study `s`'s plan, when it is a plan inside a folder every reader may read through
- * (`readableFolders`), by the registry rule's own containment test (`isInside`), that parsed with a
- * mode; else null.
+ * The plan of the row `s`, read through `folder` (`src/study-folder.ts`, which follows no link and
+ * enters no folder that is not one inside `repro/`): its mode study when the plan parsed with a
+ * mode; a link on the way to it; else nothing.
  */
-const modeStudyOf = (paper, s, deps, readable) => {
+export const readModeStudy = (s, folder, codec) => {
     const plan = s.plan;
-    const text = plan === undefined ||
-        !readable(s.folder) ||
-        !isInside(plan) ||
-        plan.includes("\0")
-        ? null
-        : textAt(deps.files, join(paper, REPRO_DIR, s.folder, plan));
-    if (plan === undefined || text === null)
-        return null;
-    const parsed = deps.codec.parsePlan(text, s.kind);
+    if (plan === undefined)
+        return { kind: "none" };
+    const read = folder.read(s.folder, plan);
+    if (read.kind === "linked")
+        return read;
+    if (read.kind === "absent")
+        return { kind: "none" };
+    const parsed = codec.parsePlan(read.text, s.kind);
     if (parsed.kind === "unreadable" || parsed.plan.mode === undefined)
-        return null;
+        return { kind: "none" };
     const empty = parsed.kind === "draft" ? parsed.empty : [];
-    return { row: s, plan, mode: parsed.plan.mode, empty };
+    return {
+        kind: "mode",
+        study: { row: s, plan, mode: parsed.plan.mode, empty },
+    };
 };
 /**
- * Every study of the paper folder `paper` whose plan declares a mode, in registry order. A plan that
- * does not parse is `repro/study-registered`'s to report; here it declares nothing.
+ * Every study of the registry `r` whose plan declares a mode, in registry order. A plan that does
+ * not parse, or is reached through a link, is `repro/study-registered`'s to report; here it declares
+ * nothing.
  */
-export const modeStudies = (paper, deps) => {
-    const r = registryOf(paper, deps);
-    const readable = readableFolders(paper, deps);
-    return (r.kind === "read" ? r.registry.studies : []).flatMap((s) => {
-        const m = modeStudyOf(paper, s, deps, readable);
-        return m === null ? [] : [m];
-    });
-};
+export const modeStudies = (r, folder, codec) => pipe(studiesOf(r), map((s) => readModeStudy(s, folder, codec)), filter(isMode), map((m) => m.study));
+/** A plan read that declared a mode. */
+const isMode = (m) => m.kind === "mode";
 //# sourceMappingURL=study-modes.js.map

package/dist/study-modes.js.map

@@ -1 +1 @@
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package/dist/study-registry-rule.d.ts

@@ -4,17 +4,13 @@ import type { FolderRuleModule } from "./folder-venue-rule.ts";
 import type { Files } from "./ports/files.ts";
 import type { ListEntries } from "./ports/list-entries.ts";
 import type { StudyRegistryCodec } from "./ports/study-registry-codec.ts";
+import type { StudyFolder } from "./ports/study-folder.ts";
 /** What the rule reads with: the disk, its listings, and the registry's parser. */
 export interface StudyRegistryDeps extends FolderLayoutDeps {
     readonly codec: StudyRegistryCodec;
     /** `repro/`'s entries, links not followed: a study folder that is a link is never read through. */
     readonly entries: ListEntries;
 }
-/**
- * The test every reader of a study's folder passes a row through: its folder is one folder name
- * inside `repro/` (`isFolderName`) and not a symbolic link, which would lead the reads anywhere.
- */
-export declare const readableFolders: (dir: string, deps: Pick<StudyRegistryDeps, "entries">) => ((folder: string) => boolean);
 /** The text of the file at `p`; null when there is none, or a directory sits there. */
 export declare const textAt: (files: Files, p: string) => string | null;
 /** The registry of the paper folder `dir`: absent, unreadable with why, or read. */
@@ -23,7 +19,7 @@ export declare function registryOf(dir: string, deps: Pick<StudyRegistryDeps, "f
  * The plan each row of `r` names, read and parsed, by `<folder>/<plan>`; a plan not there is left out.
  * A plan still named `prereg.json` is parsed by the loose schema of its old name.
