I've spent some time researching Sencha Cmd and the default setup seems simple enough however, when I try to do something a little custom, it gets very complicated and I cant find any useful information.

First I would like to know how can I build an existing project using Sencha Cmd for production (for both Ext JS and Sencha Touch)?

I also have some questions regarding file/folder structure. I dont have index.html file since the application its dynamically created by php. Here is the structure that I'm trying to achieve.

/index.php - entry for the application (this will determine whether to load desktop or mobile)
/mobile/ - this folder will encapsulate all files for mobile (including app.json, app.js, etc)
/mobile/app - contains view, model, controller, etc

/etc/sencha-touch-2.1.1/ - Here I have different versions of sencha platforms so I could switch on the fly

How can I achieve this? Could you please provide examples of config files.