@lumenflow/cli 2.13.0 → 2.14.0

package/dist/wu-delete.js

@@ -9,25 +9,30 @@
  * 2) Ensure main is clean and up-to-date with origin
  * 3) Create temp branch WITHOUT switching (main checkout stays on main)
  * 4) Create micro-worktree in /tmp pointing to temp branch
- * 5) Delete WU file and update backlog.md in micro-worktree
+ * 5) Delete WU artifacts and clean references in micro-worktree
  * 6) Commit, ff-only merge, push
  * 7) Cleanup temp branch and micro-worktree
  *
  * Usage:
- *   pnpm wu:delete --id WU-123           # Single WU deletion
- *   pnpm wu:delete --id WU-123 --dry-run # Dry run
+ *   pnpm wu:delete --id WU-123            # Single WU deletion
+ *   pnpm wu:delete --id WU-123 --dry-run  # Dry run
  *   pnpm wu:delete --batch WU-1,WU-2,WU-3 # Batch deletion
  */
 import { existsSync, readFileSync, writeFileSync, unlinkSync, readdirSync } from 'node:fs';
 import { join } from 'node:path';
 import { getGitForCwd } from '@lumenflow/core/dist/git-adapter.js';
 import { die } from '@lumenflow/core/dist/error-handler.js';
-import { parseYAML, stringifyYAML } from '@lumenflow/core/dist/wu-yaml.js';
+import { parseYAML } from '@lumenflow/core/dist/wu-yaml.js';
 import { createWUParser, WU_OPTIONS } from '@lumenflow/core/dist/arg-parser.js';
 import { WU_PATHS } from '@lumenflow/core/dist/wu-paths.js';
-import { FILE_SYSTEM, EXIT_CODES, MICRO_WORKTREE_OPERATIONS, LOG_PREFIX, WU_STATUS, } from '@lumenflow/core/dist/wu-constants.js';
+import { generateBacklog, generateStatus } from '@lumenflow/core/dist/backlog-generator.js';
+import { WUStateStore } from '@lumenflow/core/dist/wu-state-store.js';
+import { FILE_SYSTEM, EXIT_CODES, MICRO_WORKTREE_OPERATIONS, LOG_PREFIX, WU_STATUS, LUMENFLOW_PATHS, } from '@lumenflow/core/dist/wu-constants.js';
 import { ensureOnMain, ensureMainUpToDate, validateWUIDFormat, } from '@lumenflow/core/dist/wu-helpers.js';
 import { withMicroWorktree } from '@lumenflow/core/dist/micro-worktree.js';
+import { INIT_PATHS } from '@lumenflow/initiatives/dist/initiative-paths.js';
+import { INIT_PATTERNS } from '@lumenflow/initiatives/dist/initiative-constants.js';
+import { readInitiative, writeInitiative } from '@lumenflow/initiatives/dist/initiative-yaml.js';
 const PREFIX = LOG_PREFIX.DELETE || '[wu:delete]';
 const DELETE_OPTIONS = {
     dryRun: {
@@ -83,21 +88,173 @@ function getStampPath(id) {
 function stampExists(id) {
     return existsSync(getStampPath(id));
 }
-function removeFromBacklog(backlogPath, id) {
-    if (!existsSync(backlogPath)) {
+function removeEventsForDeletedWUs(eventsPath, ids) {
+    if (!existsSync(eventsPath)) {
         return false;
     }
-    const content = readFileSync(backlogPath, FILE_SYSTEM.ENCODING);
-    const wuLinkPattern = new RegExp(`^.*\\[${id}[^\\]]*\\].*$`, 'gmi');
-    const wuSimplePattern = new RegExp(`^.*${id}.*\\.yaml.*$`, 'gmi');
-    let updated = content.replace(wuLinkPattern, '');
-    updated = updated.replace(wuSimplePattern, '');
-    updated = updated.replace(/\n{3,}/g, '\n\n');
-    if (updated !== content) {
-        writeFileSync(backlogPath, updated, FILE_SYSTEM.ENCODING);
-        return true;
+    const content = readFileSync(eventsPath, FILE_SYSTEM.ENCODING);
+    const lines = content.split('\n');
+    let changed = false;
+    const retained = [];
+    for (const line of lines) {
+        if (!line.trim()) {
+            continue;
+        }
+        try {
+            const event = JSON.parse(line);
+            if (event.wuId && ids.has(event.wuId.toUpperCase())) {
+                changed = true;
+                continue;
+            }
+            retained.push(line);
+        }
+        catch {
+            // Preserve malformed lines to avoid destructive cleanup of unrelated data
+            retained.push(line);
+        }
+    }
+    if (!changed) {
+        return false;
+    }
+    const next = retained.length > 0 ? `${retained.join('\n')}\n` : '';
+    writeFileSync(eventsPath, next, FILE_SYSTEM.ENCODING);
+    return true;
+}
+function getExistingWuIds(worktreePath) {
+    const wuIds = new Set();
