@alisio/plugin-thesis 0.1.0

package/dist/research/verify.js

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+import { evidenceStatuses, } from "../types.js";
+import { parseIdentifier, } from "./client.js";
+// ---------------------------------------------------------------------------------------------
+// Text normalization (spec 8.4: lowercase, accent folding, per-language stop words)
+// ---------------------------------------------------------------------------------------------
+const stopWordLists = {
+    en: "a an and are as at be by for from in into is it of on or that the their this to with without using use via based".split(" "),
+    es: "a al ante con contra de del desde el en entre es la las lo los o para por que se segun sin sobre su sus un una uno unas unos y como mediante usando basado".split(" "),
+    pt: "a ao aos as com contra de do dos da das e em entre o os ou para pelo pela por que se sem sobre um uma uns umas como usando baseado".split(" "),
+    fr: "a au aux avec ce ces dans de des du en et la le les ou par pour sur un une sans sous comme".split(" "),
+};
+/** Lowercase, remove diacritics. */
+export function fold(text) {
+    return text.normalize("NFD").replace(/[̀-ͯ]/g, "").toLowerCase();
+}
+function stopWordsFor(language) {
+    const primary = language ? fold(language).split(/[-_]/)[0] : undefined;
+    const list = primary ? stopWordLists[primary] : undefined;
+    if (list)
+        return new Set(list);
+    return new Set([
+        ...(stopWordLists.en ?? []),
+        ...(stopWordLists.es ?? []),
+        ...(stopWordLists.pt ?? []),
+    ]);
+}
+export function titleTokens(title, language) {
+    const stop = stopWordsFor(language);
+    return new Set(fold(title)
+        .split(/[^a-z0-9]+/)
+        .filter((token) => token.length > 1 && !stop.has(token)));
+}
+export function jaccard(a, b) {
+    if (a.size === 0 && b.size === 0)
+        return 0;
+    let shared = 0;
+    for (const token of a)
+        if (b.has(token))
+            shared += 1;
+    return shared / (a.size + b.size - shared);
+}
+export function titleSimilarity(a, b, language) {
+    return jaccard(titleTokens(a, language), titleTokens(b, language));
+}
+/** Stable key for duplicate detection: folded title tokens in order, plus the year. */
+export function titleKey(title) {
+    return fold(title)
+        .split(/[^a-z0-9]+/)
+        .filter(Boolean)
+        .join(" ");
+}
+export function foldFamily(name) {
+    return fold(name).replace(/[^a-z0-9]+/g, "");
+}
+const strings = (value) => Array.isArray(value)
+    ? value
+        .filter((entry) => typeof entry === "string")
+        .map((entry) => entry.toLowerCase())
+    : [];
+export const officialDomainsFromProfile = (profile) => {
+    const result = { primary: [], indexing: [] };
+    for (const rule of profile?.rules ?? []) {
+        if (rule.kind !== "official_domain_allowlist")
+            continue;
+        const hosts = [
+            ...strings(rule.values.hostSuffixes),
+            ...strings(rule.values.explicitHosts),
+            ...strings(rule.values.otherHosts),
+        ];
+        if (rule.values.tier === "indexing")
+            result.indexing.push(...hosts);
+        else
+            result.primary.push({
+                hosts,
+                allowedTypes: strings(rule.values.allowedTypes),
+            });
+    }
+    return result;
+};
+/** The lowercase hostname of an http(s) URL without credentials; undefined otherwise. */
+export function hostOf(url) {
+    if (!url)
+        return undefined;
+    try {
+        const parsed = new URL(url);
+        if ((parsed.protocol !== "https:" && parsed.protocol !== "http:") ||
+            parsed.username ||
+            parsed.password) {
+            return undefined;
+        }
+        return parsed.hostname.toLowerCase().replace(/\.$/, "") || undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+const hostMatches = (host, entry) => host === entry || host.endsWith(`.${entry}`);
+export const primaryTypes = ["law", "standard", "report", "dataset"];
+export function classifyHost(url, type, domains) {
+    const host = hostOf(url);
+    if (!host)
+        return { tier: "none" };
+    if (domains.indexing.some((entry) => hostMatches(host, entry)))
+        return { tier: "indexing" };
