This is where it all went wrong:

./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
./checksetup.pl --check-modules
cd ..
ls -l
chmod +w Bugzilla/
ls -l
chmod 711 Bugzilla/
ls -l
chmod 644 Bugzilla/
ls -l
chmod +x Bugzilla/
ls -l
cd /usr/lib/perl5/5.8.8/
ls
mkdir Bugzilla
cp CGI.pm Bugzilla/CGI.pm
cp CGI/* Bugzilla/CGI/* .
cd Bugzilla/
ls
mkdir CGI
cp ../CGI/* CGI/* .
cp ../CGI/* CGI/ .
ls
mv *.* CGI/*.*
ls
mv Apache.pm CGI/Apache.pm
mv * CGI/ .
ls
ls CGI/
ls ../..
ls ../
cd ..
rm Bugzilla/
rm -r Bugzilla/
[download]

I know the copies don't make sense, my inability in linux forced me to do it in a File Browser when I failed to do it from the command line. Effectively I copied CGI.pm and the folder CGI into the Bugzilla foler, then deleted it. Thanks for the help.