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Let's say you want to customize the layout of the content Joomla component. To do so, just copy the com_content directory from /warp/systems/joomla/layouts to the template /layouts directory or even better create your own style and change the files to your needs. If you are using your own style, copy the directory to /styles/YOUR_STYLE/layouts. This way you won't lose any of your changes after an update of your template. Make sure to only copy the files you want to change, all other layout files will be loaded automatically from the system defaults.