@lumenflow/cli 2.15.1 → 2.16.0

package/dist/wu-done.js

@@ -32,7 +32,7 @@
  * Full migration to thin shim pending @lumenflow/core CLI export implementation.
  */
 // WU-2542: Import from @lumenflow/core to establish shim layer dependency
-import { VERSION as LUMENFLOW_VERSION } from '@lumenflow/core';
+import '@lumenflow/core';
 // WU-1153: wu:done guard for uncommitted code_paths is implemented in core package
 // The guard runs in executeWorktreeCompletion() before metadata transaction
 // See: packages/@lumenflow/core/src/wu-done-validation.ts
@@ -40,19 +40,19 @@ import { execSync } from 'node:child_process';
 import prettyMs from 'pretty-ms';
 import { runGates } from './gates.js';
 import { buildClaimRepairCommand } from './wu-claim-repair-guidance.js';
-import { getGitForCwd } from '@lumenflow/core/dist/git-adapter.js';
-import { die } from '@lumenflow/core/dist/error-handler.js';
+import { getGitForCwd, createGitForPath } from '@lumenflow/core/git-adapter';
+import { die } from '@lumenflow/core/error-handler';
 // WU-1223: Location detection for worktree check
-import { resolveLocation } from '@lumenflow/core/dist/context/location-resolver.js';
+import { resolveLocation } from '@lumenflow/core/context/location-resolver';
 import { existsSync, readFileSync, mkdirSync, appendFileSync, unlinkSync, statSync } from 'node:fs';
 import path from 'node:path';
 // WU-1825: Import from unified code-path-validator (consolidates 3 validators)
-import { validateWUCodePaths } from '@lumenflow/core/dist/code-path-validator.js';
+import { validateWUCodePaths } from '@lumenflow/core/code-path-validator';
 // WU-1983: Migration deployment utilities
-import { discoverLocalMigrations, hasMigrationChanges, formatMigrationReport, } from '@lumenflow/core/dist/migration-deployer.js';
-import { validateDocsOnly, getAllowedPathsDescription, } from '@lumenflow/core/dist/docs-path-validator.js';
-import { scanLogForViolations, rotateLog } from '@lumenflow/core/dist/commands-logger.js';
-import { rollbackFiles } from '@lumenflow/core/dist/rollback-utils.js';
+import { discoverLocalMigrations, hasMigrationChanges } from '@lumenflow/core/migration-deployer';
+import { validateDocsOnly, getAllowedPathsDescription } from '@lumenflow/core/docs-path-validator';
+import { scanLogForViolations, rotateLog } from '@lumenflow/core/commands-logger';
+import { rollbackFiles } from '@lumenflow/core/rollback-utils';
 import { validateInputs, detectModeAndPaths, defaultBranchFrom, runCleanup, validateSpecCompleteness, runPreflightTasksValidation, buildPreflightErrorMessage, 
 // WU-1805: Preflight code_paths validation before gates
 executePreflightCodePathValidation, buildPreflightCodePathErrorMessage, 
@@ -61,47 +61,47 @@ validateAllPreCommitHooks,
 // WU-2310: Type vs code_paths preflight validation
 validateTypeVsCodePathsPreflight, buildTypeVsCodePathsErrorMessage, 
 // WU-1503: Dirty-main pre-merge guard
-validateDirtyMain, buildDirtyMainErrorMessage, } from '@lumenflow/core/dist/wu-done-validators.js';
+validateDirtyMain, buildDirtyMainErrorMessage, } from '@lumenflow/core/wu-done-validators';
 // WU-1825: validateCodePathsExist moved to unified code-path-validator
-import { validateCodePathsExist } from '@lumenflow/core/dist/code-path-validator.js';
-import { BRANCHES, REMOTES, PATTERNS, DEFAULTS, LOG_PREFIX, EMOJI, GIT, SESSION, WU_STATUS, WU_EXPOSURE, PKG_MANAGER, SCRIPTS, CLI_FLAGS, FILE_SYSTEM, STDIO, EXIT_CODES, STRING_LITERALS, MICRO_WORKTREE_OPERATIONS, TELEMETRY_STEPS, SKIP_GATES_REASONS, CHECKPOINT_MESSAGES, 
+import { validateCodePathsExist } from '@lumenflow/core/code-path-validator';
