Unique out of order directory entries should be respected

[loosebazooka]

ReproducibleLayerBuilder(
       LayerEntry("a/b.txt"),
       LayerEntry("a", someCustomPermissions)
)

should produce a layer with custom permissions on a, current behavior doesn't do this, since a is prepopulated into the entries by a/b.txt

[chanseokoh]

Both this and #1270 have the same root cause. It's due to the current solution (#891) of adding all the parent directories to fix #727 and #523.

A workaround is to add a first followed by a/b.txt.

[loosebazooka]

I think this can just be considered a duplicate of #1270