@tiangong-ai/cli 0.0.42 → 0.0.44

package/dist/research/workspace/review-executor.js.map

@@ -0,0 +1 @@
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package/dist/research/workspace/runtime.js

@@ -4,7 +4,7 @@ import { basename, dirname, isAbsolute, join, relative, resolve } from "node:pat
 import { CliError } from "../../errors.js";
 import { loadCapabilityDeclarations, stageLockedCapabilities, verifyCapabilities, } from "./capabilities.js";
 import { startCapabilityBroker } from "./broker.js";
-import { commitAcquisitionAssessments, freezeEvidenceSnapshot, loadCurrentEvidenceSnapshot, loadImmutableEvidenceSnapshotChain, materializeAcquisitionAudit, parseMaterializedAcquisitionAudit, } from "./acquisition.js";
+import { commitAcquisitionAssessments, freezeEvidenceSnapshot, loadCurrentEvidenceSnapshot, loadInferenceReadyEvidenceSnapshot, loadImmutableEvidenceSnapshotChain, materializeAcquisitionAudit, parseMaterializedAcquisitionAudit, } from "./acquisition.js";
 import { stageEvidenceArtifacts } from "./artifacts.js";
 import { commitDiscoveryDecisions, materializeDiscoveryEvidence } from "./discovery.js";
 import { inspectDiscoveryProgress } from "./discovery-status.js";
@@ -13,8 +13,10 @@ import { parseEvidenceExhaustionHandoff, validateEvidenceExhaustionHandoff, } fr
 import { loadProjectEvidenceReceipts, stageProjectEvidence } from "./evidence.js";
 import { appendEvidenceLedgerEvent, evidenceLedgerPath, listEvidenceCandidates, registerProjectInputCandidates, } from "./evidence-ledger.js";
 import { executeAgent } from "./executor.js";
+import { createReviewExecutor } from "./review-executor.js";
 import { requiredDiscoveryCapabilityIds } from "./external-skills.js";
 import { renderInputLineContext } from "./input-plan.js";
+import { freezeClaimEvidenceGraph, freezeInferenceSnapshot, loadCurrentInferenceSnapshot, } from "./inference.js";
 import { appendJournalEvent, readJournal, verifyJournal } from "./journal.js";
 import { nativeActivityRecordSchema } from "./native-activity.js";
 import { calculateAgentCallTokenReservation, RESEARCH_BROKER_MAX_TURNS, RESEARCH_ESTIMATED_BYTES_PER_TOKEN, RESEARCH_MAX_REPAIR_SOURCE_BYTES, RESEARCH_REPAIR_MAX_TURNS, researchStructuredOutputMaxTurns, reservedAgentPackageCost, } from "./preflight.js";
@@ -160,14 +162,14 @@ export const researchHandoffRecordSchema = {
         },
     ],
 };
-export async function runResearchWorkspace(root, options, packageExecutor = executeAgent) {
-    return runResearchWorkspaceInternal(root, options, packageExecutor, false);
+export async function runResearchWorkspace(root, options, packageExecutor) {
+    return runResearchWorkspaceInternal(root, options, packageExecutor ?? executeAgent, false, packageExecutor === undefined);
 }
 /** @internal Test-only seam for exercising deterministic package admission with fake agents. */
 export async function runResearchWorkspaceWithInjectedProducerForTesting(root, options, packageExecutor) {
-    return runResearchWorkspaceInternal(root, options, packageExecutor, true);
+    return runResearchWorkspaceInternal(root, options, packageExecutor, true, false);
 }
-async function runResearchWorkspaceInternal(root, options, packageExecutor, allowInjectedProducerForTesting) {
+async function runResearchWorkspaceInternal(root, options, packageExecutor, allowInjectedProducerForTesting, useConfiguredReviewerExecutor) {
     validateRunOptions(options);
     const requestId = randomUUID();
     if (options.dryRun)
@@ -176,6 +178,9 @@ async function runResearchWorkspaceInternal(root, options, packageExecutor, allo
         await verifyJournal(workspacePaths(root).journal);
         const config = await loadWorkspaceConfig(root);
         assertExecutionConfiguration(config);
+        const reviewerPackageExecutor = useConfiguredReviewerExecutor
+            ? createReviewExecutor({ root, execution: config.reviewerExecution }).execute
+            : null;
         for (const project of await projectsForRun(root, options.projectId)) {
             await assertProjectPublicationPolicy(root, project);
         }
@@ -223,7 +228,7 @@ async function runResearchWorkspaceInternal(root, options, packageExecutor, allo
             if (!selected.length)
                 break;
             cycles += 1;
-            const results = await Promise.all(selected.map(({ project, workPackage }) => executeWorkPackage(root, project.id, workPackage.id, config, options, requestId, packageExecutor, doctorAttestation)));
+            const results = await Promise.all(selected.map(({ project, workPackage }) => executeWorkPackage(root, project.id, workPackage.id, config, options, requestId, packageExecutor, reviewerPackageExecutor, doctorAttestation)));