+import { BRANCHES, REMOTES, PATTERNS, DEFAULTS, LOG_PREFIX, EMOJI, GIT, SESSION, WU_STATUS, WU_EXPOSURE, PKG_MANAGER, SCRIPTS, CLI_FLAGS, FILE_SYSTEM, EXIT_CODES, STRING_LITERALS, MICRO_WORKTREE_OPERATIONS, TELEMETRY_STEPS, SKIP_GATES_REASONS, CHECKPOINT_MESSAGES, LUMENFLOW_PATHS, 
 // WU-1223: Location types for worktree detection
-CONTEXT_VALIDATION, } from '@lumenflow/core/dist/wu-constants.js';
-import { isDocumentationType } from '@lumenflow/core/dist/wu-type-helpers.js';
-import { printGateFailureBox, printStatusPreview } from '@lumenflow/core/dist/wu-done-ui.js';
-import { ensureOnMain } from '@lumenflow/core/dist/wu-helpers.js';
-import { WU_PATHS, createWuPaths } from '@lumenflow/core/dist/wu-paths.js';
-import { getConfig } from '@lumenflow/core/dist/lumenflow-config.js';
-import { writeWU, appendNote, parseYAML } from '@lumenflow/core/dist/wu-yaml.js';
-import { PLACEHOLDER_SENTINEL, validateWU, validateDoneWU, validateApprovalGates, } from '@lumenflow/core/dist/wu-schema.js';
-import { validateBacklogSync } from '@lumenflow/core/dist/backlog-sync-validator.js';
+CONTEXT_VALIDATION, } from '@lumenflow/core/wu-constants';
+import { isDocumentationType } from '@lumenflow/core/wu-type-helpers';
+import { printGateFailureBox, printStatusPreview } from '@lumenflow/core/wu-done-ui';
+import { ensureOnMain } from '@lumenflow/core/wu-helpers';
+import { WU_PATHS } from '@lumenflow/core/wu-paths';
+import { getConfig } from '@lumenflow/core/config';
+import { writeWU, appendNote, parseYAML } from '@lumenflow/core/wu-yaml';
+import { PLACEHOLDER_SENTINEL, validateWU, validateDoneWU, validateApprovalGates, } from '@lumenflow/core/wu-schema';
+import { validateBacklogSync } from '@lumenflow/core/backlog-sync-validator';
 import { executeBranchOnlyCompletion, 
 // WU-1492: Import branch-pr completion path
-executeBranchPRCompletion, } from '@lumenflow/core/dist/wu-done-branch-only.js';
-import { executeWorktreeCompletion, autoRebaseBranch, } from '@lumenflow/core/dist/wu-done-worktree.js';
-import { checkWUConsistency } from '@lumenflow/core/dist/wu-consistency-checker.js';
+executeBranchPRCompletion, } from '@lumenflow/core/wu-done-branch-only';
+import { executeWorktreeCompletion, autoRebaseBranch } from '@lumenflow/core/wu-done-worktree';
+import { checkWUConsistency } from '@lumenflow/core/wu-consistency-checker';
 // WU-1542: Use blocking mode compliance check (replaces non-blocking checkMandatoryAgentsCompliance)
-import { checkMandatoryAgentsComplianceBlocking } from '@lumenflow/core/dist/orchestration-rules.js';
-import { endSessionForWU } from '@lumenflow/agent/dist/auto-session-integration.js';
-import { runBackgroundProcessCheck } from '@lumenflow/core/dist/process-detector.js';
-import { WUStateStore } from '@lumenflow/core/dist/wu-state-store.js';
+import { checkMandatoryAgentsComplianceBlocking } from '@lumenflow/core/orchestration-rules';
+import { endSessionForWU } from '@lumenflow/agent/auto-session';
+import { runBackgroundProcessCheck } from '@lumenflow/core/process-detector';
+import { WUStateStore } from '@lumenflow/core/wu-state-store';
 // WU-1588: INIT-007 memory layer integration
-import { createCheckpoint } from '@lumenflow/memory/dist/mem-checkpoint-core.js';
-import { createSignal, loadSignals } from '@lumenflow/memory/dist/mem-signal-core.js';
+import { createCheckpoint } from '@lumenflow/memory/checkpoint';
+import { createSignal, loadSignals } from '@lumenflow/memory/signal';
 // WU-1763: Memory store for loading discoveries (lifecycle nudges)
-import { loadMemory, queryByWu } from '@lumenflow/memory/dist/memory-store.js';
