diff --git a/drupal-contrib/scripts/test-issue-branches.sh b/drupal-contrib/scripts/test-issue-branches.sh
index f8bde7f..56c56c1 100755
--- a/drupal-contrib/scripts/test-issue-branches.sh
+++ b/drupal-contrib/scripts/test-issue-branches.sh
@@ -95,6 +95,16 @@ for SPEC in "${TESTS[@]}"; do
       continue
     fi
     log "Checked out issue branch: $BRANCH"
+    DIRTY=$(git status --short 2>/dev/null)
+    if [ -n "$DIRTY" ]; then
+      log "ERROR: dirty git tree after issue branch checkout:"
+      echo "$DIRTY" | head -20
+      RESULTS["$DIR_KEY"]="FAIL (dirty git tree after checkout)"
+      DURATIONS["$DIR_KEY"]=$((SECONDS - START))
+      cd "$HOME"
+      continue
+    fi
+    log "✓ git tree clean after checkout"
   fi
 
   # --- Configure DDEV if needed ---
diff --git a/drupal-contrib/template.tf b/drupal-contrib/template.tf
index e86ed69..e093916 100644
--- a/drupal-contrib/template.tf
+++ b/drupal-contrib/template.tf
@@ -545,6 +545,12 @@ GIT_EXCLUDE_EOF
              git checkout -b "$ISSUE_BRANCH" "$REMOTE_NAME/$ISSUE_BRANCH" >> "$SETUP_LOG" 2>&1; then
             log_setup "✓ Checked out branch $ISSUE_BRANCH"
             update_status "✓ Branch checkout: Success"
+            # Ensure working tree exactly matches the checked-out branch.
+            # origin/main may be ahead of the issue branch base; git can leave
+            # files from those newer commits as modified/untracked after checkout.
+            git reset --hard HEAD >> "$SETUP_LOG" 2>&1 || true
+            git clean -fd >> "$SETUP_LOG" 2>&1 || true
+            log_setup "✓ Working tree reset to match branch"
           else
             log_setup "⚠ Warning: Could not checkout $ISSUE_BRANCH — remaining on current branch"
             update_status "⚠ Branch checkout: Warning"
diff --git a/drupal-core/scripts/test-issue-branches.sh b/drupal-core/scripts/test-issue-branches.sh
index 7f1924a..c98f613 100755
--- a/drupal-core/scripts/test-issue-branches.sh
+++ b/drupal-core/scripts/test-issue-branches.sh
@@ -105,6 +105,16 @@ for PAIR in "${TESTS[@]}"; do
       cd "$HOME"
       continue
     fi
+    DIRTY=$(git status --short 2>/dev/null)
+    if [ -n "$DIRTY" ]; then
+      log "ERROR: dirty git tree after issue branch checkout:"
+      echo "$DIRTY" | head -20
+      RESULTS["$DIR_KEY"]="FAIL (dirty git tree after checkout)"
+      DURATIONS["$DIR_KEY"]=$((SECONDS - START))
+      cd "$HOME"
+      continue
+    fi
+    log "✓ git tree clean after checkout"
   elif [ "$TARGET_BRANCH" != "main" ]; then
     log "Checking out $TARGET_BRANCH..."
     if ! (git checkout -b "$TARGET_BRANCH" "origin/$TARGET_BRANCH" 2>&1 || \
diff --git a/drupal-core/scripts/update-drupal-cache b/drupal-core/scripts/update-drupal-cache
index 6cfa224..70c32d8 100755
--- a/drupal-core/scripts/update-drupal-cache
+++ b/drupal-core/scripts/update-drupal-cache
@@ -56,6 +56,10 @@ echo ""
 echo "Fetching Drupal core git objects..."
 git -C "$SEED_DIR" fetch --all --prune
 
+echo "Fast-forwarding local main branch..."
+git -C "$SEED_DIR" merge --ff-only origin/main || \
+  echo "Warning: could not fast-forward main (local changes?); objects still updated."
+
 echo ""
 echo "=== Seed cache updated successfully ==="
 echo "Completed: $(date)"
diff --git a/drupal-core/template.tf b/drupal-core/template.tf
index 5e52230..0aaa06e 100644
--- a/drupal-core/template.tf
+++ b/drupal-core/template.tf
@@ -635,6 +635,13 @@ STATUS_HEADER
             if git -C "$DRUPAL_DIR" checkout -b "$ISSUE_BRANCH" "issue/$ISSUE_BRANCH" >> "$SETUP_LOG" 2>&1 || \
                git -C "$DRUPAL_DIR" checkout "$ISSUE_BRANCH" >> "$SETUP_LOG" 2>&1; then
               log_setup "  ✓ Checked out branch: $ISSUE_BRANCH"
+              # Ensure the working tree exactly matches the checked-out branch.
+              # When cloning with --reference, origin/main may be ahead of the
+              # issue branch base; git updates the index but can leave working tree
+              # files from those newer main commits behind as modified/untracked.
+              git -C "$DRUPAL_DIR" reset --hard HEAD >> "$SETUP_LOG" 2>&1 || true
+              git -C "$DRUPAL_DIR" clean -fd >> "$SETUP_LOG" 2>&1 || true
+              log_setup "  ✓ Working tree reset to match branch"
             else
               log_setup "✗ Failed to check out branch $ISSUE_BRANCH"
               SETUP_FAILED=true