paperlint 10.2.0 → 10.4.0

package/dist/domain/study-registry.js

@@ -10,12 +10,16 @@
  * ── JSON, NEVER MARKDOWN ─────────────────────────────────────────────────────────
  * The registry is data: its text is parsed once, where it enters, against the schema in
  * `src/adapters/study-registry/` (`StudyRegistryCodec`). The index in `repro/README.md` is OUTPUT: it is
- * generated from the registry and compared as a string, between two fixed markers. Nothing parses it.
+ * generated from the registry, the plans' modes and git's history (src/domain/index-columns.ts), and
+ * compared cell by cell between two fixed markers, the two columns read from git left out. Nothing
+ * else parses it.
  *
  * Pure: the caller lists `repro/`, reads the registry and the README, and says which result files exist.
  */
 import { isAbsolute, posix, win32 } from "node:path";
 import { STUDIES_FILE, STUDY_SLUG } from "./repro-layout.js";
+import { needsMode } from "./study-mode.js";
+import { decisionCell, firstOutputCell, modeCell, } from "./index-columns.js";
 /** The registry, at the top of the paper's `repro/`; the layout allows it there. */
 export { STUDIES_FILE };
 export const STUDY_KINDS = [
@@ -47,6 +51,76 @@ export const INDEX_BEGIN = "<!-- studies:begin — generated from studies.json b
 export const INDEX_END = "<!-- studies:end -->";
 /** The README written when `repro/` has none. */
 const INDEX_HEADING = "# Reproduction index";
+/** What a measurement is to the paper: the claim it carries, or what that claim is compared with. */
+export const MEASUREMENT_ROLES = ["headline", "baseline"];
+/**
+ * The statuses of a study that has run: its plan was due before the first run. A `designing` study
+ * has not run yet, and a `dropped` one never will.
+ */
+export const RAN_STATUSES = [
+    "running",
+    "done",
+    "stopped",
+    "superseded",
+];
+/** The file `paperlint studies new` writes a study's plan to, beside its README.md. */
+export const PLAN_FILE = "plan.json";
+/** The plan's name before it was a plan: still read as one, and reported by `repro/study-plan-name`. */
+export const LEGACY_PLAN_FILE = "prereg.json";
+/** The top-level fields of a plan: none of them may be a key of `extra`. */
+export const PLAN_FIELDS = [
+    "question",
+    "population",
+    "arms",
+    "primary_outcome",
+    "author_check",
+    "extra",
+    "mode",
+];
+/** The texts a plan must fill before the study runs, in the order they are named. */
+export const PLAN_TEXT_FIELDS = [
+    "question",
+    "population.source",
+    "population.draw.method",
+    "primary_outcome",
+    "mode",
+    "mode.outputs",
+    "mode.decision.file",
+    "mode.decision.note",
+    "mode.reason",
+];
+/** The decision file `paperlint studies new` names for a study in `folder`, relative to the paper. */
+export const decisionPath = (folder) => `repro/${folder}/${DECISION_FILE}`;
+/** The decision file's name, beside the plan. */
+export const DECISION_FILE = "decision.md";
+/**
+ * The plan `paperlint studies new` writes for a study of `kind` in `folder`: every field present, its
+ * value to fill. Its draw is of all the population (a census); a sampled study changes it to
+ * `{ "kind": "seeded", "method", "seed" }`. A study that must declare its mode gets the default one,
+ * decided before the run, its decision file named and its outputs and note to fill.
+ */
+export const planTemplate = (kind, folder) => ({
+    question: "",
+    population: { source: "", draw: { kind: "all", method: "" } },
+    arms: [],
+    primary_outcome: "",
+    author_check: null,
+    ...(needsMode(kind)
+        ? {
+            mode: {
+                kind: "decide_before_run",
+                outputs: [],
+                decision: { file: decisionPath(folder), note: "" },
+            },
+        }
+        : {}),
+});
+/** A plan's text as `paperlint studies new` writes it: JSON, two-space indented, a final newline. */
+export const planText = (p) => `${JSON.stringify(p, null, 2)}\n`;
+/** The findings `repro/study-plan-name` reports, a warning; every other is `repro/study-registered`'s. */
+export const PLAN_NAME_PROBLEMS = [
+    "legacy-plan",
+];
 /** The number of an id of `prefix` (`P1-S07` → 7); null for an id of another shape. */
 function idNumber(prefix, id) {
     const m = new RegExp(`^${prefix}-S(\\d{2,})$`, "u").exec(id);
@@ -73,12 +147,27 @@ export const titleWords = (title) => title.split(/\s+/u).filter((w) => w !== "")
  * Whether `path` stays inside the folder it is relative to. A backslash or a Windows absolute path
  * is refused outright: `posix.normalize` does not resolve `..\\`, while the host's `join` may.