+import { loadMemory, queryByWu } from '@lumenflow/memory/store';
 // WU-1943: Checkpoint warning helper
-import { hasSessionCheckpoints } from '@lumenflow/core/dist/wu-done-worktree.js';
+import { hasSessionCheckpoints } from '@lumenflow/core/wu-done-worktree';
 // WU-1603: Atomic lane locking - release lock on WU completion
-import { releaseLaneLock } from '@lumenflow/core/dist/lane-lock.js';
+import { releaseLaneLock } from '@lumenflow/core/lane-lock';
 // WU-1747: Checkpoint and lock for concurrent load resilience
-import { createPreGatesCheckpoint as createWU1747Checkpoint, markGatesPassed, canSkipGates, clearCheckpoint, } from '@lumenflow/core/dist/wu-checkpoint.js';
+import { createPreGatesCheckpoint as createWU1747Checkpoint, markGatesPassed, canSkipGates, clearCheckpoint, } from '@lumenflow/core/wu-checkpoint';
 // WU-1946: Spawn registry for tracking sub-agent spawns
-import { SpawnRegistryStore } from '@lumenflow/core/dist/spawn-registry-store.js';
-import { SpawnStatus } from '@lumenflow/core/dist/spawn-registry-schema.js';
+import { SpawnRegistryStore } from '@lumenflow/core/spawn-registry-store';
+import { SpawnStatus } from '@lumenflow/core/spawn-registry-schema';
 // WU-1999: Exposure validation for UI pairing
 // WU-2022: Feature accessibility validation (blocking)
-import { validateExposure, validateFeatureAccessibility, } from '@lumenflow/core/dist/wu-validation.js';
+import { validateExposure, validateFeatureAccessibility } from '@lumenflow/core/wu-validation';
 import { ensureCleanWorktree } from './wu-done-check.js';
 // WU-1366: Auto cleanup after wu:done success
 // WU-1533: commitCleanupChanges auto-commits dirty state files after cleanup
@@ -120,8 +120,7 @@ const MEMORY_CHECKPOINT_NOTES = {
     PRE_GATES: 'Pre-gates checkpoint for recovery if gates fail',
 };
 const MEMORY_SIGNAL_WINDOW_MS = 60 * 60 * 1000; // 1 hour for recent signals
-// Path constant for wu-events.jsonl (used in multiple places)
-const WU_EVENTS_PATH = '.lumenflow/state/wu-events.jsonl';
+// WU-1539: Use centralized LUMENFLOW_PATHS.WU_EVENTS instead of local constant
 /**
  * WU-1804: Preflight validation for claim metadata before gates.
  *
@@ -146,7 +145,7 @@ async function validateClaimMetadataBeforeGates(id, worktreePath, yamlStatus) {
     // Check 2: State store must show WU as in_progress
     const resolvedWorktreePath = path.resolve(worktreePath);
     const stateDir = path.join(resolvedWorktreePath, '.lumenflow', 'state');
-    const eventsPath = path.join(resolvedWorktreePath, WU_EVENTS_PATH);
+    const eventsPath = path.join(resolvedWorktreePath, LUMENFLOW_PATHS.WU_EVENTS);
     try {
         const store = new WUStateStore(stateDir);
         await store.load();
@@ -273,10 +272,10 @@ export function buildGatesCommand(options) {
     }
     return `${PKG_MANAGER} ${SCRIPTS.GATES}`;
 }
-async function assertWorktreeWUInProgressInStateStore(id, worktreePath) {
+async function _assertWorktreeWUInProgressInStateStore(id, worktreePath) {
     const resolvedWorktreePath = path.resolve(worktreePath);
     const stateDir = path.join(resolvedWorktreePath, '.lumenflow', 'state');
-    const eventsPath = path.join(resolvedWorktreePath, WU_EVENTS_PATH);
+    const eventsPath = path.join(resolvedWorktreePath, LUMENFLOW_PATHS.WU_EVENTS);
     const store = new WUStateStore(stateDir);
     try {
         await store.load();
@@ -475,7 +474,7 @@ export async function isBranchAlreadyMerged(branch) {
 // WU-1281: isDocsOnlyByPaths removed - use shouldSkipWebTests from path-classifiers.ts
 // The validators already use shouldSkipWebTests via detectDocsOnlyByPaths wrapper.
