@tiangong-ai/cli 0.0.60 → 0.0.62

package/dist/research/workspace/setup-upgrade.js.map

@@ -0,0 +1 @@
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package/dist/research/workspace/setup.d.ts

@@ -84,8 +84,17 @@ export interface ResearchSetupPlan {
         target: string;
         reason: string;
     }>;
+    upgrade?: ResearchSetupUpgradeBinding;
     planSha256: string;
 }
+export interface ResearchSetupUpgradeBinding {
+    schemaVersion: 1;
+    cliRuntimeSha256: string;
+    parentPlanSha256: string;
+    parentRuntimeLockSha256: string;
+    parentConfigSha256: string;
+    parentMarkerSha256: string;
+}
 export interface ResearchSetupState {
     schemaVersion: 1;
     planSha256: string;
@@ -126,6 +135,8 @@ export interface ResearchSetupPlanInput {
     declarativeConfigurationSha256?: string;
     environment?: NodeJS.ProcessEnv;
     targetRoots?: Partial<Record<ResearchSetupAgent, string>>;
+    /** Internal candidate creation; never a public bypass of plan verification. */
+    upgrade?: ResearchSetupUpgradeBinding;
 }
 export interface SetupCommandResult {
     exitCode: number;
@@ -146,6 +157,16 @@ export interface ApplyResearchSetupOptions {
     sleeper?: (milliseconds: number) => Promise<unknown>;
     executor?: DoctorOptions["executor"];
     skipDoctor?: boolean;
+    upgradeCheckpoint?: (point: string) => Promise<void>;
+    /** Setup-upgrade preparation only; no public CLI flag exposes these paths. */
+    sourceCacheWorkspace?: string;
+    installerCacheDirectory?: string;
+}
+export interface ApplyResearchSetupResult {
+    schemaVersion: 1;
+    plan: ResearchSetupPlan;
+    state: ResearchSetupState;
+    report: Awaited<ReturnType<typeof doctorResearchSetup>> | null;
 }
 export type ResearchSetupCompanionInput = {
     workspace: string;
@@ -169,30 +190,16 @@ export interface RunResearchSetupCompanionOptions {
 }
 export declare function createResearchSetupPlan(input: ResearchSetupPlanInput): Promise<ResearchSetupPlan>;
 export declare function loadAndVerifyResearchSetupPlan(planPath: string): Promise<ResearchSetupPlan>;
+export declare function loadHashVerifiedResearchSetupPlan(planPath: string): Promise<ResearchSetupPlan>;
 export declare function createResearchSetupUpgradePlan(input: {
     workspace: string;
     acceptedLicenseIds: string[];
     confirmUpgrade: boolean;
     environment?: NodeJS.ProcessEnv;
 }): Promise<ResearchSetupPlan>;
-export declare function applyResearchSetupPlan(planPath: string, options?: ApplyResearchSetupOptions): Promise<{
-    schemaVersion: 1;
-    plan: ResearchSetupPlan;
-    state: ResearchSetupState;
-    report: null;
-} | {
-    schemaVersion: 1;
-    plan: ResearchSetupPlan;
-    state: ResearchSetupState;
-    report: Record<string, unknown> & {
-        readiness: "READY" | "BLOCKED";
-        researchReadiness: "READY" | "BLOCKED";
-        preprocessingReadiness: SetupDomainReadiness;
-        acquisitionReadiness: SetupDomainReadiness;
-        authoringReadiness: SetupDomainReadiness;
-        overallReadiness: "READY" | "PARTIALLY_READY" | "BLOCKED";
-    };
-}>;
+export declare function researchSetupUpgradeCandidatePath(plan: ResearchSetupPlan): string;
+export declare function assertUpgradeParent(plan: ResearchSetupPlan): Promise<ResearchSetupPlan>;
+export declare function applyResearchSetupPlan(planPath: string, options?: ApplyResearchSetupOptions): Promise<ApplyResearchSetupResult>;
 export declare function inspectResearchSetupStatus(workspace: string, environment?: NodeJS.ProcessEnv): Promise<{
     schemaVersion: 1;
