[BUG] Fixing configuration del, in, and set

- Fixes to conform to new configuration structure
- Makes "in" keyword and __contains__ work properly
- Makes deep and shallow deletes work properly.
- Makes deep and shallow set work in the same key order as get.
[DEV] Minor tweaks to loggers warnings

Warning print format now includes files and is set properly.
[VER] Version Bump and Release Notes
Merge branch 'release/0.3.2' into develop