gistfile1.txt

git clone git://github.com/croogo/app myapp
cd myapp
git submodule add -f --name Croogo -b 1.6 git://github.com/croogo/croogo Vendor/croogo/croogo
git submodule add -f --name CakePHP git://github.com/cakephp/cakephp Vendor/cakephp/cakephp
git submodule add -f --name Search git://github.com/CakeDC/search Plugin/Search
git submodule add -f --name Migrations git://github.com/CakeDC/migrations Plugin/Migrations

set your vhost DocumentRoot to myapp/webroot and the install process should work
so, basically myapp is your own repo, which you can later customize and push to your own project repo
while croogo and cakephp are in Vendor, and should not be modified.