I like limited root directory of owncloud,

I have a server with owncloud and would like the owncloud root directory is limited to 2GB per folder.
To understand my scenario this server HD is separated to the root of owncloud and configure per-user external storage.
Thus the user's quota is only for external storage and not to the root of owncloud.
So I need to limit the owncloud the user folders.

If you connect each user individually to the external storage, you can use the quota-settings of the external storage. Or use LVM and create individual mount points for each user (http://serverfault.com/questions/100596/linux-quota-per-directory).