+    const wuDir = join(worktreePath, WU_PATHS.WU_DIR());
+    if (!existsSync(wuDir)) {
+        return wuIds;
+    }
+    for (const file of readdirSync(wuDir)) {
+        if (!file.endsWith('.yaml')) {
+            continue;
+        }
+        const id = file.slice(0, -'.yaml'.length).toUpperCase();
+        if (id.startsWith('WU-')) {
+            wuIds.add(id);
+        }
+    }
+    return wuIds;
+}
+function removeOrphanedEvents(eventsPath, existingWuIds) {
+    if (!existsSync(eventsPath)) {
+        return 0;
+    }
+    const content = readFileSync(eventsPath, FILE_SYSTEM.ENCODING);
+    const lines = content.split('\n');
+    let removed = 0;
+    const retained = [];
+    for (const line of lines) {
+        if (!line.trim()) {
+            continue;
+        }
+        try {
+            const event = JSON.parse(line);
+            if (event.wuId && !existingWuIds.has(event.wuId.toUpperCase())) {
+                removed++;
+                continue;
+            }
+            retained.push(line);
+        }
+        catch {
+            // Preserve malformed lines to avoid destructive cleanup of unrelated data
+            retained.push(line);
+        }
+    }
+    if (removed === 0) {
+        return 0;
     }
-    return false;
+    const next = retained.length > 0 ? `${retained.join('\n')}\n` : '';
+    writeFileSync(eventsPath, next, FILE_SYSTEM.ENCODING);
+    return removed;
+}
+function removeDeletedWUsFromInitiatives(worktreePath, ids) {
+    const modified = [];
+    const initiativesDir = join(worktreePath, INIT_PATHS.INITIATIVES_DIR());
+    if (!existsSync(initiativesDir)) {
+        return modified;
+    }
+    const initiativeFiles = readdirSync(initiativesDir).filter((file) => file.endsWith('.yaml'));
+    for (const fileName of initiativeFiles) {
+        const initId = fileName.replace(/\.yaml$/, '');
+        if (!INIT_PATTERNS.INIT_ID.test(initId)) {
+            continue;
+        }
+        const initiativePath = join(initiativesDir, fileName);
+        try {
+            const initDoc = readInitiative(initiativePath, initId);
+            if (!Array.isArray(initDoc.wus)) {
+                continue;
+            }
+            const before = initDoc.wus.length;
+            initDoc.wus = initDoc.wus.filter((wuId) => !ids.has(String(wuId).toUpperCase()));
+            if (initDoc.wus.length === before) {
+                continue;
+            }
+            writeInitiative(initiativePath, { ...initDoc, id: initDoc.id || initId });
+            modified.push(INIT_PATHS.INITIATIVE(initId));
+        }
+        catch (err) {
+            // Non-blocking: malformed initiative files should not block WU delete operation
+            console.warn(`${PREFIX} ⚠️  Could not update initiative ${initId}: ${err.message}`);
+        }
+    }
+    return modified;
+}
+export async function cleanupDeletedWUsInWorktree({ worktreePath, ids }) {
+    const normalizedIds = new Set(ids.map((id) => id.toUpperCase()));
+    const modified = new Set();
+    for (const id of normalizedIds) {
+        const wuRelPath = WU_PATHS.WU(id);
+        const wuAbsPath = join(worktreePath, wuRelPath);
+        if (existsSync(wuAbsPath)) {
+            unlinkSync(wuAbsPath);
+            modified.add(wuRelPath);
+            console.log(`${PREFIX} ✅ Deleted ${id}.yaml`);
+        }
+        const stampRelPath = getStampPath(id);
+        const stampAbsPath = join(worktreePath, stampRelPath);
+        if (existsSync(stampAbsPath)) {
+            unlinkSync(stampAbsPath);
+            modified.add(stampRelPath);
+            console.log(`${PREFIX} ✅ Deleted stamp ${id}.done`);
+        }
+    }
+    const eventsRelPath = LUMENFLOW_PATHS.WU_EVENTS;
+    const eventsAbsPath = join(worktreePath, eventsRelPath);
+    if (removeEventsForDeletedWUs(eventsAbsPath, normalizedIds)) {
+        modified.add(eventsRelPath);
+        console.log(`${PREFIX} ✅ Removed ${normalizedIds.size} WU event stream(s) from wu-events.jsonl`);
+    }
+    const existingWuIds = getExistingWuIds(worktreePath);
+    const orphanedRemoved = removeOrphanedEvents(eventsAbsPath, existingWuIds);
