How to replace default source folders with gradle?

You need to add some lines to build.gradle:

To replace the default source folders, you will want to use srcDirs instead, which takes an array of paths.

    sourceSets {
        main.java.srcDirs = ['src/java']
        main.resources.srcDirs = ['src/resources']
    }

Another way to do this:

    sourceSets {
        main {
            java {
                srcDir 'src/java'
            }
            resources {
                srcDir 'src/resources'
            }
        }
    }

The same applies to the test folder.