Enhance upgrade workflow with tomli-w installation

Added installation of tomli-w and updated pyproject.toml overrides.

.github/workflows/upgrade-deps.yml

@@ -17,6 +17,14 @@ jobs:
         with:
           enable-cache: true
 
+      - name: Install tomli-w
+        run: |
+          uv install tomli-w
+
+      - name: Update overrides in pyproject.toml (if any)
+        run: |
+          python src/tools//apply_overrides.py
+
       - name: Calculate Cutoff Date
         id: date
         run: |
@@ -37,7 +45,7 @@ jobs:
           # git diff --quiet returns 0 if there are no changes, and 1 if there are changes.
           if git diff --quiet uv.lock; then
             echo "has_changes=false" >> $GITHUB_OUTPUT
-            echo "No older-than-14-days updates found. Skipping PR."
+            echo "No changes found. Skipping PR."
           else
             echo "has_changes=true" >> $GITHUB_OUTPUT
             echo "Lockfile updated. Proceeding to PR generation."
@@ -48,10 +56,10 @@ jobs:
         uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          commit-message: "chore: lockfile dependency upgrade (${{ steps.date.outputs.cutoff_date }})"
+          commit-message: "chore: dependency upgrades (${{ steps.date.outputs.cutoff_date }})"
           title: "Dependency Upgrade: Quarantine Buffer Applied"
           body: |
-            Updates the `uv.lock` file to the latest package versions available as of **${{ steps.date.outputs.cutoff_date }}**.
+            Updates the `uv.lock` and `pyproject.toml` files to the latest package versions available as of **${{ steps.date.outputs.cutoff_date }}**.
             
             - **Single Source of Truth:** Dependencies are still read from `pyproject.toml`.
             - **14-Day Buffer:** Only releases older than 2 weeks are included.