This is still an issue in Gradle 2.13.
In my case it seems only a clean build will work.

Hey Scott, do you have a reproducible example? This should have been marked as fixed in 2.5-rc-2. Here's the minimum test we extracted from the forum post: https://github.com/gradle/gradle/blob/master/subprojects/core/src/integTest/groovy/org/gradle/api/tasks/ArchiveIntegrationTest.groovy#L122

This is the gist of what is failing for me. It appears to make a difference if you do a clean build or not:

    dependencies {
        appDist group: 'example.group', name:'app', version: '1.0.0', classifier: 'dist-linux',  ext: 'tgz', transitive: false
    }
    
    task copyToStagingArea(type: Copy) {
        into "${buildDir}/staging"
        from { configurations.appDist.findAll { it.name.endsWith(".tgz") }.collect { tarTree(it) } }
    }

Thanks. Could the tgz's have read-only permissions on some files inside them?

Absolutely.

tar -tvf path_to_tgz_in_gradle_cache
...
-rw-rw-r-- qoduser/qoduser 148557 2016-02-11 13:16 DITZ/app/openjfx-dialogs-1.0.2.jar
-rwxr-xr-x qoduser/qoduser  10551 2016-02-11 13:16 DITZ/DITZ
-r--r--r-- qoduser/qoduser 598358 2016-02-11 13:16 DITZ/libpackager.so
...
drwxrwxr-x qoduser/qoduser        0 2016-02-11 13:16 DITZ/runtime/lib/amd64/server/
-r-xr-xr-x qoduser/qoduser    11052 2016-02-11 13:16 DITZ/runtime/lib/amd64/server/libjsig.so
-r-xr-xr-x qoduser/qoduser 16918647 2016-02-11 13:16 DITZ/runtime/lib/amd64/server/libjvm.so
-r--r--r-- qoduser/qoduser     1423 2016-02-11 13:16 DITZ/runtime/lib/amd64/server/Xusage.txt
...

The tgz is a simple distribution image created with javapackager.

The question now becomes... What is the right way to handle this? It is inefficient to delete the destination files always, only to copy over the exact same files that were already there. Only rarely will the files actually be different. I looked, but the Copy task doesn't seem to have an 'force overwrite' setting.

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Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.