+    if (orphanedRemoved > 0) {
+        modified.add(eventsRelPath);
+        console.log(`${PREFIX} ✅ Removed ${orphanedRemoved} orphaned event(s) for missing WU specs`);
+    }
+    const initiativeFiles = removeDeletedWUsFromInitiatives(worktreePath, normalizedIds);
+    for (const file of initiativeFiles) {
+        modified.add(file);
+    }
+    if (initiativeFiles.length > 0) {
+        console.log(`${PREFIX} ✅ Removed deleted WU references from ${initiativeFiles.length} initiative file(s)`);
+    }
+    const stateDir = join(worktreePath, '.lumenflow', 'state');
+    const store = new WUStateStore(stateDir);
+    await store.load();
+    const backlogRelPath = WU_PATHS.BACKLOG();
+    const statusRelPath = WU_PATHS.STATUS();
+    const backlogAbsPath = join(worktreePath, backlogRelPath);
+    const statusAbsPath = join(worktreePath, statusRelPath);
+    const backlogContent = await generateBacklog(store);
+    writeFileSync(backlogAbsPath, backlogContent, FILE_SYSTEM.ENCODING);
+    modified.add(backlogRelPath);
+    const statusContent = await generateStatus(store);
+    writeFileSync(statusAbsPath, statusContent, FILE_SYSTEM.ENCODING);
+    modified.add(statusRelPath);
+    console.log(`${PREFIX} ✅ Regenerated backlog.md and status.md from state store`);
+    return Array.from(modified);
 }
 async function deleteSingleWU(id, dryRun) {
     console.log(`${PREFIX} Starting WU delete for ${id}`);
@@ -111,7 +268,10 @@ async function deleteSingleWU(id, dryRun) {
     if (dryRun) {
         console.log(`\n${PREFIX} 🔍 DRY RUN: Would delete ${id}`);
         console.log(`${PREFIX}   - Delete file: ${wuPath}`);
-        console.log(`${PREFIX}   - Update: ${WU_PATHS.BACKLOG()}`);
+        console.log(`${PREFIX}   - Delete events from: ${LUMENFLOW_PATHS.WU_EVENTS}`);
+        console.log(`${PREFIX}   - Regenerate: ${WU_PATHS.BACKLOG()}`);
+        console.log(`${PREFIX}   - Regenerate: ${WU_PATHS.STATUS()}`);
+        console.log(`${PREFIX}   - Remove initiative links from: ${INIT_PATHS.INITIATIVES_DIR()}`);
         if (stampExists(id)) {
             console.log(`${PREFIX}   - Delete stamp: ${getStampPath(id)}`);
         }
@@ -131,27 +291,12 @@ async function deleteSingleWU(id, dryRun) {
             id: id,
             logPrefix: PREFIX,
             execute: async ({ worktreePath, gitWorktree }) => {
-                const wuFilePath = join(worktreePath, wuPath);
-                const backlogFilePath = join(worktreePath, WU_PATHS.BACKLOG());
-                unlinkSync(wuFilePath);
-                console.log(`${PREFIX} ✅ Deleted ${id}.yaml`);
-                const stampPath = join(worktreePath, getStampPath(id));
-                if (existsSync(stampPath)) {
-                    unlinkSync(stampPath);
-                    console.log(`${PREFIX} ✅ Deleted stamp ${id}.done`);
-                }
-                const removedFromBacklog = removeFromBacklog(backlogFilePath, id);
-                if (removedFromBacklog) {
-                    console.log(`${PREFIX} ✅ Removed ${id} from backlog.md`);
-                }
-                else {
-                    console.log(`${PREFIX} ℹ️  ${id} was not found in backlog.md`);
-                }
+                const files = await cleanupDeletedWUsInWorktree({ worktreePath, ids: [id] });
                 await gitWorktree.add('.');
                 const commitMessage = `docs: delete ${id.toLowerCase()}`;
                 return {
                     commitMessage,
-                    files: [],
+                    files,
                 };
             },
         });
@@ -186,6 +331,13 @@ async function deleteBatchWUs(ids, dryRun) {
     }
     if (dryRun) {
         console.log(`\n${PREFIX} 🔍 DRY RUN: Would delete ${ids.length} WU(s)`);
+        console.log(`${PREFIX}   - Delete events from: ${LUMENFLOW_PATHS.WU_EVENTS}`);
+        console.log(`${PREFIX}   - Regenerate: ${WU_PATHS.BACKLOG()}`);
+        console.log(`${PREFIX}   - Regenerate: ${WU_PATHS.STATUS()}`);
+        console.log(`${PREFIX}   - Remove initiative links from: ${INIT_PATHS.INITIATIVES_DIR()}`);
+        if (stampsToDelete.length > 0) {