  */
-const isInside = (path) => {
+export const isInside = (path) => {
     if (path.includes("\\") || isAbsolute(path) || win32.isAbsolute(path))
         return false;
     const n = posix.normalize(path);
     return n !== ".." && !n.startsWith("../");
 };
+/**
+ * Whether `folder` names one folder directly inside `repro/`: not empty, not `.` or `..`, and no
+ * separator or NUL. Every command and rule that reads a study's folder reads only such a one: a row
+ * naming `../x` would have them read and write outside the paper.
+ */
+export const isFolderName = (folder) => folder !== "." && folder !== ".." && /^[^/\\\0]+$/u.test(folder);
+/**
+ * The `<folder>/<plan>` of each row whose plan lies inside its folder: the files the judge needs read
+ * (`StudyInput.plans`). A plan outside its folder is reported without being read.
+ */
+export const planKeys = (r) => planRefs(r).map((p) => p.key);
+/** Each plan `planKeys` names, with the kind of the study whose row names it: what its parser needs. */
+export const planRefs = (r) => r.studies.flatMap((s) => s.plan !== undefined && isInside(s.plan) && isFolderName(s.folder)
+    ? [{ key: `${s.folder}/${s.plan}`, folder: s.folder, kind: s.kind }]
+    : []);
 /** Whether the row is the first of the registry with its value of `key`. */
 const isFirst = ({ r, s, i }, key) => r.studies.findIndex((o) => key(o) === key(s)) === i;
 const badId = ({ r, s }) => idNumber(r.prefix, s.id) === null
@@ -139,6 +228,82 @@ const noSuccessor = ({ r, s }) => {
         ? { problem: "no-successor", id: s.id, superseded_by: by }
         : null;
 };
+/** A row's `measurement`, when the registry declares its measurements, names one of them. */
+const unknownMeasurement = ({ r, s }) => r.measurements === undefined ||
+    s.measurement === undefined ||
+    r.measurements.some((m) => m.id === s.measurement)
+    ? null
+    : { problem: "unknown-measurement", id: s.id, measurement: s.measurement };
+/** The state of the plan the row names (absent when outside its folder); null when it names none. */
+const planOf = ({ s, input }) => {
+    if (s.plan === undefined)
+        return null;
+    return isInside(s.plan)
+        ? (input.plans.get(`${s.folder}/${s.plan}`) ?? { kind: "absent" })
+        : { kind: "absent" };
+};
+const hasRun = (s) => RAN_STATUSES.includes(s.status);
+/** The finding for the plan `path` of `s`, in the state its folder holds it; null when it stands. */
+const planFinding = (s, path, state) => {
+    const at = { problem: "bad-plan", id: s.id, path };
+    switch (state.kind) {
+        case "absent":
+            return { ...at, why: "missing" };
+        case "unreadable":
+            return { ...at, why: "unreadable", reasons: state.why };
+        case "draft":
+            return hasRun(s)
+                ? { ...at, why: "unfilled", fields: state.empty, status: s.status }
+                : null;
+        case "ready":
+            return null;
+    }
+};
+/** The plan a row names is a file inside its folder, of the schema, and ready once the study has run. */
+const badPlan = ({ s, input }) => {
+    const path = s.plan;
+    if (path === undefined)
+        return null;
+    if (!isInside(path))
+        return { problem: "bad-plan", id: s.id, path, why: "outside" };
+    return planFinding(s, path, input.plans.get(`${s.folder}/${path}`) ?? { kind: "absent" });
+};
+/** A plan under its old name: read, and named for renaming. */
+const legacyPlan = ({ s }) => s.plan !== undefined && posix.basename(s.plan) === LEGACY_PLAN_FILE
+    ? { problem: "legacy-plan", id: s.id, path: s.plan }
+    : null;
+/**
+ * A study of a headline measurement that has run carries the author's check of its drawn units in
+ * its plan, by the registry's author when it names one. A plan that cannot be read is `badPlan`'s.
