Did you mean "print $out1" ?
Anyway, a couple of things may be going wrong. One thing is that it's possible that the backticks don't interpret the command's output as UTF8.
Try this:
#!/usr/bin/perl
use warnings;
use strict;
print "Content-type: text/html;charset=utf-8", "\n\n";
# open command and explicitly request utf-8
open (COMMAND,"-|:encoding(UTF-8)","java -classpath /usr/local/lib/CS.
+jar csearch/CorpusSearch 'HTMLQ((naġ Exists))") or die $!;
my $out1 = join('',<COMMAND>); # put all lines in one string
binmode(STDOUT,":utf8"); # this marks the output as accepting utf8
print $out1;
You may also need to be careful about how you're reading the input data.
See also http://perldoc.perl.org/functions/open.html
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