  */
-export declare const plansOf: (dir: string, r: RegistryState, deps: Pick<StudyRegistryDeps, "files" | "codec">, readable: (folder: string) => boolean) => ReadonlyMap<string, PlanState>;
+export declare const plansOf: (r: RegistryState, folder: StudyFolder, codec: StudyRegistryCodec) => ReadonlyMap<string, PlanState>;
 /** Every finding of the paper folder `dir`'s study registry — THE function behind both rules. */
 export declare function studyFindings(dir: string, deps: StudyRegistryDeps): readonly StudyFinding[];
 /**

package/dist/study-registry-rule.d.ts.map

@@ -1 +1 @@
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package/dist/study-registry-rule.js

@@ -18,25 +18,14 @@
  * file in `repro/`.
  */
 import { basename, dirname, join, posix } from "node:path";
+import { filter, map, pipe } from "remeda";
 import { callerPath } from "./caller-path.js";
 import { README, REPRO_BYPRODUCTS, REPRO_DIR, REPRO_DIRS, } from "./domain/repro-layout.js";
-import { LEGACY_PLAN_FILE, PLAN_NAME_PROBLEMS, STUDIES_FILE, isFolderName, judgeStudies, planRefs, studyMessage, } from "./domain/study-registry.js";
+import { LEGACY_PLAN_FILE, PLAN_NAME_PROBLEMS, STUDIES_FILE, judgeStudies, folderKey, planRefs, studiesOf, studyMessage, } from "./domain/study-registry.js";
 import { reproEntriesOf } from "./repro-layout-rule.js";
+import { studyFolder } from "./study-folder.js";
 import { rulePageUrl } from "./venue-rules.js";
 const STATUS_FILE = "PIPELINE-STATUS.md";
-/** The names at the top of `<dir>/repro/` that are symbolic links. */
-const linksIn = (dir, deps) => new Set(deps
-    .entries(callerPath(join(dir, REPRO_DIR)))
-    .filter((e) => e.kind === "symlink")
-    .map((e) => e.name));
-/**
- * The test every reader of a study's folder passes a row through: its folder is one folder name
- * inside `repro/` (`isFolderName`) and not a symbolic link, which would lead the reads anywhere.
- */
-export const readableFolders = (dir, deps) => {
-    const links = linksIn(dir, deps);
-    return (folder) => isFolderName(folder) && !links.has(folder);
-};
 /** The text of the file at `p`; null when there is none, or a directory sits there. */
 export const textAt = (files, p) => {
     const b = files.isFile(callerPath(p)) ? files.readBytes(callerPath(p)) : null;
@@ -58,45 +47,47 @@ const studyFolders = (dir, deps) => reproEntriesOf(dir, deps)
     !REPRO_DIRS.includes(e.name) &&
     !REPRO_BYPRODUCTS.includes(e.name))
     .map((e) => e.name);
-/** Each `<folder>/<result_file>` of `r` that is a file. */
-const existingResults = (dir, r, files, readable) => new Set((r.kind === "read" ? r.registry.studies : [])
-    // A row whose folder is not one inside `repro/`, or is a link, is never read through.
-    .filter((s) => readable(s.folder))
-    .flatMap((s) => s.result_file === undefined ? [] : [`${s.folder}/${s.result_file}`])
-    // A NUL is no path the disk can hold, and probing one throws: such a row reads as missing.
-    .filter((p) => !p.includes("\0") &&
-    files.isFile(callerPath(join(dir, REPRO_DIR, p)))));
+/** What each `<folder>/<result_file>` of `r`'s rows is, as the study folder's reader finds it. */
+const resultsOf = (r, folder) => pipe(studiesOf(r), filter(hasResultFile), map((s) => [
+    folderKey(s.folder, s.result_file),
+    folder.locate(s.folder, s.result_file),
+]), (entries) => new Map(entries));
+/** A row that names a result file. */
+const hasResultFile = (s) => s.result_file !== undefined;
 /**
  * The plan each row of `r` names, read and parsed, by `<folder>/<plan>`; a plan not there is left out.
  * A plan still named `prereg.json` is parsed by the loose schema of its old name.
  */
-export const plansOf = (dir, r, deps, readable) => new Map((r.kind === "read" ? planRefs(r.registry) : [])
-    // A NUL is no path the disk can hold, and probing one throws: such a plan reads as missing. A
-    // folder that is a link is never read through.
