Fix LoRA weight exports to save merged full checkpoints

[taivu1998]

Summary

• merge LoRA deltas into full trainer weight exports before HF serialization so weights/step_<N> stays a standalone checkpoint
• keep save_adapter_separately=true additive by still writing lora_adapters/ alongside the merged full checkpoint
• add focused merge-math coverage plus full-checkpoint assertions for the existing SFT LoRA integration path
• clarify the checkpoint/config contract for LoRA exports in the trainer config and checkpointing docs

Closes #1707.

Testing

• python3 -m py_compile src/prime_rl/trainer/lora.py src/prime_rl/trainer/weights.py src/prime_rl/trainer/ckpt.py src/prime_rl/configs/trainer.py tests/unit/train/test_lora.py tests/integration/test_sft_lora.py
• git diff --check -- src/prime_rl/trainer/lora.py src/prime_rl/trainer/weights.py src/prime_rl/trainer/ckpt.py src/prime_rl/configs/trainer.py docs/checkpointing.md tests/unit/train/test_lora.py tests/integration/test_sft_lora.py
• attempted: UV_CACHE_DIR=/tmp/uv-cache uv run pytest tests/unit/train/test_lora.py -q
  • this could not be completed locally because the repo lockfile only supports Linux environments while this workspace is macOS

---

Note

Medium Risk
Changes the semantics of LoRA weight exports by merging adapter deltas into the main weights/step_<N> checkpoint, which could affect downstream consumers if any relied on the previous unmerged format; adds test coverage to reduce regression risk.

Overview
Ensures LoRA weight exports always produce a standalone Hugging Face-compatible merged checkpoint at weights/step_<N> by merging LoRA deltas into the gathered full-model state dict before HF serialization.

Makes ckpt.weights.save_adapter_separately additive (writes weights/step_<N>/lora_adapters as a sidecar without altering the main checkpoint), removes LoRA-cleanup from gather_weights_on_master, and adds unit + expanded integration tests (including a new merged-only CI config) to assert both adapter exports and merged full checkpoints are HF-compatible.

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