Because reference.conf is fully resolved before merging with main config, the following doesn't work:

reference.conf:

myapp {
    storageDir = "."
}
myappinternal {
    file1 = ${myapp.storageDir}/file1
    file2 = ${myapp.storageDir}/file2
}

aplication.conf:

myapp {
    storageDir = "mydir"
}

file1 and file2 will not be "mydir/file1" paths but "./file1" instead.