Here's what I did in Android Studio Beta (0.8.14)
- Changed the package name manually in the manifest file
- Navigated to build -> source -> r -> release and drilled down until I found R.java
- Selected the file and pressed F6 to rename
- Then from the Build menu selected Make Project
- Clicked the first error and pressed Shift+F6 on the package name and renamed which updated all my source files
- Selected my project name in Android Studio, right clicked -> Refactor -> Rename and changed the name there too.
- Next went to app -> build.gradle and updated my applicationId
- Navigate to .idea -> .name file and rename your Android Studio project in there too
- Just to clean up I deleted the old package folder inside build -> source -> r -> release
And vola, my package name has now changed and builds successfully.