Refactor code structure for improved readability and maintainability and also added the mask ROI

Refactor A1 evaluation protocols to focus exclusively on Protocol C; update documentation and scripts accordingly.

Fix duplicate --feature-num-workers/--num-fit-workers args in parser

Add instruct-tuning (LoRA), multi-model fit, comparison viz; fix missing flags

added the test run for HF job

Merge hf/master: restore run_a1 files and hf_jobs