@alisio/plugin-thesis 0.1.0

package/dist/checks/design.js

@@ -0,0 +1,107 @@
+import { parseProtocol } from "../protocol.js";
+import { fold } from "../research/verify.js";
+const file = "research/protocol.md";
+const isObject = (value) => typeof value === "object" && value !== null && !Array.isArray(value);
+const filled = (value) => typeof value === "string" && value.trim().length > 0;
+const error = (message, hint) => ({
+    code: "DSN-001",
+    gate: "G1",
+    severity: "error",
+    file,
+    message,
+    ...(hint ? { hint } : {}),
+});
+function strings(value) {
+    return Array.isArray(value)
+        ? value
+            .filter((entry) => typeof entry === "string")
+            .map((entry) => fold(entry).trim())
+        : [];
+}
+/** G1: the protocol is complete (DSN-001) and its objective verbs are verifiable (DSN-002). */
+export function checkDesign(project) {
+    if (project.protocolText === undefined)
+        return [];
+    const parsed = parseProtocol(project.protocolText);
+    if (!parsed.data)
+        return [error(parsed.error ?? "protocol.md cannot be read")];
+    const data = parsed.data;
+    const findings = [];
+    const hint = "Run /thesis:design again, or fix the front matter of research/protocol.md.";
+    if (!filled(data.problem))
+        findings.push(error("The protocol has no problem statement", hint));
+    if (!Array.isArray(data.researchQuestions) || !data.researchQuestions.some(filled)) {
+        findings.push(error("The protocol has no research question", hint));
+    }
+    const general = data.generalObjective;
+    if (!isObject(general) || !filled(general.text)) {
+        findings.push(error("The protocol has no general objective", hint));
+    }
+    const objectives = Array.isArray(data.specificObjectives) ? data.specificObjectives : [];
+    if (objectives.length < 2 || objectives.length > 6) {
+        findings.push(error(`The protocol must have 2 to 6 specific objectives (found ${objectives.length})`, hint));
+    }
+    objectives.forEach((objective, index) => {
+        if (!isObject(objective) ||
+            !filled(objective.id) ||
+            !filled(objective.verb) ||
+            !filled(objective.object) ||
+            !filled(objective.deliverable)) {
+            findings.push(error(`Specific objective ${index + 1} needs an id, a verb, an object and a deliverable`, hint));
+        }
+    });
+    const justification = data.justification;
+    if (!isObject(justification) ||
+        !["relevance", "novelty", "feasibility", "beneficiaries"].every((key) => filled(justification[key]))) {
+        findings.push(error("The justification must state relevance, novelty, feasibility and beneficiaries", hint));
+    }
+    const methodology = data.methodology;
+    if (!isObject(methodology) || !filled(methodology.design) || !filled(methodology.analysisPlan)) {
+        findings.push(error("The methodology needs at least a design and an analysis plan", hint));
+    }
+    // DSN-002: verbs against the approved list of the thesis language (warning, never blocking).
+    const profile = project.profile;
+    const rule = profile?.rules.find((entry) => entry.kind === "objective_verbs");
+    if (profile && !rule) {
+        findings.push({
+            code: "DSN-002",
+            gate: "G1",
+            severity: "info",
+            file,
+            message: `No approved objective-verb list exists for language ${profile.inputs.language}; verbs were not checked`,
+        });
+    }
+    else if (profile && rule) {
+        const recommended = new Set(Object.values(isObject(rule.values.recommendedByLevel) ? rule.values.recommendedByLevel : {}).flatMap(strings));
+        const unverifiable = new Set([
+            ...strings(rule.values.avoid),
+            ...strings(rule.values.ambiguous),
+        ]);
+        const downgrade = isObject(rule.values.qualitativeDowngrade)
+            ? rule.values.qualitativeDowngrade
+            : undefined;
+        const downgraded = new Set(strings(downgrade?.verbs));
+        const qualitative = profile.inputs.approach === "qualitative";
+        for (const objective of objectives) {
+            if (!isObject(objective) || !filled(objective.verb))
+                continue;
+            const verb = fold(String(objective.verb)).trim();
+            const id = filled(objective.id) ? String(objective.id) : "objective";
+            if (recommended.has(verb) && !unverifiable.has(verb))
+                continue;
+            const soft = qualitative && downgraded.has(verb);
+            findings.push({
+                code: "DSN-002",
+                gate: "G1",
+                severity: soft ? "info" : "warning",
+                file,
+                message: unverifiable.has(verb)
+                    ? `${id}: the verb "${String(objective.verb)}" is not verifiable; use a measurable action verb`
+                    : `${id}: the verb "${String(objective.verb)}" is not in the approved list for ${profile.inputs.language}`,
+                hint: `Approved verbs come from ${rule.ruleId}; see /thesis:pack explain ${rule.ruleId}.`,
+            });
+        }
+    }
+    return findings;
+}
+//# sourceMappingURL=design.js.map

