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Themes are explored in full in the Design Guide: http://doc.prestashop.com/display/PS15PS16/Designer+Guide (link to the 1.5 version).
Modules and the override system are explored in this Developer Guide, starting with the "Concepts" section below. You can learn more about each in the following chapters:

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Overriding is a system in itself. PrestaShop uses completely object-oriented code. One of the advantages of this is that, with the right code architecture, you can easily replace or extend parts of the core code with your own custom code, without having to touch the core code. Your code thus overrides the core code, making PrestaShop behave as you prefer it to.
It is not recommended to use an override in a module that you intend to distribute (for instance through the PrestaShop Addons marketplace), and they are forbidden in partner modules. Keep them for your own shop.

PrestaShop's technical architecture

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