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.
Merge pull request #1169 from sbt/wip/fix-override-default

Fix overwrite default to true in deprecated method calls.