Nice work, overall. The bit in the middle violates Don't Repeat Yourself, though.
sub print_diff {
my ( $decor, $dir, @filename ) = @_;
my $prefix = (
( $opt_plain ? "$decor " : '' )
. ( defined $dir ? "$dir " : '' )
);
print map "$prefix$_\n", @filename;
}
if ( not( $opt_bonly or $opt_jonly ) ) {
print_diff '<', $dirname1, diff( \@dir1, \@dir2 );
}
if ( not( $opt_aonly or $opt_jonly ) ) {
print_diff '>', $dirname2, diff( \@dir2, \@dir1 );
}
if ( $opt_inter or $opt_jonly ) {
print_diff '=', '', isect( \@dir1, \@dir2 );
}
Makeshifts last the longest.
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