mustflow 2.18.20 → 2.21.1

package/dist/cli/commands/classify.js

@@ -1,6 +1,6 @@
-import { mkdirSync, writeFileSync } from 'node:fs';
 import path from 'node:path';
 import { createChangeClassificationReport, } from '../../core/change-classification.js';
+import { writeJsonFileInsideWithoutSymlinks } from '../../core/safe-filesystem.js';
 import { printUsageError, renderHelp } from '../lib/cli-output.js';
 import { requireGitChangedFiles } from '../lib/git-changes.js';
 import { t } from '../lib/i18n.js';
@@ -111,8 +111,7 @@ function resolveWritePath(projectRoot, inputPath) {
 }
 function writeClassifyOutput(projectRoot, inputPath, output) {
     const outputPath = resolveWritePath(projectRoot, inputPath);
-    mkdirSync(path.dirname(outputPath), { recursive: true });
-    writeFileSync(outputPath, `${JSON.stringify(output, null, 2)}\n`, 'utf8');
+    writeJsonFileInsideWithoutSymlinks(projectRoot, outputPath, output);
 }
 export function runClassify(args, reporter, lang = 'en') {
     if (args.includes('--help') || args.includes('-h')) {

package/dist/cli/commands/doctor.js

@@ -5,7 +5,9 @@ import { getAgentContext, } from '../lib/agent-context.js';
 import { t } from '../lib/i18n.js';
 import { getLocalIndexDatabasePath } from '../lib/local-index.js';
 import { resolveMustflowRoot } from '../lib/project-root.js';
-import { checkMustflowProject } from '../lib/validation.js';
+import { checkMustflowProjectReport } from '../lib/validation.js';
+import { findCommandEnvInheritanceWarnings } from '../../core/command-contract-validation.js';
+import { readCommandContract } from '../../core/config-loading.js';
 import { summarizeSkillRouteAlignment } from '../../core/skill-route-alignment.js';
 const DOCTOR_SCHEMA_VERSION = '1';
 export function getDoctorHelp(lang = 'en') {
@@ -46,6 +48,7 @@ function createDiagnostics(output) {
     const localIndexExists = existsSync(getLocalIndexDatabasePath(output.mustflow_root));
     const runnableIntentCount = output.context.runnable_intents.length;
     const skillRouteAlignment = summarizeSkillRouteAlignment(output.check.issues);
+    const inheritedEnvIntentCount = output.command_environment.inherited_intents.length;
     diagnostics.push({
         id: 'install',
         status: output.installed ? 'ok' : 'fail',
@@ -55,7 +58,9 @@ function createDiagnostics(output) {
     diagnostics.push({
         id: 'validation',
         status: output.check.ok ? 'ok' : 'fail',
-        summary: `${output.check.issue_count} ${pluralize(output.check.issue_count, 'issue', 'issues')}`,
+        summary: output.check.warning_count === 0
+            ? `${output.check.issue_count} ${pluralize(output.check.issue_count, 'issue', 'issues')}`
+            : `${output.check.issue_count} ${pluralize(output.check.issue_count, 'issue', 'issues')}, ${output.check.warning_count} ${pluralize(output.check.warning_count, 'warning', 'warnings')}`,
         action: output.check.ok ? null : checkCommand,
     });
     diagnostics.push({
@@ -72,6 +77,16 @@ function createDiagnostics(output) {
             : 'missing',
         action: output.context.command_contract_exists ? 'mf help commands' : 'mf init --dry-run',
     });
+    diagnostics.push({
+        id: 'environment',
+        status: output.context.command_contract_exists ? (inheritedEnvIntentCount > 0 ? 'warn' : 'ok') : 'info',
+        summary: output.context.command_contract_exists
+            ? inheritedEnvIntentCount === 0
+                ? 'no inherited host-environment intents'
+                : `${inheritedEnvIntentCount} inherited host-environment ${pluralize(inheritedEnvIntentCount, 'intent', 'intents')}: ${output.command_environment.inherited_intents.join(', ')}`
+            : 'command contract missing',
+        action: inheritedEnvIntentCount > 0 ? 'mf check --strict --json' : null,
+    });
     diagnostics.push({
         id: 'read_order',
         status: output.context.missing_read_order.length === 0 ? 'ok' : 'fail',
@@ -124,15 +139,37 @@ function getNextSteps(output) {
     }
     return nextSteps;
 }
+function readCommandEnvironmentSummary(projectRoot) {
+    try {
+        const contract = readCommandContract(projectRoot);
+        const warnings = findCommandEnvInheritanceWarnings(contract);
+        return {
+            inherited_intents: warnings.map((warning) => warning.intentName).sort((left, right) => left.localeCompare(right)),
+            inherited_network_intents: warnings
+                .filter((warning) => warning.network)
+                .map((warning) => warning.intentName)
+                .sort((left, right) => left.localeCompare(right)),
+        };
+    }
+    catch {
+        return {
+            inherited_intents: [],
+            inherited_network_intents: [],
+        };
+    }
+}
 function createDoctorOutput(strict) {
     const mustflowRoot = resolveMustflowRoot();
     const context = getAgentContext(mustflowRoot);
-    const issues = checkMustflowProject(mustflowRoot, { strict });
+    const checkReport = checkMustflowProjectReport(mustflowRoot, { strict });
     const check = {
-        ok: issues.length === 0,
-        issue_count: issues.length,
-        issues,
+        ok: checkReport.issues.length === 0,
+        issue_count: checkReport.issues.length,
+        issues: checkReport.issues,
+        warning_count: checkReport.warnings.length,
+        warnings: checkReport.warnings,
     };
+    const commandEnvironment = readCommandEnvironmentSummary(mustflowRoot);
     const baseOutput = {
         schema_version: DOCTOR_SCHEMA_VERSION,
         command: 'doctor',
@@ -150,6 +187,7 @@ function createDoctorOutput(strict) {
             missing_optional_read_order: context.optional_read_order.filter((entry) => !entry.exists).map((entry) => entry.path),
             latest_run_exists: context.latest_run.exists,
         },
+        command_environment: commandEnvironment,
         effective_policy: context.effective_policy,
         state_policy: context.state_policy,
         blocked_actions: context.blocked_actions,
@@ -171,6 +209,8 @@ function getDiagnosticLabel(id, lang) {
             return t(lang, 'doctor.diagnostic.skillRoutes');
         case 'commands':
             return t(lang, 'doctor.diagnostic.commands');
+        case 'environment':
+            return t(lang, 'doctor.diagnostic.environment');
         case 'read_order':
             return t(lang, 'doctor.diagnostic.readOrder');
         case 'optional_read_order':

