Adding release notes.

Also updating the prep script for things that need to happen to go from
3.0 to 3.1 (which isn't a lot!).
Merge branch 'master' into release_notes
Release notes and README updates.
Fixing bug in prep script.

The prep script fixes an issue with running create_default_collections
on older databases which haven't had their indexes fixed.
Merge pull request #226 from crits/release_notes

Release notes
Merge branch 'master' into stable_3