I suggest you take a look at the tutorials broquaint suggested; this should all become less mysterious. As for your question, the same principle applies as above: if you've got a reference in $ref put the sigil for the relevant type before it to dereference it. You'll get something like %$ref, @$ref, $$ref.

my $hierarchy = get_hierarchy(@dirs);
while ( my ( $directory, $contents ) = each %$hierarchy ) {
    ... # do your thing here
}
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