When you begin a new project in Android studio, the project's structure will appear with almost all the files held within the SDK directory, this switch to a Gradle based management system offers an even greater flexibility to the build process.
With the recent release of Android Studio v0.1, there are a lot of questions with the android-studio tag, and a lot of them are duplicates or have the answer "It's alpha software, it's not supposed to be perfect!" or perhaps "Report the bug to Google, not here."