@tiangong-ai/cli 0.0.35 → 0.0.36

package/dist/research/orchestration.js

@@ -11,6 +11,7 @@ import { configureExternalSkillProfile, doctorExternalCapabilities, EXTERNAL_SKI
 import { appendJournalEvent } from "./workspace/journal.js";
 import { fetchNativeCandidateSource } from "./workspace/broker.js";
 import { registerEvidenceArtifact } from "./workspace/artifacts.js";
+import { exportProjectAuditBundle, verifyProjectAuditBundle } from "./workspace/audit-bundle.js";
 import { loadCurrentEvidenceSnapshot } from "./workspace/acquisition.js";
 import { inspectDiscoveryProgress } from "./workspace/discovery-status.js";
 import { recordDiscoveryAssessmentBatch } from "./workspace/discovery.js";
@@ -25,6 +26,8 @@ import { approveResearchPolicy, initializeResearchPolicy, inspectResearchPolicyC
 import { resolveInstalledResearchPolicySource, runInteractiveResearchPolicyWizard, } from "./workspace/research-policy-wizard.js";
 import { abortNativeResearchStage, inspectNativeResearchStage, prepareNativeResearchStage, requestResearchHandoff, resolveResearchHandoff, runResearchWorkspace, submitNativeResearchStage, } from "./workspace/runtime.js";
 import { schemaForStage } from "./workspace/schemas.js";
+import { readAndVerifyScientificDesign, scientificDesignSchema, } from "./workspace/scientific-design.js";
+import { inspectScientificReviewStatus, prepareScientificReview, scientificGateAssessmentSchema, scientificReviewSchema, submitScientificReview, } from "./workspace/scientific-review.js";
 import { pathExists, sha256Text, workspacePaths } from "./workspace/storage.js";
 import { doctorResearchWorkspace, initializeResearchWorkspace, requireResearchWorkspace, withWorkspaceLock, } from "./workspace/workspace.js";
 const COMMON_OPTIONS = { help: "boolean", json: "boolean" };
@@ -78,16 +81,21 @@ export function researchOrchestrationHelp() {
   tiangong-ai research publication review submit <project-id> --role evidence|methods-reproducibility|domain-novelty|journal-editor --review <absolute-json> [--workspace <path>] [--json]
   tiangong-ai research publication status <project-id> [--workspace <path>] [--json]
   tiangong-ai research publication close <project-id> [--workspace <path>] [--json]
-  tiangong-ai research project init <project-id> --question <question> [--goal evidence-report|top-journal] [--requirements <absolute-json>] [--input-plan <absolute-json>] [--confirm-budget] [--workspace <path>] [--json]
-  tiangong-ai research project preflight --question <question> [--goal evidence-report|top-journal] [--policy-project <project-id>] [--requirements <absolute-json>] [--input-plan <absolute-json>] [--workspace <path>] [--json]
+  tiangong-ai research project init <project-id> --question <question> [--goal evidence-report|top-journal] [--design <absolute-json> --design-producer-agent codex|claude --design-producer-session <opaque-id>] [--requirements <absolute-json>] [--input-plan <absolute-json>] [--confirm-budget] [--workspace <path>] [--json]
+  tiangong-ai research project preflight --question <question> [--goal evidence-report|top-journal] [--policy-project <project-id> --design <absolute-json>] [--requirements <absolute-json>] [--input-plan <absolute-json>] [--workspace <path>] [--json]
   tiangong-ai research project input add <project-id> --path <absolute-file> [--role primary|reference|replication] [--trust-status verified-owner-input|unverified-owner-input|reference-only|replication-candidate] [--independently-reproduced] [--workspace <path>] [--json]
   tiangong-ai research project retry <project-id> [--package <package-id>] [--workspace <path>] [--json]
-  tiangong-ai research project fork <source-project-id> --to <target-project-id> [--resume-through discover|acquire|analyze|synthesize] [--workspace <path>] [--json]
-  tiangong-ai research project addendum <closed-project-id> --to <target-project-id> [--workspace <path>] [--json]
+  tiangong-ai research project fork <source-project-id> --to <target-project-id> [--resume-through discover|acquire|analyze|synthesize] [--design <absolute-json> --design-producer-agent codex|claude --design-producer-session <opaque-id>] [--workspace <path>] [--json]
+  tiangong-ai research project addendum <closed-project-id> --to <target-project-id> [--design <absolute-json> --design-producer-agent codex|claude --design-producer-session <opaque-id>] [--workspace <path>] [--json]