package/dist/checks/design.js.map

@@ -0,0 +1 @@
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package/dist/checks/document.d.ts

@@ -0,0 +1,17 @@
+import { type Assembled } from "../render/assemble.js";
+import type { ThesisDocument } from "../render/model.js";
+import type { Finding } from "../types.js";
+import type { LoadedProject } from "./project.js";
+/** The full-scope document of a project, parsed once per loaded project. */
+export declare function documentOf(project: LoadedProject): Assembled | undefined;
+/** XRF-001, XRF-002 and MTH-001. */
+export declare function modelFindings(doc: ThesisDocument): Finding[];
+/** G7: HYG-001 from the dialect (raw HTML, raw Typst, placeholders, unknown attributes) and label notes. */
+export declare function checkDocumentHygiene(project: LoadedProject): Finding[];
+/** G8: cross-references and math. */
+export declare function checkDocumentModel(project: LoadedProject): Finding[];
+/** G8 BLD-001: the last recorded build must have succeeded (nothing is reported before a first build). */
+export declare function checkBuildReport(project: LoadedProject): Finding[];
+/** FIG-001 to FIG-003: every chart spec under figures/ against the supported subset (G8). */
+export declare function checkCharts(project: LoadedProject): Finding[];
+//# sourceMappingURL=document.d.ts.map

package/dist/checks/document.d.ts.map

@@ -0,0 +1 @@
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package/dist/checks/document.js