+ */
+const authorCheck = (row) => {
+    const { r, s } = row;
+    const m = r.measurements?.find((o) => o.id === s.measurement);
+    if (m?.role !== "headline" || !hasRun(s))
+        return null;
+    const at = {
+        problem: "author-check",
+        id: s.id,
+        measurement: m.id,
+        status: s.status,
+    };
+    const state = planOf(row);
+    if (state === null)
+        return { ...at, why: "no-plan" };
+    const wrong = state.kind === "ready" || state.kind === "draft"
+        ? checkProblem(r, state.plan)
+        : null;
+    return wrong === null ? null : { ...at, ...wrong };
+};
+/** What a read plan's author check lacks: it is not there, or it is not the registry's author's. */
+const checkProblem = (r, plan) => {
+    const check = plan.author_check;
+    if (check === null)
+        return { why: "missing" };
+    return r.author === undefined || check.by === r.author
+        ? null
+        : { why: "not-author", by: check.by, author: r.author };
+};
 /** The checks of a row, in the order their findings are reported. */
 const ROW_CHECKS = [
     badId,
@@ -150,17 +315,60 @@ const ROW_CHECKS = [
     noResult,
     resultFile,
     noSuccessor,
+    unknownMeasurement,
+    badPlan,
+    legacyPlan,
+    authorCheck,
 ];
+/** A headline measurement's approval: missing, or not the registry's author's; null when it stands. */
+const headlineApproval = (r, m) => {
+    if (m.role !== "headline")
+        return null;
+    const author = r.author ?? null;
+    if (m.approval === undefined)
+        return {
+            problem: "headline-approval",
+            measurement: m.id,
+            why: "missing",
+            author,
+        };
+    return author === null || m.approval.by === author
+        ? null
+        : {
+            problem: "headline-approval",
+            measurement: m.id,
+            why: "not-author",
+            by: m.approval.by,
+            author,
+        };
+};
+/** What is wrong with one measurement: no study, a requirement not held, a headline not approved. */
+const judgeMeasurement = (r, m) => {
+    const approval = headlineApproval(r, m);
+    return [
+        ...(r.studies.some((s) => s.measurement === m.id)
+            ? []
+            : [{ problem: "empty-measurement", measurement: m.id }]),
+        ...(m.requirements ?? [])
+            .filter((id) => !(r.requirements ?? []).some((q) => q.id === id))
+            .map((requirement) => ({
+            problem: "unknown-requirement",
+            measurement: m.id,
+            requirement,
+        })),
+        ...(approval === null ? [] : [approval]),
+    ];
+};
 /** What is wrong with a row, in a fixed order. */
 const judgeRow = (row) => ROW_CHECKS.map((check) => check(row)).filter((f) => f !== null);
 /** Whether the README's index is the one `r` generates; the finding when not. */
-function judgeIndex(r, readme) {
+function judgeIndex(r, readme, plans) {
     if (readme === null)
         return { problem: "stale-index", why: "no-readme" };
     const block = embeddedIndex(readme);
     if (block === null)
         return { problem: "stale-index", why: "no-markers" };
-    return indexInSync(readme, r)
+    return indexInSync(readme, r, { plans, history: new Map() })
         ? null
         : { problem: "stale-index", why: "differs" };
 }
@@ -178,7 +386,7 @@ export function judgeStudies(input) {
         return [{ problem: "unreadable", why: state.why }];
     const r = state.registry;
     const next = nextStudyId(r);
-    const index = judgeIndex(r, input.readme);
+    const index = judgeIndex(r, input.readme, input.plans);
     return [
         ...input.folders
             .filter((f) => !r.studies.some((s) => s.folder === f))
@@ -188,21 +396,50 @@ export function judgeStudies(input) {
             next,
         })),