   tiangong-ai research project archive <project-id> --reason <text> [--workspace <path>] [--json]
   tiangong-ai research project abandon <project-id> --reason <text> [--workspace <path>] [--json]
   tiangong-ai research project handoff request <project-id> --record <absolute-json> [--workspace <path>] [--json]
   tiangong-ai research project handoff resolve <project-id> --note <text> [--workspace <path>] [--json]
+  tiangong-ai research project scientific review prepare <project-id> --role research-design|evidence-construct|pilot-methods --assessment <absolute-json> --reviewer-agent codex|claude --reviewer-session <opaque-id> [--workspace <path>] [--json]
+  tiangong-ai research project scientific review submit <project-id> --role research-design|evidence-construct|pilot-methods --review <absolute-json> [--workspace <path>] [--json]
+  tiangong-ai research project scientific status <project-id> [--workspace <path>] [--json]
+  tiangong-ai research project audit export <project-id> --output <absolute-new-directory> [--workspace <path>] [--json]
+  tiangong-ai research project audit verify --bundle <absolute-directory> [--json]
   tiangong-ai research project stage prepare <project-id> --stage discover|acquire|analyze|synthesize --host-agent codex|claude [--workspace <path>] [--json]
   tiangong-ai research project stage submit <project-id> --session <id> --output <absolute-json> [--confirm-model <id>] [--workspace <path>] [--json]
   tiangong-ai research project stage abort <project-id> --session <id> [--workspace <path>] [--json]
@@ -97,7 +105,7 @@ export function researchOrchestrationHelp() {
   tiangong-ai research project evidence assessment record <project-id> --record <absolute-json> [--workspace <path>] [--json]
   tiangong-ai research project evidence download bind <project-id> --candidate <id> --record <absolute-json> [--workspace <path>] [--json]
   tiangong-ai research project evidence artifact register <project-id> --candidate <id> --path <absolute-file> [--download-binding <id> | --derived-from-artifact <id>] [--media-type <type>] [--source-url <https-url>] [--license <declared-license>] [--license-url <https-url>] [--host-type <type>] [--article-version <version>] [--workspace <path>] [--json]
-  tiangong-ai research schema show <discover|acquire|analyze|synthesize|review|doctor|publication-assessment|publication-review-evidence|publication-review-methods-reproducibility|publication-review-domain-novelty|publication-review-journal-editor> [--json]
+  tiangong-ai research schema show <discover|acquire|analyze|synthesize|review|doctor|scientific-design|scientific-assessment-research-design|scientific-assessment-evidence-construct|scientific-assessment-pilot-methods|scientific-review-research-design|scientific-review-evidence-construct|scientific-review-pilot-methods|publication-assessment|publication-review-evidence|publication-review-methods-reproducibility|publication-review-domain-novelty|publication-review-journal-editor> [--compatibility claude-code] [--json]
   tiangong-ai research status [--project <project-id>] [--all] [--workspace <absolute-path>] [--json]
   tiangong-ai research run [--project <project-id>] [--max-parallel <1-8>] [--max-cycles <1-100>] [--dry-run] [--progress-jsonl] [--workspace <absolute-path>] [--json]
 
@@ -303,33 +311,74 @@ async function runSchema(argv, io) {
         return writeHelp(io);
     if (action !== "show")
         throw unknownAction("research schema", action);
-    const args = parseStrictArgs(rest, COMMON_OPTIONS, "research schema show");
+    const args = parseStrictArgs(rest, { ...COMMON_OPTIONS, compatibility: "string" }, "research schema show");
     if (strictBoolean(args, "help"))
         return writeHelp(io);
     const stage = onePositional(args.positionals, "research schema show");
-    if (stage === "publication-assessment") {
-        writeJson(io, publicationAssessmentSchema(), args);
-        return 0;
+    let schema;
+    if (stage === "scientific-design") {
+        schema = scientificDesignSchema();
+    }
+    else if (stage.startsWith("scientific-assessment-")) {
+        const role = scientificReviewRole(stage.slice("scientific-assessment-".length));
+        schema = scientificGateAssessmentSchema(role);
+    }
+    else if (stage.startsWith("scientific-review-")) {
+        const role = scientificReviewRole(stage.slice("scientific-review-".length));
