Oh. I don't have much trouble with organizing files that a plugin should have. Generally, I will have
-> Plugin main file on root folder(which should be).
-> Dev files on root folder.
-> Assets folder containing plugin assets. Subfolders js, CSS, img and subfolder admin, frontend if only the plugin is large.
-> Languages folder for pot file.
-> Includes for all other files. Subfolders admin, templates, third-parties and any groupism if required.
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