         ...r.studies.flatMap((s, i) => judgeRow({ r, s, i, input })),
+        ...(r.measurements ?? []).flatMap((m) => judgeMeasurement(r, m)),
         ...(index === null ? [] : [index]),
     ];
 }
 // ── the index ─────────────────────────────────────────────────────────────────────
 /** A cell's text: one line, a backslash and then a pipe escaped, so `a\\|b` stays one cell. */
 const cell = (s) => s.replace(/\r?\n/gu, " ").replace(/\\/gu, "\\\\").replace(/\|/gu, "\\|");
-/** The columns of the index: each one's header, and its cell for a study. */
+/** The mode the plan of `s` declares; null when it names none, or the plan is absent or unreadable. */
+const declaredMode = (s, plans) => {
+    const state = s.plan !== undefined && isInside(s.plan)
+        ? plans.get(`${s.folder}/${s.plan}`)
+        : undefined;
+    return state === undefined ||
+        state.kind === "absent" ||
+        state.kind === "unreadable"
+        ? null
+        : (state.plan.mode ?? null);
+};
+/** What the index shows of `s` beyond its row. */
+const factsOf = (s, at) => ({
+    mode: declaredMode(s, at.plans),
+    history: at.history.get(s.id) ?? null,
+});
+/**
+ * The columns of the index: each one's header, its cell for a study, and whether git's history is
+ * where the cell comes from — those two are never compared (src/domain/index-columns.ts).
+ */
 const COLUMNS = [
-    { head: "id", of: (s) => s.id },
-    { head: "title", of: (s) => cell(s.title) },
-    { head: "status", of: (s) => s.status },
-    { head: "result", of: (s) => cell(s.result ?? "—") },
-    { head: "in paper", of: (s) => s.in_paper },
-    { head: "folder", of: (s) => `[${s.folder}/](${s.folder}/)` },
+    { head: "id", of: (s) => s.id, fromGit: false },
+    { head: "title", of: (s) => cell(s.title), fromGit: false },
+    { head: "status", of: (s) => s.status, fromGit: false },
+    { head: "result", of: (s) => cell(s.result ?? "—"), fromGit: false },
+    { head: "in paper", of: (s) => s.in_paper, fromGit: false },
+    { head: "mode", of: (_, f) => cell(modeCell(f)), fromGit: false },
+    { head: "decision", of: (_, f) => decisionCell(f), fromGit: true },
+    { head: "first output", of: (_, f) => firstOutputCell(f), fromGit: true },
+    {
+        head: "folder",
+        of: (s) => `[${s.folder}/](${s.folder}/)`,
+        fromGit: false,
+    },
 ];
+/** The positions of the columns read from git: left out when an index is compared. */
+const FROM_GIT = COLUMNS.flatMap((c, i) => (c.fromGit ? [i] : []));
 /** The width a cell takes: its code points. */
 const widthOf = (s) => Array.from(s).length;
 /** `t` padded to `width`. */
@@ -212,16 +449,17 @@ const padded = (t, width) => t + " ".repeat(width - widthOf(t));
  * widest cell (at least 3), the way prettier writes a table — so formatting the README leaves it as
  * it is.
  */
-export function studyIndex(r) {
+export function studyIndex(r, at) {
+    const studies = r.studies.map((s) => ({ s, f: factsOf(s, at) }));
     const sized = COLUMNS.map((c) => ({
         ...c,
-        width: Math.max(3, widthOf(c.head), ...r.studies.map((s) => widthOf(c.of(s)))),
+        width: Math.max(3, widthOf(c.head), ...studies.map(({ s, f }) => widthOf(c.of(s, f)))),
     }));
     const line = (cells) => `| ${cells.join(" | ")} |`;
     return [
         line(sized.map((c) => padded(c.head, c.width))),
         line(sized.map((c) => "-".repeat(c.width))),
-        ...r.studies.map((s) => line(sized.map((c) => padded(c.of(s), c.width)))),
+        ...studies.map(({ s, f }) => line(sized.map((c) => padded(c.of(s, f), c.width)))),
     ].join("\n");
 }
 /**
@@ -229,7 +467,7 @@ export function studyIndex(r) {
  * `---`. The index is judged on this, because the padding belongs to the formatter: prettier sizes a
  * column by display width, so a wide character pads differently from a code-point count.
