fix: catch TimeoutExpired in parallel runner wait loop

The initial wait loop used proc.wait(timeout=0.5) which could raise
subprocess.TimeoutExpired and crash the runner. Added a try/except and
increased timeout to 5s so the runner polls correctly without crashing.

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Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

scripts/run_molecule_parallel.py

@@ -106,7 +106,10 @@ def cli(pairs: tuple[str, ...]) -> None:
         if not finished_indices:
             # No process finished yet, wait a bit
             for proc in processes:
-                proc.wait(timeout=0.5)
+                try:
+                    proc.wait(timeout=5)
+                except subprocess.TimeoutExpired:
+                    pass
             continue
 
         # Remove finished processes from the list