sneakoscope 3.1.8 → 3.1.10

package/dist/core/codex-native/project-skill-dedupe.js

@@ -17,8 +17,16 @@ export async function dedupeProjectSkills(input) {
         const userEntries = group.filter((entry) => !entry.managed_by_sks);
         const managedEntries = group.filter((entry) => entry.managed_by_sks);
         if (userEntries.length > 0 && managedEntries.length > 0) {
-            for (const user of userEntries)
-                actions.push(actionRow(canonical, 'kept', user, null, 'user-authored skill preserved'));
+            const keepUser = userEntries[0];
+            if (keepUser)
+                actions.push(actionRow(canonical, 'kept', keepUser, null, 'user-authored skill preserved'));
+            const shouldMoveUserDuplicates = fix && yes && input.quarantineUserDuplicates === true;
+            for (const duplicateUser of userEntries.slice(1)) {
+                const quarantine = shouldMoveUserDuplicates ? await quarantineSkill(root, canonical, duplicateUser, 'user-authored duplicate skill') : null;
+                actions.push(actionRow(canonical, quarantine ? 'quarantined' : 'reported', duplicateUser, quarantine, 'user-authored duplicate skill requires --quarantine-user-duplicates --yes'));
+            }
+            if (userEntries.length > 1 && !shouldMoveUserDuplicates)
+                unresolvedUserDuplicates.push(canonical);
             for (const managed of managedEntries) {
                 const quarantine = await maybeQuarantine(root, canonical, managed, fix, 'managed collision with user-authored skill');
                 actions.push(actionRow(canonical, quarantine ? 'quarantined' : 'reported', managed, quarantine, 'managed collision with user-authored skill'));
@@ -49,7 +57,11 @@ export async function dedupeProjectSkills(input) {
         }
     }
     const duplicateNames = [...new Set(actions.filter((action) => action.action !== 'kept').map((action) => action.canonical_name))].sort();
-    const blockers = unresolvedUserDuplicates.map((name) => `user_duplicate_requires_confirmation:${name}`);
+    const afterLedger = await buildSkillRegistryLedger({ root, reportPath: null });
+    const blockers = [
+        ...unresolvedUserDuplicates.map((name) => `user_duplicate_requires_confirmation:${name}`),
+        ...afterLedger.duplicate_active_canonical_names.map((name) => `duplicate_active_skill_name:${name}`)
+    ];
     const report = {
         schema: 'sks.project-skill-dedupe.v1',
         generated_at: nowIso(),
@@ -58,6 +70,9 @@ export async function dedupeProjectSkills(input) {
         fix,
         yes,
         actions,
+        active_unique_by_canonical_name: afterLedger.active_unique_by_canonical_name,
+        active_entries: afterLedger.active_entries,
+        duplicate_active_canonical_names: afterLedger.duplicate_active_canonical_names,
         duplicate_canonical_names: duplicateNames,
         unresolved_user_duplicates: unresolvedUserDuplicates,
         blockers

package/dist/core/codex-native/skill-registry-ledger.js

@@ -56,13 +56,20 @@ export async function buildSkillRegistryLedger(input) {
                 entry.status = entry.status === 'user-owned' ? 'duplicate' : 'duplicate';
         });
     }
-    const blockers = duplicates.map((name) => `duplicate_skill_name:${name}`);
+    const activeEntries = entries.filter((entry) => entry.status !== 'quarantined');
+    const activeGrouped = groupByCanonical(activeEntries);
+    const duplicateActiveNames = [...activeGrouped.entries()].filter(([, group]) => group.length > 1).map(([name]) => name).sort();
+    const activeUnique = duplicateActiveNames.length === 0;
+    const blockers = duplicateActiveNames.map((name) => `duplicate_active_skill_name:${name}`);
     const ledger = {
         schema: 'sks.skill-registry-ledger.v1',
         generated_at: nowIso(),
-        ok: blockers.length === 0,
+        ok: activeUnique,
         root,
         entries,
+        active_unique_by_canonical_name: activeUnique,
+        active_entries: activeEntries,
+        duplicate_active_canonical_names: duplicateActiveNames,
         duplicate_canonical_names: duplicates,
         blockers
     };

package/dist/core/commands/basic-cli.js

@@ -1,6 +1,6 @@
 import path from 'node:path';
 import { spawnSync } from 'node:child_process';
-import { COMMANDS } from '../../cli/command-registry.js';
+import { COMMANDS, LEGACY_COMMAND_ALIASES } from '../../cli/command-registry.js';
 import { flag } from '../../cli/args.js';
 import { printJson, sksTextLogo } from '../../cli/output.js';
 import { PACKAGE_VERSION, ensureDir, exists, nowIso, projectRoot, readJson, sksRoot, tmpdir, writeJsonAtomic } from '../fsx.js';
@@ -55,6 +55,9 @@ export function dollarCommandsCommand(args = []) {
 export function aliasesCommand() {
     console.log('Aliases');
     console.log('- sks, sneakoscope');
+    console.log('- CLI compatibility aliases:');
+    for (const [alias, canonical] of Object.entries(LEGACY_COMMAND_ALIASES))
+        console.log(`  sks ${alias} -> sks ${canonical}`);
     console.log('- $ aliases:');
     for (const entry of DOLLAR_COMMAND_ALIASES)
         console.log(`  ${entry.app_skill} -> ${entry.canonical}`);
@@ -182,7 +185,9 @@ export async function initCommand(args = []) {
 export async function fixPathCommand(args = []) {
     const root = await projectRoot();
     const installScope = installScopeFromArgs(args);
-    await initProject(root, { installScope, localOnly: flag(args, '--local-only'), globalCommand: 'sks', force: true });
+    await withSecretPreservationGuard(root, 'fix-path-command', async () => {
+        await initProject(root, { installScope, localOnly: flag(args, '--local-only'), globalCommand: 'sks', force: true });
+    });
     const result = {
         schema: 'sks.fix-path.v1',
         ok: true,

