feat(FN-4157): remove composite checkout, add workflow-level checkout steps

Fixes overlap merge checkout logic by removing the composite checkout approach and replacing it with explicit workflow-specific checkout steps, with a new CI job to guard against regressions and a test hardening the temporary directory cleanup path.

Fusion-Task-Id: FN-4157

.github/actions/setup-node-pnpm/action.yml

@@ -1,5 +1,5 @@
 name: setup-node-pnpm
-description: "Checkout, install pnpm, setup Node.js, install dependencies"
+description: "Install pnpm, setup Node.js, install dependencies"
 inputs:
   node-version:
     description: Node.js version
@@ -12,9 +12,6 @@ inputs:
 runs:
   using: composite
   steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-
     - name: Install pnpm
       uses: pnpm/action-setup@v4