chore: split protocol.py into own folder/files

No other changes apart from just moving code around.

Code review checklist (for code reviewer to complete)

[ ] Pull request represents a single change (i.e. not fixing disparate/unrelated things in a single PR)
[ ] Title summarizes what is changing
[ ] Commit messages are meaningful (see this for details)
[ ] Tests have been included and/or updated, as appropriate
[ ] Docstrings have been included and/or updated, as appropriate
[ ] Standalone docs have been updated accordingly