Could not determine the dependencies of task ':app:crashlyticsStoreDeobsDebug' if I enable the proguard
Full combo of build/ clean project + build/ rebuild project + file/ Invalidate caches / restart works for me!
I had the same issue a few days ago and I found this thread Twitter Developer Forum that points to some incompatibility with versions of gradle/build-tools/crashalics.
My problem was slightly different from yours as I'm not using alpha-3 I'm using 1.5. But on my update I also changed to the latest gradle distribution gradle-2.9-all.zip.
So probably/maybe you can fix it by changing to the latest gradle version. But If it does not work, you'll really have to be patient and wait until build tools V2.0 is not in alpha anymore OR the Crashalitycs team, fix the incompatibility.
I was facing the same issue when integrating Firebase Cloud Store in my project.Inside the project level gradle, I added
classpath 'com.google.gms:google-services:4.0.1'that fixed the issue.