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@hash{@alphafiles}=();
foreach (keys %hash){
my $patt=substr($_,0,index($_,"xml"));
@matched=grep(/^$patt/,@gammafiles);
$hash{$_} = $matched[0];
}

@sortalpha= sort @alphafiles;
@sortgamma= sort @gammafiles;
...
$hash{$sortalpha[$i]}=$sortgamma[$i];
$i++;
}