I want to start a empty project with Gradle in Intellij IDEA but it seems not so convenient as Eclipse does.
What I did is File->New Project->Gradle. And a project s
When creating new Gradle project, select "Create directories for empty content roots automatically".

New project will have those directories.

In latest IntelliJ IDEA Community Edition(2018.1), there's no Create directories for empty content roots automatically option available in New Project dialog. But we can go to Preferences...->Build, Execution, Deployment->Gradle and check the underlined option in the screenshot below.