This worked for us also although rather than catching the individual journals and redirecting to sub directories we used the existing catch all.
We have all but one journal on http://journals.knowledgearc.com/, so http://journals.knowledgearc.com/journal1, http://journals.knowledgearc.com/journal2, etc. However, one of our journals, journal3, is on a completely different domain, I.e. http://completely.different.domain. So we used the following in htaccess:
RewriteEngine On
RewriteBase /
## journal3
RewriteCond %{SERVER_NAME} ^completely.different.domain
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/journal3/$1 [QSA,L]
## All other journals
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/$1 [QSA,L]
The first checks for completely.different.domain and redirects to journal3. All other journals just get sent to http://journals.knowledgearc.com.
In config.inc.php
base_url[journal3] = http://completely.different.domain
we didn’t need to set base_url[index].