fix: address linting & protobuf issues

[Jonathansumner]

• Creates tools package to manually include linter + dependencies, forming a space to add any future build tools
• Improve Makefile to avoid docker issues with linting
• Add basic version check and warning to Makefile
• Address protobuf generation config, which was complaining about versioning

Issues: linter known as Depsguard complains after these changes

[Jonathansumner]

Causes issues locally without these two lines

[pbukva]

LGTM (later we might need reevaluate all these disabled linters)