-    .filter(({ key, folder }) => !key.includes("\0") && readable(folder))
-    .flatMap(({ key, kind }) => {
-    const text = textAt(deps.files, join(dir, REPRO_DIR, key));
-    if (text === null)
-        return [];
-    return [
-        [
-            key,
-            posix.basename(key) === LEGACY_PLAN_FILE
-                ? deps.codec.parseLegacyPlan(text)
-                : deps.codec.parsePlan(text, kind),
-        ],
-    ];
+export const plansOf = (r, folder, codec) => new Map((r.kind === "read" ? planRefs(r.registry) : []).flatMap((ref) => {
+    const state = planStateOf(ref, folder, codec);
+    return state === null
+        ? []
+        : [[folderKey(ref.folder, ref.plan), state]];
 }));
+/** The state of the plan `ref` names, read through `folder`; null when it is not there. */
+const planStateOf = ({ folder: of, plan, kind }, folder, codec) => {
+    const read = folder.read(of, plan);
+    switch (read.kind) {
+        case "absent":
+            return null;
+        case "linked":
+            return { kind: "linked", link: read.link };
+        case "text":
+            return posix.basename(plan) === LEGACY_PLAN_FILE
+                ? codec.parseLegacyPlan(read.text)
+                : codec.parsePlan(read.text, kind);
+    }
+};
 /** Every finding of the paper folder `dir`'s study registry — THE function behind both rules. */
 export function studyFindings(dir, deps) {
-    const readable = readableFolders(dir, deps);
     const registry = registryOf(dir, deps);
+    const folder = studyFolder(dir, deps);
     return judgeStudies({
         folders: studyFolders(dir, deps),
         registry,
         readme: textAt(deps.files, join(dir, REPRO_DIR, README)),
-        existingResults: existingResults(dir, registry, deps.files, readable),
-        plans: plansOf(dir, registry, deps, readable),
+        results: resultsOf(registry, folder),
+        plans: plansOf(registry, folder, deps.codec),
     });
 }
 /** The problems `repro/study-registered` reports, each its own message id; the text is `studyMessage`. */

package/dist/study-registry-rule.js.map

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package/docs/design/study-modes.md

@@ -67,8 +67,9 @@ decision that is a directory, a decision its own outputs match). A runner calls
 npx paperlint studies gate papers/my-paper P1-S03 && ./run.sh
 ```
 
-For an exploratory study it exits 0 and says it has no gate. A study that declares no mode, or whose
-plan is still a draft, is refused.
+For an exploratory study it exits 0 and says it has no gate. A study that declares no mode, whose
+plan is still a draft, or whose id two rows of the registry share (the gate answers for exactly one
+study), is refused.
 
 ### 3. `repro/outputs-before-decision` — the proof of order a reviewer can re-run
 
@@ -132,17 +133,31 @@ make a command or a rule read, judge or write files that belong to nothing in it
 
 Every command and rule that reads a study's folder — `studies gate`, `studies index` and `new`,
 `repro/outputs-before-decision`, and `repro/study-registered`'s reads of plans and result files —
-reads a row only through one predicate, `readableFolders` (`src/study-registry-rule.ts`): its
-`folder` is one folder directly inside `repro/` (`isFolderName`: not empty, not `.` or `..`, no
-separator or NUL) and not a symbolic link (`ListEntries`, read without following links). Such a row
-is never read through: `studies index` and `new` refuse the registry, the gate refuses the study,
-the order rule treats it as no study, and `repro/study-registered` reads its plan and results as
-missing. A plan's path is held inside its folder by the registry rule's own `isInside`, the same on
-every platform (a backslash is refused outright); the decision file is held inside the paper by the
-schema (`staysInside`) and must be a regular file on disk — a directory or a symbolic link is refused
-by the gate and reported by the rule (`decision-not-file`). Only a **ready** plan's mode decides
-anything: the gate refuses a draft, naming its empty fields, and the order rule judges no draft — a
-draft may name no outputs, or an empty decision file.
+goes through one reader, `studyFolder` (`src/study-folder.ts`), built once per run from the paper's
+folder over `ListEntries`, which does not follow links. It decides first whether a row's folder may
+be entered at all (`refusal`): its `folder` is one folder directly inside `repro/` (`isFolderName`:
+not empty, not `.` or `..`, no separator or NUL) and not a symbolic link. Such a row is never read
+through: `studies index` and `new` refuse the registry, the gate refuses the study, the order rule
+treats it as no study, and `repro/study-registered` reads its plan and results as missing.
