Does the sync task work at all? I'm trying it out with Gradle 2.12 and even when preceding tasks are not up-to-date it still fails to remove files not copied.

The issue came up recently again. Here are some additional notes and a use case:

Workaround: create custom tasks that explicitly define the output directory as an input so it can detect changes:
======

task mySync {
    inputs.files = files(“$buildDir/configuration”)
    inputs.files = filed(“$rootDir/../../upoint/configuration/core/Apps/Benefits/Portal/config")

    sync {
        from (“$rootDir/../../upoint/configuration/core/Apps/Benefits/Portal/config")
        into “$buildDir/configuration”
    }
}

Use Case
======
1. run a syc from one directory into a buildDir/someOutput

task syncSomething(type: Sync) {
    from “a”
    into "$buildDir/someOutput"
}

2. Manually delete one file from buildDir/someOutput

3. Re-run the sync task and it says up to date. Per our understanding if anything in a or the output changes the task should re-run. Here is a coded example that will also recreate the issue.

task init << {
        mkdir('a')
        def file1 = file('a/test1.txt')
        file1.text = "I am file 1!"

        mkdir('b')
        def file2 = file('b/test2.txt')
        file2.text = "I am file 2!"

        mkdir('c')
        def file3 = file('c/test3.txt')
        file3.text = "I am file 3!"
}

task run(type: Sync, dependsOn: 'init') {
        from('a')
        from('b')
        into 'out1'
}

task update(type: Copy, dependsOn: 'run') {
        from('c')
        into 'out1'
} 

./gradlew update 
./gradlew run 

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This is still an issue in recent Gradle.

Moved to https://github.com/gradle/gradle/issues/1349