How do I only allow logged in users to see Wiki?

I have set up a server and the website, but it only works if you forward the urls, in the DNS machine records, to the public ip address of my of my router. I only want to allow logged in users to be able to click on a wiki homepage link to see it. Also, typing in the internal ip address of a device on my network doesn't get me to my server unless I allow the Internet to see the wiki.
So I would like to...
1. Make users log in to be able to see anything, like people, profiles, and wikis.
2. Allow intranet access to server with host names and server ip address
3. Allow logged in VPN users to see the site (I'm guessing this would go along with number 2)
4. If I need to add a custom site, how would I add the site so it would pop up when the URL is typed in and have a login window to be able to go the wiki site
5. I don't want to mess up Profile Manager either
I've tried many different things and can get one thing to work, but not the other.
Thanks in advance!!!

Files to change:
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclientbase/pu blic/javascripts/sprockets.js
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/app/co ntrollers/application_controller.rb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/app/he lpers/entity_url_helper.rb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/app/mo dels/sources/my_documents.rb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/app/mo dels/sources/my_favorites.rb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/app/vi ews/layouts/application.html.erb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/config /routes.rb
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclient/config /initializers/register_apple_plugins.rb
Folder to delete to remove iPad version of wiki
/Applications/Server.app/Contents/ServerRoot/usr/share/collabd/coreclientmobile/ public
There are way to many lines of code in these files that are different to go through one by one.  I have put the files in google docs (server 2.2.1 mods). 
There is a great program at the mac app store called CompareMerge you can go through the files line by line to see what is different. 
Before doing anything I recommend coping all files that you are changing/deleting some where safe so if something goes wrong you can go back to the originals.
Once all files have been replaced/deleted you have to open the server app and stop/start wikis

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