In projects that use the Gradle build system, what you want to change is the applicationId in the build.gradle file. The build system uses this value to override anything specified by hand in the manifest file when it does the manifest merge and build.
For example, your module's build.gradle file looks something like this:
apply plugin: 'com.android.application' android { compileSdkVersion 20 buildToolsVersion "20.0.0" defaultConfig { // CHANGE THE APPLICATION ID BELOW applicationId "com.example.fred.myapplication" minSdkVersion 10 targetSdkVersion 20 versionCode 1 versionName "1.0" } }
applicationId is the name the build system uses for the property that eventually gets written to the package attribute of the manifest tag in the manifest file. It was renamed to prevent confusion with the Java package name (which you have also tried to modify), which has nothing to do with it.