             executed.push(...results);
         }
         const result = await summarizeRun(root, requestId, cycles, executed, options.maxCycles, options.projectId);
@@ -234,6 +239,22 @@ async function runResearchWorkspaceInternal(root, options, packageExecutor, allo
         return result;
     });
 }
+function capsuleDispositionForHost(hostAgent) {
+    return hostAgent === "workbuddy" || hostAgent === "codebuddy"
+        ? "retained-outer-sandbox"
+        : "deleted";
+}
+function nativeCapsuleDisposition(session) {
+    return capsuleDispositionForHost(session.packet.hostAgent);
+}
+async function releaseNativeStageSession(root, projectId, session) {
+    const disposition = nativeCapsuleDisposition(session);
+    await rm(nativeStageSessionPath(root, projectId), { force: true });
+    if (disposition === "deleted") {
+        await rm(session.capsuleRoot, { recursive: true, force: true });
+    }
+    return disposition;
+}
 export async function inspectNativeResearchStage(root, project) {
     const path = nativeStageSessionPath(root, project.id);
     if (!(await pathExists(path))) {
@@ -314,7 +335,11 @@ export async function prepareNativeResearchStage(input) {
             await registerProjectInputCandidates(input.root, project.id, project.inputs);
         }
         if (input.stage === "analyze" || input.stage === "synthesize") {
-            await loadCurrentEvidenceSnapshot(input.root, project.id);
+            await loadInferenceReadyEvidenceSnapshot(input.root, project.id);
+            if (input.stage === "analyze")
+                await freezeInferenceSnapshot(input.root, project.id);
+            else
+                await loadCurrentInferenceSnapshot(input.root, project.id);
         }
         if (config.mode === "production-research" &&
             config.budget.maxCostUsd > config.budget.confirmationCostUsd &&
@@ -753,7 +778,7 @@ export async function submitNativeResearchStage(input) {
                 details: { state: project.handoff.state, reasonCode: project.handoff.reasonCode },
             });
         }
-        await assertNoUnresolvedNativeChallenge(input.root, project.id);
+        await assertNoUnresolvedNativeChallenge(input.root, project.id, session.packet.stage, raw);
         const workPackage = packageById(project, session.packet.packageId);
         if (workPackage.status !== "running" || workPackage.executor !== "producer") {
             throw new CliError("The bound native producer package is no longer running.", {
@@ -795,6 +820,11 @@ export async function submitNativeResearchStage(input) {
                 await freezeEvidenceSnapshot(input.root, project);
                 outputs.push(await fileRecord(join(projectRoot(input.root, project.id), "outputs", "evidence-snapshot.json"), "outputs/evidence-snapshot.json"));
             }
+            if (workPackage.stage === "analyze") {
+                const analysis = JSON.parse(await readFile(join(projectRoot(input.root, project.id), "outputs", "analysis.json"), "utf8"));
+                await freezeClaimEvidenceGraph(input.root, project.id, analysis);
+                outputs.push(await fileRecord(join(projectRoot(input.root, project.id), "outputs", "claim-evidence-graph.json"), "outputs/claim-evidence-graph.json"));
+            }
             await commitStageEvidenceBindings(input.root, project, workPackage);
             applyUsage(project, result);
             workPackage.status = "complete";
@@ -828,6 +858,7 @@ export async function submitNativeResearchStage(input) {
                 accountingMode: "reserved-native-host",
             });
             const usage = { ...usageSlice(result), accountingMode: "reserved-native-host" };
+            const capsuleDisposition = nativeCapsuleDisposition(session);
             await appendJournalEvent(workspacePaths(input.root).journal, "native.stage.completed", project.id, {
                 sessionId: session.packet.sessionId,
                 packetSha256: session.packet.packetSha256,
@@ -836,9 +867,10 @@ export async function submitNativeResearchStage(input) {
                 stage: workPackage.stage,
                 outputs,
                 usage,
+                capsuleDisposition,
+                retainedCapsuleId: capsuleDisposition === "retained-outer-sandbox" ? basename(session.capsuleRoot) : null,
             });
-            await rm(nativeStageSessionPath(input.root, project.id), { force: true });
-            await rm(session.capsuleRoot, { recursive: true, force: true });
+            await releaseNativeStageSession(input.root, project.id, session);
             return {
