If you have knowledge with pointer (C/C++) it is pretty much the same in Perl.

sub clear {
    my ($ref) = @_;
    $ref = []; # now ref is made to point to new object (array)
    @$ref = ();  # what ref points to is modified
}
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$ref is a pointer(reference) variable, it stores only address(so as to speak). So when $ref is assigned to point to another object, subroutine caller does not see the change. On the other hand, if you assign what $ref points to (deference), the change is reflected in caller.