Add another java source directory to gradle script

I agree with @JB Nizet about respecting standard conventions. If you still insist on being an Anarchist though:

You already have src declared in your sourceset, why not add src1 and src2 as well? You can add them to the same sourceset, or define a sourceset per module if you want.

sourceSets {
    main {
        java {
            srcDirs 'src'
            srcDirs 'src1'
            srcDirs 'src2'
        }
    }
 }

To reference files outside the project, see this answer.