Just updated Android-Studio to version 0.2.7 an now I get the error message from the title:
You do not want to manage gradle at a system level, it is better handled per project. Android Studio projects already setup gradle wrapper handling when creating new projects but if you have an older one you can add the same file that Android Studio does. Think of this as an gradle bootstrap file that will download the correct gradle version per project. You can also read up on Gradle Wrapper and generate a shell script called gradlew that will provide gradle-free bootstrapping.
In gradle/wrapper/gradle-wrapper.properties
in your project directory make sure you have:
#
#Tue Oct 08 13:40:54 CEST 2013
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
distributionUrl=http\://services.gradle.org/distributions/gradle-1.7-bin.zip
Then when you go into Gradle you can set it to use the gradle wrapper. This is the default when creating new projects in Android Studio.
There are at least three approaches to migration or adding Gradle properly and using the new project structure Google and Android Studio has introduced.
For now I'm copying the files over to a new project until the tools get a bit better.