Deprecate public fields and members that should not be accessible

This PR aims to deprecate many members that should not be publicly accessible. Mainly, this includes public fields, for which it adds getters and sometimes setters. A benefit of this is that if there ever is a ST5, we can tell people to upgrade to 4.3 first, fix all the deprecation warnings, and then upgrade to ST5. I am submitting this PR early to allow some review; more changes will be added over time as I work through the codebase.