package/dist/core/commands/mad-sks-command.js

@@ -30,6 +30,7 @@ export async function madHighCommand(args = [], deps = {}) {
         return madSksSubcommand(subcommand, args.filter((arg) => String(arg) !== subcommand));
     const cleanArgs = stripMadLaunchOnlyArgs(args);
     const rawArgs = (args || []).map((arg) => String(arg));
+    const madDbGrant = resolveMadLaunchMadDbGrant(rawArgs);
     const dryRun = rawArgs.includes('--dry-run');
     if (args.includes('--json') && !dryRun) {
         const profile = buildMadHighLaunchProfileNoWrite();
@@ -133,13 +134,6 @@ export async function madHighCommand(args = [], deps = {}) {
     // later when the Zellij session opens. All filesystem/permission/EPERM/symlink/ACL
     // readability + repair checks still run. SKS_LAUNCH_FULL_CODEX_PROBE=1 restores the
     // old behavior.
-    const madDbRequested = rawArgs.includes('--mad-db');
-    const madDbAck = readOption(rawArgs, '--ack', '');
-    if (madDbRequested && madDbAck !== MAD_DB_ACK) {
-        console.error(`SKS MAD-DB launch blocked. Required --ack ${JSON.stringify(MAD_DB_ACK)}`);
-        process.exitCode = 2;
-        return { ok: false, status: 'blocked', reason: 'mad_db_ack_phrase_required', required_ack: MAD_DB_ACK };
-    }
     const allowMadRepair = rawArgs.includes('--repair-config') || rawArgs.includes('--fix') || rawArgs.includes('--yes-repair');
     const launchPreflight = await runCodexLaunchPreflight(launchRoot, { fix: allowMadRepair, launchFast: process.env.SKS_LAUNCH_FULL_CODEX_PROBE !== '1', profile: profile.profile_name, sandbox: 'danger-full-access', serviceTier: 'fast' });
     const afterPreflightUi = beforeUi ? await writeCodexAppUiSnapshot(launchRoot, `mad-after-preflight-${uiSnapshotId}`).catch(() => null) : null;
@@ -160,18 +154,38 @@ export async function madHighCommand(args = [], deps = {}) {
         return launchPreflight;
     }
     const madLaunch = await activateMadZellijPermissionState(process.cwd(), args);
-    const madDbCapability = madDbRequested
-        ? await createMadDbCapability(madLaunch.root, { missionId: madLaunch.mission_id, ack: madDbAck, cwd: process.cwd() })
+    const madDbCapability = madDbGrant.enabled
+        ? await createMadDbCapability(madLaunch.root, { missionId: madLaunch.mission_id, ack: madDbGrant.ack, cwd: process.cwd() })
         : null;
     if (madDbCapability) {
+        const grantReport = {
+            schema: 'sks.mad-sks-launch-grants.v1',
+            generated_at: nowIso(),
+            mission_id: madLaunch.mission_id,
+            mad_sks_active: true,
+            mad_db_active: true,
+            mad_db_default_grant: madDbGrant.source === 'sks_mad_default',
+            mad_db_grant_source: madDbGrant.source,
+            mad_db_one_cycle_only: true,
+            mad_db_capability_file: 'mad-db-capability.json',
+            mad_db_cycle_id: madDbCapability.cycle_id,
+            mad_db_expires_at: madDbCapability.expires_at,
+            standalone_mad_db_enable_still_requires_ack: true
+        };
+        await writeJsonAtomic(path.join(madLaunch.dir, 'mad-sks-launch-grants.json'), grantReport);
         await setCurrent(madLaunch.root, {
             mission_id: madLaunch.mission_id,
             mad_db_active: true,
             mad_db_cycle_id: madDbCapability.cycle_id,
             mad_db_capability_file: 'mad-db-capability.json',
-            mad_db_break_glass: true
+            mad_db_break_glass: true,
+            mad_db_default_grant: madDbGrant.source === 'sks_mad_default',
+            mad_db_grant_source: madDbGrant.source,
+            mad_db_one_cycle_only: true,
+            mad_db_priority_override_active: true,
+            mad_sks_launch_grants_file: 'mad-sks-launch-grants.json'
         });
-        await appendJsonlBounded(path.join(madLaunch.dir, 'events.jsonl'), { ts: nowIso(), type: 'mad_db.capability_created', cycle_id: madDbCapability.cycle_id, expires_at: madDbCapability.expires_at });
+        await appendJsonlBounded(path.join(madLaunch.dir, 'events.jsonl'), { ts: nowIso(), type: 'mad_db.capability_created', grant_source: madDbGrant.source, cycle_id: madDbCapability.cycle_id, expires_at: madDbCapability.expires_at });
     }
     const updateNotice = await checkSksUpdateNotice({
         packageName: deps.packageName || 'sneakoscope',
@@ -192,10 +206,10 @@ export async function madHighCommand(args = [], deps = {}) {
     await appendJsonlBounded(path.join(madLaunch.dir, 'events.jsonl'), { ts: nowIso(), type: 'mad_sks.update_notice_checked', non_blocking: true, update_available: updateNotice.update_available === true, source: updateNotice.source });
     console.log(`SKS MAD ready: ${madHighProfileName()} | gate ${madLaunch.mission_id}`);
     if (madDbCapability)
-        console.log(`MAD-DB one-cycle capability active; expires ${madDbCapability.expires_at}.`);
+        console.log(`MAD-DB one-cycle capability active (${madDbGrant.source}); expires ${madDbCapability.expires_at}.`);
     if (updateNotice.update_available === true)
         console.log(`SKS update notice: ${updateNotice.latest_version} available (non-blocking).`);
-    console.log('Scoped high-power maintenance authority active; add explicit --allow-* flags for packages, services, network, browser/Computer Use, generated assets, file permissions, DB writes, or system/admin scopes. Catastrophic guards remain.');
+    console.log('Scoped high-power maintenance authority active; add explicit --allow-* flags for packages, services, network, browser/Computer Use, generated assets, file permissions, or system/admin scopes. MAD-DB one-cycle DB break-glass is already active for this launch; protected-core, audit, and one-cycle bounds remain.');
     const launchLb = lb.status === 'present' ? { ...lb, status: 'configured' } : lb;
     const madSksEnv = {
         SKS_PROTECTED_CORE_POLICY: madLaunch.gate.protected_core_policy,
@@ -260,6 +274,15 @@ export async function madHighCommand(args = [], deps = {}) {
         console.log('MAD launch running headless: live_panes=false.');
     return launch;
 }
+export function resolveMadLaunchMadDbGrant(args = []) {
+    const list = (args || []).map((arg) => String(arg));
+    return {
+        enabled: true,
+        source: list.includes('--mad-db') ? 'sks_mad_explicit_redundant_flag' : 'sks_mad_default',
+        ack: MAD_DB_ACK,
+        one_cycle_only: true
+    };
+}
 export async function startMadNativeSwarm(root, madLaunch, args = [], profile = {}, opts = {}) {
     const swarm = resolveMadNativeSwarmOptions(args, profile, opts);
     const dir = madLaunch.dir || missionDirLike(root, madLaunch.mission_id);

