File structure for packaging
From Joomla! Documentation
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The most basic files, such as index.php, component.php, templateDetails.xml, template_thumbnail.png, favicon.ico, params.ini should be placed directly in your template folder. The most common is to place images, CSS files, JavaScript files etc in separate folders. Joomla override files must be placed in folders in the folder "html".
When making the template folder, your language files should be copied to your template folder. The ones for the front end site should be placed directly in the template folder. If you have language files for the back end, these should be placed in a folder, named for instance "admin". All the language files will be copied automatically to the right folders if stated correctly in the templateDetails.xml.