Consolidate deprecation handling during reconfigure to use new deprecation list

TLDR: We are consolidating all deprecation handling to a single place. In addition, we will abort reconfigure if sensitive (~= breaking || causing data loss) configuration is being used even after their removals. Non-sensitive configuration will be dropped at their removal version and we will not bother about them anymore.

In this MR, in addition to consolidating deprecations, I am removing deprecation warnings for two non-sensitive configuration that have been deprecated since 10.1 (and has been unused since an even earlier version) - git_timeout and git_max_size.

I've opened !2532 (merged), !2522 (merged) and !2520 (merged) for discussing other removals.

Closes #3515 (closed)