Split lib_main was defined multiple times

Recovery:

Deleting the (projectFolder)/app/build folder and re-building worked for me. (as answered by @AskQ)

I wonder if Build > Clean Project would have worked as well; from the Android Studio GUI menus.

Avoidance:

In my case the problem seems to have occurred because I had copy pasted a project, so 2 projects had the same name.
There are like other causes too, learning what they are can help users avoid this concern.

I ran into this issue after refactoring and changing app name in gradle. Following AskQ's lead, I rebuilt the project (following a slightly different path):

Build-> Clean Project

followed by

Build-> Rebuild Project

Solved the issue

Just delete build folder of appmodule and Rebuild the project!

This will fix the issue!.

For those who wonder what InstantRun is (first setting in the picture):

And yes disabling that setting fixes the issue.

Edit 01/19/16

'com.android.tools.build:gradle:2.0.0-alpha6' was released three days ago. Using that new version, the "Split lib_main was defined multiple times" error is gone and installation of the app succeeds but now I get a runtime error:

java.lang.RuntimeException: Unable to instantiate application
com.android.tools.fd.runtime.BootstrapApplication:
java.lang.ClassNotFoundException: Didn't find class
"com.android.tools.fd.runtime.BootstrapApplication" on path:
DexPathList[[zip file "/data/app/com.onegravity.k10.pro2-2/base.apk",
zip file "/data/app/com.onegravity.k10.pro2-/split_lib_main.apk"]

Caused by: java.lang.ClassNotFoundException: Didn't find class
"com.android.tools.fd.runtime.BootstrapApplication" on path:
DexPathList[[zip file "/data/app/com.onegravity.k10.pro2-2/base.apk",
zip file "/data/app/com.onegravity.k10.pro2-2/split_lib_main.apk"]

Suppressed: java.io.IOException: No original dex files found for dex location
/data/app/com.onegravity.k10.pro2-2/base.apk

Suppressed: java.lang.ClassNotFoundException:
com.android.tools.fd.runtime.BootstrapApplication

Turning off instant run eliminates that error. Let's wait for com.android.tools.build:gradle:2.0.0-alpha7...

Edit 01/25/16

'com.android.tools.build:gradle:2.0.0-alpha7' was released two days ago.

Getting the same exception as with 2.0.0-alpha6