     workspace: string;
@@ -327,29 +334,14 @@ export declare function retryResearchSetup(input: {
     step: string;
     clearStaleLock?: boolean;
     options?: ApplyResearchSetupOptions;
-}): Promise<{
-    schemaVersion: 1;
-    plan: ResearchSetupPlan;
-    state: ResearchSetupState;
-    report: null;
-} | {
-    schemaVersion: 1;
-    plan: ResearchSetupPlan;
-    state: ResearchSetupState;
-    report: Record<string, unknown> & {
-        readiness: "READY" | "BLOCKED";
-        researchReadiness: "READY" | "BLOCKED";
-        preprocessingReadiness: SetupDomainReadiness;
-        acquisitionReadiness: SetupDomainReadiness;
-        authoringReadiness: SetupDomainReadiness;
-        overallReadiness: "READY" | "PARTIALLY_READY" | "BLOCKED";
-    };
-}>;
-export declare function checkResearchSetupUpdates(workspace: string, environment?: NodeJS.ProcessEnv): Promise<{
+}): Promise<ApplyResearchSetupResult>;
+export declare function checkResearchSetupUpdates(workspace: string, environment?: NodeJS.ProcessEnv, candidateVersion?: string): Promise<{
     schemaVersion: 1;
     workspace: string;
     checkedAt: string;
-    updateAvailable: boolean;
+    updateAvailable: boolean | null;
+    releaseCandidate: import("./setup-release.js").ResearchCliReleaseInspection | null;
+    candidateUpgradeCommand: string | null;
     cliVersionDrift: {
         planned: string;
         active: string;
@@ -528,9 +520,9 @@ declare function runAcademicPaperCompanion(input: {
     source?: never;
     validation?: never;
 } | {
+    error?: never;
     artifactCommitted?: never;
     sourcesTried?: never;
-    error?: never;
     schemaVersion: 1;
     kind: "research-setup-companion-result";
     status: "complete";

package/dist/research/workspace/setup.js

@@ -7,6 +7,8 @@ import { setTimeout as sleep } from "node:timers/promises";
 import { CliError } from "../../errors.js";
 import { loadCapabilityDeclarations } from "./capabilities.js";
 import { inspectResearchContext } from "./context.js";
+import { inspectExactResearchCliRelease } from "./setup-release.js";
+import { researchSetupRuntimeSha256, assertResearchSetupRuntimeIntegrity, } from "./setup-runtime-integrity.js";
 import { inspectCapabilityCredentialEnvironment, loadCapabilityCredentialMapForIds, reconcileCapabilityCredentialEnvironment, setCapabilityCredentialValue, } from "./credentials.js";
 import { configureExternalSkillProfile, configureTiangongDatabaseCapability, doctorExternalCapabilities, EXTERNAL_SKILL_CONTEXT_PROFILE, EXTERNAL_SKILL_MEDIA_PROFILE, EXTERNAL_SKILL_PROFILE, reconcileSetupManagedCapabilities, } from "./external-skills.js";
 import { appendJournalEvent } from "./journal.js";
@@ -16,7 +18,7 @@ import { configuredResearchSecrets, isSensitiveEnvironmentName, sanitizeResearch
 import { inspectResearchSetupCatalog, RESEARCH_SETUP_CREDENTIALS, RESEARCH_SETUP_INSTALLER, RESEARCH_SETUP_SETTINGS, RESEARCH_SETUP_SKILLS, resolveSetupSkills, setupSkill, setupSource, setupTargetRoot, verifyResearchSetupRuntimeContract, } from "./setup-catalog.js";
 import { inspectResearchSetupInstructionRouting, isResearchSetupInstructionRoutingPlan, planResearchSetupInstructionRouting, reconcileResearchSetupInstructionRouting, } from "./setup-instructions.js";
 import { acquireFileLock, canonicalJson, ensureDirectory, fileSize, hashRegularTree, isObject, pathExists, REGULAR_TREE_HASH_ALGORITHM, readJsonFile, sha256File, sha256Text, workspacePaths, writeJsonAtomic, writeTextAtomic, } from "./storage.js";
-import { packageRoot, packageVersion, RESEARCH_PACKAGE_NAME } from "./constants.js";
