Thanks for letting me know. Last Friday I updated the sample code to build with Android Studio 1.0.2. I also renamed the repo, and it looks like a file in the .idea directory that still pointed at the old name. This caused a warning prompt for me when I did a clean checkout just now, though the app still built and ran once I continued.
I've just updated that repo. If you do a clean checkout now it should work without the warning. I also updated the README instructions, which previously specified a particular project directory name. You can now clone the project more simply like this:
$ git clone firstname.lastname@example.org:exosite-garage/AndroidThermostat.git
Let me know if you have any questions.