package/dist/core/commands/naruto-command.js

@@ -114,6 +114,7 @@ async function narutoRun(parsed) {
         prompt: parsed.prompt,
         requestedClones: roster.agent_count,
         totalWorkItems: parsed.workItems,
+        honorExplicitTotalWorkItems: parsed.workItemsExplicit,
         readonly: parsed.readonly,
         writeCapable,
         leaseBasePath: patchEnvelopeBasePath,
@@ -127,6 +128,7 @@ async function narutoRun(parsed) {
         prompt: parsed.prompt,
         requestedClones: roster.agent_count,
         totalWorkItems: parsed.workItems,
+        honorExplicitTotalWorkItems: parsed.workItemsExplicit,
         readonly: parsed.readonly,
         writeCapable,
         leaseBasePath: patchEnvelopeBasePath,
@@ -791,6 +793,7 @@ function parseNarutoArgs(args = []) {
     const json = hasFlag(args, '--json');
     const requestedClones = Number(readOption(args, '--clones', readOption(args, '--agents', DEFAULT_NARUTO_CLONES)));
     const clones = clampClones(requestedClones);
+    const workItemsExplicit = hasOption(args, '--work-items');
     const workItems = clampWorkItems(Number(readOption(args, '--work-items', clones * 2)), clones);
     const concurrency = normalizeConcurrency(readOption(args, '--concurrency', readOption(args, '--target-active-slots', null)), clones);
     const useOllama = hasFlag(args, '--ollama') || hasFlag(args, '--local-model');
@@ -831,7 +834,7 @@ function parseNarutoArgs(args = []) {
     const messages = normalizeMessages(readOption(args, '--messages', '8'));
     const valueFlags = new Set(['--clones', '--agents', '--work-items', '--concurrency', '--target-active-slots', '--backend', '--write-mode', '--max-write-agents', '--service-tier', '--mission', '--mission-id', '--ollama-model', '--local-model-model', '--ollama-base-url', '--local-model-base-url', '--parallelism', '--messages']);
     const prompt = positionalArgs(rest, valueFlags).join(' ').trim() || 'Naruto shadow clone swarm run';
-    return { action, prompt, clones, workItems, concurrency, backend, backendExplicit, mock, real, readonly, ollamaEnabled: useOllama && !noOllama, noOllama, ollamaModel, ollamaBaseUrl, writeMode, applyPatches, dryRunPatches, maxWriteAgents, fastMode, serviceTier, noFast, json, missionId, noOpenZellij, attach, smoke, parallelism, messages };
+    return { action, prompt, clones, workItems, workItemsExplicit, concurrency, backend, backendExplicit, mock, real, readonly, ollamaEnabled: useOllama && !noOllama, noOllama, ollamaModel, ollamaBaseUrl, writeMode, applyPatches, dryRunPatches, maxWriteAgents, fastMode, serviceTier, noFast, json, missionId, noOpenZellij, attach, smoke, parallelism, messages };
 }
 function normalizeParallelism(value) {
     const text = String(value || 'extreme').toLowerCase();