package/dist/cli/commands/run/output.js

@@ -46,7 +46,7 @@ export function writeStreamChunk(reporter, stream, chunk) {
     reporter.stderr(chunk.toString());
 }
 export function createOutputLimitError(stream, maxOutputBytes) {
-    return Object.assign(new Error(`${stream} exceeded max_output_bytes (${maxOutputBytes})`), {
+    return Object.assign(new Error(`${stream} exceeded per-stream max_output_bytes (${maxOutputBytes})`), {
         code: OUTPUT_LIMIT_ERROR_CODE,
     });
 }

package/dist/cli/commands/run/receipt.js

@@ -16,6 +16,7 @@ export function assembleRunReceipt(input) {
         envPolicy: input.plan.envPolicy,
         envAllowlist: input.plan.envAllowlist,
         timeoutSeconds: input.plan.timeoutSeconds,
+        killAfterSeconds: input.plan.killAfterSeconds,
         maxOutputBytes: input.plan.maxOutputBytes,
         successExitCodes: input.plan.successExitCodes,
         exitCode: input.exitCode,

package/dist/cli/commands/verify.js

@@ -1,11 +1,12 @@
 import { createHash } from 'node:crypto';
-import { mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { readFileSync } from 'node:fs';
 import path from 'node:path';
 import { createClassifyOutput } from './classify.js';
 import { runRun } from './run.js';
 import { createChangeVerificationReport, } from '../../core/change-verification.js';
+import { writeJsonFileInsideWithoutSymlinks } from '../../core/safe-filesystem.js';
 import { createVerifyCompletionVerdict, } from '../../core/completion-verdict.js';
-import { atomicWriteJsonFile, createStateRunId } from '../../core/atomic-state-write.js';
+import { createStateRunId } from '../../core/atomic-state-write.js';
 import { createExternalEvidenceRisks, } from '../../core/external-evidence.js';
 import { createRepeatedFailureRisks, createVerificationFailureFingerprint, updateRepeatedFailureState, } from '../../core/repeated-failure.js';
 import { countReproEvidenceVerdictEffects, createReproEvidenceRisks, } from '../../core/repro-evidence.js';
@@ -16,7 +17,7 @@ import { readCommandContract } from '../../core/config-loading.js';
 import { DEFAULT_VERIFY_PARALLELISM, parseVerifyArgs } from './verify/args.js';
 import { printUsageError, renderHelp } from '../lib/cli-output.js';
 import { t } from '../lib/i18n.js';
-import { readLocalCommandEffectGraph, readLocalPathSurfaces, readLocalSourceAnchorVerdictRisks, } from '../lib/local-index.js';
+import { readLocalCommandEffectGraphs, readLocalPathSurfaces, readLocalSourceAnchorVerdictRisks, } from '../lib/local-index.js';
 import { resolveMustflowRoot } from '../lib/project-root.js';
 const VERIFY_SCHEMA_VERSION = '1';
 const RUN_STATE_DIR = path.join('.mustflow', 'state', 'runs');
@@ -545,8 +546,7 @@ function createInputFromChanged(projectRoot) {
 }
 function writeChangedPlan(projectRoot, inputPath, plan) {
     const planPath = resolvePlanPath(projectRoot, inputPath);
-    mkdirSync(path.dirname(planPath), { recursive: true });
-    writeFileSync(planPath, `${JSON.stringify(plan, null, 2)}\n`, 'utf8');
+    writeJsonFileInsideWithoutSymlinks(projectRoot, planPath, plan);
 }
 export function planErrorMessageKey(code) {
     switch (code) {
@@ -578,6 +578,20 @@ function skippedResult(candidate) {
         receipt: null,
     };
 }
+function stoppedAfterFailedBatchResult(entry, verificationPlanId) {
+    return {
+        intent: entry.intent,
+        status: 'skipped',
+        skipped: true,
+        reason: 'stopped_after_failed_batch',
+        detail: 'Skipped because an earlier verification batch failed and the schedule failure policy stops before the next batch.',
+        exit_code: null,
+        verification_plan_id: verificationPlanId,
+        receipt_path: null,
+        receipt_sha256: null,
+        receipt: null,
+    };
+}
 function candidateResultKey(candidate) {
     return candidate.intent
         ? `intent:${candidate.intent}`
@@ -670,21 +684,40 @@ async function runVerificationEntriesInParallelChunks(entries, parallelism, lang
     }
     return results;
 }
+function verificationResultFailed(result) {
+    return (!result.skipped &&
+        (result.status === 'failed' ||
+            result.status === 'timed_out' ||
+            result.status === 'start_failed' ||
+            result.status === 'output_limit_exceeded'));
+}
 async function runScheduledVerificationIntents(report, lang, verificationPlanId, scheduledTestTargets, parallelism) {
-    if (parallelism <= DEFAULT_VERIFY_PARALLELISM) {
-        return runVerificationEntriesSequentially(report.schedule.entries, lang, verificationPlanId, scheduledTestTargets);
-    }
     const results = [];
-    for (const batch of report.schedule.batches) {
+    for (let batchIndex = 0; batchIndex < report.schedule.batches.length; batchIndex += 1) {
