You just want to separate the core from your app folder?  Just edit
your app/webroot/index.php, and change the CAKE_CORE_INCLUDE_PATH
define.  I currently have
define('CAKE_CORE_INCLUDE_PATH',
'C:'.DS.'Subversion'.DS.'MyProject'.DS.'trunk'.DS.'libs'.DS.'cake_1.2.x.x_branch'
 );

when my core cake libs are in
c:\Subversion\MyProject\trunk\libs\cake_1.2.x.x_branch
and my app is in
c:\Subversion\MyProject\trunk\src


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