package/dist/core/commands/pipeline-command.js

@@ -1,7 +1,7 @@
 import path from 'node:path';
-import { projectRoot, readJson, writeJsonAtomic } from '../fsx.js';
+import { projectRoot, readJson } from '../fsx.js';
 import { missionDir, stateFile } from '../mission.js';
-import { buildPipelinePlan, PIPELINE_PLAN_ARTIFACT, projectGateStatus } from '../pipeline.js';
+import { PIPELINE_PLAN_ARTIFACT, projectGateStatus, writePipelinePlan } from '../pipeline.js';
 import { routePrompt } from '../routes.js';
 import { flag, positionalArgs, readFlagValue, resolveMissionId } from './command-utils.js';
 export async function pipelineCommand(args = []) {
@@ -33,14 +33,13 @@ export async function pipelineCommand(args = []) {
                 force: flag(args, '--force-agents'),
                 noAgents: flag(args, '--no-agents')
             };
-            const plan = buildPipelinePlan({
+            const plan = await writePipelinePlan(dir, {
                 missionId: id,
                 route,
                 task: routeContext.task || mission.prompt || state.prompt || '',
                 required: Boolean(routeContext.context7_required || state.context7_required),
                 agents
             });
-            await writeJsonAtomic(path.join(dir, PIPELINE_PLAN_ARTIFACT), plan);
             if (flag(args, '--json'))
                 return console.log(JSON.stringify({ schema: 'sks.pipeline-plan.v1', ok: true, mission_id: id, plan }, null, 2));
             console.log(`Pipeline plan written: .sneakoscope/missions/${id}/${PIPELINE_PLAN_ARTIFACT}`);