+        const batch = report.schedule.batches[batchIndex];
         const entries = entriesForScheduleBatch(report.schedule.entries, batch);
         if (entries.length === 0) {
             continue;
         }
+        let batchResults;
         if (entries.length > 1 && entries.every((entry) => entry.parallelEligible)) {
-            results.push(...(await runVerificationEntriesInParallelChunks(entries, parallelism, lang, verificationPlanId, scheduledTestTargets)));
+            batchResults =
+                parallelism > DEFAULT_VERIFY_PARALLELISM
+                    ? await runVerificationEntriesInParallelChunks(entries, parallelism, lang, verificationPlanId, scheduledTestTargets)
+                    : await runVerificationEntriesSequentially(entries, lang, verificationPlanId, scheduledTestTargets);
+        }
+        else {
+            batchResults = await runVerificationEntriesSequentially(entries, lang, verificationPlanId, scheduledTestTargets);
+        }
+        results.push(...batchResults);
+        if (!batchResults.some(verificationResultFailed)) {
             continue;
         }
-        results.push(...(await runVerificationEntriesSequentially(entries, lang, verificationPlanId, scheduledTestTargets)));
+        const remainingEntries = report.schedule.batches
+            .slice(batchIndex + 1)
+            .flatMap((remainingBatch) => entriesForScheduleBatch(report.schedule.entries, remainingBatch));
+        results.push(...remainingEntries.map((entry) => stoppedAfterFailedBatchResult(entry, verificationPlanId)));
+        break;
     }
     return results;
 }
@@ -1026,7 +1059,6 @@ function writeVerifyRunReceipts(projectRoot, output, report, sourceAnchorRisks,
     const statePaths = createVerifyRunStatePaths(projectRoot);
     const receipts = [];
     const results = [];
-    mkdirSync(statePaths.absoluteIntentDir, { recursive: true });
     for (const [index, result] of output.results.entries()) {
         let receiptPath = null;
         let receiptSha256 = null;
@@ -1042,7 +1074,7 @@ function writeVerifyRunReceipts(projectRoot, output, report, sourceAnchorRisks,
             };
             const receiptContent = `${JSON.stringify(receipt, null, 2)}\n`;
             receiptSha256 = hashTextSha256(receiptContent);
-            atomicWriteJsonFile(absoluteReceiptPath, receipt);
+            writeJsonFileInsideWithoutSymlinks(projectRoot, absoluteReceiptPath, receipt);
         }
         receipts.push({
             intent: result.intent,
@@ -1148,7 +1180,7 @@ function writeVerifyRunReceipts(projectRoot, output, report, sourceAnchorRisks,
         ...(outputWithReceiptPaths.external_checks ? { external_checks: outputWithReceiptPaths.external_checks } : {}),
         receipts,
     };
-    atomicWriteJsonFile(statePaths.absoluteManifestPath, manifest);
+    writeJsonFileInsideWithoutSymlinks(projectRoot, statePaths.absoluteManifestPath, manifest);
     const latest = {
         schema_version: '1',
         command: 'verify',
@@ -1169,7 +1201,7 @@ function writeVerifyRunReceipts(projectRoot, output, report, sourceAnchorRisks,
         run_dir: statePaths.runDir,
         manifest_path: statePaths.manifestPath,
     };
-    atomicWriteJsonFile(path.join(projectRoot, LATEST_RUN_RECEIPT_PATH), latest);
+    writeJsonFileInsideWithoutSymlinks(projectRoot, path.join(projectRoot, LATEST_RUN_RECEIPT_PATH), latest);
     return outputWithReceiptPaths;
 }
 async function createVerifyOutput(input, planSource, projectRoot, lang, reproEvidence = null, externalChecks = [], parallelism = DEFAULT_VERIFY_PARALLELISM) {
@@ -1276,14 +1308,11 @@ async function createPlanOnlyOutput(input, projectRoot) {
     if (!firstEntry) {
         return { ...report, verification_plan_id: verificationPlanId, requirements };
     }
-    const firstGraph = await readLocalCommandEffectGraph(projectRoot, firstEntry.intent);
-    const graphsByIntent = new Map([[firstEntry.intent, firstGraph]]);
-    if (firstGraph.status === 'fresh') {
-        for (const entry of report.schedule.entries.slice(1)) {
-            if (!graphsByIntent.has(entry.intent)) {
-                graphsByIntent.set(entry.intent, await readLocalCommandEffectGraph(projectRoot, entry.intent));
-            }
-        }
+    const scheduledIntents = Array.from(new Set(report.schedule.entries.map((entry) => entry.intent)));
+    const graphsByIntent = await readLocalCommandEffectGraphs(projectRoot, scheduledIntents);
+    const firstGraph = graphsByIntent.get(firstEntry.intent);
+    if (!firstGraph) {
+        return { ...report, verification_plan_id: verificationPlanId, requirements };
     }
     return {
         ...report,