+    const matching = domains.primary.filter((group) => group.hosts.some((entry) => hostMatches(host, entry)));
+    if (matching.length === 0)
+        return { tier: "none" };
+    const allowed = type !== undefined &&
+        primaryTypes.includes(type) &&
+        matching.some((group) => group.allowedTypes.length === 0 || group.allowedTypes.includes(type));
+    return allowed ? { tier: "primary" } : { tier: "type_not_allowed" };
+}
+export const similarityThreshold = 0.85;
+function compact(value) {
+    return Object.fromEntries(Object.entries(value).filter(([, entry]) => entry !== undefined && entry !== null));
+}
+function draftFromScholar(record, status, metadataMatch, retracted, now) {
+    const type = record.type === "other" ? "web_page" : record.type;
+    return compact({
+        type,
+        title: record.title,
+        authors: record.authors.map((author) => compact({
+            family: author.family,
+            given: author.given ?? undefined,
+            orcid: author.orcid ?? undefined,
+        })),
+        year: record.year,
+        containerTitle: record.containerTitle ?? undefined,
+        volume: record.volume ?? undefined,
+        issue: record.issue ?? undefined,
+        pages: record.pages ?? undefined,
+        publisher: record.publisher ?? undefined,
+        placeOfPublication: record.placeOfPublication ?? undefined,
+        doi: record.doi ?? undefined,
+        isbn: record.isbn ?? undefined,
+        issn: record.issn ?? undefined,
+        url: record.url ?? record.oaUrl ?? undefined,
+        language: record.language ?? undefined,
+        verification: {
+            method: record.source,
+            metadataMatch: Math.round(metadataMatch * 1000) / 1000,
+            retracted,
+            checkedAt: now.toISOString(),
+        },
+        status,
+    });
+}
+function classifyResolved(record) {
+    switch (record.type) {
+        case "journal_article":
+        case "conference_paper":
+            return "VERIFIED_PEER_REVIEWED";
+        case "book":
+        case "chapter":
+        case "report":
+        case "dataset":
+        case "standard":
+            return "VERIFIED_AUTHORITATIVE_GREY";
+        default:
+            return "CONTEXTUAL_ONLY";
+    }
+}
+/** First-author and year checks of spec 8.4. A claim without authors cannot match an authored record. */
+function mismatch(candidate, record) {
+    const similarity = titleSimilarity(candidate.title, record.title, record.language ?? candidate.language);
+    if (similarity < similarityThreshold)
+        return `title similarity ${similarity.toFixed(2)} is below ${similarityThreshold}`;
+    const first = record.authors[0];
+    if (first) {
+        const claimed = candidate.firstAuthor ? foldFamily(candidate.firstAuthor) : "";
+        if (claimed !== foldFamily(first.family))
+            return "first author does not match";
+    }
+    if (record.year === null)
+        return "the source has no publication year";
+    if (Math.abs(record.year - candidate.year) > 1)
+        return `year ${candidate.year} is not within one year of ${record.year}`;
+    return undefined;
+}
+/** The status code would give a resolved record whose metadata matches (spec 8.4). */
+export function suggestStatus(record, domains, extraUrl) {
+    // A DOI-resolved report, standard or dataset can still be primary when an official URL backs it.
+    const type = record.type === "other" ? "web_page" : record.type;
+    for (const url of [extraUrl, record.url]) {
+        if (classifyHost(url, type, domains).tier === "primary")
+            return "VERIFIED_PRIMARY";
+    }
+    return classifyResolved(record);
+}
+/**
+ * Resolve an identifier; after a Crossref hit also ask OpenAlex so `is_retracted` is honored.
+ * Throws the client's fixed error messages when a source is unavailable.
+ */
+export async function resolveChecked(client, identifier, signal, crossCheck = true) {
+    const resolved = await client.resolve(identifier, signal);
+    if (!resolved)
+        return undefined;
+    let retracted = resolved.retracted;
+    if (!retracted && crossCheck && resolved.record.source === "crossref" && resolved.record.doi) {
+        try {
+            const other = await client.resolve({ kind: "openalex", value: `doi:https://doi.org/${resolved.record.doi}` }, signal);
