Thank you for the answer Tom. I still haven't had time to play around more with the skin folder (since i am more of a developer than designer), but as i can see your answer makes pretty good point about keeping own JS files into the skin directory. I just want to avoid for some reason overriding the template files before the layouts, cause of the way Magento calls the theme. It first calls the layout which i would first extend, then it calls the templates which i would extend as a second option. It's like telling Magento: OK let me take the control from here. And the sooner you take the control in your hands the more options you will have. Please correct me if i am wrong, cause i have been using this technique a lot especially while dealing with CodeIgniter framework and it showed up as a good thing so far.
Thank you again!
Zoran
Thank you for the answer Tom. I still haven't had time to play around more with the skin folder (since i am more of a developer than designer), but as i can see your answer makes pretty good point about keeping own JS files into the skin directory. I just want to avoid for some reason overriding the template files before the layouts, cause of the way Magento calls the theme. It first calls the layout which i would first extend, then it calls the templates which i would extend as a second option. It's like telling Magento: OK let me take the control from here. And the sooner you take the control in your hands the more options you will have. Please correct me if i am wrong, cause i have been using this technique a lot especially while dealing with CodeIgniter framework and it showed up as a good thing so far.
Thank you again!
Zoran