Fix overwrite default to true in deprecated method calls.

We cannot break existing users, but we can deprecate the improper usage.
This is part #2 of the workaround for #1156.  This ensures that
users will stop using the legacy methods after 0.13.2 is out.
Add introduction to the setting system.

Conflicts:
	src/sphinx/Architecture/Core-Principles.rst
Fix spelling issues in architecture document.
Add changes documentation for 0.13.1->0.13.2