Shifted the opac out of koha so its now /usr/lib/cgi-bin/opac and /usr/lib/cgi-bin...
tree844edcdeb500c299f05c65b4bf52af497d11e44b
-rwxr-xr-x 295 .htaccess
drwxr-xr-x - C4
-rw-r--r-- 97 MANIFEST.SKIP
-rwxr-xr-x 7954 Makefile.PL
-rw-r--r-- 3515 README.txt
-rwxr-xr-x 3194 about.pl
drwxr-xr-x - acqui
drwxr-xr-x - admin
drwxr-xr-x - authorities
drwxr-xr-x - catalogue
drwxr-xr-x - cataloguing
-rwxr-xr-x 942 changelanguage.pl
-rwxr-xr-x 919 check_sysprefs.pl
drwxr-xr-x - circ
-rwxr-xr-x 3667 edithelp.pl
drwxr-xr-x - etc
-rwxr-xr-x 1779 help.pl
-rw-r--r-- 1646 install-CPAN.pl
drwxr-xr-x - installer
drwxr-xr-x - koha-tmpl
-rw-r--r-- 508 kohaversion.pl
drwxr-xr-x - labels
-rwxr-xr-x 1968 mainpage.pl
drwxr-xr-x - members
drwxr-xr-x - misc
drwxr-xr-x - opac
drwxr-xr-x - reports
drwxr-xr-x - reserve
drwxr-xr-x - reviews
-rw-r--r-- 3792 rewrite-config.PL
drwxr-xr-x - rss
drwxr-xr-x - serials
drwxr-xr-x - sms
drwxr-xr-x - suggestion
drwxr-xr-x - svc
drwxr-xr-x - t
drwxr-xr-x - tmp
drwxr-xr-x - tools
drwxr-xr-x - virtualshelves