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

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

1 and 3, yes. 2, no, because /includes/modules/pages/ files are not overrideable - there is no processing structure to use a "template" copy of these. At least some of the filenames are also fixed, so you probably cannot prefix them with your company tag. You can and should note your name, date and relevant comments in the file contents, though.

There are some other override folders as well, for deeper structures, two at least named simply /overrides/:
/includes/autoloaders/overrides/
/includes/init_includes/overrides/

The wiki should have some articles about using these and others.

good advices，thank gjh42

http://www.zen-cart.com/search.php?do=process&search_type=1&contenttypeid=24&query=overrides