  */
-const cellsOf = (table) => table
+const cellsOf = (table, skip) => table
     .trim()
     .split("\n")
     .map((line) => line
@@ -237,15 +475,26 @@ const cellsOf = (table) => table
     .replace(/^\||\|$/gu, "")
     .split(/(?<!\\)\|/u)
     .map((c) => c.trim().replace(/^:?-{3,}:?$/u, "---"))
+    .filter((_, i) => !skip.includes(i))
     .join("|"))
     .join("\n");
-/** Whether `readme` holds the index of `r`, whatever padding a formatter gave its table. */
-export function indexInSync(readme, r) {
+/** Whether `readme` holds the index of `r` in every column but those at `skip`, whatever its padding. */
+const sameCells = (readme, index, skip) => {
     const block = readme === null ? null : embeddedIndex(readme);
-    return block !== null && cellsOf(block) === cellsOf(studyIndex(r));
-}
+    return block !== null && cellsOf(block, skip) === cellsOf(index, skip);
+};
+/**
+ * Whether `readme` holds the index of `r`, whatever padding a formatter gave its table and whatever
+ * its two columns read from git say: what `repro/study-registered` checks.
+ */
+export const indexInSync = (readme, r, at) => sameCells(readme, studyIndex(r, at), FROM_GIT);
+/**
+ * Whether `readme` holds the index of `r` in every column, whatever its padding: when it does,
+ * `studies index` leaves the README as it is, so the padding a formatter gave the table stays.
+ */
+export const indexCurrent = (readme, r, at) => sameCells(readme, studyIndex(r, at), []);
 /** The index between its markers, a blank line on each side. */
-export const indexBlock = (r) => `${INDEX_BEGIN}\n\n${studyIndex(r)}\n\n${INDEX_END}`;
+export const indexBlock = (r, at) => `${INDEX_BEGIN}\n\n${studyIndex(r, at)}\n\n${INDEX_END}`;
 /**
  * Where `marker` stands alone on a line of `text`, at or after `from`; -1 when it does not. A marker
  * counts only there, where the generator writes it: prose can mention it and a cell can carry it, but
@@ -266,15 +515,16 @@ export function embeddedIndex(readme) {
  * `readme` with its index regenerated from `r`: the block replaced in place, appended when the README
  * has none, a README of its own when there is none.
  */
-export function withIndex(readme, r) {
+export function withIndex(readme, r, at) {
+    const fresh = indexBlock(r, at);
     if (readme === null)
-        return `${INDEX_HEADING}\n\n${indexBlock(r)}\n`;
+        return `${INDEX_HEADING}\n\n${fresh}\n`;
     const block = embeddedIndex(readme);
     if (block === null)
-        return `${readme.trimEnd()}\n\n${indexBlock(r)}\n`;
+        return `${readme.trimEnd()}\n\n${fresh}\n`;
     const begin = markerAt(readme, INDEX_BEGIN);
     const after = begin + INDEX_BEGIN.length + block.length + INDEX_END.length;
-    return `${readme.slice(0, begin)}${indexBlock(r)}${readme.slice(after)}`;
+    return `${readme.slice(0, begin)}${fresh}${readme.slice(after)}`;
 }
 /** The registry's text as `paperlint studies new` writes it: JSON, two-space indented, a final newline. */
 export const registryText = (r) => `${JSON.stringify(r, null, 2)}\n`;
@@ -284,6 +534,13 @@ const NEW_STUDY = '`npx paperlint studies new <paper-dir> "<title>"`';
 const RUN_INDEX = "What to do: run `npx paperlint studies index <paper-dir>`; the block is generated, never edited by hand.";
 const RENAME = "give each other row the next free id and rename its folder to match";
 const tick = (s) => `\`${s}\``;
+/** `a`, `b` and `c`: names in backticks, the last joined by "and". */
+const listed = (names) => {
+    const t = names.map(tick);
+    return [t.slice(0, -1).join(", "), ...t.slice(-1)]
+        .filter((part) => part !== "")
+        .join(" and ");
+};
 const STALE_HEAD = {
     differs: `The index in \`repro/README.md\` (between the \`studies:begin\` and \`studies:end\` markers) is not the one ${REGISTRY} generates.`,
     "no-markers": "`repro/README.md` has no index of the studies (the `studies:begin` and `studies:end` markers).",