                 projectId: project.id,
                 packageId: workPackage.id,
@@ -858,7 +890,7 @@ export async function submitNativeResearchStage(input) {
         }
     });
 }
-async function assertNoUnresolvedNativeChallenge(root, projectId) {
+async function assertNoUnresolvedNativeChallenge(root, projectId, stage, rawOutput) {
     const events = await readJournal(evidenceLedgerPath(root, projectId));
     const lastChallengeIndex = events.findLastIndex((event) => event.type === "activity.recorded" &&
         event.payload.status === "blocked" &&
@@ -867,6 +899,11 @@ async function assertNoUnresolvedNativeChallenge(root, projectId) {
         return;
     const lastResolutionIndex = events.findLastIndex((event) => event.type === "handoff.resolved");
     if (lastResolutionIndex < lastChallengeIndex) {
+        if (stage === "acquire") {
+            const output = parseStructuredStageOutput("acquire", rawOutput).value;
+            if (Array.isArray(output.gaps) && output.gaps.length > 0)
+                return;
+        }
         throw new CliError("A login, MFA, CAPTCHA, paywall, security, or authorization challenge requires a durable user handoff before stage submission.", {
             code: "RESEARCH_PROJECT_HANDOFF_REQUIRED",
             exitCode: 3,
@@ -904,9 +941,12 @@ export async function abortNativeResearchStage(input) {
             projectId: project.id,
             packageId: workPackage.id,
             stage: workPackage.stage,
+            capsuleDisposition: nativeCapsuleDisposition(session),
+            retainedCapsuleId: nativeCapsuleDisposition(session) === "retained-outer-sandbox"
+                ? basename(session.capsuleRoot)
+                : null,
         });
-        await rm(nativeStageSessionPath(input.root, project.id), { force: true });
-        await rm(session.capsuleRoot, { recursive: true, force: true });
+        await releaseNativeStageSession(input.root, project.id, session);
         return {
             projectId: project.id,
             packageId: workPackage.id,
@@ -988,12 +1028,15 @@ export async function requestResearchHandoff(input) {
             requestedAt,
             interruptedSessionId: session?.packet.sessionId ?? null,
             interruptedPackageId: session?.packet.packageId ?? null,
+            capsuleDisposition: session ? nativeCapsuleDisposition(session) : null,
+            retainedCapsuleId: session && nativeCapsuleDisposition(session) === "retained-outer-sandbox"
+                ? basename(session.capsuleRoot)
+                : null,
         };
         await appendEvidenceLedgerEvent(input.root, project.id, "handoff.requested", eventPayload);
         await appendJournalEvent(workspacePaths(input.root).journal, "project.handoff.requested", project.id, { projectId: project.id, ...eventPayload });
         if (session) {
-            await rm(activePath, { force: true });
-            await rm(session.capsuleRoot, { recursive: true, force: true });
+            await releaseNativeStageSession(input.root, project.id, session);
         }
         return {
             projectId: project.id,
@@ -1115,7 +1158,7 @@ function parseHandoffRequest(value) {
         accessRequests,
     };
 }
-async function executeWorkPackage(root, projectId, packageId, config, options, requestId, packageExecutor, doctorAttestation) {
+async function executeWorkPackage(root, projectId, packageId, config, options, requestId, packageExecutor, reviewerPackageExecutor, doctorAttestation) {
     const project = await loadProject(root, projectId);
     const workPackage = packageById(project, packageId);
     await assertScientificGateForStage(root, project, workPackage.stage);
@@ -1141,6 +1184,8 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
     const runId = randomUUID();
     const startedAt = new Date().toISOString();
     let capsuleRoot;
+    let capsuleDisposition = null;
+    let retainedCapsuleId = null;
     let broker;
     let accountedResult;
     let promotedOutputs = [];
@@ -1154,7 +1199,11 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
         }
         else {
             if (["analyze", "synthesize", "review"].includes(workPackage.stage)) {
-                await loadCurrentEvidenceSnapshot(root, project.id);
+                await loadInferenceReadyEvidenceSnapshot(root, project.id);
+                if (workPackage.stage === "analyze")
+                    await freezeInferenceSnapshot(root, project.id);
+                else
+                    await loadCurrentInferenceSnapshot(root, project.id);
             }
             const discovery = workPackage.stage === "discover"
                 ? await inspectDiscoveryProgress(root, project, config)