+import { packageRoot, packageVersion, RESEARCH_PACKAGE_NAME, SETUP_UPGRADING_MARKER, } from "./constants.js";
 import { inspectReviewerBridgeStatus } from "./review-executor.js";
 import { exactResearchCliCommand, pinResearchCliCommand, researchSetupApplyCommand, researchSetupRetryCommand, } from "./setup-invocation.js";
 import { doctorResearchWorkspace, initializeResearchWorkspace, loadWorkspaceConfig, } from "./workspace.js";
@@ -213,6 +215,7 @@ export async function createResearchSetupPlan(input) {
             agentSmokeCost: input.agentSmoke === true,
         },
         mutations: setupMutations(root, targets, selected, instructionRouting),
+        ...(input.upgrade ? { upgrade: input.upgrade } : {}),
     };
     const plan = {
         ...unsigned,
@@ -222,6 +225,13 @@ export async function createResearchSetupPlan(input) {
     await ensureDirectory(paths.control);
     const release = await acquireFileLock(paths.setupLock, setupLockPayload(plan.planSha256));
     try {
+        if (plan.upgrade) {
+            await assertUpgradeParent(plan);
+            const candidatePath = researchSetupUpgradeCandidatePath(plan);
+            await assertNoSymlinkedExistingPath(dirname(candidatePath), root);
+            await writeJsonAtomic(candidatePath, plan, 0o444);
+            return plan;
+        }
         if ((await pathExists(paths.setupPlan)) && !input.replacePlan) {
             throw setupError({
                 code: "RESEARCH_SETUP_PLAN_EXISTS",
@@ -275,7 +285,7 @@ export async function loadAndVerifyResearchSetupPlan(planPath) {
     assertPlanMatchesCatalog(plan);
     return plan;
 }
-async function loadHashVerifiedResearchSetupPlan(planPath) {
+export async function loadHashVerifiedResearchSetupPlan(planPath) {
     if (!isAbsolute(planPath)) {
         throw setupError({
             code: "RESEARCH_SETUP_PLAN_INVALID",
@@ -327,7 +337,28 @@ export async function createResearchSetupUpgradePlan(input) {
     }
     const prior = await loadHashVerifiedResearchSetupPlan(workspacePaths(root).setupPlan);
     const selected = resolveSetupSkills(prior.selection.skillIds);
-    validateLicenseAcceptances(selected, input.acceptedLicenseIds);
+    const acceptedLicenseIds = [
+        ...new Set([
+            ...input.acceptedLicenseIds,
+            ...prior.acceptedLicenses
+                .filter((accepted) => selected.some((skill) => skill.id === accepted.skillId && skill.license.id === accepted.licenseId))
+                .map((accepted) => accepted.licenseId),
+        ]),
+    ];
+    validateLicenseAcceptances(selected, acceptedLicenseIds);
+    const paths = workspacePaths(root);
+    for (const path of [paths.runtimeLock, paths.config, paths.marker]) {
+        await assertNoSymlinkedExistingPath(path, root);
+    }
+    const currentConfig = await loadWorkspaceConfig(root);
+    const upgrade = {
+        schemaVersion: 1,
+        cliRuntimeSha256: await researchSetupRuntimeSha256(),
+        parentPlanSha256: prior.planSha256,
+        parentRuntimeLockSha256: await sha256File(paths.runtimeLock),
+        parentConfigSha256: await sha256File(paths.config),
+        parentMarkerSha256: await sha256File(paths.marker),
+    };
     return createResearchSetupPlan({
         workspace: root,
         name: prior.workspace.name,
@@ -336,10 +367,18 @@ export async function createResearchSetupUpgradePlan(input) {
         skillIds: prior.selection.skillIds.filter((id) => !BRAVE_PROFILE_SKILLS[prior.selection.evidenceProfile].includes(id)),
         scope: prior.install.scope,