package/dist/cli/i18n/en.js

@@ -488,6 +488,7 @@ export const enMessages = {
     "doctor.diagnostic.validation": "Validation",
     "doctor.diagnostic.skillRoutes": "Skill routes",
     "doctor.diagnostic.commands": "Command specification",
+    "doctor.diagnostic.environment": "Environment",
     "doctor.diagnostic.readOrder": "Read order",
     "doctor.diagnostic.optionalReadOrder": "Optional read order",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/i18n/es.js

@@ -488,6 +488,7 @@ export const esMessages = {
     "doctor.diagnostic.validation": "Validación",
     "doctor.diagnostic.skillRoutes": "Rutas de skills",
     "doctor.diagnostic.commands": "Especificación de comandos",
+    "doctor.diagnostic.environment": "Entorno",
     "doctor.diagnostic.readOrder": "Orden de lectura",
     "doctor.diagnostic.optionalReadOrder": "Orden de lectura opcional",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/i18n/fr.js

@@ -488,6 +488,7 @@ export const frMessages = {
     "doctor.diagnostic.validation": "Validation",
     "doctor.diagnostic.skillRoutes": "Routage des skills",
     "doctor.diagnostic.commands": "Spécification des commandes",
+    "doctor.diagnostic.environment": "Environnement",
     "doctor.diagnostic.readOrder": "Ordre de lecture",
     "doctor.diagnostic.optionalReadOrder": "Ordre de lecture optionnel",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/i18n/hi.js