@@ -1163,6 +1212,9 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
             const reservation = reservePackageBudget(project, workPackage, config, discovery?.plan.reservedDiscoverTokens);
             const capsule = await createCapsule(root, project, workPackage, runId, config);
             capsuleRoot = capsule.capsuleRoot;
+            capsuleDisposition = capsuleDispositionForHost(config.producer.agent);
+            retainedCapsuleId =
+                capsuleDisposition === "retained-outer-sandbox" ? basename(capsuleRoot) : null;
             if (capsule.reviewPacketRecord) {
                 await appendJournalEvent(workspacePaths(root).journal, "review.packet.persisted", projectId, {
                     requestId,
@@ -1174,6 +1226,9 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
             }
             const stageContextContent = await stageContextForPackage(capsule.projectRoot, project, workPackage, config);
             const route = workPackage.executor === "reviewer" ? config.reviewer : config.producer;
+            const selectedPackageExecutor = workPackage.executor === "reviewer" && reviewerPackageExecutor
+                ? reviewerPackageExecutor
+                : packageExecutor;
             executor = route.agent;
             broker =
                 workPackage.stage === "discover"
@@ -1203,7 +1258,7 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
                 expectedRuntime: runtimeForRoute(doctorAttestation, route),
             });
             assertPreCallTokenReservation(project, workPackage, config, primaryRequest, 0, true);
-            result = await withHeartbeat(packageExecutor(primaryRequest), options, requestId, project, workPackage, config);
+            result = await withHeartbeat(selectedPackageExecutor(primaryRequest), options, requestId, project, workPackage, config);
             accountedResult = result;
             assertExecutorSucceeded(result);
             assertActualPackageBudget(project, workPackage, config, result, stageOutputTokens);
@@ -1237,7 +1292,7 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
                     expectedRuntime: runtimeForRoute(doctorAttestation, route),
                 });
                 assertPreCallTokenReservation(project, workPackage, config, repairRequest, result.tokens, false);
-                const repair = await withHeartbeat(packageExecutor(repairRequest), options, requestId, project, workPackage, config);
+                const repair = await withHeartbeat(selectedPackageExecutor(repairRequest), options, requestId, project, workPackage, config);
                 accountedResult = combineExecutionResults(result, repair);
                 assertExecutorSucceeded(repair);
                 assertActualPackageBudget(project, workPackage, config, accountedResult, stageOutputTokens + config.budget.maxRepairTokens);
@@ -1256,6 +1311,11 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
                 await freezeEvidenceSnapshot(root, project);
                 promotedOutputs.push(await fileRecord(join(projectRoot(root, project.id), "outputs", "evidence-snapshot.json"), "outputs/evidence-snapshot.json"));
             }
+            if (workPackage.stage === "analyze") {
+                const analysis = JSON.parse(await readFile(join(projectRoot(root, project.id), "outputs", "analysis.json"), "utf8"));
+                await freezeClaimEvidenceGraph(root, project.id, analysis);
+                promotedOutputs.push(await fileRecord(join(projectRoot(root, project.id), "outputs", "claim-evidence-graph.json"), "outputs/claim-evidence-graph.json"));
+            }
             await commitStageEvidenceBindings(root, project, workPackage);
         }
         const completedAt = new Date().toISOString();
@@ -1288,6 +1348,8 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
             failureKind: null,
             failureDetails: null,
             runtime: accountedResult.runtime,
+            isolation: accountedResult.isolation,
+            reviewAttestation: accountedResult.reviewAttestation,
             telemetry: accountedResult.telemetry,
         });
         const usage = usageSlice(accountedResult);
@@ -1300,6 +1362,9 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
             outputs: promotedOutputs,
             usage,
             runtime: accountedResult.runtime,
+            reviewerExecution: accountedResult.reviewAttestation ?? accountedResult.isolation ?? null,
+            capsuleDisposition,
+            retainedCapsuleId,
         });
