Bump to v0.3.1

1) Change readme to reflect new file structure. 2) Fix `truffle init` / 

fixes ConsenSys-archive#69. 3) Add message for 0.2.x users that tells them to upgrade their dapps.

Bump Truffle version to reflect changes to README.

Bump the version number, and use the latest version of Pudding.

Better messaging when a processor doesn't export the function correctly.

Bump version

Prepare for release.

Should have been in with the last commit.

Fix an issue where the provider wasn't being set in some cases.

Bumping up to 0.0.12 to update readme.