package/dist/core/commands/qa-loop-command.js

@@ -5,7 +5,7 @@ import { getCodexInfo, runCodexExec } from '../codex-adapter.js';
 import { createMission, loadMission, setCurrent, stateFile } from '../mission.js';
 import { writeQuestions } from '../questions.js';
 import { sealContract } from '../decision-contract.js';
-import { buildQaLoopQuestionSchema, buildQaLoopPrompt, evaluateQaGate, qaStatus, qaUiRequired, writeMockQaResult, writeQaLoopArtifacts, writeQaNativeAgentLedger } from '../qa-loop.js';
+import { buildQaLoopQuestionSchema, buildQaLoopPrompt, ensureQaLoopVisualEvidenceContract, evaluateQaGate, qaGptImage2AnnotatedReviewRequired, qaStatus, qaUiRequired, writeMockQaResult, writeQaLoopArtifacts, writeQaNativeAgentLedger } from '../qa-loop.js';
 import { containsUserQuestion, noQuestionContinuationReason } from '../no-question-guard.js';
 import { ROUTES, routePrompt, stripVisibleDecisionAnswerBlocks } from '../routes.js';
 import { codexChromeExtensionStatus } from '../codex-app.js';
@@ -124,6 +124,8 @@ async function qaLoopRun(args) {
     const contract = await readJson(contractPath, {});
     if (!(await exists(path.join(dir, 'qa-ledger.json'))))
         await writeQaLoopArtifacts(dir, mission, contract);
+    else
+        await ensureQaLoopVisualEvidenceContract(dir, mission, contract);
     const safetyScan = await scanDbSafety(root);
     if (!safetyScan.ok) {
         console.error('QA-LOOP cannot run: SKS safety scan found unsafe project data-tool configuration.');
@@ -148,6 +150,7 @@ async function qaLoopRun(args) {
     const reportFile = qaGate.qa_report_file;
     const executionProfile = await readJson(path.join(dir, 'qa-loop', 'execution-profile.json'), null);
     const uiRequired = qaUiRequired(contract.answers || {});
+    const gptImage2ReviewRequired = qaGptImage2AnnotatedReviewRequired(contract, mission.prompt);
     const capabilityArtifact = await writeCodex0138CapabilityArtifacts(root, { missionId: id }).catch((err) => ({ error: err?.message || String(err), report: null }));
     const usageArtifact = await writeCodexAccountUsageArtifacts(root, { missionId: id }).catch((err) => ({ error: err?.message || String(err), snapshot: null }));
     const budgetPolicy = buildQaLoopBudgetPolicy({ usage: usageArtifact?.snapshot || null, provider: 'codex-sdk' });
@@ -253,6 +256,16 @@ async function qaLoopRun(args) {
                 ui_chrome_extension_evidence: false,
                 ui_computer_use_evidence: false,
                 ui_evidence_source: 'blocked_chrome_extension_setup_required',
+                ui_chrome_extension_screenshot_required: true,
+                ui_chrome_extension_screenshot_captured: false,
+                ui_chrome_extension_screenshot_artifact: null,
+                ui_chrome_extension_screenshot_sha256: null,
+                gpt_image_2_annotated_review_required: gptImage2ReviewRequired,
+                gpt_image_2_annotated_review_generated: false,
+                gpt_image_2_annotated_review_artifact: null,
+                gpt_image_2_annotated_review_sha256: null,
+                gpt_image_2_annotated_review_model: gptImage2ReviewRequired ? null : 'not_required',
+                gpt_image_2_annotated_review_provider: gptImage2ReviewRequired ? null : 'not_required',
                 blocker: 'codex_chrome_extension_setup_required',
                 blockers: Array.from(new Set([...(qaGate.blockers || []), 'codex_chrome_extension_setup_required', ...(chrome.blockers || [])])),
                 evidence: [...(qaGate.evidence || []), 'Codex Chrome Extension preflight failed before web QA execution.'],
@@ -277,6 +290,28 @@ async function qaLoopRun(args) {
     const nativeAgentRun = await runNativeAgentOrchestrator({ root, missionId: id, route: '$QA-LOOP', prompt: mission.prompt || 'QA-LOOP run', backend: mock ? 'fake' : 'codex-sdk', mock, agents: requestedAgents, targetActiveSlots, desiredWorkItemCount, minimumWorkItems, maxQueueExpansion, concurrency: Math.min(requestedAgents, 5), readonly: !(applyPatches && writeMode !== 'off'), profile, writeMode: writeMode, applyPatches, dryRunPatches, maxWriteAgents, roster: nativeRoster, routeCommand: 'sks qa-loop run', routeBlackboxKind: 'actual_qa_command', env: { SKS_CODEX_APP_EXECUTION_PROFILE: executionProfile?.mode || 'unknown', SKS_CODEX_AGENT_ROLE_STRATEGY: executionProfile?.agent_role_strategy || 'message-role' } });
     await writeJsonAtomic(path.join(dir, 'qa-native-agent-run.json'), nativeAgentRun);
     await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'qaloop.native_agents.completed', backend: nativeAgentRun.backend, ok: nativeAgentRun.ok, proof: nativeAgentRun.proof?.status });
+    if (flag(args, '--native-proof-only')) {
+        const proofOnlyGate = {
+            schema: 'sks.qa-native-proof-only-gate.v1',
+            ok: nativeAgentRun.proof?.ok === true,
+            native_agent_proof: nativeAgentRun.proof?.ok === true,
+            proof_status: nativeAgentRun.proof?.status || null,
+            blockers: nativeAgentRun.proof?.blockers || []
+        };
+        if (flag(args, '--json'))
+            return console.log(JSON.stringify({
+                schema: 'sks.qa-loop-run.v1',
+                ok: proofOnlyGate.ok,
+                status: proofOnlyGate.ok ? 'native_proof_ready' : 'blocked',
+                mission_id: id,
+                gate: proofOnlyGate,
+                proof: nativeAgentRun.proof,
+                native_agent_run: nativeAgentRun,
+                native_proof_only: true
+            }, null, 2));
+        console.log(`QA-LOOP native proof ready: ${id}`);
+        return;
+    }
     if (mock) {
         let gate = await writeMockQaResult(dir, mission, contract);
         const needsVisual = uiRequired;