@@ -0,0 +1,213 @@
+import { assembleDocument } from "../render/assemble.js";
+import { checkChartSpec } from "../render/charts.js";
+import { validateLatex } from "../render/math.js";
+import { allBlockLists, walkBlocks, walkInlines } from "../render/walk.js";
+/** Checks over the renderer-neutral document model (spec 10.0): no output format is involved. */
+const cache = new WeakMap();
+/** The full-scope document of a project, parsed once per loaded project. */
+export function documentOf(project) {
+    if (!cache.has(project)) {
+        cache.set(project, assembleDocument(project, { scope: "full", sections: project.sections ?? {} }));
+    }
+    return cache.get(project);
+}
+const at = (file, block) => ({
+    ...(file === undefined ? {} : { file }),
+    ...(block.line === undefined ? {} : { line: block.line }),
+});
+/** XRF-001, XRF-002 and MTH-001. */
+export function modelFindings(doc) {
+    const findings = [];
+    const lists = allBlockLists(doc);
+    const defined = new Map();
+    for (const { file, blocks } of lists) {
+        walkBlocks(blocks, (block) => {
+            if (!("label" in block) || !block.label)
+                return;
+            const previous = defined.get(block.label);
+            if (previous) {
+                findings.push({
+                    code: "XRF-001",
+                    gate: "G8",
+                    severity: "error",
+                    ...at(file, block),
+                    message: `Label ${block.label} is defined more than once (first at ${previous.file ?? "unknown"}${previous.line ? `:${previous.line}` : ""})`,
+                });
+            }
+            else
+                defined.set(block.label, { file, line: block.line });
+        });
+    }
+    const referenced = new Set();
+    for (const { file, blocks } of lists) {
+        walkInlines(blocks, (inline, owner) => {
+            if (inline.kind === "crossref") {
+                referenced.add(inline.label);
+                if (!defined.has(inline.label)) {
+                    findings.push({
+                        code: "XRF-001",
+                        gate: "G8",
+                        severity: "error",
+                        ...at(file, owner),
+                        message: `Reference @${inline.label} does not match any label`,
+                        hint: "Label figures, tables, equations and headings with {#fig-x}, {#tbl-x}, {#eq-x} and {#sec-x}.",
+                    });
+                }
+            }
+            if (inline.kind === "math") {
+                const problem = validateLatex(inline.latex);
+                if (problem) {
+                    findings.push({
+                        code: "MTH-001",
+                        gate: "G8",
+                        severity: "error",
+                        ...at(file, owner),
+                        message: problem,
+                    });
+                }
+            }
+        });
+        walkBlocks(blocks, (block) => {
+            if (block.kind === "equation") {
+                const problem = validateLatex(block.latex);
+                if (problem) {
+                    findings.push({
+                        code: "MTH-001",
+                        gate: "G8",
+                        severity: "error",
+                        ...at(file, block),
+                        message: problem,
+                    });
+                }
+            }
+        });
+    }
+    // FIG-004: a chart needs a caption and a source line.
+    for (const { file, blocks } of lists) {
+        walkBlocks(blocks, (block) => {
+            if (block.kind !== "figure" || block.asset.kind !== "chart")
+                return;
+            if (block.caption.length === 0) {
+                findings.push({
+                    code: "FIG-004",
+                    gate: "G8",
+                    severity: "error",
+                    ...at(file, block),
+                    message: `Chart ${block.asset.path} has no caption`,
+                    hint: "Write the caption as the figure's alt text: ![Caption. Source: ...](chart.vl.json).",
+                });
+            }
+            if (!block.source) {
+                findings.push({
+                    code: "FIG-004",
+                    gate: "G8",
+                    severity: "error",
+                    ...at(file, block),
+                    message: `Chart ${block.asset.path} has no source line`,
+                    hint: 'End the caption with "Source: ..." (Fuente: / Fonte:), for example "Source: own elaboration."',
+                });
+            }
+        });
+    }
+    // XRF-003: a heading level may not skip a level (for example # followed by ###).
+    let previous = 0;
+    for (const section of [...doc.body, ...doc.annexes]) {
+        walkBlocks(section.blocks, (block) => {
+            if (block.kind !== "heading")
+                return;
+            if (block.level > previous + 1) {
+                findings.push({
+                    code: "XRF-003",
+                    gate: "G8",
+                    severity: "warning",
+                    ...at(section.path, block),
+                    message: previous === 0
+                        ? `The first heading is level ${block.level}; start with a level 1 heading`
+                        : `Heading level jumps from ${previous} to ${block.level}`,
+                    hint: "Use consecutive heading levels so the table of contents and numbering stay meaningful.",
+                });
+            }
+            previous = block.level;
+        });
+    }
+    for (const { file, blocks } of lists) {
+        walkBlocks(blocks, (block) => {
+            if ((block.kind === "figure" || block.kind === "table") &&
+                block.label &&
+                !referenced.has(block.label)) {
+                findings.push({
+                    code: "XRF-002",
+                    gate: "G8",
+                    severity: "warning",
+                    ...at(file, block),
+                    message: `${block.kind === "figure" ? "Figure" : "Table"} ${block.label} is never referenced in the text`,
+                    hint: `Mention it with @${block.label}.`,
+                });
+            }
+        });
+    }
+    return findings;
+}
+/** G7: HYG-001 from the dialect (raw HTML, raw Typst, placeholders, unknown attributes) and label notes. */
+export function checkDocumentHygiene(project) {
+    const assembled = documentOf(project);
+    return assembled ? assembled.findings.filter((finding) => finding.gate === "G7") : [];
+}
+/** G8: cross-references and math. */
+export function checkDocumentModel(project) {
+    const assembled = documentOf(project);
+    if (!assembled)
+        return [];
+    return modelFindings(assembled.document);
+}
+/** G8 BLD-001: the last recorded build must have succeeded (nothing is reported before a first build). */
+export function checkBuildReport(project) {
+    if (project.buildReportText === undefined)
+        return [];
+    let report;
+    try {
+        report = JSON.parse(project.buildReportText);
+    }
+    catch {
+        return [
+            {
+                code: "BLD-001",
+                gate: "G8",
+                severity: "error",
+                file: "build/build-report.json",
+                message: "The build report is unreadable; run /thesis:build again",
+            },
+        ];
+    }
+    if (report.ok === true)
+        return [];
+    return [
+        {
+            code: "BLD-001",
+            gate: "G8",
+            severity: "error",
+            file: "build/build-report.json",
+            message: `The last build (${typeof report.scope === "string" ? report.scope : "unknown scope"}) failed with ${typeof report.errors === "number" ? report.errors : "some"} error(s)`,
+            hint: "Run /thesis:build and fix the reported errors.",
+        },
+    ];
+}
+/** FIG-001 to FIG-003: every chart spec under figures/ against the supported subset (G8). */
+export function checkCharts(project) {
+    const dataFiles = new Set(project.dataFiles);
+    const findings = [];
+    for (const spec of project.chartSpecs) {
+        for (const issue of checkChartSpec(spec.content, { dataFiles }).issues) {
+            findings.push({
+                code: issue.code,
+                gate: "G8",
+                severity: "error",
+                file: spec.path,
+                message: issue.message,
+                ...(issue.hint ? { hint: issue.hint } : {}),
+            });
+        }
+    }
+    return findings;
+}
+//# sourceMappingURL=document.js.map

