[WIP] Modify quickrun to allow resuming

[IAlibay]

Minimal changes to quickrun in order to allow resuming by serializing ProtocolDAGs.
Related to & requires OpenFreeEnergy/gufe#738

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[IAlibay]

pre-commit.ci autofix

[github-actions]

No API break detected ✅

[IAlibay]

Here and everywhere else I'm doing a tmpdir -> tmp_path change, turns out tmpdir's implementation in pytest doesn't implement all the pathlib.Path features, so it's better to use tmp_path.

As far as I'm aware the slow tests aren't affected by this because we wrap them around Path calls.

[IAlibay]

I don't know what's up with the tyk2 CLI test, but locally the restart is working!