+
+A plan's path is held inside its folder by the registry rule's own `isInside`, the same on every
+platform (a backslash is refused outright). The reader walks the path one component at a time, and a
+plan or a result file whose path passes through a symbolic link — the file itself, or a directory
+above it — is never read. The gate refuses it naming the link, the order rule treats the study as
+declaring no mode, and `repro/study-registered` reports it (`bad-plan`, `result-file`) with the link.
+
+The decision file is held inside the paper by the schema (`staysInside`) and is judged by the same
+walk (`decisionEntry`, `entryAt`): every component of its path must be a real directory and the last
+a regular file. A directory or a symbolic link as the file itself is refused by the gate and reported
+by the rule (`decision-not-file`); a symbolic link above the file is refused naming that link
+(`decision-linked`).
+
+The plan reads, the result-file existence checks and the decision's path check take a `StudyFolder`
+and not `Files`, so a read that follows a link is not what those readers are handed. A study's
+outputs are listed through it too (`StudyFolder.list`).
+
+Only a **ready** plan's mode decides anything: the gate refuses a draft, naming its empty fields, and
+the order rule judges no draft — a draft may name no outputs, or an empty decision file.
 
 ### 6. Legacy plans
 
@@ -220,21 +235,24 @@ Read for this note (2026-10-16):
 
 ## Where each part lives
 
-| part                                                          | file                                  | layer   |
-| ------------------------------------------------------------- | ------------------------------------- | ------- |
-| the modes, what is an output, which decision a mode waits on  | `src/domain/study-mode.ts`            | domain  |
-| the order judge and its messages                              | `src/domain/decide-first.ts`          | domain  |
-| the index's mode columns and the history they show            | `src/domain/index-columns.ts`         | domain  |
-| the index, which columns the lint compares, `isFolderName`    | `src/domain/study-registry.ts`        | domain  |
-| the schema of `mode`; readiness by kind                       | `src/adapters/study-registry/`        | adapter |
-| git: committed state, first commits, ancestry, shallow        | `src/adapters/git/`                   | adapter |
-| what the app asks of git                                      | `src/ports/git-history.ts`            | port    |
-| a directory's entries, links not followed                     | `src/ports/list-entries.ts`           | port    |
-| the studies with a mode, and the files under a study's folder | `src/study-modes.ts`                  | app     |
-| the order rule                                                | `src/outputs-before-decision-rule.ts` | app     |
-| the plans and histories `studies index` and `new` write from  | `src/study-index-input.ts`            | app     |
-| `gate`; `new` and `index`                                     | `src/study-gate.ts`, `src/studies.ts` | app     |
-| wiring: git with PATH and HOME, the clock                     | `src/cli.ts`                          | root    |
+| part                                                         | file                                  | layer   |
+| ------------------------------------------------------------ | ------------------------------------- | ------- |
+| the modes, what is an output, which decision a mode waits on | `src/domain/study-mode.ts`            | domain  |
+| the order judge and its messages                             | `src/domain/decide-first.ts`          | domain  |
+| the index's mode columns and the history they show           | `src/domain/index-columns.ts`         | domain  |
+| the index, which columns the lint compares, `isFolderName`   | `src/domain/study-registry.ts`        | domain  |
+| the schema of `mode`; readiness by kind                      | `src/adapters/study-registry/`        | adapter |
+| git: committed state, first commits, ancestry, shallow       | `src/adapters/git/`                   | adapter |
+| what the app asks of git                                     | `src/ports/git-history.ts`            | port    |
+| a directory's entries, links not followed                    | `src/ports/list-entries.ts`           | port    |
+| the studies with a mode, and how a decision's path stands    | `src/study-modes.ts`                  | app     |
+| what the study readers need of a study's folder              | `src/ports/study-folder.ts`           | port    |
+| what the study readers are handed                            | `src/ports/study-deps.ts`             | port    |
+| the one reader of a study's folder, links not followed       | `src/study-folder.ts`                 | app     |
+| the order rule                                               | `src/outputs-before-decision-rule.ts` | app     |
+| the plans and histories `studies index` and `new` write from | `src/study-index-input.ts`            | app     |
+| `gate`; `new` and `index`                                    | `src/study-gate.ts`, `src/studies.ts` | app     |
+| wiring: git with PATH and HOME, the clock                    | `src/cli.ts`                          | root    |
 
 ## What it does not check
 

package/docs/rules/repro/outputs-before-decision.md

@@ -36,6 +36,9 @@ A study decided before its run — its plan's `mode` is `decide_before_run`, the
   a directory with the commits of anything under it, and records a link rather than the file it
   points to, so no order is read from either. (A path that names the paper's folder
   itself, `.`, or ends in `/` is refused when the plan is parsed.)