@@ -488,6 +488,7 @@ export const hiMessages = {
     "doctor.diagnostic.validation": "सत्यापन",
     "doctor.diagnostic.skillRoutes": "स्किल रूट",
     "doctor.diagnostic.commands": "कमांड विनिर्देश",
+    "doctor.diagnostic.environment": "एनवायरनमेंट",
     "doctor.diagnostic.readOrder": "पढ़ने का क्रम",
     "doctor.diagnostic.optionalReadOrder": "वैकल्पिक पढ़ने का क्रम",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/i18n/ko.js

@@ -488,6 +488,7 @@ export const koMessages = {
     "doctor.diagnostic.validation": "검증",
     "doctor.diagnostic.skillRoutes": "스킬 라우팅",
     "doctor.diagnostic.commands": "명령",
+    "doctor.diagnostic.environment": "실행 환경",
     "doctor.diagnostic.readOrder": "읽기 순서",
     "doctor.diagnostic.optionalReadOrder": "선택적 읽기 순서",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/i18n/zh.js

@@ -488,6 +488,7 @@ export const zhMessages = {
     "doctor.diagnostic.validation": "验证",
     "doctor.diagnostic.skillRoutes": "技能路由",
     "doctor.diagnostic.commands": "命令规范",
+    "doctor.diagnostic.environment": "环境",
     "doctor.diagnostic.readOrder": "读取顺序",
     "doctor.diagnostic.optionalReadOrder": "可选读取顺序",
     "doctor.diagnostic.repoMap": "REPO_MAP.md",

package/dist/cli/lib/git-changes.js

@@ -1,5 +1,7 @@
 import { spawnSync } from 'node:child_process';
 import { parseGitStatusOutput } from '../../core/change-classification.js';
+const GIT_STATUS_TIMEOUT_MS = 10_000;
+const GIT_STATUS_MAX_BUFFER_BYTES = 16 * 1024 * 1024;
 export class GitChangedFilesError extends Error {
     result;
     constructor(result) {
@@ -9,9 +11,13 @@ export class GitChangedFilesError extends Error {
     }
 }
 export function readGitChangedFiles(projectRoot) {
-    const result = spawnSync('git', ['status', '--short', '--untracked-files=all'], {
+    const result = spawnSync('git', ['status', '--porcelain=v1', '-z', '--untracked-files=all'], {
         cwd: projectRoot,
         encoding: 'utf8',
+        input: '',
+        maxBuffer: GIT_STATUS_MAX_BUFFER_BYTES,
+        stdio: ['ignore', 'pipe', 'pipe'],
+        timeout: GIT_STATUS_TIMEOUT_MS,
         windowsHide: true,
     });
     if (result.status !== 0 || typeof result.stdout !== 'string') {

