Standardize Input Names Across PET prep piplines

[bendhouseart]

PET pipelines should follow BIDS app naming conventions and formatting:

• use positional arguments over flagged arguments for bids_dir, output_dir and participant_level
• subjects should be referred to participants/subjects uniformly across apps.

See nipreps guide, petprep_hmc, and petprep_extract_tacs for examples both conforming and non-conforming.

[bendhouseart]

@mnoergaard are we sticking with --flags or moving over to positional args as outlined above?