         emitProgress(options, progressEvent("package.completed", requestId, projectId, packageId, remainingBudget(project, config), { outputs: promotedOutputs, usage }));
         return { projectId, packageId, status: "complete" };
@@ -1348,6 +1413,8 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
                 failureKind: classification.kind,
                 failureDetails,
                 runtime: accountedResult.runtime,
+                isolation: accountedResult.isolation,
+                reviewAttestation: accountedResult.reviewAttestation,
                 telemetry: accountedResult.telemetry,
             });
         }
@@ -1365,6 +1432,8 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
             details: failureDetails,
             outputs: promotedOutputs,
             usage,
+            capsuleDisposition,
+            retainedCapsuleId,
         });
         emitProgress(options, progressEvent("package.failed", requestId, projectId, packageId, remainingBudget(failedProject, config), {
             retryable,
@@ -1379,8 +1448,9 @@ async function executeWorkPackage(root, projectId, packageId, config, options, r
     finally {
         if (broker)
             await broker.stop();
-        if (capsuleRoot)
+        if (capsuleRoot && capsuleDisposition !== "retained-outer-sandbox") {
             await rm(capsuleRoot, { recursive: true, force: true });
+        }
     }
 }
 async function stagePublicationPolicy(root, project, capsuleProject) {
@@ -1611,7 +1681,10 @@ async function writeReviewPacket(root, capsuleProject, project, inputManifest, e
         "outputs/evidence.json",
         "outputs/acquisition.json",
         "outputs/evidence-snapshot.json",
+        "outputs/content-snapshot.json",
+        "outputs/inference-snapshot.json",
         "outputs/analysis.json",
+        "outputs/claim-evidence-graph.json",
         "outputs/report.md",
     ];
     const evidenceFiles = new Map();
@@ -1657,7 +1730,9 @@ async function writeReviewPacket(root, capsuleProject, project, inputManifest, e
         evidenceFiles: [...evidenceFiles.values()].sort((left, right) => left.path.localeCompare(right.path)),
         environment,
         environmentFile: await fileRecord(join(capsuleProject, "inputs", "runtime-fingerprint.json"), "inputs/runtime-fingerprint.json"),
-        artifacts: await Promise.all(artifactPaths.map((logicalPath) => fileRecord(resolveContained(capsuleProject, logicalPath), logicalPath))),
+        artifacts: (await Promise.all(artifactPaths.map(async (logicalPath) => (await pathExists(resolveContained(capsuleProject, logicalPath)))
+            ? fileRecord(resolveContained(capsuleProject, logicalPath), logicalPath)
+            : null))).filter((record) => record !== null),
     };
     const packetSha256 = sha256Text(canonicalJson(packet));
     const completePacket = {
@@ -2251,7 +2326,7 @@ async function validateOutputShape(root, project, workPackage, path, reviewPacke
     }
     const { value } = parseStructuredStageOutput(workPackage.stage, content, reviewPacketSha256);
     if (workPackage.stage === "analyze") {
-        await validateFindings(path, value.findings);
+        await validateAnalysis(path, value);
     }
     if (workPackage.stage === "review") {
         if (value.decision !== "pass") {
@@ -2322,30 +2397,88 @@ async function validateEvidenceSources(root, project, sources) {
         sourceIds.add(id);
     }
 }
-async function validateFindings(path, findings) {
-    const evidencePath = join(dirname(path), "evidence-snapshot.json");
-    const evidence = JSON.parse(await readFile(evidencePath, "utf8"));
-    if (!isObject(evidence) || !Array.isArray(evidence.sources)) {
-        throw deterministicError("Analysis requires a frozen evidence-snapshot.json.");
+async function validateAnalysis(path, value) {
+    const inferencePath = join(dirname(path), "inference-snapshot.json");
+    const inference = JSON.parse(await readFile(inferencePath, "utf8"));
+    if (!isObject(inference) ||
+        typeof inference.snapshotSha256 !== "string" ||
+        !Array.isArray(inference.sources) ||
+        !Array.isArray(inference.atoms) ||
+        !Array.isArray(inference.claims) ||
+        !Array.isArray(inference.artifactSha256s) ||
+        !Array.isArray(inference.implementationArtifactSha256s) ||
+        !Array.isArray(inference.environmentLockSha256s)) {
+        throw deterministicError("Analysis requires a frozen inference-snapshot.json.");
     }
-    const sourceIds = new Set(evidence.sources
+    if (value.inferenceSnapshotSha256 !== inference.snapshotSha256) {
+        throw new StructuredOutputError("Analysis does not bind the current inference snapshot.");
+    }
