You can clone with
HTTPS or Subversion.
If a package is in a repository but still in the AUR cower refuses to download it.
For packages in official repositories this should not be a problem, since their PKGBUILDs should be in the ABS and not in the AUR. However packages from inofficial repositories usually have their PKGBUILDs in the AUR.
$ grep -A3 adslgr32 /etc/pacman.conf
## The Hellenic (Greek) archlinux unofficial repository with many
## interesting packages.
Server = http://archlinuxgr.tiven.org/archlinux/$arch
$ cower -d cower
warning: cower is available in adslgr32
$ pacman -Slq adslgr32 | grep cower
$ pacman -Si cower-git
Repository : adslgr32
Name : cower-git
Version : 20110818-1
URL : http://github.com/falconindy/cower
Licenses : MIT
Groups : None
Provides : cower
Depends On : curl pacman yajl
Optional Deps : None
Conflicts With : cower
Replaces : None
Download Size : 21.16 K
Installed Size : 100.00 K
Packager : Axilleas P <markeleas @ gmail.com>
Architecture : i686
Build Date : 2011-08-18T16:16:57 CEST
MD5 Sum : 3720111674d41335f44922228c8968a3
Description : A simple AUR agent with a pretentious name
While it is correct for cower-git to provide cower, in this case cower itself should probably be in the repository as it has a stable release. However the general problem with PKGBUILDs of packages from unofficial repositories remains.
I added the --ignorerepo flag to cower for just this reason.