I wonder how CMS(Wordpress) know the default template and plugins to run.
Should I store the default value for template in MySQL database or just using file_put_content to store the default value for template/plugins ?
Or, is there any better way ?

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for the template name or style name, you can either store it in database or in xml file.

Can you tell me which one is preferred to do ?

Most are using database, but I prefer storing it as xml file similar to how the symfony2 stores its AsseticBundle configurations as xml files.

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