This worked for me in Eclipse Neon:
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Right click on project and add the Gradle nature
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File -> Export -> Android -> Generate Gradle build files
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In the root directory of your project, create a local.properties file and set sdk.dir. See: Where does local.properties go for android project?
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Right click on project -> Gradle -> Refresh Gradle Project
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Enable code shrinking in build.gradle. See: https://developer.android.com/studio/build/shrink-code.html
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Put your Proguard configuration in proguard-rules.pro (or in a different file if you set the proguardFiles property in build.gradle accordingly)
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Open the Gradle Tasks view and run the assembleRelease task. Check the console to see if it ran successfully. If it went well, refresh your project directory and the .apk file(s) will be in the build/outputs/apk subdirectory.
solved Proguard claims to obfuscate the .apk, but does not