+            retracted = other?.retracted === true;
+        }
+        catch {
+            // Fail open: the Crossref answer stands when OpenAlex is unavailable.
+        }
+    }
+    return { record: resolved.record, retracted };
+}
+export async function verifyCandidate(candidate, context) {
+    const now = context.now();
+    let identifier;
+    try {
+        identifier = parseIdentifier(candidate.identifier);
+    }
+    catch {
+        return { status: "UNVERIFIED", reason: "invalid_identifier" };
+    }
+    if (identifier.kind === "url")
+        return verifyOfficialUrl(candidate, identifier.value, context, now);
+    let resolved;
+    try {
+        resolved = await resolveChecked(context.client, identifier, context.signal, context.crossCheckRetraction !== false);
+    }
+    catch (error) {
+        return { status: "UNVERIFIED", reason: "source_unavailable", detail: error.message };
+    }
+    if (!resolved)
+        return {
+            status: "UNVERIFIED",
+            reason: identifier.kind === "doi" ? "doi_not_found" : "not_found",
+        };
+    const { record, retracted } = resolved;
+    const problem = candidate.userSupplied ? undefined : mismatch(candidate, record);
+    const similarity = candidate.userSupplied
+        ? 1
+        : titleSimilarity(candidate.title, record.title, record.language ?? candidate.language);
+    if (problem) {
+        return {
+            status: "UNVERIFIED",
+            reason: identifier.kind === "doi" ? "doi_mismatch" : "metadata_mismatch",
+            detail: problem,
+            record: draftFromScholar(record, "UNVERIFIED", similarity, retracted, now),
+        };
+    }
+    if (record.year === null)
+        return { status: "UNVERIFIED", reason: "no_year" };
+    const abstract = record.abstract?.slice(0, 600);
+    if (retracted) {
+        return {
+            status: "REJECTED",
+            reason: "retracted",
+            record: draftFromScholar(record, "REJECTED", similarity, true, now),
+        };
+    }
+    const status = suggestStatus(record, context.domains, candidate.url);
+    if (status === "VERIFIED_PRIMARY") {
+        const draft = draftFromScholar(record, status, similarity, false, now);
+        const type = record.type === "other" ? "web_page" : record.type;
+        draft.url = [candidate.url, record.url].find((url) => classifyHost(url, type, context.domains).tier === "primary");
+        return { status, record: draft, ...(abstract ? { abstract } : {}) };
+    }
+    return {
+        status,
+        record: draftFromScholar(record, status, similarity, false, now),
+        ...(abstract ? { abstract } : {}),
+    };
+}
+function verifyOfficialUrl(candidate, url, context, now) {
+    const decision = classifyHost(url, candidate.type, context.domains);
+    if (decision.tier === "indexing")
+        return { status: "UNVERIFIED", reason: "indexing_only" };
+    if (decision.tier === "type_not_allowed")
+        return { status: "UNVERIFIED", reason: "type_not_primary" };
+    if (decision.tier === "none")
+        return { status: "UNVERIFIED", reason: "not_official_domain" };
+    const record = compact({
+        type: candidate.type,
+        title: candidate.title,
+        authors: candidate.firstAuthor ? [{ family: candidate.firstAuthor }] : [],
+        year: candidate.year,
+        url,
+        language: candidate.language,
+        verification: {
+            method: "official_domain",
+            metadataMatch: 1,
+            retracted: false,
+            checkedAt: now.toISOString(),
+        },
+        status: "VERIFIED_PRIMARY",
+    });
+    return { status: "VERIFIED_PRIMARY", record };
+}
+// ---------------------------------------------------------------------------------------------
+// Auditor limits: a status may be downgraded, never upgraded
+// ---------------------------------------------------------------------------------------------
+/** Lower is stronger. */
+export const statusRank = (status) => evidenceStatuses.indexOf(status);
+export function isUpgrade(from, to) {
+    return statusRank(to) < statusRank(from);
+}
+export function applyAuditorStatus(assigned, requested) {
+    if (!requested || isUpgrade(assigned, requested))
+        return assigned;
+    return requested;
+}
+//# sourceMappingURL=verify.js.map

