Document the change to use a directory for .vagrant in CHANGELOG.md

Prior to 1.1.0 .vagrant was a file, and once you run Vagrant 1.1+ on a
project, Vagrant 1.0.x will stop working.  This change happened at
approximately commit 4e649cc98792c192c1589a0bd86e8433e90f60cd.

Addresses https://github.com/mitchellh/vagrant/issues/3558