package/dist/cli/lib/local-index/index.js

@@ -1,4 +1,4 @@
-import { existsSync, mkdirSync, readFileSync, statSync, writeFileSync } from 'node:fs';
+import { existsSync, readFileSync, statSync } from 'node:fs';
 import { createHash } from 'node:crypto';
 import path from 'node:path';
 import { isRecord, readCommandContract, readString, readStringArray } from '../command-contract.js';
@@ -8,6 +8,7 @@ import { collectSourceAnchorIndexRecords, hasHighRiskSourceAnchorRiskTags, } fro
 import { listSourceAnchorFiles } from '../../../core/source-anchors.js';
 import { normalizeCommandEffects } from '../../../core/command-effects.js';
 import { listChangeClassificationRuleDescriptors } from '../../../core/change-classification.js';
+import { writeFileInsideWithoutSymlinks } from '../../../core/safe-filesystem.js';
 import { DEFAULT_DATABASE_RELATIVE_PATH, DEFAULT_PROMPT_CACHE_STABLE_READ, DEFAULT_PROMPT_CACHE_TASK_SOURCES, DEFAULT_PROMPT_CACHE_VOLATILE_SOURCES, INDEX_CONFIG_RELATIVE_PATH, LOCAL_INDEX_CONTENT_MODE, LOCAL_INDEX_EXCLUDED_RAW_DATA_KINDS, LOCAL_INDEX_PARSER_VERSION, LOCAL_INDEX_SCHEMA_VERSION, LOCAL_INDEX_STORE_FULL_CONTENT, LATEST_RUN_STATE_RELATIVE_PATH, MAX_SEARCH_MATCH_SNIPPET_CHARS, MAX_SNIPPET_BYTES_PER_DOCUMENT, MUSTFLOW_RELATIVE_PATH, SEARCH_BACKEND_FTS5, SEARCH_BACKEND_TABLE_SCAN, SEARCH_MATCH_CONTEXT_AFTER_CHARS, SEARCH_MATCH_CONTEXT_BEFORE_CHARS, SEARCH_MATCH_TRUNCATION_MARKER, SEARCH_NGRAM_MAX_GRAMS_PER_TARGET, SEARCH_NGRAM_MAX_LENGTH, SEARCH_NGRAM_MAX_TOKEN_CHARS, SEARCH_NGRAM_MIN_LENGTH, SOURCE_INDEX_MAX_FILE_BYTES, TEST_DISABLE_FTS5_ENV, } from './constants.js';
 import { loadSqlJs } from './sql.js';
 export function getLocalIndexDatabasePath(projectRoot) {
@@ -331,16 +332,16 @@ function collectSourceAnchorCandidatePaths(projectRoot, sourceConfig) {
         excludeGeneratedOrVendor: true,
     });
 }
-function collectFastPreflightIndexedFileMetadataRecords(projectRoot, includeSource, sourceConfig) {
+function collectFastPreflightIndexedFileRecords(projectRoot, includeSource, sourceConfig) {
     const records = new Map();
     for (const relativePath of getExistingIndexablePaths(projectRoot)) {
-        records.set(relativePath, readIndexedFileMetadataRecord(projectRoot, relativePath, 'workflow'));
+        records.set(relativePath, readIndexedFileRecord(projectRoot, relativePath, 'workflow'));
     }
     if (includeSource) {
         try {
             for (const sourcePath of collectSourceAnchorCandidatePaths(projectRoot, sourceConfig)) {
                 if (!records.has(sourcePath)) {
-                    records.set(sourcePath, readIndexedFileMetadataRecord(projectRoot, sourcePath, 'source_anchor'));
+                    records.set(sourcePath, readIndexedFileRecord(projectRoot, sourcePath, 'source_anchor'));
                 }
             }
         }
@@ -349,7 +350,7 @@ function collectFastPreflightIndexedFileMetadataRecords(projectRoot, includeSour
         }
     }
     if (existsSync(path.join(projectRoot, ...LATEST_RUN_STATE_RELATIVE_PATH.split('/')))) {
-        records.set(LATEST_RUN_STATE_RELATIVE_PATH, readIndexedFileMetadataRecord(projectRoot, LATEST_RUN_STATE_RELATIVE_PATH, 'state'));
+        records.set(LATEST_RUN_STATE_RELATIVE_PATH, readIndexedFileRecord(projectRoot, LATEST_RUN_STATE_RELATIVE_PATH, 'state'));
     }
     return [...records.values()].sort((left, right) => left.path.localeCompare(right.path));
 }
@@ -2053,27 +2054,6 @@ function createStoredLocalIndexResult(projectRoot, databasePath, dryRun, indexMo
         indexed_paths: readStoredIndexedPaths(database),
     };
 }
-function indexedFileMetadataMatch(database, currentFiles) {
-    const rows = queryRows(database, 'SELECT path, source_scope, size_bytes, mtime_ms, parser_version FROM indexed_files ORDER BY path');
-    if (rows.length !== currentFiles.length) {
-        return false;
-    }
-    const currentByPath = new Map(currentFiles.map((file) => [file.path, file]));
-    for (const row of rows) {
-        const storedPath = toSearchString(row.path);
-        const current = currentByPath.get(storedPath);
-        if (!current) {
-            return false;
-        }
-        if (normalizeIndexedFileSourceScope(row.source_scope) !== current.sourceScope ||
-            row.size_bytes !== current.sizeBytes ||
-            row.mtime_ms !== current.mtimeMs ||
-            toSearchString(row.parser_version) !== LOCAL_INDEX_PARSER_VERSION) {
-            return false;
-        }
-    }
-    return true;
-}
 function indexedFilesMatch(database, currentFiles) {
     const rows = queryRows(database, 'SELECT path, source_scope, content_hash, parser_version FROM indexed_files ORDER BY path');
     if (rows.length !== currentFiles.length) {
@@ -2116,7 +2096,7 @@ async function readIncrementalPreflightReuse(SQL, databasePath, projectRoot, cur
         if (!hasTable(database, 'indexed_files')) {
             return { result: null, rebuildReason: 'indexed_files_missing' };
         }
-        if (!indexedFileMetadataMatch(database, currentFiles)) {
+        if (!indexedFilesMatch(database, currentFiles)) {
             return { result: null, rebuildReason: 'file_fingerprint_mismatch' };
         }
         const capabilities = readStoredSearchCapabilities(database);
@@ -2190,7 +2170,7 @@ export async function createLocalIndex(projectRoot, options = {}) {
     capabilities = detectLocalSearchCapabilities(capabilityDatabase);
     capabilityDatabase.close();
     if (incremental) {
-        const preflightFiles = collectFastPreflightIndexedFileMetadataRecords(projectRoot, includeSource, sourceConfig);
+        const preflightFiles = collectFastPreflightIndexedFileRecords(projectRoot, includeSource, sourceConfig);
         const preflightReuse = await readIncrementalPreflightReuse(SQL, databasePath, projectRoot, preflightFiles, sourceScopeHash, dryRun, indexMode);
         if (preflightReuse.result) {
             return preflightReuse.result;
@@ -2223,8 +2203,7 @@ export async function createLocalIndex(projectRoot, options = {}) {
         const database = new SQL.Database();
         createSchema(database, capabilities);
         populateDatabase(database, capabilities, documents, skills, skillRoutes, commandIntents, sourceAnchors, indexedFiles, verificationEvidence, indexMode, sourceScopeHash, includeSource, new Date().toISOString());
-        mkdirSync(path.dirname(databasePath), { recursive: true });
-        writeFileSync(databasePath, database.export());
+        writeFileInsideWithoutSymlinks(projectRoot, databasePath, database.export());
         database.close();
     }
     return {

