while (<>) {
 chomp if /^CLI\b/;
 print;
}
# or without all those default variables
while (my $line = <$FILEHANDLE>) {
 chomp($line) if $line =~ /^CLI\b/;
 print $line;
}

##</code><code>##

my @lines;
my $last_line_was_CLI = 0;
while (<>) {
 chomp;
 if ($last_line_was_CLI) {
  $lines[-1] .= $_;
  $last_line_was_CLI = 0;
 } elsif (/^CLI\b/) {
  $last_line_was_CLI = 1;
  push @lines, $_;
 } else {
  push @lines, $_;
 }
}