+        schema = scientificReviewSchema(role);
+    }
+    else if (stage === "publication-assessment") {
+        schema = publicationAssessmentSchema();
     }
-    if (stage.startsWith("publication-review-")) {
+    else if (stage.startsWith("publication-review-")) {
         const role = publicationReviewRole(stage.slice("publication-review-".length));
-        writeJson(io, publicationReviewSchema(role), args);
-        return 0;
+        schema = publicationReviewSchema(role);
+    }
+    else if (stage === "discover" ||
+        stage === "acquire" ||
+        stage === "analyze" ||
+        stage === "synthesize" ||
+        stage === "review" ||
+        stage === "doctor") {
+        schema = schemaForStage(stage);
     }
-    if (stage !== "discover" &&
-        stage !== "acquire" &&
-        stage !== "analyze" &&
-        stage !== "synthesize" &&
-        stage !== "review" &&
-        stage !== "doctor") {
+    else {
         throw new CliError(`Unsupported research schema stage: ${stage}`, {
             code: "RESEARCH_SCHEMA_INVALID",
             exitCode: 2,
         });
     }
-    writeJson(io, schemaForStage(stage), args);
+    writeJson(io, compatibleSchema(schema, strictString(args, "compatibility")), args);
     return 0;
 }
+function compatibleSchema(schema, compatibility) {
+    if (!compatibility)
+        return schema;
+    if (compatibility !== "claude-code") {
+        throw new CliError(`Unsupported schema compatibility target: ${compatibility}`, {
+            code: "RESEARCH_SCHEMA_COMPATIBILITY_INVALID",
+            exitCode: 2,
+            details: { supported: ["claude-code"] },
+        });
+    }
+    const compatible = structuredClone(schema);
+    const stripMetadata = (value) => {
+        if (Array.isArray(value)) {
+            for (const item of value)
+                stripMetadata(item);
+            return;
+        }
+        if (!value || typeof value !== "object")
+            return;
+        const record = value;
+        delete record.$schema;
+        delete record.$id;
+        for (const item of Object.values(record))
+            stripMetadata(item);
+    };
+    stripMetadata(compatible);
+    return compatible;
+}
 async function runContext(argv, io) {
     const [action, ...rest] = argv;
     if (!action || action === "--help" || action === "-h")
@@ -520,6 +569,41 @@ async function runProject(argv, io) {
     const [action, ...rest] = argv;
     if (!action || action === "--help" || action === "-h")
         return writeHelp(io);
+    if (action === "audit") {
+        const [auditAction, ...auditRest] = rest;
+        if (auditAction === "export") {
+            const args = parseStrictArgs(auditRest, { ...WORKSPACE_OPTIONS, output: "string" }, "research project audit export");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project audit export");
+            const destination = strictString(args, "output");
+            if (!destination) {
+                throw new CliError("Audit export requires --output.", {
+                    code: "RESEARCH_AUDIT_BUNDLE_PATH_INVALID",
+                    exitCode: 2,
+                });
+            }
+            const root = await workspaceFromArgs(args);
+            writeJson(io, await exportProjectAuditBundle({ root, projectId, destination }), args);
+            return 0;
+        }
+        if (auditAction === "verify") {
+            const args = parseStrictArgs(auditRest, { ...COMMON_OPTIONS, bundle: "string" }, "research project audit verify");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            rejectPositionals(args.positionals, "research project audit verify");
+            const bundlePath = strictString(args, "bundle");
+            if (!bundlePath) {
+                throw new CliError("Audit verification requires --bundle.", {
+                    code: "RESEARCH_AUDIT_BUNDLE_PATH_INVALID",
+                    exitCode: 2,
+                });
+            }
+            writeJson(io, await verifyProjectAuditBundle(bundlePath), args);
+            return 0;
+        }
+        throw unknownAction("research project audit", auditAction ?? "");
+    }
     if (action === "handoff") {
         const [handoffAction, ...handoffRest] = rest;
         if (handoffAction === "request") {
@@ -559,6 +643,71 @@ async function runProject(argv, io) {
