Your Drupal Multisite as subfolder does not work? (http://www.mydomain.com/mymultisitealias)
If you already have a correct sites.php in the "sites" folder ("sites/sites.php") then the solution may be to create a symlink in the drupal home directory.
In the example above that means your sites.php looks like this:
$sites['mydomain.com'] = 'default';
$sites['mydomain.com/mymultisitealias'] = 'mydomain.com.mymultisitealias';
?>
and you have a symlink in your index directory (where index.php is located):
Link (shortcut file): "mymultisitealias"
Pointing to "."
Your multisite must be placed in "mydomain.com.mymultisitealias" then.
Did this fix your Problem? :)
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