diff --git a/src/resources/extensions/gsd/auto-recovery.ts b/src/resources/extensions/gsd/auto-recovery.ts
index 40a6df7e7..f3124a2da 100644
--- a/src/resources/extensions/gsd/auto-recovery.ts
+++ b/src/resources/extensions/gsd/auto-recovery.ts
@@ -96,13 +96,13 @@ export function resolveExpectedArtifactPath(unitType: string, unitId: string, ba
  * skipped writing the UAT file (see #176).
  */
 export function verifyExpectedArtifact(unitType: string, unitId: string, base: string): boolean {
-  // Clear stale directory listing cache so artifact checks see fresh disk state (#431)
-  clearPathCache();
-
   // Hook units have no standard artifact — always pass. Their lifecycle
   // is managed by the hook engine, not the artifact verification system.
   if (unitType.startsWith("hook/")) return true;
 
+  // Clear stale directory listing cache so artifact checks see fresh disk state (#431).
+  // Moved after hook check to avoid unnecessary cache clears for hook units.
+  clearPathCache();
 
   if (unitType === "rewrite-docs") {
     const overridesPath = resolveGsdRootFile(base, "OVERRIDES");
@@ -296,7 +296,8 @@ export function persistCompletedKey(base: string, key: string): void {
       keys = JSON.parse(readFileSync(file, "utf-8"));
     }
   } catch (e) { /* corrupt file — start fresh */ void e; }
-  if (!keys.includes(key)) {
+  const keySet = new Set(keys);
+  if (!keySet.has(key)) {
     keys.push(key);
     // Atomic write: tmp file + rename prevents partial writes on crash
     const tmpFile = file + ".tmp";
@@ -310,12 +311,15 @@ export function removePersistedKey(base: string, key: string): void {
   const file = completedKeysPath(base);
   try {
     if (existsSync(file)) {
-      let keys: string[] = JSON.parse(readFileSync(file, "utf-8"));
-      keys = keys.filter(k => k !== key);
-      // Atomic write: tmp file + rename prevents partial writes on crash
-      const tmpFile = file + ".tmp";
-      writeFileSync(tmpFile, JSON.stringify(keys), "utf-8");
-      renameSync(tmpFile, file);
+      const keys: string[] = JSON.parse(readFileSync(file, "utf-8"));
+      const filtered = keys.filter(k => k !== key);
+      // Only write if the key was actually present
+      if (filtered.length !== keys.length) {
+        // Atomic write: tmp file + rename prevents partial writes on crash
+        const tmpFile = file + ".tmp";
+        writeFileSync(tmpFile, JSON.stringify(filtered), "utf-8");
+        renameSync(tmpFile, file);
+      }
     }
   } catch (e) { /* non-fatal: removePersistedKey failure */ void e; }
 }
@@ -360,8 +364,11 @@ export function reconcileMergeState(basePath: string, ctx: ExtensionContext): bo
   } else {
     // Still conflicted — try auto-resolving .gsd/ state file conflicts (#530)
     const conflictedFiles = unmerged.trim().split("\n").filter(Boolean);
-    const gsdConflicts = conflictedFiles.filter(f => f.startsWith(".gsd/"));
-    const codeConflicts = conflictedFiles.filter(f => !f.startsWith(".gsd/"));
+    const gsdConflicts: string[] = [];
+    const codeConflicts: string[] = [];
+    for (const f of conflictedFiles) {
+      (f.startsWith(".gsd/") ? gsdConflicts : codeConflicts).push(f);
+    }
 
     if (gsdConflicts.length > 0 && codeConflicts.length === 0) {
       // All conflicts are in .gsd/ state files — auto-resolve by accepting theirs
diff --git a/src/resources/extensions/gsd/guided-flow.ts b/src/resources/extensions/gsd/guided-flow.ts
index 6bc822ea7..198c8f7b3 100644
--- a/src/resources/extensions/gsd/guided-flow.ts
+++ b/src/resources/extensions/gsd/guided-flow.ts
@@ -132,6 +132,7 @@ export function checkAutoStartAfterDiscuss(): boolean {
 