+            console.log(`${PREFIX}   - Delete ${stampsToDelete.length} stamp(s)`);
+        }
         console.log(`${PREFIX} No changes made.`);
         process.exit(EXIT_CODES.SUCCESS);
     }
@@ -202,31 +354,13 @@ async function deleteBatchWUs(ids, dryRun) {
             id: `batch-${ids.length}`,
             logPrefix: PREFIX,
             execute: async ({ worktreePath, gitWorktree }) => {
-                const backlogFilePath = join(worktreePath, WU_PATHS.BACKLOG());
-                for (const { id, wuPath } of wusToDelete) {
-                    const wuFilePath = join(worktreePath, wuPath);
-                    unlinkSync(wuFilePath);
-                    console.log(`${PREFIX} ✅ Deleted ${id}.yaml`);
-                }
-                for (const id of stampsToDelete) {
-                    const stampPath = join(worktreePath, getStampPath(id));
-                    if (existsSync(stampPath)) {
-                        unlinkSync(stampPath);
-                        console.log(`${PREFIX} ✅ Deleted stamp ${id}.done`);
-                    }
-                }
-                for (const { id } of wusToDelete) {
-                    const removed = removeFromBacklog(backlogFilePath, id);
-                    if (removed) {
-                        console.log(`${PREFIX} ✅ Removed ${id} from backlog.md`);
-                    }
-                }
+                const files = await cleanupDeletedWUsInWorktree({ worktreePath, ids });
                 await gitWorktree.add('.');
                 const idList = ids.map((id) => id.toLowerCase()).join(', ');
                 const commitMessage = `chore(repair): delete ${ids.length} orphaned wus (${idList})`;
                 return {
                     commitMessage,
-                    files: [],
+                    files,
                 };
             },
         });
@@ -243,7 +377,7 @@ async function deleteBatchWUs(ids, dryRun) {
     console.log(`${PREFIX} ✅ Successfully deleted ${ids.length} WU(s)`);
     console.log(`${PREFIX} Changes pushed to origin/main`);
 }
-async function main() {
+export async function main() {
     const opts = parseArgs();
     const { id, dryRun, batch } = opts;
     if (!id && !batch) {
@@ -263,8 +397,10 @@ async function main() {
         await deleteSingleWU(id, dryRun);
     }
 }
-main().catch((err) => {
-    console.error(`${PREFIX} ❌ ${err.message}`);
-    process.exit(EXIT_CODES.ERROR);
-});
+if (import.meta.main) {
+    void main().catch((err) => {
+        console.error(`${PREFIX} ❌ ${err.message}`);
+        process.exit(EXIT_CODES.ERROR);
+    });
+}
 //# sourceMappingURL=wu-delete.js.map

package/dist/wu-delete.js.map

@@ -1 +1 @@
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package/dist/wu-done.js

@@ -59,7 +59,9 @@ executePreflightCodePathValidation, buildPreflightCodePathErrorMessage,
 // WU-2308: Pre-commit hooks with worktree context
 validateAllPreCommitHooks, 
 // WU-2310: Type vs code_paths preflight validation
-validateTypeVsCodePathsPreflight, buildTypeVsCodePathsErrorMessage, } from '@lumenflow/core/dist/wu-done-validators.js';
+validateTypeVsCodePathsPreflight, buildTypeVsCodePathsErrorMessage, 
+// WU-1503: Dirty-main pre-merge guard
+validateDirtyMain, buildDirtyMainErrorMessage, } from '@lumenflow/core/dist/wu-done-validators.js';
 // 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, 
@@ -559,6 +561,23 @@ async function ensureCleanWorkingTree() {
             `  - Leftover changes from previous session`);
     }
 }
+const INTERNAL_LIFECYCLE_DIRTY_FILES = new Set([
+    '.lumenflow/flow.log',
+    '.lumenflow/skip-gates-audit.log',
+    '.lumenflow/skip-cos-gates-audit.log',
+]);
+function parsePorcelainPath(line) {
+    if (line.length < 4)
+        return null;
+    const pathPart = line.slice(3).trim();
+    if (!pathPart)
+        return null;
+    const renameIndex = pathPart.indexOf(' -> ');
+    if (renameIndex !== -1) {
+        return pathPart.slice(renameIndex + 4);
+    }
+    return pathPart;
+}
 /**
  * WU-1084: Check for uncommitted changes on main after merge completes.
