You can clone with
HTTPS or Subversion.
unauthorized modules (i.e. module names that conflict with a previous version) should not be searched for.
Not sure though how to find out, which one is authorized and which is not in an efficient way (note: we have to check this for each upload).
Does the 02packages file help? My idea is to look the module name up in the 02packages file and see whether the mentioned release matches the release I'm processing right now. But that would leave me with the problem that it doesn't contain data about the backpan. Is there a 02packages file for the backpan? On the other hand those should probably be marked as unauthorized anyway, because they are not installable via any cpan client.
This would solve the issue that there are currently 3 unauthorized results before the authorized: http://beta.metacpan.org/search?q=pod+parser
fixed a long time ago...