         agents: prior.install.agents,
-        acceptedLicenseIds: input.acceptedLicenseIds,
+        acceptedLicenseIds,
         credentialEnvironment: Object.fromEntries(prior.credentialSources.map((credential) => [credential.id, credential.fromEnvironment])),
         settings: prior.settings,
-        agentRoutes: prior.agentRoutes,
+        agentRoutes: {
+            producerAgent: currentConfig.producer.agent,
+            reviewerAgent: currentConfig.reviewer.agent,
+            producerModel: currentConfig.producer.model,
+            reviewerModel: currentConfig.reviewer.model,
+            producerPricing: currentConfig.producer.pricing ?? null,
+            reviewerPricing: currentConfig.reviewer.pricing ?? null,
+        },
+        reviewerExecution: currentConfig.reviewerExecution,
         liveChecks: prior.checks.live,
         allowSyntheticUnstructureUpload: prior.checks.allowSyntheticUnstructureUpload,
         agentSmoke: prior.checks.agentSmoke,
@@ -347,12 +386,40 @@ export async function createResearchSetupUpgradePlan(input) {
         confirmGlobalMutation: prior.install.scope === "global",
         confirmAgentSmokeCost: prior.checks.agentSmoke,
         replacePlan: true,
+        upgrade,
         targetRoots: Object.fromEntries(prior.install.targets.map((target) => [target.agent, target.root])),
         ...(input.environment === undefined ? {} : { environment: input.environment }),
     });
 }
+export function researchSetupUpgradeCandidatePath(plan) {
+    return join(workspacePaths(plan.workspace.path).control, "setup-candidates", `${plan.planSha256}.json`);
+}
+export async function assertUpgradeParent(plan) {
+    const paths = workspacePaths(plan.workspace.path);
+    const prior = await loadHashVerifiedResearchSetupPlan(paths.setupPlan);
+    if (!plan.upgrade ||
+        prior.planSha256 !== plan.upgrade.parentPlanSha256 ||
+        (await sha256File(paths.runtimeLock)) !== plan.upgrade.parentRuntimeLockSha256 ||
+        (await sha256File(paths.config)) !== plan.upgrade.parentConfigSha256 ||
+        (await sha256File(paths.marker)) !== plan.upgrade.parentMarkerSha256) {
+        throw setupError({
+            code: "RESEARCH_SETUP_UPGRADE_CONFLICT",
+            step: "upgrade-parent",
+            reason: "The active generation changed after this upgrade was planned.",
+            minimumAction: "Inspect the current setup and create a new reviewed upgrade candidate.",
+            retryCommand: `tiangong-ai research setup status --workspace ${plan.workspace.path} --json`,
+            exitCode: 3,
+        });
+    }
+    return prior;
+}
 export async function applyResearchSetupPlan(planPath, options = {}) {
     const plan = await loadAndVerifyResearchSetupPlan(resolve(planPath));
+    if (plan.upgrade) {
+        await assertResearchSetupRuntimeIntegrity(plan.upgrade.cliRuntimeSha256);
+        const { applyManagedSetupUpgrade } = await import("./setup-upgrade.js");
+        return applyManagedSetupUpgrade(plan, options);
+    }
     const root = plan.workspace.path;
     const paths = workspacePaths(root);
     const environment = options.environment ?? process.env;
@@ -360,7 +427,10 @@ export async function applyResearchSetupPlan(planPath, options = {}) {
     const release = await acquireFileLock(paths.setupLock, setupLockPayload(plan.planSha256));
     let installerCacheDirectory;
     try {
-        installerCacheDirectory = await mkdtemp(join(tmpdir(), "tiangong-research-npm-cache-"));
+        installerCacheDirectory =
+            options.installerCacheDirectory ??