+    const sourceIds = new Set(inference.sources
         .filter((source) => isObject(source))
         .map((source) => source.id)
         .filter((id) => typeof id === "string"));
+    const atomSources = new Map(inference.atoms.flatMap((atom) => isObject(atom) && typeof atom.atomId === "string" && typeof atom.sourceId === "string"
+        ? [[atom.atomId, atom.sourceId]]
+        : []));
+    const claimIds = new Set(inference.claims.flatMap((claim) => isObject(claim) && typeof claim.id === "string" ? [claim.id] : []));
+    const allowedInputSha256s = new Set(inference.artifactSha256s.filter((sha256) => typeof sha256 === "string"));
+    const allowedImplementationSha256s = new Set(inference.implementationArtifactSha256s.filter((sha256) => typeof sha256 === "string"));
+    const allowedEnvironmentSha256s = new Set(inference.environmentLockSha256s.filter((sha256) => typeof sha256 === "string"));
+    const run = value.analysisRun;
+    if (!isObject(run))
+        throw new StructuredOutputError("Analysis run binding is invalid.");
+    const implementationSha256s = run.implementationSha256s;
+    const environmentSha256s = run.environmentSha256s;
+    const inputArtifactSha256s = run.inputArtifactSha256s;
+    if (implementationSha256s.some((sha256) => !allowedImplementationSha256s.has(sha256)) ||
+        environmentSha256s.some((sha256) => !allowedEnvironmentSha256s.has(sha256)) ||
+        inputArtifactSha256s.some((sha256) => !allowedInputSha256s.has(sha256))) {
+        throw new StructuredOutputError("Analysis run refers to an artifact outside the inference snapshot.");
+    }
+    if (run.mode === "qualitative") {
+        if (run.status !== "not-applicable" ||
+            run.command !== null ||
+            run.randomSeed !== null ||
+            implementationSha256s.length > 0 ||
+            environmentSha256s.length > 0) {
+            throw new StructuredOutputError("Qualitative analysis run metadata is inconsistent.");
+        }
+    }
+    else if (run.status !== "reproduced" ||
+        typeof run.command !== "string" ||
+        run.command.trim().length < 1 ||
+        typeof run.randomSeed !== "string" ||
+        run.randomSeed.trim().length < 1 ||
+        implementationSha256s.length < 1 ||
+        environmentSha256s.length < 1) {
+        throw new StructuredOutputError("Computational analysis requires exact reproduced run metadata.");
+    }
+    const findings = value.findings;
     const findingIds = new Set();
     for (const finding of findings) {
+        const findingEvidence = isObject(finding) && Array.isArray(finding.evidence) ? finding.evidence : [];
         if (!isObject(finding) ||
             typeof finding.id !== "string" ||
             findingIds.has(finding.id) ||
             !Array.isArray(finding.evidence) ||
-            finding.evidence.some((id) => typeof id !== "string" || !sourceIds.has(id))) {
+            finding.evidence.some((id) => typeof id !== "string" || !sourceIds.has(id)) ||
+            !Array.isArray(finding.evidenceAtomIds) ||
+            finding.evidenceAtomIds.some((atomId) => typeof atomId !== "string" ||
+                !atomSources.has(atomId) ||
+                !findingEvidence.includes(atomSources.get(atomId))) ||
+            !Array.isArray(finding.claimIds) ||
+            finding.claimIds.some((claimId) => typeof claimId !== "string" || !claimIds.has(claimId))) {
             throw new StructuredOutputError("analyze output contains an invalid or untraceable finding.", {
                 validation: [
-                    "finding IDs must be unique and evidence IDs must reference admitted sources",
+                    "finding IDs must be unique; source, atom, and design-claim IDs must bind the inference snapshot",
                 ],
                 admittedEvidenceIds: [...sourceIds].sort(),
             });
         }
+        if (inference.scientificReview !== null &&
+            (finding.evidenceAtomIds.length < 1 || finding.claimIds.length < 1)) {
+            throw new StructuredOutputError("Top-journal findings require at least one evidence atom and design claim.");
+        }
         findingIds.add(finding.id);
     }
 }
@@ -2723,13 +2856,19 @@ async function commitStageEvidenceBindings(root, project, workPackage) {
             if (!isObject(finding) ||
                 typeof finding.id !== "string" ||
                 !Array.isArray(finding.evidence) ||
-                finding.evidence.some((sourceId) => typeof sourceId !== "string")) {
+                finding.evidence.some((sourceId) => typeof sourceId !== "string") ||
+                !Array.isArray(finding.evidenceAtomIds) ||