@@ -304,11 +561,47 @@ const HEADS = {
     "result-file": (f) => `${REGISTRY}: the \`result_file\` of ${tick(f.id)}, ${tick(f.path)}, ${f.why === "missing" ? "is not a file in its folder" : "is outside its folder"}. What to do: name a file that exists, relative to the study's folder.`,
     "no-successor": (f) => `${REGISTRY}: ${tick(f.id)} is \`superseded\` ${f.superseded_by === null ? "without `superseded_by`" : `by ${tick(f.superseded_by)}, which is no study in the registry`}. What to do: name the id of the study that replaced it.`,
     "stale-index": (f) => `${STALE_HEAD[f.why]} ${RUN_INDEX}`,
+    "unknown-measurement": (f) => `${REGISTRY}: the row ${tick(f.id)} names the measurement ${tick(f.measurement)}, which is not in \`measurements\`. What to do: add the measurement to \`measurements\`, or correct the row's \`measurement\`.`,
+    "empty-measurement": (f) => `${REGISTRY}: no row names the measurement ${tick(f.measurement)}, and a measurement is made of studies. What to do: set \`"measurement": "${f.measurement}"\` on the rows of its studies, or remove the measurement.`,
+    "unknown-requirement": (f) => `${REGISTRY}: the measurement ${tick(f.measurement)} must meet the requirement ${tick(f.requirement)}, which is not in \`requirements\`. What to do: add the requirement — the author's words verbatim in \`text\`, with its \`date\` and \`source\` — or correct the measurement's \`requirements\`.`,
+    "headline-approval": (f) => f.why === "missing"
+        ? `${REGISTRY}: the measurement ${tick(f.measurement)} is a \`headline\` one and has no \`approval\`. What to do: record ${f.author === null ? "the author's approval" : `the approval of ${f.author}, the registry's \`author\``} — \`by\`, \`date\`, and their words in \`quote\` — or make it a \`baseline\`.`
+        : `${REGISTRY}: the measurement ${tick(f.measurement)} is a \`headline\` one, and its \`approval\` is by ${f.by}, not by the registry's \`author\`, ${f.author}. What to do: only the author approves a headline measurement; record their own approval.`,
+    "bad-plan": (f) => {
+        const of = `the \`plan\` of ${tick(f.id)}, ${tick(f.path)},`;
+        const plan = `The plan of ${tick(f.id)}, ${tick(f.path)} in its folder,`;
+        switch (f.why) {
+            case "missing":
+                return `${REGISTRY}: ${of} is not a file in its folder. What to do: write the plan there (its fields are on the rule's page), or correct the row's \`plan\`.`;
+            case "outside":
+                return `${REGISTRY}: ${of} is outside its folder. What to do: keep the plan in the study's folder, as \`${PLAN_FILE}\`, and name it relative to the folder.`;
+            case "unreadable":
+                return `${plan} is not a study plan: ${f.reasons}. What to do: give it the fields on the rule's page — \`question\`, \`population\`, \`arms\`, \`primary_outcome\`, and for a measurement its \`mode\`.`;
+            case "unfilled":
+                return `${plan} leaves ${listed(f.fields)} empty, and the study is ${tick(f.status)}: a plan is written before the runs. What to do: fill them in, or set the study back to \`designing\`.`;
+        }
+    },
+    "author-check": (f) => {
+        const head = `${tick(f.id)} is ${tick(f.status)} in the headline measurement ${tick(f.measurement)}, and`;
+        switch (f.why) {
+            case "no-plan":
+                return `${head} its row names no plan to hold the author's check of the drawn units. What to do: write its plan (\`${PLAN_FILE}\` in its folder, named in the row's \`plan\`) with \`author_check\` — \`by\`, \`date\`, and the author's words in \`quote\`.`;
+            case "missing":
+                return `${head} its plan has no \`author_check\`. What to do: show the author the drawn units, then record their answer in the plan's \`author_check\` — \`by\`, \`date\`, and their words in \`quote\`.`;
+            case "not-author":
