How do I completely re-install PAM security?

reply is:

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
 there is nothing to do

pacdiff was unknown, and when i tried to install it with sudo pacman -Sy pacdiff it says target not found.

I have never heard of or used pacdiff


Moderator edit: In the future, please use proper formatting: [HowTo] Post command output and file content as formatted text

i used the GUI add/remove to add pacdiff. 

this was the result to pacdiff -o

/usr/share/icons/default/index.theme.pacnew
/etc/passwd.pacnew
/etc/shells.pacnew
/etc/gdm/custom.conf.pacsave
/etc/locale.gen.pacnew
/etc/default/grub.pacnew
/etc/mkinitcpio.conf.pacnew
/etc/pacman.conf.pacnew
/etc/php/php.ini.pacnew
/etc/pam.d/polkit-1.pacsave
/etc/default/useradd.pacnew

If you think i have hosed my system, i can try to backup everything and re-install Manjaro fresh. I have dozens of hours into setting up the webserver which is working great including cgi-bin with python. That took me a while to get running so i hate to wipe it and start over.

I thought i was being 'good' and i updated pretty much everytime it showed me that something could be updated using the gui.