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I used to have to work with my own custom *.conf file in order to get my multi-site to work off a non root install of drupal but now have moved it to root ,I don't need that file anymore as system reads the .htaccess.

So while my subdomains work fine in sites folder, my other domain name in sites folder refuses to work without symlink. Which I always thought was only necessary in tandem with *.conf file for virtualDocument hosts.

So my question is --

Why won't my other domain work like other sites in sites folder?

Why must it have a symlink to work?

And why do other sites have clean-urls working along with main install site but not other domain name?

My set up is

mainsite.com/sites/

                  subdomain.mainsite.com 
                  subdomain2.mainsite.com
                  otherdomain.com

If I symlink otherdomain.com while in www folder:

ln -s /var/www/html/ /var/www/html/otherdomain.com

It works but without clean-urls

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I have the answer now.

The symlink is necessary so two separate domains can share the one IP along with your server's records. Obviously the subdomains share the same name and so are fine just listed in sites directory. The symlink links the other domain or any number of domains to the same html folder where the root installation of drupal resides.

The clean urls for the symlink multi-site domain on my Centos 6.4 linux system running httpd require the default httpd.conf file in etc/httpd/conf to change AllowOverride NONE to All for directories. Then the service must be restarted for changes to take effect service httpd restart

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