package/dist/research/verify.js.map

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package/dist/resources.d.ts

@@ -0,0 +1,15 @@
+import type { ResourceRole } from "./types.js";
+export declare const resourcePaths: {
+    readonly agents: "../.agents/agents";
+    readonly skills: "../.agents/skills";
+};
+/** Skills each agent loads. The same files are the registered resources and the child instructions. */
+export declare const roleSkills: Record<ResourceRole, string[]>;
+interface ParsedResource {
+    frontmatter: Record<string, unknown>;
+    body: string;
+}
+export declare function parseResource(source: string, label: string): ParsedResource;
+export declare function loadRoleInstructions(role: ResourceRole): Promise<string>;
+export {};
+//# sourceMappingURL=resources.d.ts.map

package/dist/resources.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"resources.d.ts","sourceRoot":"","sources":["../src/resources.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAE/C,eAAO,MAAM,aAAa;aACxB,MAAM,EAAE,mBAAmB;aAC3B,MAAM,EAAE,mBAAmB;CACnB,CAAC;AAEX,uGAAuG;AACvG,eAAO,MAAM,UAAU,EAAE,MAAM,CAAC,YAAY,EAAE,MAAM,EAAE,CAcrD,CAAC;AAEF,UAAU,cAAc;IACtB,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACrC,IAAI,EAAE,MAAM,CAAC;CACd;AAcD,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,cAAc,CA6B3E;AAkED,wBAAsB,oBAAoB,CAAC,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,CAe9E"}

package/dist/resources.js

@@ -0,0 +1,148 @@
+import { readFile } from "node:fs/promises";
+import { fileURLToPath } from "node:url";
+export const resourcePaths = {
+    agents: "../.agents/agents",
+    skills: "../.agents/skills",
+};
+/** Skills each agent loads. The same files are the registered resources and the child instructions. */
+export const roleSkills = {
+    "thesis-coordinator": ["thesis-intake", "thesis-policy", "thesis-build"],
+    "thesis-methodologist": ["thesis-methodology", "thesis-policy", "thesis-institution-norms"],
+    "thesis-librarian": ["thesis-search", "thesis-evidence"],
+    "thesis-evidence-auditor": ["thesis-evidence", "thesis-citations"],
+    "thesis-architect": ["thesis-outline", "thesis-evidence"],
+    "thesis-writer": ["thesis-writing", "thesis-citations", "thesis-figures", "thesis-math"],
+    "thesis-editor": [
+        "thesis-editing",
+        "thesis-citations",
+        "thesis-csl-authoring",
+        "thesis-institution-norms",
+    ],
+    "thesis-reviewer": ["thesis-review", "thesis-citations", "thesis-evidence"],
+};
+function scalar(source) {
+    const value = source.trim();
+    if (value === "true")
+        return true;
+    if (value === "false")
+        return false;
+    if (/^\d+$/.test(value))
+        return Number(value);
+    if (value.startsWith("[") && value.endsWith("]")) {
+        const inner = value.slice(1, -1).trim();
+        return inner ? inner.split(",").map((item) => item.trim().replace(/^['"]|['"]$/g, "")) : [];
+    }
+    return value.replace(/^['"]|['"]$/g, "");
+}
+export function parseResource(source, label) {
+    const normalized = source.replace(/\r\n/g, "\n");
+    const match = /^---\n([\s\S]*?)\n---\n([\s\S]+)$/.exec(normalized);
+    if (!match)
+        throw new Error(`Malformed resource frontmatter: ${label}`);
+    const frontmatter = {};
+    let parent;
+    for (const [index, line] of (match[1] ?? "").split("\n").entries()) {
+        if (!line.trim() || line.trimStart().startsWith("#"))
+            continue;
+        if (/\t|[&*!>|]/.test(line))
+            throw new Error(`Unsupported frontmatter syntax in ${label}`);
+        const nested = /^ {2}([A-Za-z][\w-]*):\s*(.*)$/.exec(line);
+        if (nested && parent) {
+            parent[nested[1]] = scalar(nested[2]);
+            continue;
+        }
+        const entry = /^([A-Za-z][\w-]*):\s*(.*)$/.exec(line);
+        if (!entry)
+            throw new Error(`Malformed frontmatter line ${index + 1} in ${label}`);
+        const key = entry[1];
+        const raw = entry[2];
+        if (!raw) {
+            parent = {};
+            frontmatter[key] = parent;
+        }
+        else {
+            frontmatter[key] = scalar(raw);
+            parent = undefined;
+        }
+    }
+    const body = (match[2] ?? "").trim();
+    if (!body)
+        throw new Error(`Resource body is empty: ${label}`);
+    return { frontmatter, body };
+}
