It isn’t good idea to include some plugins directly in your theme, because you loose oportunity to update plugin etc. If you do so manually and update whole theme you can try to put folder with plugin eg. my-plugin in your themes root directory and in functions.php just include main my-plugin.php (folder name and main php file always have the same name). It may be good idea if you develop your own plugin for theme and update whole theme if you do changes.
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