+                return `${head} the \`author_check\` in its plan is by ${f.by}, not by the registry's \`author\`, ${f.author}. What to do: only the author approves the drawn units of a headline measurement; record their own answer.`;
+        }
+    },
+    "legacy-plan": (f) => `The plan of ${tick(f.id)} is ${tick(f.path)}, its old name; it is read as the plan. What to do: rename it to \`${PLAN_FILE}\` in the study's folder (\`git mv\`) and set the row's \`plan\` to \`${PLAN_FILE}\`.`,
 };
 /** The head of finding `f` of problem `p`: the lookup, typed by the problem. */
 const headOf = (p, f) => HEADS[p](f);
+/** The rule that reports finding `f`. */
+const ruleOf = (f) => PLAN_NAME_PROBLEMS.includes(f.problem)
+    ? "repro/study-plan-name"
+    : "repro/study-registered";
 /** The one text a finding is reported with: what is wrong, what to do, and the rule's page. */
-export const studyMessage = (f) => `${headOf(f.problem, f)}\nRule repro/study-registered: https://github.com/zernie/paperlint/blob/main/docs/rules/repro/study-registered.md`;
+export const studyMessage = (f) => `${headOf(f.problem, f)}\nRule ${ruleOf(f)}: https://github.com/zernie/paperlint/blob/main/docs/rules/${ruleOf(f)}.md`;
 // ── a new study ───────────────────────────────────────────────────────────────────
 /** Whether `s` names a kind of study. */
 export const isStudyKind = (s) => STUDY_KINDS.some((k) => k === s);
@@ -325,7 +618,7 @@ function titleProblem(title) {
 }
 /**
  * `r` with a new study appended: the next id, the folder `<id>-<slug>`, `status: designing`,
- * `in_paper: no` and an empty question; or why the title cannot make one.
+ * `in_paper: no`, an empty question and its plan, `plan.json`; or why the title cannot make one.
  */
 export function addStudy(r, n) {
     const title = n.title.trim().replace(/\s+/gu, " ");
@@ -342,6 +635,7 @@ export function addStudy(r, n) {
         status: "designing",
         date: n.date,
         in_paper: "no",
+        plan: PLAN_FILE,
     };
     return {
         ok: true,
@@ -361,6 +655,10 @@ export const studyReadme = (s) => [
     `Its row in \`../${STUDIES_FILE}\` holds its status. When the study ends, set \`status\`, \`result\`,`,
     "`result_file` and `in_paper` there, then run `npx paperlint studies index <paper-dir>`.",
     "",
+    `Its plan is \`${PLAN_FILE}\`: what it measures, the population and the draw, the arms and the primary`,
+    "outcome, filled in before the first run; the author's check of the drawn units goes in its",
+    "`author_check`.",
+    "",
     "## Question",
     "",
     "## How to run",

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

@@ -1 +1 @@
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package/dist/outputs-before-decision-rule.d.ts

@@ -0,0 +1,17 @@
+import { type StudyDeps } from "./study-modes.ts";
+import { type DecideFirstStudy } from "./domain/decide-first.ts";
+import type { FolderRuleModule } from "./folder-venue-rule.ts";
+import type { GitOrder } from "./ports/git-history.ts";
+/** What the rule reads with: the registry's, and git's order. */
+export interface OrderDeps extends StudyDeps {
+    readonly git: GitOrder;
+}
+/** Every decide-first study of the paper folder `paper`, with its tree and its history's order. */
+export declare const decideFirstStudies: (paper: string, deps: OrderDeps) => readonly DecideFirstStudy[];
+/** The rule, reading the folder and git through `deps`. */
+export declare const outputsBeforeDecisionRules: (deps: OrderDeps) => Readonly<Record<"outputs-before-decision", FolderRuleModule>>;
+/** Its level in paperlint's own config: an error. */
+export declare const ORDER_RULE_LEVELS: Readonly<{
+    "repro/outputs-before-decision": "error";
+}>;
+//# sourceMappingURL=outputs-before-decision-rule.d.ts.map

package/dist/outputs-before-decision-rule.d.ts.map

@@ -0,0 +1 @@
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