+                finding.evidenceAtomIds.some((atomId) => typeof atomId !== "string") ||
+                !Array.isArray(finding.claimIds) ||
+                finding.claimIds.some((claimId) => typeof claimId !== "string")) {
                 throw deterministicError("Analysis contains an invalid claim binding.");
             }
             const binding = {
                 claimId: finding.id,
                 snapshotId: snapshot.snapshotId,
                 sourceIds: [...finding.evidence].sort(),
+                atomIds: [...finding.evidenceAtomIds].sort(),
+                designClaimIds: [...finding.claimIds].sort(),
                 claimSha256: sha256Text(canonicalJson(finding)),
             };
             const bindingSha256 = sha256Text(canonicalJson(binding));
@@ -2814,6 +2953,16 @@ async function outputRecords(root, project, logicalPaths) {
     return Promise.all(logicalPaths.map((logicalPath) => fileRecord(resolveContained(projectRoot(root, project.id), logicalPath), logicalPath)));
 }
 async function stageContextForPackage(capsuleProject, project, workPackage, config) {
+    let analyzeFallbackContext = [];
+    if (workPackage.stage === "analyze") {
+        const inference = JSON.parse(await readFile(resolveContained(capsuleProject, "outputs/inference-snapshot.json"), "utf8"));
+        if (isObject(inference) &&
+            Array.isArray(inference.atoms) &&
+            inference.atoms.length === 0 &&
+            (await pathExists(resolveContained(capsuleProject, "inputs/evidence-artifact-context.txt")))) {
+            analyzeFallbackContext = ["inputs/evidence-artifact-context.txt"];
+        }
+    }
     const logicalPaths = workPackage.stage === "discover" && project.lineage.kind === "addendum"
         ? ["outputs/base-evidence-snapshot.json"]
         : workPackage.stage === "acquire"
@@ -2822,25 +2971,19 @@ async function stageContextForPackage(capsuleProject, project, workPackage, conf
                 ...(project.lineage.kind === "addendum" ? ["outputs/base-evidence-snapshot.json"] : []),
             ]
             : workPackage.stage === "analyze"
-                ? [
-                    "outputs/evidence-snapshot.json",
-                    ...((await pathExists(resolveContained(capsuleProject, "inputs/evidence-artifact-context.txt")))
-                        ? ["inputs/evidence-artifact-context.txt"]
-                        : []),
-                ]
+                ? ["outputs/inference-snapshot.json", ...analyzeFallbackContext]
                 : workPackage.stage === "synthesize"
                     ? [
-                        "outputs/evidence-snapshot.json",
+                        "outputs/inference-snapshot.json",
                         "outputs/analysis.json",
-                        ...((await pathExists(resolveContained(capsuleProject, "inputs/evidence-artifact-context.txt")))
-                            ? ["inputs/evidence-artifact-context.txt"]
-                            : []),
+                        "outputs/claim-evidence-graph.json",
                     ]
                     : workPackage.stage === "review"
                         ? [
                             "inputs/review-evidence-context.txt",
-                            "outputs/evidence-snapshot.json",
+                            "outputs/inference-snapshot.json",
                             "outputs/analysis.json",
+                            "outputs/claim-evidence-graph.json",
                             "outputs/report.md",
                         ]
                         : [];
@@ -2879,8 +3022,8 @@ function packagePrompt(project, workPackage, inputs, stagedSkills, capabilityDoc
     const stageInstructions = {
         discover: "Assess candidates incrementally through the packet's recordAssessment command; do not accumulate a source-sized final response. The control plane has already assigned every immutable input and broker result a candidateId and retains its title, URL, DOI, dates, receipt, locator, JSON Pointer, hashes, and retrieval metadata. Reference candidateId; never repeat or invent those deterministic fields. Give each admitted candidate a concise sourceId plus source type, relevance, quality, applicability, coverage dimensions, and limitations. Record meaningful explicit rejections; omitted candidates remain unassessed for later gap filling. Native Web or Browser discoveries are supplemental candidates only and cannot be admitted until an immutable broker receipt is attached to the same canonical URL or DOI. After broad search, strict assessment, and focused gap filling, return only the small closeout object with one judgment for every reviewed dimension plus limitations and remaining gaps. The CLI mechanically joins the latest recorded assessments to provenance, derives counts/date range/coverage, and rejects unknown or unformalized candidates.",
