Android. Gradle. Change the package of the classes. Manifest, customviews, custom prefereces - all these xmls will be changed too. Only thing you have todo, enable your proguard and add "-applymapping ./build/mapping.txt" to your proguard. Also change "somepackage" and "targetpackage" to yours

build.gradle

android.applicationVariants.all { variant ->
    File mappingFile = file("${buildDir}/mapping.txt")

    if (variant.getBuildType().isMinifyEnabled()) {
        variant.mergeResources.doLast {
            if (!mappingFile.exists()) mappingFile.createNewFile()
            println "minify replacePackageInResources"
            replaceResources(variant, "com.somepackage", "com.targetpackage")
            replaceResources(variant, "com.somepackage2", "com.targetpackage2")
        }
        variant.assemble.doLast {
            if (!mappingFile.exists()) mappingFile.createNewFile()
            println "minify printMappingFile"

            String text = mappingFile.getText('UTF-8')
            boolean rebuild = text.trim().isEmpty()
            replacePackage(variant, "com.somepackage", "com.targetpackage")
            replacePackage(variant, "com.somepackage2", "com.targetpackage2")
            if (rebuild || !text.equals(mappingFile.getText('UTF-8'))) {
                File[] files = file("${buildDir}").listFiles()
                for (File file : files) {
                    if (file.name.contains("mapping")) continue;
                    GFileUtils.deleteDirectory(file)
                }
                throw new GradleException('Rebuild project')
            }
        }

        variant.outputs.each { output ->
            output.processManifest.doLast {
                if (!mappingFile.exists()) mappingFile.createNewFile()
                println "minify replacePackagesInManifest"
                replaceManifest(output, "com.somepackage", "com.targetpackage")
                replaceManifest(output, "com.somepackage2", "com.targetpackage2")
            }
        }
    }
}

def replacePackage(variant, String currentPackage, String targetPackage) {
    //Copy classes by generating proguard mapping file.
    File mappingFile = file("${buildDir}/mapping.txt")

    File generatedMappingFile = file("${buildDir}/outputs/mapping/${variant.dirName}/mapping.txt")
    if (!generatedMappingFile.exists()) return;
    String generatedMap = generatedMappingFile.getText('UTF-8')
    Pattern pattern = Pattern.compile("(" + currentPackage + ".*?) -> .*?:")
    Matcher m = pattern.matcher(generatedMap)

    StringBuilder b = new StringBuilder(mappingFile.getText('UTF-8'));
    while (m.find()) {
        def pack = m.group(1)
        def targetPack = pack.replaceAll(currentPackage, targetPackage)
        if (b.contains(pack)) continue;
        b.append(pack).append(" -> ").append(targetPack).append(":\n")
    }
    mappingFile.write(b.toString(), 'UTF-8')
}

def replaceResources(variant, String currentPackage, String targetPackage) {
    //Rename packages in layouts
    replaceRes(variant, currentPackage, targetPackage, "layout")
    replaceRes(variant, currentPackage, targetPackage, "menu")
    replaceRes(variant, currentPackage, targetPackage, "xml")

}

def replaceRes(variant, String currentPackage, String targetPackage, String fileName) {
    File valuesFile = file("${buildDir}/intermediates/res/merged/${variant.dirName}/${fileName}")
    for (File file : valuesFile.listFiles()) {
        String content = file.getText('UTF-8')
        content = content.replaceAll(currentPackage, targetPackage)
        file.write(content, 'UTF-8')
    }
}

def replaceManifest(variant, String currentPackage, String targetPackage) {
    println "replaceManifest"
    //Rename packages in manifest
    File valuesFile = file("${buildDir}/intermediates/manifests/full/${variant.dirName}/AndroidManifest.xml")
    String content = valuesFile.getText('UTF-8')
    Pattern pattern = Pattern.compile("<application.*?</application>", Pattern.DOTALL | Pattern.MULTILINE)
    Matcher matcher = pattern.matcher(content)
    if (matcher.find()) {
        String application = matcher.group()
        application = application.replaceAll(currentPackage, targetPackage)
        content = pattern.matcher(content).replaceAll(application);
        valuesFile.write(content, 'UTF-8')
    }
}