 // Keeping the export for backward compatibility but re-exporting the canonical function.
-export { shouldSkipWebTests as isDocsOnlyByPaths } from '@lumenflow/core/dist/path-classifiers.js';
+export { shouldSkipWebTests as isDocsOnlyByPaths } from '@lumenflow/core/path-classifiers';
 /**
  * WU-1234: Pre-flight check for backlog state consistency
  * Fails fast if the WU appears in both Done and In Progress sections.
@@ -543,7 +542,7 @@ function getCommitHeaderLimit() {
  * Context: WU-635 (multi-agent coordination)
  * See: CLAUDE.md §2.2
  */
-async function ensureCleanWorkingTree() {
+async function _ensureCleanWorkingTree() {
     const status = await getGitForCwd().getStatus();
     if (status.trim()) {
         die(`Working tree is not clean. Cannot proceed with wu:done.\n\n` +
@@ -567,6 +566,17 @@ const INTERNAL_LIFECYCLE_DIRTY_FILES = new Set([
     '.lumenflow/skip-gates-audit.log',
     '.lumenflow/skip-cos-gates-audit.log',
 ]);
+/**
+ * WU-1554: Prefixes for metadata files that wu:done manages.
+ * These files may be dirty after merge+rebase when wu:claim used push-only mode
+ * or when concurrent agents advance origin/main. Instead of blocking wu:done,
+ * these are auto-committed by the caller.
+ */
+const METADATA_LIFECYCLE_PREFIXES = [
+    '.lumenflow/state/',
+    '.lumenflow/stamps/',
+    '.lumenflow/archive/',
+];
 function parsePorcelainPath(line) {
     if (line.length < 4)
         return null;
@@ -579,6 +589,20 @@ function parsePorcelainPath(line) {
     }
     return pathPart;
 }
+/**
+ * WU-1554: Check if a file is a metadata lifecycle file.
+ * Metadata files are managed by wu:done (wu-events.jsonl, status.md, backlog.md,
+ * WU YAML, stamps, archives) and may be dirty after merge+rebase.
+ */
+function isMetadataLifecycleFile(filePath, metadataDir) {
+    if (METADATA_LIFECYCLE_PREFIXES.some((prefix) => filePath.startsWith(prefix))) {
+        return true;
+    }
+    if (metadataDir && filePath.startsWith(metadataDir + '/')) {
+        return true;
+    }
+    return false;
+}
 /**
  * WU-1084: Check for uncommitted changes on main after merge completes.
  *
@@ -586,26 +610,34 @@ function parsePorcelainPath(line) {
  * outside the WU's code_paths during worktree work. These changes survive
  * the merge and would be silently left behind when the worktree is removed.
  *
+ * WU-1554: Added metadataDir parameter and metadataFiles return field.
+ * Metadata files (wu-events.jsonl, status.md, backlog.md, WU YAML, stamps)
+ * may be dirty after merge+rebase when wu:claim used push-only mode.
+ * These are returned separately for auto-commit by the caller.
+ *
  * @param gitStatus - Output from git status (porcelain format)
  * @param wuId - The WU ID for error messaging
- * @returns Object with isDirty flag and optional error message
+ * @param metadataDir - Optional task directory prefix for metadata file detection
+ * @returns Object with isDirty flag, file categories, and optional error message
  */
-export function checkPostMergeDirtyState(gitStatus, wuId) {
+export function checkPostMergeDirtyState(gitStatus, wuId, metadataDir) {
     // WU-1522: Split before trimming to preserve leading spaces in porcelain format.
