I have a basic setup that I am constantly improving, including all the basic things that I need for my projects. The cascading file system used by Kohana makes this very easy. You can see something like this at http://github.com/synapsestudios/kohana-projecttemplate .
I converted from CI and stayed because everything was simpler using the PHP5 OOP concepts the way they should be. In addition, ORM helped me quickly set up models.
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