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ROOT/cms/cacheContains cached images, style sheets and JavaScript files. Images that are scaled using CONTENIDOs image functions (TODO include link to article describing image functions) are stored in this folder using a hash as name. Module specific style sheets and JavaScripts that are used for a template are merged to a single file each and stored using the templates name.
ROOT/cms/cache/codeThis folder contains the code cache (TODO add link describing the code cache functionality). When displaying an article in frontend, the PHP code of all its modules is merged into a single file, that is stored in this folder. TODO describe the naming conventions for these files.
ROOT/cms/cache/templates_cWhen using the Smarty plugin, templates are usually precompiled and stored in this folder.
ROOT/cms/cssWhen developing a layout, its style sheets are often outsourced (which is really a good idea!) and should be located in this folder. This folder can have arbitrary subfolders. You can e.g. put all files for a single layout in its own folder. This folder should also be used to store any CSS framework (e.g. Blueprint et.al.) you might use.
ROOT/cms/data 
ROOT/cms/data/config The config folder contains client specific configuration files. These are structured by defined environments as subfolders. By default there is just the production environment, but this can e.g. be extended by development, testing or staging.
ROOT/cms/data/layouts Layouts that can be created using the CONTENIDO backend are stored in this folder. They have each an own folder with a single HTML file, both having the same name as the layout.
ROOT/cms/data/logs 
ROOT/cms/data/modules 
ROOT/cms/data/version 
ROOT/cms/imagesWhen developing a layout, its images should be located in this folder. This folder even can have arbitrary subfolders. You can e.g. put all files for a single layout in its own folder.
ROOT/cms/includes 
ROOT/cms/jsWhen developing a layout, its JavaScripts are often outsourced (which is really a good idea!) and should be located in this folder. This folder can have arbitrary subfolders. You can e.g. put all files for a single layout in its own folder. This folder should also be used to store any JavaScript framework (e.g. jQuery, prototype et.al.) you might use.
ROOT/cms/templatesThis folder contains cTemplate and Smarty templates. This could be either templates for content types as CMS_FILELIST or CMS_TEASER or even templates that are used by more than one module.
ROOT/cms/uploadAll files that are uploaded using CONTENIDOs file manager or the content types CMS_IMGEDITOR or CMS_LINKEDITOR are stored in this folder. This folder can have arbitrary subfolders.
ROOT/cms/xml 

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