     // Porcelain lines like ' M .lumenflow/flow.log' use the leading space as a status
     // indicator (working tree vs staging area). Trimming the whole string first strips
     // the leading space from the first line, corrupting parsePorcelainPath output.
     const lines = gitStatus.split('\n').filter((line) => line.length >= 4);
     if (lines.length === 0) {
-        return { isDirty: false, internalOnlyFiles: [], unrelatedFiles: [] };
+        return { isDirty: false, internalOnlyFiles: [], metadataFiles: [], unrelatedFiles: [] };
     }
     const dirtyFiles = lines
         .map((line) => parsePorcelainPath(line))
         .filter((value) => Boolean(value));
+    // WU-1554: Three-category classification
     const internalOnlyFiles = dirtyFiles.filter((file) => INTERNAL_LIFECYCLE_DIRTY_FILES.has(file));
-    const unrelatedFiles = dirtyFiles.filter((file) => !INTERNAL_LIFECYCLE_DIRTY_FILES.has(file));
+    const metadataFiles = dirtyFiles.filter((file) => !INTERNAL_LIFECYCLE_DIRTY_FILES.has(file) && isMetadataLifecycleFile(file, metadataDir));
+    const unrelatedFiles = dirtyFiles.filter((file) => !INTERNAL_LIFECYCLE_DIRTY_FILES.has(file) && !isMetadataLifecycleFile(file, metadataDir));
     if (unrelatedFiles.length === 0) {
-        return { isDirty: false, internalOnlyFiles, unrelatedFiles: [] };
+        return { isDirty: false, internalOnlyFiles, metadataFiles, unrelatedFiles: [] };
     }
     const displayStatus = gitStatus.trim();
     const error = `Main branch has uncommitted changes after merge:\n\n${displayStatus}\n\n` +
@@ -616,7 +648,7 @@ export function checkPostMergeDirtyState(gitStatus, wuId) {
         `  1. Review and commit the changes: git add . && git commit -m "format: fix formatting"\n` +
         `  2. Discard if unwanted: git checkout -- .\n` +
         `  3. Then re-run: pnpm wu:done --id ${wuId} --skip-worktree-completion`;
-    return { isDirty: true, internalOnlyFiles, unrelatedFiles, error };
+    return { isDirty: true, internalOnlyFiles, metadataFiles, unrelatedFiles, error };
 }
 /**
  * Extract completed WU IDs from git log output.
@@ -828,9 +860,10 @@ function runTripwireCheck() {
     rotateLog();
     process.exit(EXIT_CODES.ERROR);
 }
-async function listStaged() {
-    // WU-1235: Use getGitForCwd() to capture current directory (worktree after chdir)
-    const gitCwd = getGitForCwd();
+async function listStaged(gitAdapter) {
+    // WU-1541: Use explicit gitAdapter if provided, otherwise fall back to getGitForCwd()
+    // WU-1235: getGitForCwd() captures current directory (legacy behavior)
+    const gitCwd = gitAdapter ?? getGitForCwd();
     const raw = await gitCwd.raw(['diff', '--cached', '--name-only']);
     return raw ? raw.split(/\r?\n/).filter(Boolean) : [];
 }
@@ -1018,8 +1051,9 @@ async function runGatesInWorktree(worktreePath, id, options = {}) {
         die(`Gates failed in ${worktreePath}. Fix issues in the worktree and try again.`);
     }
 }
-async function validateStagedFiles(id, isDocsOnly = false) {
-    const staged = await listStaged();
+async function validateStagedFiles(id, isDocsOnly = false, gitAdapter, options = {}) {
+    // WU-1541: Accept optional gitAdapter to avoid process.chdir dependency
+    const staged = await listStaged(gitAdapter);
     // WU-1311: Use config-based paths instead of hardcoded docs/04-operations paths
     const config = getConfig();
     const wuPath = `${config.directories.wuDir}/${id}.yaml`;
@@ -1028,8 +1062,10 @@ async function validateStagedFiles(id, isDocsOnly = false) {
         wuPath,
         config.directories.statusPath,
         config.directories.backlogPath,
-        WU_EVENTS_PATH,
+        LUMENFLOW_PATHS.WU_EVENTS,
     ];
+    const metadataAllowlist = (options.metadataAllowlist ?? []).filter((file) => typeof file === 'string' && file.length > 0);
+    const whitelistSet = new Set([...whitelist, ...metadataAllowlist]);
     if (isDocsOnly) {