+                (await mkdtemp(join(tmpdir(), "tiangong-research-npm-cache-")));
+        await ensureDirectory(installerCacheDirectory);
     }
     catch (error) {
         await release();
@@ -420,7 +490,9 @@ export async function applyResearchSetupPlan(planPath, options = {}) {
             const sourceDirectories = new Map();
             for (const sourceId of requiredSourceIds) {
                 try {
-                    sourceDirectories.set(sourceId, await ensureSetupSourceCheckout(plan, sourceId, runner, setupInstallerEnvironment));
+                    sourceDirectories.set(sourceId, await ensureSetupSourceCheckout(options.sourceCacheWorkspace
+                        ? { ...plan, workspace: { ...plan.workspace, path: options.sourceCacheWorkspace } }
+                        : plan, sourceId, runner, setupInstallerEnvironment));
                 }
                 catch (error) {
                     throw await annotateSetupSourceCheckoutFailure(error, plan, sourceId);
@@ -562,7 +634,8 @@ export async function applyResearchSetupPlan(planPath, options = {}) {
     }
     finally {
         try {
-            await rm(installerCacheDirectory, { recursive: true, force: true });
+            if (!options.installerCacheDirectory)
+                await rm(installerCacheDirectory, { recursive: true, force: true });
         }
         finally {
             await release();
@@ -572,6 +645,42 @@ export async function applyResearchSetupPlan(planPath, options = {}) {
 export async function inspectResearchSetupStatus(workspace, environment = process.env) {
     const requestedRoot = requireAbsoluteWorkspace(resolve(workspace));
     const requestedPaths = workspacePaths(requestedRoot);
+    const marker = (await pathExists(requestedPaths.marker))
+        ? await readJsonFile(requestedPaths.marker, "Research workspace marker")
+        : null;
+    if (isObject(marker) && marker.kind === SETUP_UPGRADING_MARKER) {
+        const candidateHash = marker.setupUpgradePlanSha256;
+        let recovery = {};
+        if (typeof candidateHash === "string" && /^[a-f0-9]{64}$/.test(candidateHash)) {
+            const planPath = join(requestedPaths.control, "setup-candidates", `${candidateHash}.json`);
+            const candidate = await loadHashVerifiedResearchSetupPlan(planPath).catch(() => null);
+            const canonicalRoot = await realpath(requestedRoot).catch(() => requestedRoot);
+            if (candidate?.upgrade &&
+                candidate.planSha256 === candidateHash &&
+                candidate.workspace.path === canonicalRoot) {
+                recovery = {
+                    planPath,
+                    retryCommand: researchSetupApplyCommand({ version: candidate.cli.version, planPath }),
+                    rollbackCommand: exactResearchCliCommand([
+                        "research",
+                        "setup",
+                        "upgrade",
+                        "--rollback",
+                        "--candidate",
+                        planPath,
+                        "--workspace",
+                        canonicalRoot,
+                        "--json",
+                    ], candidate.cli.version),
+                };
+            }
+        }
+        throw new CliError("Complete or roll back the recorded setup upgrade before inspecting readiness.", {
+            code: "RESEARCH_SETUP_UPGRADE_PENDING",
+            exitCode: 3,
+            details: recovery,
+        });
+    }
     const plan = await loadAndVerifyResearchSetupPlan(requestedPaths.setupPlan);
     const canonicalRequestedRoot = await realpath(requestedRoot).catch(() => requestedRoot);
     if (canonicalRequestedRoot !== plan.workspace.path) {
@@ -1726,7 +1835,7 @@ export async function retryResearchSetup(input) {
     }).catch(() => undefined);
     return applyResearchSetupPlan(paths.setupPlan, input.options);
 }
-export async function checkResearchSetupUpdates(workspace, environment = process.env) {
+export async function checkResearchSetupUpdates(workspace, environment = process.env, candidateVersion) {
     const root = requireAbsoluteWorkspace(resolve(workspace));
     const plan = await loadHashVerifiedResearchSetupPlan(workspacePaths(root).setupPlan);
     const catalog = await inspectResearchSetupCatalog({
@@ -1753,12 +1862,37 @@ export async function checkResearchSetupUpdates(workspace, environment = process
     const cliVersionDrift = plan.cli.version === packageVersion()
         ? null
         : { planned: plan.cli.version, active: packageVersion() };
-    const updateAvailable = drift.length > 0 || cliVersionDrift !== null;
+    const releaseCandidate = candidateVersion === undefined
+        ? null
+        : await inspectExactResearchCliRelease(candidateVersion, {
+            installedVersion: plan.cli.version,
+            environment,
+        });
+    const candidateUpgradeCommand = releaseCandidate?.status === "newer"
+        ? exactResearchCliCommand([
+            "research",
+            "setup",
+            "upgrade",
+            "--plan",
+            "--confirm-upgrade",
+            "--workspace",
+            root,
+            "--json",
+        ], releaseCandidate.requestedVersion).replace(/^npx /, "npx --registry=https://registry.npmjs.org --@tiangong-ai:registry=https://registry.npmjs.org --strict-ssl=true ")
+        : null;
+    const localUpdateAvailable = drift.length > 0 || cliVersionDrift !== null;
+    const updateAvailable = localUpdateAvailable || releaseCandidate?.status === "newer"
+        ? true
+        : releaseCandidate?.status === "unavailable"
+            ? null
+            : false;
     return {
         schemaVersion: 1,
         workspace: root,
         checkedAt: new Date().toISOString(),
         updateAvailable,
+        releaseCandidate,
+        candidateUpgradeCommand,
         cliVersionDrift,
         drift,
         currentInstaller: RESEARCH_SETUP_INSTALLER,
@@ -1766,9 +1900,13 @@ export async function checkResearchSetupUpdates(workspace, environment = process
         policy: {
             automaticUpdate: false,
             floatingUpdate: false,
-            minimumAction: updateAvailable
-                ? "Use the active exact CLI release to create, review, and apply a replacement immutable plan; upgrade never runs a floating CLI or Skills update."
