diff --git a/scripts/provision-worktree.sh b/scripts/provision-worktree.sh
index 14acc040..861a6037 100644
--- a/scripts/provision-worktree.sh
+++ b/scripts/provision-worktree.sh
@@ -335,6 +335,18 @@ disable_seeded_routines() {
 
 disable_seeded_routines
 
+list_base_node_modules_paths() {
+  cd "$base_cwd" &&
+    find . \
+      -mindepth 1 \
+      -maxdepth 4 \
+      -type d \
+      -name node_modules \
+      ! -path './.git/*' \
+      ! -path './.paperclip/*' \
+      | sed 's#^\./##'
+}
+
 if [[ -f "$worktree_cwd/package.json" && -f "$worktree_cwd/pnpm-lock.yaml" ]]; then
   needs_install=0
 
@@ -342,32 +354,56 @@ if [[ -f "$worktree_cwd/package.json" && -f "$worktree_cwd/pnpm-lock.yaml" ]]; t
     [[ -n "$relative_path" ]] || continue
     target_path="$worktree_cwd/$relative_path"
 
-    if [[ -L "$target_path" ]]; then
-      rm "$target_path"
+    if [[ -L "$target_path" || ! -e "$target_path" ]]; then
       needs_install=1
-      continue
+      break
     fi
-
-    if [[ ! -e "$target_path" ]]; then
-      needs_install=1
-    fi
-  done < <(
-    cd "$base_cwd" &&
-      find . \
-        -mindepth 1 \
-        -maxdepth 3 \
-        -type d \
-        -name node_modules \
-        ! -path './.git/*' \
-        ! -path './.paperclip/*' \
-        | sed 's#^\./##'
-  )
+  done < <(list_base_node_modules_paths)
 
   if [[ "$needs_install" -eq 1 ]]; then
+    backup_suffix=".paperclip-backup-$BASHPID"
+    moved_symlink_paths=()
+
+    while IFS= read -r relative_path; do
+      [[ -n "$relative_path" ]] || continue
+      target_path="$worktree_cwd/$relative_path"
+      if [[ -L "$target_path" ]]; then
+        backup_path="${target_path}${backup_suffix}"
+        rm -rf "$backup_path"
+        mv "$target_path" "$backup_path"
+        moved_symlink_paths+=("$relative_path")
+      fi
+    done < <(list_base_node_modules_paths)
+
+    restore_moved_symlinks() {
+      local relative_path target_path backup_path
+      for relative_path in "${moved_symlink_paths[@]}"; do
+        target_path="$worktree_cwd/$relative_path"
+        backup_path="${target_path}${backup_suffix}"
+        [[ -L "$backup_path" ]] || continue
+        rm -rf "$target_path"
+        mv "$backup_path" "$target_path"
+      done
+    }
+
+    cleanup_moved_symlinks() {
+      local relative_path target_path backup_path
+      for relative_path in "${moved_symlink_paths[@]}"; do
+        target_path="$worktree_cwd/$relative_path"
+        backup_path="${target_path}${backup_suffix}"
+        [[ -L "$backup_path" ]] && rm "$backup_path"
+      done
+    }
+
     (
       cd "$worktree_cwd"
       pnpm install --frozen-lockfile
-    )
+    ) || {
+      restore_moved_symlinks
+      exit 1
+    }
+
+    cleanup_moved_symlinks
   fi
 
   exit 0
@@ -384,13 +420,5 @@ while IFS= read -r relative_path; do
   mkdir -p "$(dirname "$target_path")"
   ln -s "$source_path" "$target_path"
 done < <(
-  cd "$base_cwd" &&
-    find . \
-      -mindepth 1 \
-      -maxdepth 3 \
-      -type d \
-      -name node_modules \
-      ! -path './.git/*' \
-      ! -path './.paperclip/*' \
-      | sed 's#^\./##'
+  list_base_node_modules_paths
 )
diff --git a/server/src/services/heartbeat.ts b/server/src/services/heartbeat.ts
index f585b834..0a3a1479 100644
--- a/server/src/services/heartbeat.ts
+++ b/server/src/services/heartbeat.ts
@@ -779,6 +779,8 @@ function enrichWakeContextSnapshot(input: {
     contextSnapshot[WAKE_COMMENT_IDS_KEY] = wakeCommentIds;
     contextSnapshot.commentId = latestCommentId;
     contextSnapshot.wakeCommentId = latestCommentId;
+    // Once comment ids are normalized into the snapshot, rebuild the structured
+    // wake payload from those ids later instead of carrying forward stale data.
     delete contextSnapshot[PAPERCLIP_WAKE_PAYLOAD_KEY];
   } else if (!readNonEmptyString(contextSnapshot["wakeCommentId"]) && wakeCommentId) {
     contextSnapshot.wakeCommentId = wakeCommentId;
@@ -814,6 +816,8 @@ export function mergeCoalescedContextSnapshot(
     merged[WAKE_COMMENT_IDS_KEY] = mergedCommentIds;
     merged.commentId = latestCommentId;
     merged.wakeCommentId = latestCommentId;
+    // The merged context should carry canonical comment ids; the next wake will
+    // regenerate any structured payload from those ids.
     delete merged[PAPERCLIP_WAKE_PAYLOAD_KEY];
   }
   return merged;