         }
         throw unknownAction("research project handoff", handoffAction ?? "");
     }
+    if (action === "scientific") {
+        const [scientificAction, ...scientificRest] = rest;
+        if (scientificAction === "status") {
+            const args = parseStrictArgs(scientificRest, WORKSPACE_OPTIONS, "research project scientific status");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project scientific status");
+            const root = await workspaceFromArgs(args);
+            writeJson(io, await inspectScientificReviewStatus(root, projectId), args);
+            return 0;
+        }
+        if (scientificAction !== "review") {
+            throw unknownAction("research project scientific", scientificAction ?? "");
+        }
+        const [reviewAction, ...reviewRest] = scientificRest;
+        if (reviewAction === "prepare") {
+            const args = parseStrictArgs(reviewRest, {
+                ...WORKSPACE_OPTIONS,
+                role: "string",
+                assessment: "string",
+                "reviewer-agent": "string",
+                "reviewer-session": "string",
+            }, "research project scientific review prepare");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project scientific review prepare");
+            const assessmentPath = strictString(args, "assessment");
+            const reviewerSessionId = strictString(args, "reviewer-session");
+            if (!assessmentPath || !reviewerSessionId) {
+                throw new CliError("Scientific review prepare requires --assessment, --reviewer-agent, and --reviewer-session.", { code: "RESEARCH_SCIENTIFIC_REVIEW_ARGUMENT_REQUIRED", exitCode: 2 });
+            }
+            const root = await workspaceFromArgs(args);
+            writeJson(io, await prepareScientificReview({
+                root,
+                projectId,
+                role: scientificReviewRole(strictString(args, "role")),
+                assessmentPath,
+                reviewerAgent: publicationAgent(strictString(args, "reviewer-agent"), "reviewer"),
+                reviewerSessionId,
+            }), args);
+            return 0;
+        }
+        if (reviewAction === "submit") {
+            const args = parseStrictArgs(reviewRest, { ...WORKSPACE_OPTIONS, role: "string", review: "string" }, "research project scientific review submit");
+            if (strictBoolean(args, "help"))
+                return writeHelp(io);
+            const projectId = onePositional(args.positionals, "research project scientific review submit");
+            const reviewPath = strictString(args, "review");
+            if (!reviewPath) {
+                throw new CliError("Scientific review submit requires --review.", {
+                    code: "RESEARCH_SCIENTIFIC_REVIEW_ARGUMENT_REQUIRED",
+                    exitCode: 2,
+                });
+            }
+            const root = await workspaceFromArgs(args);
+            writeJson(io, await submitScientificReview({
+                root,
+                projectId,
+                role: scientificReviewRole(strictString(args, "role")),
+                reviewPath,
+            }), args);
+            return 0;
+        }
+        throw unknownAction("research project scientific review", reviewAction ?? "");
+    }
     if (action === "stage") {
         const [stageAction, ...stageRest] = rest;
         if (stageAction === "prepare") {
@@ -800,6 +949,9 @@ async function runProject(argv, io) {
             goal: "string",
             requirements: "string",
             "input-plan": "string",
+            design: "string",
+            "design-producer-agent": "string",
+            "design-producer-session": "string",
             "confirm-budget": "boolean",
         }, "research project init");
         if (strictBoolean(args, "help"))
@@ -816,7 +968,26 @@ async function runProject(argv, io) {
         const goal = researchGoal(strictString(args, "goal"));
         const requirementsPath = strictString(args, "requirements");
         const inputPlanPath = strictString(args, "input-plan");
-        const project = await initializeProject(root, projectId, question, requirementsPath ? await readEvidenceRequirements(requirementsPath) : undefined, strictBoolean(args, "confirm-budget"), inputPlanPath ? await readAndVerifyProjectInputPlan(inputPlanPath) : undefined, goal === "top-journal" ? await loadApprovedResearchPolicy(root, projectId) : undefined);
