fix(ci): restore broken YAML structure in 3 workflows, revert aggressive STALE_HOURS

- pr-auto-response.yml: restore permissions, steps, and checkout in
  contributor-tier-issues job (broken by runner swap)
- pr-check-stale.yml: restore steps block and step name
- pr-intake-checks.yml: restore steps block, checkout, and timeout
- pr-check-status.yml: revert STALE_HOURS from 4 to 48 (not a cost
  optimization; 4h is too aggressive), switch to ubuntu-latest per
  PR description

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

.github/workflows/pr-check-status.yml

@@ -13,13 +13,13 @@ concurrency:
 
 jobs:
   nudge-stale-prs:
-    runs-on: blacksmith-2vcpu-ubuntu-2404
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       pull-requests: write
       issues: write
     env:
-      STALE_HOURS: "4"
+      STALE_HOURS: "48"
     steps:
       - name: Checkout repository
         uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4