         // For docs-only WUs, validate that all staged files are in allowed paths
         const docsResult = validateDocsOnly(staged);
@@ -1041,10 +1077,10 @@ async function validateStagedFiles(id, isDocsOnly = false) {
     }
     const unexpected = staged.filter((file) => {
         // Whitelist exact matches
-        if (whitelist.includes(file))
+        if (whitelistSet.has(file))
             return false;
-        // Whitelist .lumenflow/stamps/** pattern
-        if (file.startsWith('.lumenflow/stamps/'))
+        // Whitelist stamps directory pattern
+        if (file.startsWith(`${LUMENFLOW_PATHS.STAMPS_DIR}/`))
             return false;
         // WU-1072: Whitelist apps/docs/**/*.mdx for auto-generated docs from turbo docs:generate
         if (file.startsWith('apps/docs/') && file.endsWith('.mdx'))
@@ -1054,13 +1090,14 @@ async function validateStagedFiles(id, isDocsOnly = false) {
     if (unexpected.length > 0) {
         // WU-1311: Use config-based pattern for WU YAML detection
         const wuDirPattern = config.directories.wuDir.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+        // eslint-disable-next-line security/detect-non-literal-regexp -- config path escaped for regex; not user input
         const wuYamlRegex = new RegExp(`^${wuDirPattern}/WU-\\d+\\.yaml$`);
         const otherWuYamlOnly = unexpected.every((f) => wuYamlRegex.test(f));
         if (otherWuYamlOnly) {
             console.warn(`${LOG_PREFIX.DONE} Warning: other WU YAMLs are staged; proceeding and committing only current WU files.`);
         }
         else {
-            die(`Unexpected files staged (only current WU YAML, status.md, backlog.md, .lumenflow/stamps/<id>.done allowed):\n  ${unexpected.join(`${STRING_LITERALS.NEWLINE}  `)}`);
+            die(`Unexpected files staged (only current WU metadata, current parent initiative YAML, and .lumenflow/stamps/<id>.done allowed):\n  ${unexpected.join(`${STRING_LITERALS.NEWLINE}  `)}`);
         }
     }
 }
@@ -1579,6 +1616,16 @@ async function executePreFlightChecks({ id, args, isBranchOnly, isDocsOnly, docM
                 }
                 else if (dirtyResult.relatedFiles.length > 0) {
                     console.log(`${LOG_PREFIX.DONE} ${EMOJI.INFO} WU-1503: ${dirtyResult.relatedFiles.length} related dirty file(s) on main (allowed)`);
+                    // WU-1554: Auto-restore related dirty files so ff-only merge can proceed.
+                    // These files will be overwritten by the merge commit anyway.
+                    // Without this, git merge --ff-only refuses to overwrite dirty tracked files.
+                    try {
+                        await gitAdapter.raw(['checkout', '--', ...dirtyResult.relatedFiles]);
+                        console.log(`${LOG_PREFIX.DONE} ${EMOJI.INFO} WU-1554: Auto-restored ${dirtyResult.relatedFiles.length} related file(s) for clean merge`);
+                    }
+                    catch (restoreErr) {
+                        console.warn(`${LOG_PREFIX.DONE} ${EMOJI.WARNING} WU-1554: Could not auto-restore related files: ${restoreErr.message}`);
+                    }
                 }
             }
         }
@@ -1589,7 +1636,7 @@ async function executePreFlightChecks({ id, args, isBranchOnly, isDocsOnly, docM
         // which causes the auto-rebase to fail with "You have unstaged changes"
         if (derivedWorktree) {
             try {
-                execSync(`git -C "${derivedWorktree}" restore "${WU_EVENTS_PATH}"`);
+                execSync(`git -C "${derivedWorktree}" restore "${LUMENFLOW_PATHS.WU_EVENTS}"`);
             }
             catch {
                 // Non-fatal: file might not exist or already clean
@@ -1812,7 +1859,7 @@ async function executeGates({ id, args, isBranchOnly, isDocsOnly, worktreePath,
     // This restores the file to HEAD state - checkpoint data is preserved in memory store
     if (worktreePath) {
