how to construct a zencart web site with a lot of secondary developments

Question

I am new to my company now, my company site has been created based on 1.3.8a, and there are lot of zencart core files changed , and a lot of new secondary developed files added . now my boss want to update the company site to zencart 1.5.1, and want to construct the site starting from scratch, the new verson of company site should be clear in structure and easy to update.

can any good people give some suggestions ? and any good theads telling about that ? some thoughts of mine:
1.if new classes files added ,should be placed in includes/classes/jy_class.xxx.php (jy is my company name);
2.if new includes/modules/pages/xxx/header_php.php ,should be placed in includes/modules/jy/pages/xxx/header_php.php
3.if new functions ,should be placed in includes/functions/extra_functions/jy_functions_xxx.php

I know that this question is a opened question , but it is very important for me. I want some zencart developing experts give me some good advices.

Answer 1

Suggestions 1 and 3 are fine. Suggestion 2 won't work; the page cannot be in the subdirectory jy - it must be in includes/modules/pages/xxx/header_php.php. You also want to initiate this activity as soon as possible; Zen Cart 1.3.8a has been compromised for a long time and is not secure.