print $1 if $line =~ m/<!-- USER \d+ - ([^\s]+)/i;
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This is good, but it \S is shorter than [^\s], so:

print $1 if $line =~ m/<!-- USER \d+ - (\S+)/i;
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Although to get a little closer to the original specification, I'd put:

my $user=undef;
for (@site) {
  if (/<!--.*USER.* (\S+) -->/) {
    print "joe:\n";
    $user = $1;
    last;
  }
}
print "user = $user\n";
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