When you create a "fresh" slave sites with Joomla Installation, you receive a new website without any extensions installed.
The only extensions that are automatically shared by JMS is the template (themes) and the language files because Joomla does not use anything from the database to recognize them.
For the component, modules and plugin, you have to re-install them into a slave site to allow those kind of extension fill the database with their specific content.
When you replicate a website usiing the JMS "website template" menu, you replicate all the tables of a website and therefore all the content of the pre-installed extension present in this website to replicate.
In summary, if you replicate a website, you have all the extension present in this website automatically replicate.
If you create a fresh slave site with the Joomla Installation, you have to re-install the extension.
Only the themes and language extension are automatically shared between the websites.
If you want specific themes for a specific slave site, you have an option in the slave site definition that allow you give a speific folder for that.
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