+async function load(path) {
+    const url = new URL(path, import.meta.url);
+    return parseResource(await readFile(fileURLToPath(url), "utf8"), path);
+}
+function validateAgent(resource, role, skillNames) {
+    const front = resource.frontmatter;
+    const permission = front.permission;
+    const declaredSkills = Array.isArray(front.skills) ? front.skills : undefined;
+    if (front.name !== role ||
+        typeof front.description !== "string" ||
+        !front.description ||
+        !Array.isArray(front.tools) ||
+        !Array.isArray(front.disallowedTools) ||
+        !front.disallowedTools.includes("task") ||
+        (role === "thesis-coordinator" ? front.mode !== "primary" : front.mode !== "subagent") ||
+        typeof front.maxTurns !== "number" ||
+        typeof front.readOnly !== "boolean" ||
+        !permission ||
+        typeof permission !== "object" ||
+        Array.isArray(permission) ||
+        !declaredSkills ||
+        !skillNames.every((skillName) => declaredSkills.includes(skillName))) {
+        throw new Error(`Invalid agent resource: ${role}`);
+    }
+}
+function validateSkill(resource, skillName) {
+    const front = resource.frontmatter;
+    const metadata = front.metadata;
+    const headings = [
+        "## Activation Contract",
+        "## Hard Rules",
+        "## Decision Gates",
+        "## Execution Steps",
+        "## Output Contract",
+        "## References",
+    ];
+    let cursor = -1;
+    for (const heading of headings) {
+        const next = resource.body.indexOf(heading);
+        if (next <= cursor)
+            throw new Error(`Invalid skill section order: ${skillName}`);
+        cursor = next;
+    }
+    if (front.name !== skillName ||
+        typeof front.description !== "string" ||
+        !front.description.startsWith("Trigger:") ||
+        front.description.length > 250 ||
+        front.license !== "MIT" ||
+        !metadata ||
+        typeof metadata !== "object" ||
+        Array.isArray(metadata) ||
+        !("author" in metadata) ||
+        !("version" in metadata) ||
+        typeof metadata.author !== "string" ||
+        typeof metadata.version !== "string") {
+        throw new Error(`Invalid skill resource: ${skillName}`);
+    }
+}
+export async function loadRoleInstructions(role) {
+    const skillNames = roleSkills[role];
+    if (!skillNames)
+        throw new Error(`Unknown thesis role: ${role}`);
+    const [agent, ...skills] = await Promise.all([
+        load(`../.agents/agents/${role}.md`),
+        ...skillNames.map((skillName) => load(`../.agents/skills/${skillName}/SKILL.md`)),
+    ]);
+    validateAgent(agent, role, skillNames);
+    for (const [index, skill] of skills.entries()) {
+        validateSkill(skill, skillNames[index]);
+    }
+    return [
+        agent.body,
+        ...skills.flatMap((skill, index) => [`# Loaded skill: ${skillNames[index]}`, skill.body]),
+    ].join("\n\n");
+}
+//# sourceMappingURL=resources.js.map

package/dist/resources.js.map

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

@@ -0,0 +1,22 @@
+import { type Loaded, type WorkflowContext } from "./context.js";
+import type { DraftFlow } from "./draft.js";
+import type { ReviewFinding } from "./types.js";
+export declare function readFindings(base: string): Promise<ReviewFinding[]>;
+export declare class ReviewFlow {
+    private readonly context;
+    private readonly drafts;
+    private readonly afterChange;
+    constructor(context: WorkflowContext, drafts: DraftFlow, afterChange: (loaded: Loaded) => Promise<void>);
+    private get now();
+    run(workspace: string, sessionId: string, target: string): Promise<string>;
+    private load;
+    private close;
+    /** `/thesis:approve FND-xxxx -- reason`: the user dismisses a finding with a reason. */
+    dismiss(workspace: string, sessionId: string, id: string, reason: string | undefined): Promise<string>;
+    /** Route a finding to the role that owns the fix (spec 7.5). */
+    revise(workspace: string, sessionId: string, id: string, extra: string | undefined): Promise<string>;
+    private advice;
+    /** The architect revises the section's dossier so the redraft follows an improved argument. */
+    private reviseDossier;
+}
+//# sourceMappingURL=review.d.ts.map

package/dist/review.d.ts.map

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