+- **`decision-linked`** — the decision path passes through a symbolic link above the file: git
+  records the link, not the files behind it, so no order is read from it, and the finding names the
+  link.
 - **`shallow`** — the clone is shallow, so every file's first commit is the clone's: no order can be
   read, and the rule says so instead of judging.
 - **`no-history`** — git could not answer (not installed, not a repository).

package/docs/rules/repro/study-registered.md

@@ -209,7 +209,7 @@ The rule reports:
   must meet a requirement the registry does not hold (`unknown-requirement`);
 - a `headline` measurement with no `approval`, or, when the registry names its `author`, one approved
   by anyone else (`headline-approval`);
-- a row's `plan` that is outside its folder, not a file, or not of the plan's shape — and, once the
+- a row's `plan` that is outside its folder, not a file, reached through a symbolic link, or not of the plan's shape — and, once the
   study has run (`running`, `done`, `stopped`, `superseded`), a plan that leaves `question`,
   `population.source`, `population.draw.method` or `primary_outcome` empty, or — for a measurement —
   declares no `mode` or leaves one of its texts empty (`bad-plan`);
@@ -316,7 +316,8 @@ No rule options.
 - Whether the paper cites a study: `in_paper` is declared, not detected.
 - The index's `decision` and `first output` cells: they name commits a squash merge renames.
 - Inside a study folder that is a symbolic link: nothing is read through it, so its plan and its
-  result file read as missing.
+  result file read as missing. A plan or a result file whose path passes through a link inside the
+  folder is not read either, and is reported naming the link (`bad-plan`, `result-file`).
 - What may stand at the top of `repro/` besides the study folders, and whether a study folder has a
   `README.md`: that is [`repro/allowed-files-only`](allowed-files-only.md).
 

package/docs/rules/tex/heading-case.md

@@ -376,7 +376,7 @@ author wrote. Two corpora, 2026-10-03, both measured on headings, before the rul
 - **The accepted paper in this repository**, `fixtures/accepted-papers/agenticdev-acm26`: 9
   headings, 6 of them in sentence case, which the vendor's checklist does not accept. The rule
   reports 18 words, every one a true positive, and its fixes write the six corrected
-  headings ([`fixtures/accepted-papers/README.md`](../../../fixtures/accepted-papers/README.md)).
+  headings ([`fixtures/accepted-papers/README.md`](https://github.com/zernie/paperlint/blob/main/fixtures/accepted-papers/README.md)).
   Its `\title` and short title, read since 2026-10-04, are already in headline style and add no
   finding.
 - **277 `acmart` sources from arXiv** (authors' versions of papers whose arXiv comment names an ACM

package/eslint.config.mjs

@@ -212,27 +212,33 @@ export const IO_MODULES = [
   "readline/promises",
 ].flatMap((m) => [m, `node:${m}`]);
 
-/** What the inside may import from outside the repository: types, pure path arithmetic, hashing. */
-export const INSIDE_EXTERNALS = [
-  "ts-essentials",
-  "path",
-  "node:path",
-  "crypto",
-  "node:crypto",
-];
-/** What the flat app files may import besides: Node's pure helpers, measured on the first v7 run. */
-export const APP_EXTERNALS = [
-  ...INSIDE_EXTERNALS,
-  "util",
-  "node:util",
-  "url",
-  "node:url",
-  "module",
-  "node:module",
-];
+/**
+ * The npm packages that exist because of ONE external program or format, from `dependencies` in
+ * package.json: only that tool's adapter (or `src/cli.ts`, the root) imports them; the domain, a
+ * port and the app take a port. A package that exists because of one external tool goes here in the
+ * same PR that adds its adapter. A pure utility library (remeda, zod, ts-essentials) needs nothing:
+ * the inside may import every package and Node built-in that is not listed here and is not an effect
+ * (`IO_MODULES`).
