Security vulnerabilities and automated fixes for checkpoint security issues
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A high-severity deserialization vulnerability was fixed in `skills/packs/pipeline-phase-5-pretrain-code/scripts/trainer.py` where `torch.save()` was used to serialize model checkpoints. Because PyTorch's save mechanism relies on Python's `pickle` module internally, any checkpoint file loaded later could execute arbitrary code. The fix replaces `torch.save()` with `np.savez()` for model weights and a JSON file for metadata, eliminating the pickle-based serialization entirely.