package/dist/core/commands/research-command.js

@@ -40,6 +40,38 @@ export async function researchCommand(sub, args = []) {
 export async function autoresearchCommand(sub, args = []) {
     return researchCommand(sub || 'status', args);
 }
+function hasFlagOption(args = [], name) {
+    return args.includes(name) || args.some((arg) => String(arg).startsWith(`${name}=`));
+}
+function limitResearchNativeWorkGraph(graph, limit) {
+    const count = Math.max(1, Math.min(Number(graph?.work_items?.length || 0) || 1, Math.floor(Number(limit) || 1)));
+    const workItems = (graph.work_items || []).slice(0, count).map((item) => {
+        const selectedIds = new Set((graph.work_items || []).slice(0, count).map((row) => String(row.id || '')));
+        return {
+            ...item,
+            dependencies: (item.dependencies || []).map(String).filter((id) => selectedIds.has(id)),
+            can_run_in_parallel_with: (item.can_run_in_parallel_with || []).map(String).filter((id) => selectedIds.has(id))
+        };
+    });
+    const selectedIds = new Set(workItems.map((item) => String(item.id || '')));
+    const activeWaves = (graph.active_waves || [])
+        .map((wave) => ({
+        ...wave,
+        work_item_ids: (wave.work_item_ids || []).map(String).filter((id) => selectedIds.has(id)),
+        write_paths: (wave.write_paths || []).map(String),
+        conflict_count: Number(wave.conflict_count || 0)
+    }))
+        .filter((wave) => wave.work_item_ids.length > 0);
+    return {
+        ...graph,
+        requested_clones: Math.min(Number(graph.requested_clones || count), count),
+        total_work_items: workItems.length,
+        work_items: workItems,
+        active_waves: activeWaves,
+        mixed_work_kinds: [...new Set(workItems.map((item) => item.kind))],
+        write_allowed_count: workItems.filter((item) => item.write_allowed === true).length
+    };
+}
 async function researchPrepare(args) {
     const root = await sksRoot();
     if (!(await exists(path.join(root, '.sneakoscope'))))
@@ -139,10 +171,16 @@ async function researchRun(args) {
     const mock = flag(args, '--mock');
     const researchWorkGraph = await writeResearchWorkGraph(dir, plan);
     const graphWorkItemCount = Math.max(1, Number(researchWorkGraph.total_work_items || researchWorkGraph.work_items?.length || 0));
+    const explicitWorkItems = hasFlagOption(args, '--work-items');
+    const effectiveDesiredWorkItemCount = explicitWorkItems ? desiredWorkItemCount : Math.max(desiredWorkItemCount, graphWorkItemCount);
+    const effectiveMinimumWorkItems = Math.min(effectiveDesiredWorkItemCount, explicitWorkItems ? minimumWorkItems : Math.max(minimumWorkItems, Math.min(graphWorkItemCount, targetActiveSlots)));
+    const nativeResearchWorkGraph = explicitWorkItems
+        ? limitResearchNativeWorkGraph(researchWorkGraph, effectiveDesiredWorkItemCount)
+        : researchWorkGraph;
     await runResearchCycle(dir, researchWorkGraph, { cycle: 0, status: mock ? 'mock_native_orchestrator_planned' : 'native_orchestrator_planned' });
     await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_RUNNING_NO_QUESTIONS', questions_allowed: false, implementation_allowed: false, research_real_run_required: !mock, research_cycle_timeout_minutes: cycleTimeoutMinutes });
     await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.run.started', maxCycles, mock, cycleTimeoutMinutes, real_run_required: !mock });
-    const nativeAgentRun = await runNativeAgentOrchestrator({ root, missionId: id, route: flag(args, '--autoresearch') ? '$AutoResearch' : '$Research', prompt: mission.prompt || plan.prompt || 'Research run', backend: mock ? 'fake' : 'codex-sdk', mock, agents: requestedAgents, targetActiveSlots, desiredWorkItemCount: Math.max(desiredWorkItemCount, graphWorkItemCount), minimumWorkItems: Math.max(minimumWorkItems, Math.min(graphWorkItemCount, targetActiveSlots)), maxQueueExpansion, concurrency: Math.min(requestedAgents, 5), readonly: true, profile, writeMode: writeMode, applyPatches: false, dryRunPatches, maxWriteAgents, roster: plan.native_agent_plan, routeCommand: 'sks research run', routeBlackboxKind: 'actual_research_command', narutoWorkGraph: researchWorkGraph });
+    const nativeAgentRun = await runNativeAgentOrchestrator({ root, missionId: id, route: flag(args, '--autoresearch') ? '$AutoResearch' : '$Research', prompt: mission.prompt || plan.prompt || 'Research run', backend: mock ? 'fake' : 'codex-sdk', mock, agents: requestedAgents, targetActiveSlots, desiredWorkItemCount: effectiveDesiredWorkItemCount, minimumWorkItems: effectiveMinimumWorkItems, maxQueueExpansion, concurrency: Math.min(requestedAgents, 5), readonly: true, profile, writeMode: writeMode, applyPatches: false, dryRunPatches, maxWriteAgents, roster: plan.native_agent_plan, routeCommand: 'sks research run', routeBlackboxKind: 'actual_research_command', narutoWorkGraph: researchWorkGraph });
     await writeJsonAtomic(path.join(dir, 'research-native-agent-run.json'), nativeAgentRun);
     await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.native_agents.completed', backend: nativeAgentRun.backend, ok: nativeAgentRun.ok, proof: nativeAgentRun.proof?.status });
     if (!nativeAgentRun.ok) {
@@ -151,6 +189,28 @@ async function researchRun(args) {
         process.exitCode = 2;
         return;
     }
+    if (flag(args, '--native-proof-only')) {
+        const proofOnlyGate = {
+            schema: 'sks.research-native-proof-only-gate.v1',
+            ok: nativeAgentRun.proof?.ok === true,
+            native_agent_proof: nativeAgentRun.proof?.ok === true,
+            proof_status: nativeAgentRun.proof?.status || null,
+            blockers: nativeAgentRun.proof?.blockers || []
+        };
+        if (flag(args, '--json'))
+            return console.log(JSON.stringify({
+                schema: flag(args, '--autoresearch') ? 'sks.autoresearch-run.v1' : 'sks.research-run.v1',
+                ok: proofOnlyGate.ok,
+                mission_id: id,
+                gate: proofOnlyGate,
+                proof: nativeAgentRun.proof,
+                native_agent_run: nativeAgentRun,
+                research_work_graph: nativeResearchWorkGraph,
+                native_proof_only: true
+            }, null, 2));
+        console.log(`Research native proof ready: ${id}`);
+        return;
+    }
     const legacyResearchCycle = flag(args, '--legacy-research-cycle') || process.env.SKS_RESEARCH_LEGACY_CYCLE === '1';
     const sourceMutationBaseline = await researchCodeMutationSnapshot(root, id);
     if (!legacyResearchCycle) {

