Install the right numpy version matching PyTorch CI (#2640)
Summary:
As pointed out in https://github.com/pytorch/benchmark/pull/2639, the new Docker image missed this step and installed numpy 2.x, which is not the same version used in PyTorch CI https://github.com/pytorch/pytorch/blob/main/.ci/docker/requirements-ci.txt. With this done, I could revert `batch-20250825.pt` back to the original `batch.pt`.
I also clean up `.github/scripts/run.sh` which is not used in CI anymore. Utilities like `cuda_utils.py` would need to be refreshed too, but I will do that later in the context of other functionality to bring back like bisection.
### Testing
[numpy==1.26.2](https://github.com/pytorch/benchmark/actions/runs/17282489625/job/49053486634) is installed in the image now.
Differential Revision: D81192556
Pulled By: huydhn
