I wish to rename my apk from gradle. I have the following lines inside build
applicationVariants.all { variant ->      
            def file = variant.outputFile
            def filename = file.name.replace("SomeXXX", "SomeYYY")
            variant.outputFile = new File(file.parent, filename)
                    }
This successfully renames the apks but not the unaligned apks. Please someone throw some light on this.
The gradle plugin has moved on since you posted this, however to get this working on with the current plugin (v1.0.0), you can use the following:-
    variant.outputs.each { output ->
        def alignedOutputFile = output.outputFile
        def unalignedOutputFile = output.packageApplication.outputFile
        // Customise APK filenames (to include build version)
        if (variant.buildType.zipAlignEnabled) {
            // normal APK
            output.outputFile = new File(alignedOutputFile.parent, alignedOutputFile.name.replace(".apk", "-" + defaultConfig.versionName + "-" + defaultConfig.versionCode + ".apk"))
        }
        // 'unaligned' APK
        output.packageApplication.outputFile = new File(unalignedOutputFile.parent, unalignedOutputFile.name.replace(".apk", "-" + defaultConfig.versionName + "-" + defaultConfig.versionCode + ".apk"))
    }
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