-                : "No catalog migration is required. Installed tree drift is reported separately by setup status/doctor.",
+            minimumAction: releaseCandidate?.status === "unavailable"
+                ? "Exact release metadata is unavailable. Preserve the active generation and retry the same explicit candidate check when access is restored; local catalog drift is reported separately."
+                : updateAvailable
+                    ? "Use the active exact CLI release to create, review, and apply a replacement immutable plan; upgrade never runs a floating CLI or Skills update."
+                    : releaseCandidate === null
+                        ? "No local catalog migration is required; no external release was checked. Pass an explicitly reviewed candidate version to check it. Installed tree drift is reported separately by setup status/doctor."
+                        : "The checked exact release is not newer and no local catalog migration is required. Installed tree drift is reported separately by setup status/doctor.",
         },
     };
 }
@@ -1905,7 +2043,8 @@ function parseResearchSetupPlan(value) {
             typeof mutation.target !== "string" ||
             typeof mutation.reason !== "string") ||
         typeof value.planSha256 !== "string" ||
-        !/^[0-9a-f]{64}$/.test(value.planSha256)) {
+        !/^[0-9a-f]{64}$/.test(value.planSha256) ||
+        (value.upgrade !== undefined && !validUpgradeBinding(value.upgrade))) {
         throw setupError({
             code: "RESEARCH_SETUP_PLAN_INVALID",
             step: "plan-validation",
@@ -1917,6 +2056,19 @@ function parseResearchSetupPlan(value) {
     }
     return value;
 }
+function validUpgradeBinding(value) {
+    if (!isObject(value) || value.schemaVersion !== 1)
+        return false;
+    const keys = [
+        "cliRuntimeSha256",
+        "parentPlanSha256",
+        "parentRuntimeLockSha256",
+        "parentConfigSha256",
+        "parentMarkerSha256",
+    ];
+    return (Object.keys(value).length === keys.length + 1 &&
+        keys.every((key) => typeof value[key] === "string" && /^[0-9a-f]{64}$/.test(String(value[key]))));
+}
 function assertPlanMatchesCatalog(plan) {
     const selected = resolveSetupSkills(plan.selection.skillIds);
     if (canonicalJson(plan.selection.skillIds) !== canonicalJson(selected.map((skill) => skill.id))) {
@@ -2345,7 +2497,16 @@ function setupAgentRoute(current, agent, executionMode, plannedModel, plannedPri
     return {
         agent,
         executionMode,
-        binary: agent === "codex" ? "codex" : agent === "claude" ? "claude" : `${agent}-native-host`,
+        binary: sameAgent
+            ? current.binary
+            : agent === "codex"
+                ? "codex"
+                : agent === "claude"
+                    ? "claude"
+                    : `${agent}-native-host`,
+        ...(sameAgent && current.wrapperTargetBinary !== undefined
+            ? { wrapperTargetBinary: current.wrapperTargetBinary }
+            : {}),
         model: plannedModel ?? (sameAgent ? current.model : null),
         effort: sameAgent ? (current.effort ?? "low") : "low",
         ...(agent === "codex" ? { verbosity: sameAgent ? (current.verbosity ?? "low") : "low" } : {}),
@@ -3131,12 +3292,30 @@ async function runAcademicPaperCompanion(input) {
         throw companionArtifactError(input.root, "The result metadata does not bind the committed PDF bytes.");
     }
     const manifest = await readJsonFile(manifestPath, "Paper manifest");
-    if (manifest.schema_version !== "academic-paper-download.artifact.v2" ||
-        manifest.file !== artifactPath ||
+    if (manifest.schema_version !== "academic-paper-download.artifact.v3") {