package/dist/core/commands/team-command.js

@@ -1,8 +1,9 @@
 import path from 'node:path';
-import { nowIso, sksRoot, writeJsonAtomic } from '../fsx.js';
+import { nowIso, readJson, sksRoot, writeJsonAtomic } from '../fsx.js';
 import { findLatestMission } from '../mission.js';
 import { narutoCommand } from './naruto-command.js';
 import { teamLegacyObserveCommand, teamLegacySubcommands } from './team-legacy-observe-command.js';
+import { SSOT_GUARD_ARTIFACT } from '../safety/ssot-guard.js';
 export async function team(args = []) {
     if (teamLegacySubcommands.has(String(args[0] || ''))) {
         return teamLegacyObserveCommand(String(args[0]), args.slice(1));
@@ -13,9 +14,13 @@ async function redirectTeamCreateToNaruto(args = []) {
     const root = await sksRoot();
     const list = (args || []).map((arg) => String(arg));
     const narutoArgs = list[0] === 'run' ? list : ['run', ...list];
+    const jsonRequested = list.includes('--json');
     console.warn('SKS Team is deprecated for new execution missions; redirecting to $Naruto.');
-    const result = await narutoCommand(narutoArgs);
+    const result = jsonRequested
+        ? await withSuppressedConsoleLog(() => narutoCommand(narutoArgs))
+        : await narutoCommand(narutoArgs);
     const missionId = result?.mission_id || await findLatestMission(root);
+    const nativeAgentRun = missionId ? await buildTeamNativeAgentCompatibility(root, missionId, result) : null;
     if (missionId) {
         await writeJsonAtomic(path.join(root, '.sneakoscope', 'missions', missionId, 'team-alias-to-naruto.json'), {
             schema: 'sks.team-alias-to-naruto.v1',
@@ -26,10 +31,65 @@ async function redirectTeamCreateToNaruto(args = []) {
             route_command: '$Naruto',
             deprecated_route: '$Team',
             parallel_write_policy: result?.parallel_write_policy || result?.run?.parallel_write_policy || null,
+            ssot_guard_artifact: SSOT_GUARD_ARTIFACT,
             created_at: nowIso(),
             args: list
         });
     }
-    return result;
+    const finalResult = {
+        ...result,
+        mock: result?.mock === true || result?.backend === 'fake',
+        ...(nativeAgentRun ? { native_agent_run: nativeAgentRun } : {})
+    };
+    if (jsonRequested)
+        console.log(JSON.stringify(finalResult, null, 2));
+    return finalResult;
+}
+async function withSuppressedConsoleLog(fn) {
+    const originalLog = console.log;
+    console.log = () => undefined;
+    try {
+        return await fn();
+    }
+    finally {
+        console.log = originalLog;
+    }
+}
+async function buildTeamNativeAgentCompatibility(root, missionId, result) {
+    const ledgerRoot = path.join(root, '.sneakoscope', 'missions', missionId, 'agents');
+    const [schedulerState, proof, parallelWritePolicy] = await Promise.all([
+        readJson(path.join(ledgerRoot, 'agent-scheduler-state.json'), null),
+        readJson(path.join(ledgerRoot, 'agent-proof-evidence.json'), null),
+        readJson(path.join(ledgerRoot, 'agent-parallel-write-policy.json'), null)
+    ]);
+    if (!schedulerState || !proof)
+        return null;
+    return {
+        schema: result?.run?.schema || 'sks.agent-run.v1',
+        ok: result?.run?.ok === true || result?.ok === true,
+        mission_id: missionId,
+        route: '$Team',
+        backend: result?.backend || result?.run?.backend || proof.backend || null,
+        ledger_root: path.relative(root, ledgerRoot),
+        target_active_slots: schedulerState.target_active_slots ?? result?.target_active_slots ?? null,
+        scheduler: {
+            state: schedulerState
+        },
+        proof: {
+            ...proof,
+            route: '$Team',
+            route_command: 'sks team',
+            route_blackbox_kind: 'actual_team_command',
+            real_route_command_used: true
+        },
+        parallel_write_policy: parallelWritePolicy || result?.parallel_write_policy || result?.run?.parallel_write_policy || null,
+        redirected_to: '$Naruto',
+        compatibility: {
+            schema: 'sks.team-native-agent-compatibility.v1',
+            ok: true,
+            source: 'team-alias-to-naruto',
+            ledger_root: path.relative(root, ledgerRoot)
+        }
+    };
 }
 //# sourceMappingURL=team-command.js.map

