Current status and recommendations:

• includes: ok
• api: Should be moved to includes/ActionApi (my preference) or includes/Api (widely used).
• specials: Can be moved directly under includes for now.
• scripts: Currently mixed use of namespaces. Could try moving the actual code to includes/MaintenanceScript and leave the scripts as simple entry point wrappers. Alternatively add prefix ContentTranslation\Maintenance(Script) to autoloader.
• tests/phpunit: Consistently use ContentTranslation\Tests namespace prefix mirroring the main namespace structure.

Benefits:

• No longer need to register each individual php file in extension.json.
• Consistent use of namespace in all code files, makes copy-pasting code easier and avoids accidentally introducing issues.
• Less top level directories, making it easier to navigate the repository.

Notes:

• This would break backwards compatibility if someone would reference our classes externally. To my knowledge this is not happening.
• This could introduce regressions if mistakes in the migration were made. Suggest using an IDE to do the changes that allows checking for such things.