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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/dataThis folder contains client specific files that change on a regular basis. It contains no files on its own but has a set of subfolders which are described below.
ROOT/cms/data/configThe 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/layoutsLayouts 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/logsThis folder is used for client specific log files. TODO explain how to enable client specific logs.
ROOT/cms/data/modulesThis is probably one of the most important folders in each client folder. It contains the installed modules which have a folder structure on their own.
ROOT/cms/data/versionWhen editing style sheets, JavaScripts, layouts, modules or templates in CONTENIDOs backend, their previous content is versioned and stored in this folder.
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/includesTODO I have no clue
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/xmlTODO I have no clue

Backend

Data

 

 

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ROOT/contenido/classes 
ROOT/contenido/cronjobs 
ROOT/contenido/external 
ROOT/contenido/images 
ROOT/contenido/includes 
ROOT/contenido/jar 
ROOT/contenido/plugins 
ROOT/contenido/scripts 
ROOT/contenido/styles 
ROOT/contenido/templates 
ROOT/contenido/templates_c 
ROOT/contenido/tools 
ROOT/contenido/xml 

Data

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ROOT/data/cacheThis folder is used for caching of client independant files that are created by some plugins (e.g. PIFA or PIXI) and modules. Also the CONTENIDO UpdateNotifier uses this folder for its files. TODO check if there are other purposes.
ROOT/data/configClient independant configuration files are located in this folder.
ROOT/data/cronlogWhen cronjobs are setup, these usually store *.job-files containing a timestamp in this folder to signal that and when they have been run last.
ROOT/data/localeThis folder contains gettext files used to localize the CONTENIDO backend.
ROOT/data/logsDepending upon configuration settings some log files are maintained that can be found in this folder.
ROOT/data/tempTODO I have no clue

On this page you get an overview of the single directories in CONTENIDO. 

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