package/dist/checks/document.js.map

@@ -0,0 +1 @@
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package/dist/checks/evidence.d.ts

@@ -0,0 +1,7 @@
+import { type Finding } from "../types.js";
+import type { LoadedProject } from "./project.js";
+/** G2: the evidence library (EVD-*). */
+export declare function checkEvidence(project: LoadedProject): Finding[];
+/** G5 (partial): references.bib is byte-identical to a fresh generation (CIT-004). */
+export declare function checkBibliography(project: LoadedProject): Finding[];
+//# sourceMappingURL=evidence.d.ts.map

package/dist/checks/evidence.d.ts.map

@@ -0,0 +1 @@
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package/dist/checks/evidence.js

@@ -0,0 +1,133 @@
+import { flattenOutline, parseOutline } from "../outline.js";
+import { generateBibtex } from "../research/bibtex.js";
+import { citableForSection, parseLibraryText } from "../research/library.js";
+import { classifyHost, officialDomainsFromProfile, primaryTypes, similarityThreshold, } from "../research/verify.js";
+import { citableStatuses, } from "../types.js";
+const libraryFile = "evidence/library.jsonl";
+const bibliographyFile = "bibliography/references.bib";
+const finding = (code, gate, severity, file, message, extra = {}) => ({ code, gate, severity, file, message, ...extra });
+/** Why a citable status is not justified by the record's own verification data (spec 8.4). */
+function statusProblem(record, domains) {
+    const { method, metadataMatch } = record.verification;
+    const viaApi = method === "crossref" || method === "openalex";
+    switch (record.status) {
+        case "VERIFIED_PEER_REVIEWED":
+            if (!viaApi)
+                return "peer-reviewed status needs Crossref or OpenAlex verification";
+            if (record.type !== "journal_article" && record.type !== "conference_paper")
+                return `peer-reviewed status needs a journal article or conference paper, not ${record.type}`;
+            if (metadataMatch < similarityThreshold)
+                return `metadata match ${metadataMatch} is below ${similarityThreshold}`;
+            return undefined;
+        case "VERIFIED_AUTHORITATIVE_GREY":
+            if (!viaApi)
+                return "authoritative grey status needs Crossref or OpenAlex verification";
+            if (metadataMatch < similarityThreshold)
+                return `metadata match ${metadataMatch} is below ${similarityThreshold}`;
+            return undefined;
+        case "VERIFIED_PRIMARY":
+            if (!primaryTypes.includes(record.type))
+                return `primary status needs a law, standard, report or dataset, not ${record.type}`;
+            if (classifyHost(record.url, record.type, domains).tier !== "primary")
+                return "primary status needs a URL on an official domain of the policy";
+            return undefined;
+        default:
+            return undefined;
+    }
+}
+const evidenceStarted = [
+    "research_approved",
+    "drafting",
+    "draft_review",
+    "approved",
+    "revising",
+];
+/** G2: the evidence library (EVD-*). */
+export function checkEvidence(project) {
+    if (project.libraryText === undefined)
+        return [];
+    const findings = [];
+    const { records, errors } = parseLibraryText(project.libraryText);
+    for (const error of errors) {
+        findings.push(finding("EVD-001", "G2", "error", libraryFile, error.message, { line: error.line }));
+    }
+    const domains = officialDomainsFromProfile(project.profile);
+    const ids = new Map();
+    const keys = new Map();
+    const dois = new Map();
+    for (const record of records) {
+        ids.set(record.id, (ids.get(record.id) ?? 0) + 1);
+        keys.set(record.citeKey, (keys.get(record.citeKey) ?? 0) + 1);
+        if (record.doi) {
+            const doi = record.doi.toLowerCase();
+            const first = dois.get(doi);
+            if (first)
+                findings.push(finding("EVD-002", "G2", "error", libraryFile, `DOI ${doi} appears in both ${first} and ${record.id}`, { hint: "Duplicates merge into the oldest evidence id; re-run /thesis:research." }));
