For those who are wondering what InstantRun is (the first setting in the picture): 
And yes, disabling this option fixes the problem.
Edit 01/19/16
'com.android.tools.build: gradle: 2.0.0-alpha6' was released three days ago. Using this new version, βSplit lib_main was detected several timesβ, the error disappeared and the installation of the application completed successfully, 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
Disabling instant start resolves this error. 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 for 2.0.0-alpha6
Emanuel Moecklin Jan 15 '16 at 18:55 2016-01-15 18:55
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