         try {
-            execSync(`git -C "${worktreePath}" restore "${WU_EVENTS_PATH}"`);
+            execSync(`git -C "${worktreePath}" restore "${LUMENFLOW_PATHS.WU_EVENTS}"`);
         }
         catch {
             // Non-fatal: file might not exist or already clean
@@ -1825,7 +1872,7 @@ async function executeGates({ id, args, isBranchOnly, isDocsOnly, worktreePath,
     const invariantsBaseDir = worktreePath || process.cwd();
     console.log(`\n${LOG_PREFIX.DONE} Running invariants check (non-bypassable)...`);
     console.log(`${LOG_PREFIX.DONE} Checking invariants in: ${invariantsBaseDir}`);
-    const { runInvariants } = await import('@lumenflow/core/dist/invariants-runner.js');
+    const { runInvariants } = await import('@lumenflow/core/invariants-runner');
     const invariantsResult = runInvariants({ baseDir: invariantsBaseDir, silent: false, wuId: id });
     if (!invariantsResult.success) {
         emitTelemetry({
@@ -2175,9 +2222,12 @@ async function main() {
             else {
                 // Worktree mode: update in worktree, commit, then merge or create PR
                 // WU-1369: Uses atomic transaction pattern
+                // WU-1541: Create worktree-aware validateStagedFiles to avoid process.chdir dependency
+                const worktreeGitForValidation = createGitForPath(worktreePath);
                 const worktreeContext = {
                     ...baseContext,
                     worktreePath,
+                    validateStagedFiles: (wuId, docsOnly, options) => validateStagedFiles(wuId, docsOnly, worktreeGitForValidation, options),
                 };
                 completionResult = await executeWorktreeCompletion(worktreeContext);
             }
@@ -2219,9 +2269,10 @@ async function main() {
         await ensureNoAutoStagedOrNoop([WU_PATH, STATUS_PATH, BACKLOG_PATH, STAMPS_DIR]);
     }
     // WU-1084: Check for uncommitted changes on main after merge
-    // This catches cases where pnpm format touched files outside code_paths
+    // WU-1554: Pass metadataDir so metadata files are classified separately
+    const metadataDir = path.dirname(STATUS_PATH);
     const postMergeStatus = await getGitForCwd().getStatus();
-    const dirtyCheck = checkPostMergeDirtyState(postMergeStatus, id);
+    const dirtyCheck = checkPostMergeDirtyState(postMergeStatus, id, metadataDir);
     if (dirtyCheck.internalOnlyFiles.length > 0) {
         const gitMain = getGitForCwd();
         try {
@@ -2232,6 +2283,21 @@ async function main() {
             console.warn(`${LOG_PREFIX.DONE} ${EMOJI.WARNING} Could not auto-restore internal lifecycle files: ${restoreErr.message}`);
         }
     }
+    // WU-1554: Auto-commit metadata files left dirty after merge+rebase
+    // This handles push-only claim mode and concurrent agent advancement
+    if (dirtyCheck.metadataFiles.length > 0) {
+        const gitMain = getGitForCwd();
+        try {
+            await gitMain.add(dirtyCheck.metadataFiles);
+            await gitMain.commit(`chore: post-merge metadata sync for ${id} [skip ci]`);
+            await gitMain.raw(['pull', '--rebase', '--autostash', 'origin', 'main']);
+            await gitMain.push('origin', 'main');
+            console.log(`${LOG_PREFIX.DONE} ${EMOJI.SUCCESS} Auto-committed post-merge metadata: ${dirtyCheck.metadataFiles.join(', ')}`);
+        }
+        catch (commitErr) {
+            console.warn(`${LOG_PREFIX.DONE} ${EMOJI.WARNING} Could not auto-commit metadata files: ${commitErr.message}`);
+        }
+    }
     if (dirtyCheck.isDirty) {
         die(dirtyCheck.error);
     }
@@ -2454,6 +2520,6 @@ async function detectChangedDocPaths(worktreePath, baseBranch) {
 // path but import.meta.url resolves to the real path - they never match
 import { runCLI } from './cli-entry-point.js';
 if (import.meta.main) {
-    runCLI(main);
+    void runCLI(main);
 }
 //# sourceMappingURL=wu-done.js.map