+            else
+                dois.set(doi, record.id);
+        }
+        if (citableStatuses.includes(record.status)) {
+            const problem = statusProblem(record, domains);
+            if (problem)
+                findings.push(finding("EVD-003", "G2", "error", libraryFile, `${record.id} is ${record.status} but ${problem}`, { hint: "Citable statuses come only from code verification (spec 8.4)." }));
+            if (record.verification.retracted)
+                findings.push(finding("EVD-004", "G2", "error", libraryFile, `${record.id} is marked retracted but still has the citable status ${record.status}`));
+        }
+    }
+    for (const [id, count] of ids)
+        if (count > 1)
+            findings.push(finding("EVD-001", "G2", "error", libraryFile, `Evidence id ${id} appears ${count} times`));
+    for (const [key, count] of keys)
+        if (count > 1)
+            findings.push(finding("EVD-001", "G2", "error", libraryFile, `Citation key ${key} appears ${count} times`));
+    // Contextual approvals must point at real records.
+    for (const [sectionId, section] of Object.entries(project.sections ?? {})) {
+        for (const id of section.contextualApprovals ?? []) {
+            if (!ids.has(id))
+                findings.push(finding("EVD-005", "G2", "error", libraryFile, `${sectionId} approves unknown evidence ${id} for contextual use`));
+        }
+    }
+    // EVD-010: evidence minimums (warning). The policy sources give a minimum for the theoretical
+    // framework as a whole, so it applies to the section(s) marked as that framework.
+    const profile = project.profile;
+    if (profile && project.outlineText !== undefined && project.sections) {
+        const outline = parseOutline(project.outlineText).outline;
+        const frameworks = outline
+            ? flattenOutline(outline.sections).filter((node) => node.requiredKey === "marco_teorico" || node.requiredKey === "estado_del_arte")
+            : [];
+        for (const rule of profile.rules.filter((entry) => entry.kind === "evidence_minimum")) {
+            const minimum = rule.values.minCitable;
+            if (rule.values.scope !== "theoretical_framework" || typeof minimum !== "number")
+                continue;
+            for (const node of frameworks) {
+                const section = project.sections[node.id];
+                if (!section || !evidenceStarted.includes(section.status))
+                    continue;
+                const citable = records.filter((record) => record.sections.includes(node.id) &&
+                    citableForSection(record, section.contextualApprovals)).length;
+                if (citable < minimum) {
+                    findings.push(finding("EVD-010", "G2", rule.values.severity === "error" ? "error" : "warning", libraryFile, `${node.id} has ${citable} citable record(s); ${rule.ruleId} suggests at least ${minimum} for this work type`, {
+                        hint: "A suggestion from the policy, not a standard; search more or override the rule with an institutional one.",
+                    }));
+                }
+            }
+        }
+    }
+    return findings;
+}
+/** G5 (partial): references.bib is byte-identical to a fresh generation (CIT-004). */
+export function checkBibliography(project) {
+    if (project.libraryText === undefined && project.bibliographyText === undefined)
+        return [];
+    const { records, errors } = parseLibraryText(project.libraryText);
+    if (errors.length > 0)
+        return [];
+    if (project.bibliographyText === generateBibtex(records))
+        return [];
+    return [
+        finding("CIT-004", "G5", "error", bibliographyFile, "references.bib differs from a fresh generation of the evidence library", {
+            hint: "references.bib is generated and never hand-edited; delete it and run /thesis:research for any section to rebuild it.",
+        }),
+    ];
+}
+//# sourceMappingURL=evidence.js.map