package/dist/cli/lib/repo-map.js

@@ -1,8 +1,9 @@
 import { spawnSync } from 'node:child_process';
 import { createHash } from 'node:crypto';
-import { existsSync, lstatSync, readdirSync, realpathSync, statSync, writeFileSync } from 'node:fs';
+import { existsSync, lstatSync, readdirSync, realpathSync, statSync } from 'node:fs';
 import path from 'node:path';
 import { toPosixPath } from './filesystem.js';
+import { writeUtf8FileInsideWithoutSymlinks } from '../../core/safe-filesystem.js';
 import { readTomlFile } from './toml.js';
 const DEFAULT_DEPTH = 3;
 const REPO_MAP_DOC_ID = 'repo-map';
@@ -691,5 +692,5 @@ export function generateRepoMap(projectRoot, options = {}) {
     ].join('\n');
 }
 export function writeRepoMap(projectRoot, content) {
-    writeFileSync(path.join(projectRoot, 'REPO_MAP.md'), content);
+    writeUtf8FileInsideWithoutSymlinks(projectRoot, path.join(projectRoot, 'REPO_MAP.md'), content);
 }

package/dist/cli/lib/run-plan.js

@@ -4,7 +4,7 @@ import { resolveSafeProjectCwd } from '../../core/command-cwd.js';
 import { resolveCommandEnv } from '../../core/command-env.js';
 import { evaluateCommandIntentEligibility, } from '../../core/command-intent-eligibility.js';
 import { isRecord, readPositiveInteger, readString, readStringArray, } from '../../core/config-loading.js';
-import { DEFAULT_COMMAND_MAX_OUTPUT_BYTES, MAX_COMMAND_OUTPUT_BYTES, commandMaxOutputBytesLimitMessage, } from '../../core/command-output-limits.js';
+import { DEFAULT_COMMAND_MAX_OUTPUT_BYTES, COMMAND_OUTPUT_LIMIT_SCOPE, MAX_COMMAND_OUTPUT_BYTES, commandMaxOutputBytesLimitMessage, } from '../../core/command-output-limits.js';
 import { t } from './i18n.js';
 function getSuccessExitCodes(intent) {
     const value = intent.success_exit_codes;
@@ -78,8 +78,10 @@ function readEffectiveMaxOutputBytes(contract, intent) {
         readPositiveInteger(contract.defaults, 'max_output_bytes') ??
         DEFAULT_COMMAND_MAX_OUTPUT_BYTES;
 }
-function readEffectiveKillAfterSeconds(contract) {
-    return readPositiveInteger(contract.defaults, 'kill_after_seconds') ?? 5;
+function readEffectiveKillAfterSeconds(contract, intent) {
+    return readPositiveInteger(intent, 'kill_after_seconds') ??
+        readPositiveInteger(contract.defaults, 'kill_after_seconds') ??
+        5;
 }
 function getMaxOutputBytesLimitDetail(contract, intent) {
     const intentValue = readPositiveInteger(intent, 'max_output_bytes');
@@ -106,7 +108,7 @@ function readRunIntentMetadata(contract, intent) {
         kind: readString(intent, 'kind') ?? null,
         configuredCwd,
         timeoutSeconds: readPositiveInteger(intent, 'timeout_seconds') ?? null,
-        killAfterSeconds: readEffectiveKillAfterSeconds(contract),
+        killAfterSeconds: readEffectiveKillAfterSeconds(contract, intent),
         maxOutputBytes: readEffectiveMaxOutputBytes(contract, intent),
         successExitCodes: getSuccessExitCodes(intent),
         commandArgv,
@@ -284,7 +286,9 @@ export function createRunPreview(plan, previewMode) {
         cwd: plan.relativeCwd,
         resolved_cwd: plan.cwd,
         timeout_seconds: plan.timeoutSeconds,
+        kill_after_seconds: plan.killAfterSeconds,
         max_output_bytes: plan.maxOutputBytes,
+        max_output_bytes_scope: plan.maxOutputBytes === null ? null : COMMAND_OUTPUT_LIMIT_SCOPE,
         mode: plan.mode,
         argv: plan.commandArgv,
         resolved_argv: plan.argvCommand,