+ */
+export const TOOL_PACKAGES = [
+  "@eslint/markdown", // ESLint's Markdown language
+  "@eslint/plugin-kit",
+  "@retorquere/bibtex-parser", // BibTeX
+  "@unified-latex/unified-latex-types", // LaTeX
+  "@unified-latex/unified-latex-util-parse",
+  "@unified-latex/unified-latex-util-visit",
+  "ajv", // JSON Schema
+  "eslint",
+  "js-yaml", // YAML
+  "markdown-it", // Markdown
+  "mp4box", // MP4
+  "srt-parser-2", // SRT subtitles
+  "typescript", // the compiler API
+  "unpdf", // PDF
+  "vigiles", // the agent harness
+].flatMap((m) => [m, `${m}/**`]);
 
 const ORIGINS = ["external", "core"];
-const modules = (source) => ({ to: { module: { origin: ORIGINS, source } } });
 const elements = (...types) => ({ element: { types: { anyOf: types } } });
 const APP = { file: { categories: "app" } };
 const ROOT = { file: { categories: "root" } };
@@ -337,14 +343,20 @@ export const layerBoundaries = (root) => ({
             allow: { to: elements("js-module") },
           },
           // ── libraries and built-ins (the plugin calls Node built-ins origin "core") ──
+          // Everyone may import any package and built-in …
           {
-            from: elements("domain", "port"),
-            allow: modules(INSIDE_EXTERNALS),
+            from: [elements("domain", "port", "adapter"), APP, ROOT],
+            allow: { to: { module: { origin: ORIGINS } } },
           },
-          { from: APP, allow: modules(APP_EXTERNALS) },
+          // … but the inside — not an adapter, not the root — not a package that exists because of
+          // one external tool (TOOL_PACKAGES). Effects are axis B's, below.
           {
-            from: [elements("adapter"), ROOT],
-            allow: { to: { module: { origin: ORIGINS } } },
+            from: [elements("domain", "port"), APP],
+            disallow: {
+              to: { module: { origin: "external", source: TOOL_PACKAGES } },
+            },
+            message:
+              "{{ dependency.source }} exists because of one external tool or format: only that tool's adapter (src/adapters/<tool>/) and src/cli.ts import it; this file takes a port (src/CLAUDE.md, layers). A new package of that kind is listed in TOOL_PACKAGES in the PR that adds its adapter.",
           },
           // Tests may import anything, fakes included …
           {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "paperlint",
-  "version": "10.4.0",
+  "version": "10.4.1",
   "description": "A linter for scientific papers written in LaTeX: catches mistakes before you submit to a conference or journal.",
   "type": "module",
   "license": "MIT",

package/skills/grade-paper-writing/SKILL.md

@@ -4,7 +4,7 @@ description: Grade how a paper reads and fix it sentence by sentence. Use when a
 allowed-tools: [Read, Write, Edit, Grep, Glob, Agent, Skill]
 ---
 
-<!-- vigiles:sha256:1897016b69f3f9b8 compiled from skills/grade-paper-writing/SKILL.md.spec.ts -->
+<!-- vigiles:sha256:2b7193c739a374e6 compiled from skills/grade-paper-writing/SKILL.md.spec.ts -->
 
 # grade-paper-writing — grade how the paper READS, then fix it sentence by sentence
 
@@ -223,7 +223,9 @@ is what happened.
    ```
 
    It measures the prose a reader sees — the files the last build read spliced in, no preamble,
-   comments, floats or inline `.bib` — so its rates are the paper's, not the source file's. Run
+   comments, floats or inline `.bib` — so its rates are the paper's, not the source file's — and, on
+   its own line, the figure captions that float outside that prose, flagging a caption sentence over
+   40 words or a caption over 100. Run
    `npx paperlint build` first: with no current build record it reads `paper.tex` alone and says so. The skill is what must ACT on it.
    Its thresholds are sourced; a FLAG means the text sits above a published human or machine
    baseline, which is a defect with a number attached, not an opinion.

package/skills/grade-paper-writing/SKILL.md.spec.ts

@@ -229,7 +229,9 @@ is what happened.
    \`\`\`
 
    It measures the prose a reader sees — the files the last build read spliced in, no preamble,
-   comments, floats or inline \`.bib\` — so its rates are the paper's, not the source file's. Run
+   comments, floats or inline \`.bib\` — so its rates are the paper's, not the source file's — and, on
+   its own line, the figure captions that float outside that prose, flagging a caption sentence over
+   40 words or a caption over 100. Run
    \`npx paperlint build\` first: with no current build record it reads \`paper.tex\` alone and says so. The skill is what must ACT on it.
    Its thresholds are sourced; a FLAG means the text sits above a published human or machine
    baseline, which is a defect with a number attached, not an opinion.