  *
@@ -571,11 +590,24 @@ async function ensureCleanWorkingTree() {
  * @returns Object with isDirty flag and optional error message
  */
 export function checkPostMergeDirtyState(gitStatus, wuId) {
-    const trimmedStatus = gitStatus.trim();
-    if (!trimmedStatus) {
-        return { isDirty: false };
-    }
-    const error = `Main branch has uncommitted changes after merge:\n\n${trimmedStatus}\n\n` +
+    // WU-1522: Split before trimming to preserve leading spaces in porcelain format.
+    // Porcelain lines like ' M .lumenflow/flow.log' use the leading space as a status
+    // indicator (working tree vs staging area). Trimming the whole string first strips
+    // the leading space from the first line, corrupting parsePorcelainPath output.
+    const lines = gitStatus.split('\n').filter((line) => line.length >= 4);
+    if (lines.length === 0) {
+        return { isDirty: false, internalOnlyFiles: [], unrelatedFiles: [] };
+    }
+    const dirtyFiles = lines
+        .map((line) => parsePorcelainPath(line))
+        .filter((value) => Boolean(value));
+    const internalOnlyFiles = dirtyFiles.filter((file) => INTERNAL_LIFECYCLE_DIRTY_FILES.has(file));
+    const unrelatedFiles = dirtyFiles.filter((file) => !INTERNAL_LIFECYCLE_DIRTY_FILES.has(file));
+    if (unrelatedFiles.length === 0) {
+        return { isDirty: false, internalOnlyFiles, unrelatedFiles: [] };
+    }
+    const displayStatus = gitStatus.trim();
+    const error = `Main branch has uncommitted changes after merge:\n\n${displayStatus}\n\n` +
         `This indicates files were modified outside the WU's code_paths.\n` +
         `Common cause: pnpm format touched files outside the WU scope.\n\n` +
         `The worktree has NOT been removed to allow investigation.\n\n` +
@@ -583,7 +615,7 @@ 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 ${wuId} --skip-worktree-completion`;
-    return { isDirty: true, error };
+    return { isDirty: true, internalOnlyFiles, unrelatedFiles, error };
 }
 /**
  * Extract completed WU IDs from git log output.