package/dist/core/change-classification.js

@@ -46,14 +46,36 @@ function uniqueSorted(values) {
     return [...new Set(values)].sort((left, right) => left.localeCompare(right));
 }
 function toPosixPath(value) {
-    return value.trim().replaceAll('\\', '/');
+    return value.replaceAll('\\', '/');
 }
 export function normalizeStatusPath(value) {
-    const pathText = toPosixPath(value);
+    const pathText = toPosixPath(value.trim());
     const renameTarget = pathText.includes(' -> ') ? (pathText.split(' -> ').pop() ?? pathText) : pathText;
     return renameTarget.replace(/^"|"$/gu, '');
 }
+function normalizePorcelainStatusPath(value) {
+    return toPosixPath(value);
+}
+function parseGitPorcelainStatusOutput(output) {
+    const paths = [];
+    const parts = output.split('\0').filter((part) => part.length > 0);
+    for (let index = 0; index < parts.length; index += 1) {
+        const entry = parts[index] ?? '';
+        const status = entry.slice(0, 2);
+        const filePath = normalizePorcelainStatusPath(entry.slice(3));
+        if (filePath.length > 0) {
+            paths.push(filePath);
+        }
+        if (status.includes('R') || status.includes('C')) {
+            index += 1;
+        }
+    }
+    return uniqueSorted(paths);
+}
 export function parseGitStatusOutput(output) {
+    if (output.includes('\0')) {
+        return parseGitPorcelainStatusOutput(output);
+    }
     const paths = output
         .split(/\r?\n/u)
         .map((line) => line.slice(3))

package/dist/core/check-issues.js

@@ -4,7 +4,7 @@ const CHECK_ISSUE_ID_RULES = [
     ['mustflow.command_contract.configured_missing_lifecycle', /^Configured intent [^\s]+ must define lifecycle$/u],
     ['mustflow.command_contract.configured_missing_run_policy', /^Configured intent [^\s]+ must define run_policy$/u],
     ['mustflow.command_contract.oneshot_missing_timeout', /^Oneshot intent [^\s]+ must define timeout_seconds$/u],
-    ['mustflow.command_contract.max_output_bytes_exceeds_limit', /^\[commands\.(?:defaults|intents\.[^\]]+)\]\.max_output_bytes must be less than or equal to \d+$/u],
+    ['mustflow.command_contract.max_output_bytes_exceeds_limit', /^\[commands\.(?:defaults|intents\.[^\]]+)\]\.max_output_bytes must be less than or equal to \d+ per output stream$/u],
     ['mustflow.command_contract.oneshot_stdin_not_closed', /^Oneshot intent [^\s]+ must set stdin = "closed"$/u],
     ['mustflow.command_contract.long_running_agent_allowed', /^Long-running intent [^\s]+ must not use run_policy = "agent_allowed"$/u],
     ['mustflow.command_contract.executable_source_missing', /^Configured intent [^\s]+ must define argv or mode = "shell" with cmd$/u],

package/dist/core/command-contract-rules.js

@@ -125,6 +125,12 @@ export function commandIntentBlockedCommandPattern(intent) {
             detail: 'Shell command contains a blocked long-running or background pattern.',
         };
     }
+    if (intent.mode === 'shell' && typeof intent.cmd === 'string' && commandTextHasLongRunningPattern(intent.cmd)) {
+        return {
+            code: 'long_running_command_pattern',
+            detail: `Shell command contains a blocked long-running pattern: ${intent.cmd}.`,
+        };
+    }
     const argv = readStringArray(intent, 'argv');
     if (!argv) {
         return null;