Nanopb Compiplation Refactor & Protobuf Cleanup

[Andrewyx]

Description

This PR seeks to address the following 3 issues:

• Refactor and document the black box nanopb.bzl
• Audit setup_software.sh to reduce hermiticity issues blocking Add macOS ARM support for Thunderscope #3496 and removed legacy version support
• Clean up optimization code relating to toolchains_protoc

Testing Done

• Compilation succeeds for deploy_robot_software
• Setup software works as previously after deleting unnecessary deps

Resolved Issues

Resolves #3484

Length Justification and Key Files to Review

• nanopb.bzl I've provided documentation on the compile process of this script and how it actually fits into our deploy pipeline. Hopefully this process makes sense now.

Review Checklist

It is the reviewers responsibility to also make sure every item here has been covered

• Function & Class comments: All function definitions (usually in the .h file) should have a javadoc style comment at the start of them. For examples, see the functions defined in thunderbots/software/geom. Similarly, all classes should have an associated Javadoc comment explaining the purpose of the class.
• Remove all commented out code
• Remove extra print statements: for example, those just used for testing
• Resolve all TODO's: All TODO (or similar) statements should either be completed or associated with a github issue

[williamckha]

LGTM very clean! Make sure to update CI so that we don't run ubuntu 22 builds any more

[Lmh-java]

Legendary work! Left some deep questions.

[Lmh-java]

LGTM. BTW, Github Action scripts should also be changed to address the CI failure.

[williamckha]

The pre-commit.yml workflow also needs to be upgraded to Ubuntu 24