@@ -827,7 +859,8 @@ export function emitTelemetry(event) {
     appendFileSync(logPath, `${line}\n`, { encoding: FILE_SYSTEM.UTF8 });
 }
 async function auditSkipGates(id, reason, fixWU, worktreePath) {
-    const auditPath = path.join('.lumenflow', 'skip-gates-audit.log');
+    const auditBaseDir = worktreePath || process.cwd();
+    const auditPath = path.join(auditBaseDir, '.lumenflow', 'skip-gates-audit.log');
     const auditDir = path.dirname(auditPath);
     if (!existsSync(auditDir))
         mkdirSync(auditDir, { recursive: true });
@@ -846,13 +879,14 @@ async function auditSkipGates(id, reason, fixWU, worktreePath) {
     };
     const line = JSON.stringify(entry);
     appendFileSync(auditPath, `${line}\n`, { encoding: FILE_SYSTEM.UTF8 });
-    console.log(`${LOG_PREFIX.DONE} ${EMOJI.MEMO} Skip-gates event logged to ${auditPath}`);
+    console.log(`${LOG_PREFIX.DONE} ${EMOJI.MEMO} Skip-gates event logged to ${path.relative(process.cwd(), auditPath) || auditPath}`);
 }
 /**
  * Audit trail for --skip-cos-gates (COS v1.3 §7)
  */
-async function auditSkipCosGates(id, reason) {
-    const auditPath = path.join('.lumenflow', 'skip-cos-gates-audit.log');
+async function auditSkipCosGates(id, reason, worktreePath) {
+    const auditBaseDir = worktreePath || process.cwd();
+    const auditPath = path.join(auditBaseDir, '.lumenflow', 'skip-cos-gates-audit.log');
     const auditDir = path.dirname(auditPath);
     if (!existsSync(auditDir))
         mkdirSync(auditDir, { recursive: true });
@@ -1521,8 +1555,32 @@ async function executePreFlightChecks({ id, args, isBranchOnly, isDocsOnly, docM
     else {
         // Worktree mode: must be on main
         await ensureOnMain(getGitForCwd());
-        // Prevent multi-agent data loss by ensuring clean working tree
-        await ensureCleanWorkingTree();
+        // WU-1503: Dirty-main pre-merge guard (replaces blanket ensureCleanWorkingTree)
+        // Distinguishes between WU-related dirty files (allowed) and unrelated dirty
+        // files (blocked with actionable guidance). Uses --force for audited bypass.
+        {
+            const gitAdapter = getGitForCwd();
+            const gitStatus = await gitAdapter.raw(['status', '--porcelain']);
+            if (gitStatus && gitStatus.trim()) {
+                const wuCodePaths = docForValidation.code_paths || [];
+                const dirtyResult = validateDirtyMain(gitStatus, id, wuCodePaths);
+                if (!dirtyResult.valid) {
+                    if (args.force) {
+                        console.log(`\n${LOG_PREFIX.DONE} ${EMOJI.WARNING} WU-1503: Dirty-main guard bypassed with --force`);
+                        console.log(`${LOG_PREFIX.DONE} Unrelated dirty files (${dirtyResult.unrelatedFiles.length}):`);
+                        for (const f of dirtyResult.unrelatedFiles) {
+                            console.log(`${LOG_PREFIX.DONE}   - ${f}`);
+                        }
+                    }
+                    else {
+                        die(buildDirtyMainErrorMessage(id, dirtyResult.unrelatedFiles));
+                    }
+                }
+                else if (dirtyResult.relatedFiles.length > 0) {
+                    console.log(`${LOG_PREFIX.DONE} ${EMOJI.INFO} WU-1503: ${dirtyResult.relatedFiles.length} related dirty file(s) on main (allowed)`);
+                }
+            }
+        }
         // Prevent coordination failures by ensuring main is up-to-date
         await ensureMainUpToDate();
         // P0 EMERGENCY FIX Part 1: Restore wu-events.jsonl BEFORE parallel completion check
@@ -1901,7 +1959,7 @@ async function executeGates({ id, args, isBranchOnly, isDocsOnly, worktreePath,
     else {
         console.log(`\n${LOG_PREFIX.DONE} ${EMOJI.WARNING} Skipping COS governance gates as requested`);
         console.log(`${LOG_PREFIX.DONE} Reason: ${args.reason || DEFAULT_NO_REASON}`);
-        await auditSkipCosGates(id, args.reason);
+        await auditSkipCosGates(id, args.reason, worktreePath);
         emitTelemetry({
             script: 'wu-done',
             wu_id: id,
@@ -2163,6 +2221,16 @@ async function main() {
     // This catches cases where pnpm format touched files outside code_paths
     const postMergeStatus = await getGitForCwd().getStatus();
     const dirtyCheck = checkPostMergeDirtyState(postMergeStatus, id);
+    if (dirtyCheck.internalOnlyFiles.length > 0) {
+        const gitMain = getGitForCwd();
+        try {
+            await gitMain.raw(['restore', '--', ...dirtyCheck.internalOnlyFiles]);
+            console.log(`${LOG_PREFIX.DONE} ${EMOJI.INFO} Restored internal lifecycle log files: ${dirtyCheck.internalOnlyFiles.join(', ')}`);
+        }
+        catch (restoreErr) {
+            console.warn(`${LOG_PREFIX.DONE} ${EMOJI.WARNING} Could not auto-restore internal lifecycle files: ${restoreErr.message}`);
+        }
+    }
     if (dirtyCheck.isDirty) {
         die(dirtyCheck.error);
     }