+        const publicationPolicy = goal === "top-journal" ? await loadApprovedResearchPolicy(root, projectId) : undefined;
+        const designPath = strictString(args, "design");
+        const designProducerAgent = strictString(args, "design-producer-agent");
+        const designProducerSession = strictString(args, "design-producer-session");
+        if (goal === "top-journal" && (!designPath || !designProducerAgent || !designProducerSession)) {
+            throw new CliError("Top-journal init requires --design, --design-producer-agent, and --design-producer-session.", { code: "RESEARCH_SCIENTIFIC_DESIGN_REQUIRED", exitCode: 2 });
+        }
+        if (goal !== "top-journal" && (designPath || designProducerAgent || designProducerSession)) {
+            throw new CliError("Scientific design options are only valid with --goal top-journal.", {
+                code: "RESEARCH_SCIENTIFIC_DESIGN_POLICY_REQUIRED",
+                exitCode: 2,
+            });
+        }
+        const project = await initializeProject(root, projectId, question, requirementsPath ? await readEvidenceRequirements(requirementsPath) : undefined, strictBoolean(args, "confirm-budget"), inputPlanPath ? await readAndVerifyProjectInputPlan(inputPlanPath) : undefined, publicationPolicy, designPath && designProducerAgent && designProducerSession
+            ? {
+                design: await readAndVerifyScientificDesign(designPath, projectId),
+                producerAgent: publicationAgent(designProducerAgent, "design producer"),
+                producerSessionId: designProducerSession,
+            }
+            : undefined);
         writeJson(io, project, args);
         return 0;
     }
@@ -828,6 +999,7 @@ async function runProject(argv, io) {
             "policy-project": "string",
             requirements: "string",
             "input-plan": "string",
+            design: "string",
         }, "research project preflight");
         if (strictBoolean(args, "help"))
             return writeHelp(io);
@@ -842,6 +1014,7 @@ async function runProject(argv, io) {
         const root = await workspaceFromArgs(args);
         const goal = researchGoal(strictString(args, "goal"));
         const policyProject = strictString(args, "policy-project");
+        let publicationPolicy = null;
         if (goal === "top-journal") {
             if (!policyProject) {
                 throw new CliError("Top-journal preflight requires --policy-project.", {
@@ -849,7 +1022,7 @@ async function runProject(argv, io) {
                     exitCode: 2,
                 });
             }
-            await loadApprovedResearchPolicy(root, policyProject);
+            publicationPolicy = await loadApprovedResearchPolicy(root, policyProject);
         }
         else if (policyProject) {
             throw new CliError("--policy-project is only valid with --goal top-journal.", {
@@ -861,7 +1034,26 @@ async function runProject(argv, io) {
         const requirements = requirementsPath ? await readEvidenceRequirements(requirementsPath) : null;
         const inputPlanPath = strictString(args, "input-plan");
         const inputPlan = inputPlanPath ? await readAndVerifyProjectInputPlan(inputPlanPath) : null;
-        const result = await evaluateProjectPreflight(root, question, requirements, inputPlan);
+        const designPath = strictString(args, "design");
+        if (goal === "top-journal" && !designPath) {
+            throw new CliError("Top-journal preflight requires --design.", {
+                code: "RESEARCH_SCIENTIFIC_DESIGN_REQUIRED",
+                exitCode: 2,
+            });
+        }
+        if (goal !== "top-journal" && designPath) {
+            throw new CliError("--design is only valid with --goal top-journal.", {
+                code: "RESEARCH_SCIENTIFIC_DESIGN_POLICY_REQUIRED",
+                exitCode: 2,
+            });
+        }
+        const scientificDesign = designPath
+            ? await readAndVerifyScientificDesign(designPath, policyProject)
+            : null;
+        const result = await evaluateProjectPreflight(root, question, requirements, inputPlan, {
+            publicationPolicy,
+            scientificDesign,
+        });
         writeJson(io, result, args);
