Upgrade dependencies

[jvmncs]

Closes #1081

Keeping notify=4.0 because of this note regarding migration. TL;DR they removed the API we were using to disambiguate filesystem events into Create/Remove/Write/Rename inforthe filesystem choreography used by rudolph. Since the reindeer are largely targeted for linux platforms I think it's ok to keep it pinned for awhile, but eventually

• fix CI on main -- the failures are a result of clippy adding some new lints for 1.63/1.64/1.65, resolved by upgrading dependencies / manually fixing errors/warnings
• resolves the following published security issues for protobuf-3.20 and pytest. both of these are vulnerabilities of the pymoose dependencies, and do not affect moose core

[yanndupis]

Looks great! I just left one comment. Thanks