I updated Android Studio to version 2.0. The build failed and also takes longer than Android Studio version 1.5 to build. Every time I run my application, I clean and reload
As suggested by @Bartek-lipinski's post, I have confirmed on my own project that downgrading Gradle plugin to v2.1.3 will solve this problem of getting "InvalidUserDataException: File specified for property does not exist."
I have filed a bug with the Android tools bugtracker website, please upvote to get some more visibility on the problem.