   pendingAutoStart = null;
   startAuto(ctx, pi, basePath, false, { step }).catch((err) => {
+    ctx.ui.notify(`Auto-start failed: ${err instanceof Error ? err.message : String(err)}`, "warning");
     if (process.env.GSD_DEBUG) console.error('[gsd] auto start error:', err);
   });
   return true;
diff --git a/src/resources/extensions/gsd/undo.ts b/src/resources/extensions/gsd/undo.ts
index dcf4b1f99..89d52f4bf 100644
--- a/src/resources/extensions/gsd/undo.ts
+++ b/src/resources/extensions/gsd/undo.ts
@@ -102,26 +102,28 @@ export async function handleUndo(args: string, ctx: ExtensionCommandContext, _pi
   // 5. Try to revert git commits from activity log
   let commitsReverted = 0;
   const activityDir = join(gsdRoot(basePath), "activity");
-  if (existsSync(activityDir)) {
-    const commits = findCommitsForUnit(activityDir, unitType, unitId);
-    if (commits.length > 0) {
-      for (const sha of commits.reverse()) {
-        try {
-          execFileSync("git", ["revert", "--no-commit", sha], { cwd: basePath, timeout: 10000, stdio: "ignore" });
-          commitsReverted++;
-        } catch {
-          // Revert conflict or already reverted — skip
-          try { execFileSync("git", ["revert", "--abort"], { cwd: basePath, timeout: 5000, stdio: "ignore" }); } catch { /* no-op */ }
-          break;
+  try {
+    if (existsSync(activityDir)) {
+      const commits = findCommitsForUnit(activityDir, unitType, unitId);
+      if (commits.length > 0) {
+        for (const sha of commits.reverse()) {
+          try {
+            execFileSync("git", ["revert", "--no-commit", sha], { cwd: basePath, timeout: 10000, stdio: "ignore" });
+            commitsReverted++;
+          } catch {
+            // Revert conflict or already reverted — skip
+            try { execFileSync("git", ["revert", "--abort"], { cwd: basePath, timeout: 5000, stdio: "ignore" }); } catch { /* no-op */ }
+            break;
+          }
         }
       }
     }
+  } finally {
+    // 6. Re-derive state — always invalidate caches even if git operations fail
+    invalidateAllCaches();
+    await deriveState(basePath);
   }
 
-  // 6. Re-derive state
-  invalidateAllCaches();
-  await deriveState(basePath);
-
   // Build result message
   const results: string[] = [`Undone: ${unitType} (${unitId})`];
   results.push(`  - Removed from completed-units.json`);
@@ -172,6 +174,7 @@ function findFileWithPrefix(dir: string, prefix: string, suffix: string): string
 
 export function findCommitsForUnit(activityDir: string, unitType: string, unitId: string): string[] {
   const safeUnitId = unitId.replace(/\//g, "-");
+  const commitSet = new Set<string>();
   const commits: string[] = [];
 
   try {
@@ -194,7 +197,8 @@ export function findCommitsForUnit(activityDir: string, unitType: string, unitId
           for (const block of blocks) {
             if (block.type === "tool_result" && typeof block.content === "string") {
               for (const sha of extractCommitShas(block.content)) {
-                if (!commits.includes(sha)) {
+                if (!commitSet.has(sha)) {
+                  commitSet.add(sha);
                   commits.push(sha);
                 }
               }
@@ -209,10 +213,12 @@ export function findCommitsForUnit(activityDir: string, unitType: string, unitId
 }
 
 export function extractCommitShas(content: string): string[] {
+  const seen = new Set<string>();
   const commits: string[] = [];
   for (const match of content.matchAll(/\[[\w/.-]+\s+([a-f0-9]{7,40})\]/g)) {
     const sha = match[1];
-    if (sha && !commits.includes(sha)) {
+    if (sha && !seen.has(sha)) {
+      seen.add(sha);
       commits.push(sha);
     }
   }