If you deleted the install directory after your last upgrade<span style="text-decoration: line-through">, you'll have to download the entire ZIP. When downloading in the Members Area, uncheck the option to download only changed files.</span>
EDIT: Changed this behavior in the Members Area. Now you don't need to download the entire ZIP just to get the install folder. Even if the aforementioned option is checked, the install folder will now always be included in the ZIP.
In your case, you will simply need to download 3.0.6 again and the install folder should be included this time.
As this was a problem with our system and not with VaultWiki itself, I've marked this as Not a Bug.