         return result.readyToInitialize ? 0 : 3;
     }
@@ -909,7 +1101,14 @@ async function runProject(argv, io) {
         return 0;
     }
     if (action === "fork") {
-        const args = parseStrictArgs(rest, { ...WORKSPACE_OPTIONS, to: "string", "resume-through": "string" }, "research project fork");
+        const args = parseStrictArgs(rest, {
+            ...WORKSPACE_OPTIONS,
+            to: "string",
+            "resume-through": "string",
+            design: "string",
+            "design-producer-agent": "string",
+            "design-producer-session": "string",
+        }, "research project fork");
         if (strictBoolean(args, "help"))
             return writeHelp(io);
         const sourceProjectId = onePositional(args.positionals, "research project fork");
@@ -921,12 +1120,41 @@ async function runProject(argv, io) {
             });
         }
         const root = await workspaceFromArgs(args);
-        const project = await forkProject(root, sourceProjectId, targetProjectId, resumeStage(strictString(args, "resume-through")));
+        const source = await loadProject(root, sourceProjectId);
+        const designPath = strictString(args, "design");
+        const designProducerAgent = strictString(args, "design-producer-agent");
+        const designProducerSession = strictString(args, "design-producer-session");
+        if (source.publicationPolicy &&
+            (!designPath || !designProducerAgent || !designProducerSession)) {
+            throw new CliError("A top-journal fork requires a target-specific approved policy plus --design, --design-producer-agent, and --design-producer-session.", { code: "RESEARCH_SCIENTIFIC_DESIGN_REAPPROVAL_REQUIRED", exitCode: 3 });
+        }
+        if (!source.publicationPolicy && (designPath || designProducerAgent || designProducerSession)) {
+            throw new CliError("Scientific reapproval options require a top-journal source project.", {
+                code: "RESEARCH_SCIENTIFIC_DESIGN_REAPPROVAL_INVALID",
+                exitCode: 2,
+            });
+        }
+        const project = await forkProject(root, sourceProjectId, targetProjectId, resumeStage(strictString(args, "resume-through")), designPath && designProducerAgent && designProducerSession
+            ? {
+                publicationPolicy: await loadApprovedResearchPolicy(root, targetProjectId),
+                scientificDesign: {
+                    design: await readAndVerifyScientificDesign(designPath, targetProjectId),
+                    producerAgent: publicationAgent(designProducerAgent, "design producer"),
+                    producerSessionId: designProducerSession,
+                },
+            }
+            : undefined);
         writeJson(io, project, args);
         return 0;
     }
     if (action === "addendum") {
-        const args = parseStrictArgs(rest, { ...WORKSPACE_OPTIONS, to: "string" }, "research project addendum");
+        const args = parseStrictArgs(rest, {
+            ...WORKSPACE_OPTIONS,
+            to: "string",
+            design: "string",
+            "design-producer-agent": "string",
+            "design-producer-session": "string",
+        }, "research project addendum");
         if (strictBoolean(args, "help"))
             return writeHelp(io);
         const sourceProjectId = onePositional(args.positionals, "research project addendum");
@@ -938,7 +1166,30 @@ async function runProject(argv, io) {
             });
         }
         const root = await workspaceFromArgs(args);
-        const project = await createProjectAddendum(root, sourceProjectId, targetProjectId);
+        const source = await loadProject(root, sourceProjectId);
+        const designPath = strictString(args, "design");
+        const designProducerAgent = strictString(args, "design-producer-agent");
+        const designProducerSession = strictString(args, "design-producer-session");
+        if (source.publicationPolicy &&
+            (!designPath || !designProducerAgent || !designProducerSession)) {
+            throw new CliError("A top-journal addendum requires a target-specific approved policy plus --design, --design-producer-agent, and --design-producer-session.", { code: "RESEARCH_SCIENTIFIC_DESIGN_REAPPROVAL_REQUIRED", exitCode: 3 });
+        }
+        if (!source.publicationPolicy && (designPath || designProducerAgent || designProducerSession)) {
