polish(nyz): fix redundant requires and vllm compatibility

[PaParaZz1]

TODO

• remove requirements in setup.py
• polish the library sequence requirements.txt
• fix lowest transformers version (4.57.1)
• fix hard requirements for vllm in code
• add an optional choice for install vllm (vllm is not necessary for this repo), like pip install ".[vllm]"
• add hint doc for install flash-attn issue (use whl or use docker)
• sync pyproject.toml with requirements.txt
• simplify gsm8k/geo3k shell, remove MLP_XXX
• other necessary doc and comments