package/dist/checks/evidence.js.map

@@ -0,0 +1 @@
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package/dist/checks/hygiene.d.ts

@@ -0,0 +1,5 @@
+import type { Finding } from "../types.js";
+import type { LoadedProject } from "./project.js";
+/** G7 (path-leak part of HYG-001): no absolute local paths in the brief or the chapters. */
+export declare function checkHygiene(project: LoadedProject): Finding[];
+//# sourceMappingURL=hygiene.d.ts.map

package/dist/checks/hygiene.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hygiene.d.ts","sourceRoot":"","sources":["../../src/checks/hygiene.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AA+BlD,4FAA4F;AAC5F,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,EAAE,CAK9D"}

package/dist/checks/hygiene.js

@@ -0,0 +1,37 @@
+// Absolute local-machine paths: POSIX home/temp roots and Windows drive paths.
+const pathPatterns = [
+    /(?<![\w.:/-])\/(?:home|Users|root|tmp|private\/var|var\/folders)\/[^\s"'`)\]}<>,;]+/g,
+    /(?<![A-Za-z0-9])[A-Za-z]:\\[^\s"'`)\]}<>,;]+/g,
+    /(?<![A-Za-z0-9])[A-Za-z]:\/(?:Users|Documents and Settings)\/[^\s"'`)\]}<>,;]+/g,
+];
+function scan(file, text) {
+    const findings = [];
+    text.split(/\r?\n/).forEach((line, index) => {
+        for (const pattern of pathPatterns) {
+            pattern.lastIndex = 0;
+            if (pattern.test(line)) {
+                findings.push({
+                    code: "HYG-001",
+                    gate: "G7",
+                    severity: "error",
+                    file,
+                    line: index + 1,
+                    message: "Absolute local path found; it leaks the author's machine layout",
+                    hint: "Use workspace-relative paths such as figures/charts/x.vl.json.",
+                });
+                break;
+            }
+        }
+    });
+    return findings;
+}
+/** G7 (path-leak part of HYG-001): no absolute local paths in the brief or the chapters. */
+export function checkHygiene(project) {
+    const findings = [];
+    if (project.briefText !== undefined)
+        findings.push(...scan("thesis.yaml", project.briefText));
+    for (const chapter of project.chapters)
+        findings.push(...scan(chapter.path, chapter.content));
+    return findings;
+}
+//# sourceMappingURL=hygiene.js.map

package/dist/checks/hygiene.js.map

@@ -0,0 +1 @@
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package/dist/checks/index.d.ts

@@ -0,0 +1,21 @@
+import { type CheckReport, type Finding, type Gate } from "../types.js";
+import type { LoadedProject } from "./project.js";
+export { type LoadedProject, type LoadProjectOptions, loadProject } from "./project.js";
+/** Each check is a pure function over the loaded project. */
+export interface CheckDefinition {
+    id: string;
+    gate: Gate;
+    run(project: LoadedProject): Finding[];
+}
+export declare const checkRegistry: readonly CheckDefinition[];
+export declare function parseGates(values: readonly string[]): Gate[];
+export interface RunOptions {
+    gates?: readonly Gate[];
+    now?: () => Date;
+    /** Keep only the findings of one section (and the files of it), as `thesis_check` offers. */
+    section?: string;
+}
+export declare function runChecks(project: LoadedProject, options?: RunOptions): CheckReport;
+/** Plain-text rendering shared by the command, the tool summary and the CLI. */
+export declare function formatReport(report: CheckReport): string;
+//# sourceMappingURL=index.d.ts.map

package/dist/checks/index.d.ts.map

@@ -0,0 +1 @@
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