+            throw new CliError("Scientific reapproval options require a top-journal source project.", {
+                code: "RESEARCH_SCIENTIFIC_DESIGN_REAPPROVAL_INVALID",
+                exitCode: 2,
+            });
+        }
+        const project = await createProjectAddendum(root, sourceProjectId, targetProjectId, designPath && designProducerAgent && designProducerSession
+            ? {
+                publicationPolicy: await loadApprovedResearchPolicy(root, targetProjectId),
+                scientificDesign: {
+                    design: await readAndVerifyScientificDesign(designPath, targetProjectId),
+                    producerAgent: publicationAgent(designProducerAgent, "design producer"),
+                    producerSessionId: designProducerSession,
+                },
+            }
+            : undefined);
         writeJson(io, project, args);
         return 0;
     }
@@ -996,6 +1247,7 @@ async function runStatus(argv, io) {
             const nativeStage = await inspectNativeResearchStage(root, current);
             const snapshot = await inspectSnapshotForStatus(root, current.id);
             const readyPackage = nextReadyPackage(current)?.id ?? null;
+            const scientificReview = await inspectScientificReviewStatus(root, current.id);
             const publication = current.publicationPolicy
                 ? await inspectPublicationForStatus(root, current.id)
                 : null;
@@ -1009,9 +1261,10 @@ async function runStatus(argv, io) {
                 evidenceState: current.evidenceState,
                 snapshot,
                 nativeStage,
+                scientificReview,
                 publication,
                 readyPackage,
-                recommendedAction: projectRecommendedAction(root, current, readyPackage, nativeStage, publication),
+                recommendedAction: projectRecommendedAction(root, current, readyPackage, nativeStage, scientificReview, publication),
                 usage: current.usage,
                 inputs: current.inputs,
                 packages: current.packages,
@@ -1079,7 +1332,7 @@ async function inspectPublicationForStatus(root, projectId) {
         };
     }
 }
-function projectRecommendedAction(root, project, readyPackage, nativeStage, publication) {
+function projectRecommendedAction(root, project, readyPackage, nativeStage, scientificReview, publication) {
     if (project.lineage.supersededBy) {
         return `Continue with superseding project ${project.lineage.supersededBy}.`;
     }
@@ -1098,6 +1351,14 @@ function projectRecommendedAction(root, project, readyPackage, nativeStage, publ
     if (nativeStage.status === "active") {
         return nativeStage.recommendedAction ?? "Resume the active native stage.";
     }
+    if (scientificReview.nextGate) {
+        const gate = scientificReview.nextGate;
+        if (gate.status === "stopped") {
+            return `Scientific ${gate.role} review stopped the project; inspect the frozen review and request user or external action instead of continuing.`;
+        }
+        const schema = `scientific-assessment-${gate.role}`;
+        return `Use the native producer App to create a bounded ${gate.role} assessment from schema ${schema}, then prepare an independent review: tiangong-ai research project scientific review prepare ${project.id} --role ${gate.role} --assessment <absolute-json> --reviewer-agent <codex|claude> --reviewer-session <fresh-opaque-id> --workspace ${root}`;
+    }
     if (project.status === "complete") {
         if (project.publicationPolicy) {
             if (publication && "code" in publication) {
@@ -1349,6 +1610,15 @@ function publicationReviewRole(value) {
     }
     throw new CliError("--role must be evidence, methods-reproducibility, domain-novelty, or journal-editor.", { code: "RESEARCH_PUBLICATION_REVIEW_ROLE_INVALID", exitCode: 2 });
 }
+function scientificReviewRole(value) {
+    if (value === "research-design" || value === "evidence-construct" || value === "pilot-methods") {
+        return value;
+    }
+    throw new CliError("--role must be research-design, evidence-construct, or pilot-methods.", {
+        code: "RESEARCH_SCIENTIFIC_REVIEW_ROLE_INVALID",
+        exitCode: 2,
+    });
+}
 function publicationAgent(value, label) {
     if (value === "codex" || value === "claude")
         return value;