package/dist/core/config/managed-config-merge.js

@@ -1,6 +1,6 @@
 import fs from 'node:fs/promises';
 import path from 'node:path';
-import { ensureDir, nowIso, writeJsonAtomic, writeTextAtomic } from '../fsx.js';
+import { ensureDir, nowIso, sha256, writeJsonAtomic, writeTextAtomic } from '../fsx.js';
 import { isProtectedSecretKey, PROTECTED_SECRET_KEYS } from './supabase-secret-preservation.js';
 export async function writeManagedJsonConfig(file, current, managed) {
     const next = safeMergeObject(current, managed);
@@ -23,13 +23,14 @@ export async function writeManagedEnvConfig(file, currentText, managedLines) {
     const next = additions.length ? `${String(currentText || '').replace(/\s*$/, '\n')}${additions.join('\n')}\n` : String(currentText || '');
     return writeMergedText(file, currentText, next, 'env', protectedKeysInText(currentText));
 }
-export function safeMergeObject(current, managed) {
+export function safeMergeObject(current, managed, prefix = '') {
     const out = { ...current };
     for (const [key, value] of Object.entries(managed)) {
-        if (isProtectedSecretKey(key) && current[key] != null)
+        const dotted = prefix ? `${prefix}.${key}` : key;
+        if (isProtectedSecretKey(dotted) && current[key] != null)
             continue;
         if (isPlainObject(value) && isPlainObject(current[key]))
-            out[key] = safeMergeObject(current[key], value);
+            out[key] = safeMergeObject(current[key], value, dotted);
         else
             out[key] = value;
     }
@@ -51,11 +52,23 @@ function upsertTomlBlockPreservingSecrets(text, block) {
             break;
         }
     }
-    const existingSecretLines = lines.slice(start + 1, end).filter((line) => {
-        const key = line.match(/^\s*([A-Za-z0-9_.-]+)\s*=/)?.[1] || '';
-        return isProtectedSecretKey(`${header}.${key}`) || isProtectedSecretKey(key);
-    });
-    lines.splice(start, end - start, ...blockLines, ...existingSecretLines.filter((line) => !blockLines.includes(line)));
+    const existingBody = lines.slice(start + 1, end);
+    const nextBody = [...existingBody];
+    for (const managedLine of blockLines.slice(1)) {
+        const managedKey = managedLine.match(/^\s*([A-Za-z0-9_.-]+)\s*=/)?.[1] || '';
+        if (!managedKey) {
+            if (!nextBody.includes(managedLine))
+                nextBody.push(managedLine);
+            continue;
+        }
+        const existingIndex = nextBody.findIndex((line) => (line.match(/^\s*([A-Za-z0-9_.-]+)\s*=/)?.[1] || '') === managedKey);
+        const protectedLine = isProtectedSecretKey(`${header}.${managedKey}`) || isProtectedSecretKey(managedKey);
+        if (existingIndex === -1)
+            nextBody.push(managedLine);
+        else if (!protectedLine)
+            nextBody[existingIndex] = managedLine;
+    }
+    lines.splice(start, end - start, blockLines[0] || `[${header}]`, ...nextBody);
     return lines.join('\n').replace(/\n{3,}/g, '\n\n');
 }
 async function writeMergedText(file, before, after, format, preserved) {
@@ -68,6 +81,7 @@ async function writeMergedText(file, before, after, format, preserved) {
         }
         await writeTextAtomic(file, after);
     }
+    const preservedSecretLineHashes = protectedSecretLineHashes(before);
     return {
         schema: 'sks.managed-config-merge.v1',
         generated_at: nowIso(),
@@ -77,6 +91,8 @@ async function writeMergedText(file, before, after, format, preserved) {
         changed: before !== after,
         backup_path: backupPath,
         protected_keys_preserved: preserved,
+        preserved_secret_lines_sha256: preservedSecretLineHashes,
+        idempotent: before === after || protectedSecretLineHashes(after).every((hash) => preservedSecretLineHashes.includes(hash)),
         blockers: []
     };
 }
@@ -88,7 +104,40 @@ function protectedKeysPresent(value) {
     return found;
 }
 function protectedKeysInText(text) {
-    return PROTECTED_SECRET_KEYS.filter((key) => new RegExp(`(^|\\n)\\s*(?:export\\s+)?${String(key).replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\s*=`).test(text)).map(String);
+    const found = new Set();
+    for (const key of PROTECTED_SECRET_KEYS) {
+        if (new RegExp(`(^|\\n)\\s*(?:export\\s+)?${String(key).replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\s*=`).test(text))
+            found.add(String(key));
+    }
+    let section = '';
+    for (const line of String(text || '').split(/\r?\n/)) {
+        const sectionMatch = line.match(/^\s*\[([^\]]+)\]\s*$/);
+        if (sectionMatch) {
+            section = String(sectionMatch[1] || '');
+            continue;
+        }
+        const key = line.match(/^\s*([A-Za-z0-9_.-]+)\s*=/)?.[1] || '';
+        if (key && section && isProtectedSecretKey(`${section}.${key}`))
+            found.add(`${section}.${key}`);
+    }
+    return [...found].sort();
+}
+function protectedSecretLineHashes(text) {
+    const hashes = [];
+    let section = '';
+    for (const line of String(text || '').split(/\r?\n/)) {
+        const sectionMatch = line.match(/^\s*\[([^\]]+)\]\s*$/);
+        if (sectionMatch) {
+            section = String(sectionMatch[1] || '');
+            continue;
+        }
+        const key = line.match(/^\s*(?:export\s+)?([A-Za-z0-9_.-]+)\s*=/)?.[1] || '';
+        if (!key)
+            continue;
+        if (isProtectedSecretKey(key) || (section && isProtectedSecretKey(`${section}.${key}`)))
+            hashes.push(sha256(line));
+    }
+    return hashes.sort();
 }
 function lookupPath(value, dotted) {
     let current = value;