+        throw companionArtifactError(input.root, "The PDF manifest must use the pinned adapter's identity-verified artifact.v3 contract; legacy structural-only metadata does not establish document identity.");
+    }
+    if (manifest.file !== artifactPath ||
         manifest.sha256 !== artifactSha256 ||
         manifest.size !== artifactInfo.size) {
         throw companionArtifactError(input.root, "The manifest does not bind the exact committed PDF.");
     }
+    const identity = manifest.identity;
+    const resolvedDoi = normalizedCompanionDoi(manifest.doi);
+    if (!resolvedDoi ||
+        normalizedCompanionDoi(result.doi) !== resolvedDoi ||
+        (doi && normalizedCompanionDoi(doi) !== resolvedDoi) ||
+        manifest.identity_status !== "matched" ||
+        result.identity_status !== "matched" ||
+        !isObject(result.identity) ||
+        !isObject(identity) ||
+        identity.schema_version !== "academic-paper-download.identity.v1" ||
+        identity.status !== "matched" ||
+        !isObject(identity.requested) ||
+        normalizedCompanionDoi(identity.requested.doi) !== resolvedDoi ||
+        canonicalJson(result.identity) !== canonicalJson(identity)) {
+        throw companionArtifactError(input.root, "The pinned adapter's document identity does not bind the requested or resolved DOI and exact manifest.");
+    }
     await verifyPdfEnvelope(artifactPath, artifactInfo.size, input.root);
     const manifestSha256 = await sha256File(manifestPath);
     await appendJournalEvent(workspacePaths(input.root).journal, "research.setup.companion.paper.completed", "workspace", {
@@ -3145,6 +3324,7 @@ async function runAcademicPaperCompanion(input) {
         skillTreeSha256: input.skill.expectedTreeSha256,
         sourceRef: setupSource(input.skill.sourceId).immutableRef,
         querySha256: sha256Text(doi ?? title),
+        documentIdentityStatus: "matched",
         source: typeof manifest.source === "string" ? manifest.source : null,
         artifact: { sha256: artifactSha256, bytes: artifactInfo.size },
         manifest: { sha256: manifestSha256, bytes: manifestInfo.size },
@@ -3162,6 +3342,7 @@ async function runAcademicPaperCompanion(input) {
         provenance: companionProvenance(input.plan, input.skill),
         validation: [
             "pinned-adapter-pypdf",
+            "pinned-adapter-pdf-identity",
             "pdf-header",
             "pdf-eof",
             "size",
@@ -3171,6 +3352,28 @@ async function runAcademicPaperCompanion(input) {
         next: "Admit the exact PDF or a derived hash-bound view as a declared research input.",
     };
 }
+function normalizedCompanionDoi(value) {
+    if (typeof value !== "string")
+        return null;
+    let raw = value.trim();
+    // Match the pinned Python adapter's urllib.parse.unquote behavior: literal
+    // percent signs survive, encoded URLs are unwrapped after one decoding pass,
+    // and URL path segments are not rewritten by WHATWG URL normalization.
+    const unquote = (text) => text.replace(/(?:%[0-9a-f]{2})+/gi, (sequence) => Buffer.from(sequence.replaceAll("%", ""), "hex").toString("utf8"));
+    const urlPrefix = /^(?:https?:\/\/)?(?:dx\.)?doi\.org\//i;
+    if (urlPrefix.test(raw)) {
+        raw = unquote(raw
+            .replace(urlPrefix, "")
+            .replace(/[\t\r\n]/g, "")
+            .split(/[?#]/, 1)[0]
+            .replace(/^\/+/, ""));
+    }
+    else {
+        raw = unquote(raw).replace(/^(?:(?:https?:\/\/)?(?:dx\.)?doi\.org\/|doi:\s*)/i, "");
+    }
+    raw = raw.trim().toLowerCase();
+    return /^10\.\d{4,9}\/\S+$/.test(raw) && !/[\u0000-\u001f]/.test(raw) ? raw : null;
+}
 function safeAcademicPaperRuntimeErrorCode(value) {
     const allowed = new Set([
         "python_incompatible",