         acquire: "Audit every provisionally admitted source exactly once. For each source, bind its ledger candidateId, list only artifactIds returned by the exact artifact registration command, and choose accepted, limited, or rejected with a concise rationale and explicit limitations. A broker receipt is an immutable discovery record but is not full text. Use an empty artifactIds array only when intentionally retaining a source as metadata/abstract evidence or when the source is an already registered local input. Put unresolved blocking acquisition or coverage deficiencies in gaps; put honest non-blocking scope constraints in limitations. Do not invent file paths, hashes, URLs, artifact IDs, or successful downloads.",
-        analyze: "Use only the complete embedded frozen evidence snapshot below and return the schema-defined analysis object. Every finding must cite source IDs present in that snapshot and state uncertainty and applicability. When the snapshot has a parent, use its mechanical delta to focus re-analysis on added, changed, and removed evidence while still returning one complete current analysis.",
-        synthesize: "Use only the complete embedded admitted evidence and findings below. Return the schema-defined object whose reportMarkdown separates supported conclusions, uncertainty, limitations, and next actions. Use real Markdown line breaks encoded exactly once for JSON; never place literal /n or double-escaped \\n markers in reportMarkdown. When the admitted publication-date range is narrower than the requested range, state the exact admitted range and missing interval prominently in the opening summary.",
+        analyze: "Use only the complete embedded inference snapshot below and return analysis schema v2. Bind the exact inference snapshot hash and one reproducible analysisRun. Every finding must cite admitted source IDs and exact evidenceAtomIds; a top-journal finding must also bind design claimIds. State uncertainty and applicability. Never promote a source-level citation when no exact atom supports the statement.",
+        synthesize: "Use only the complete embedded inference snapshot, analysis, and Claim–Evidence Graph below. Return the schema-defined object whose reportMarkdown separates supported conclusions, uncertainty, limitations, and next actions. Every material statement must remain within a graph-bound finding. Use real Markdown line breaks encoded exactly once for JSON; never place literal /n or double-escaped \\n markers in reportMarkdown.",
         review: `Independently inspect the complete embedded artifacts and globally bounded evidence excerpts. The CLI has already verified every bound full evidence object's size and SHA-256 and persistently stored the complete review packet; its hash is schema-bound even though the packet metadata is not duplicated in model context. Do not claim to have read beyond the embedded excerpts. Return the schema-defined review bound to packetSha256 ${reviewPacketSha256 ?? "unavailable"}. Use pass only when every material claim is traceable within the admitted evidence and clearly scoped to its limitations.`,
         close: "No agent action is allowed for mechanical closure.",
     };
@@ -3176,6 +3319,8 @@ function combineExecutionResults(primary, repair) {
         wallSeconds: primary.wallSeconds + repair.wallSeconds,
         model: repair.model ?? primary.model,
         runtime: repair.runtime ?? primary.runtime,
+        isolation: repair.isolation ?? primary.isolation,
+        reviewAttestation: repair.reviewAttestation ?? primary.reviewAttestation,
         telemetry: mergeTelemetry(primary.telemetry, repair.telemetry),
     };
 }
@@ -3454,9 +3599,13 @@ async function nativeStageBinding(root, project, workPackage) {
     const paths = workspacePaths(root);
     const outputRoot = join(projectRoot(root, project.id), "outputs");
     const outputs = [];
+    const stageOwnedOutputs = new Set(workPackage.expectedOutputs);
     if (await pathExists(outputRoot)) {
         for (const path of await regularTreeFiles(outputRoot)) {
-            outputs.push(await fileRecord(path, relative(projectRoot(root, project.id), path).replaceAll("\\", "/")));
+            const logicalPath = relative(projectRoot(root, project.id), path).replaceAll("\\", "/");
+            if (stageOwnedOutputs.has(logicalPath))
+                continue;
+            outputs.push(await fileRecord(path, logicalPath));
         }
     }
     return sha256Text(canonicalJson({