Update legacy Repository usage in various example files (#29085)
* Update legacy Repository usage in `examples/pytorch/text-classification/run_glue_no_trainer.py`
Marked for deprecation here https://huggingface.co/docs/huggingface_hub/guides/upload#legacy-upload-files-with-git-lfs
* Fix import order
* Replace all example usage of deprecated Repository
* Fix remaining repo call and rename args variable
* Revert removing creation of gitignore files and don't change research examples