Root directories/structure question

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Hi,

I have read the following :
- general structure documentation :http://www.concrete5.org/documentation/developers/system/directory-...
- question about core folder and overrides :http://www.concrete5.org/community/forums/customizing_c5/what-about...
-http://www.concrete5.org/community/forums/customizing_c5/models-in-... :
[package_name]/blocks/[block_name]/models vs. [package_name]/models

But something is still unclear to me : When should we use the root directories, the folders at the root of the concrete5 website folder ? For example /models ? Does it override the contents of concrete/models ? Or should one use it in case some model was shared across several packages ?