I understand that a slave site has all the extensions of a master site but can they be turned off in the slave site. Also, can I add an extension to a slave site that is not in a master site.

NO the slave site does NOT have all the extension present in the master.
You can create slave site that does NOT have any extension and that just have the standard joomla default installation.

You can uninstall extension in the slave site or use the JMS tool menu to install/share/uninstall extension.

When an extension is installed, you can also enable/disable it with the Joomla back-end.
This is the case for the module, plugin but also with the extension manage / manager / enable/disble extension.

The second part of the original question was: "Can I add an extension to a slave site that is not in a master site."

I'm still not clear on this... I want to create a slave site that inherits most of the extensions from the master site (as selected), but afterwards I want to install a unique extension on the slave site (a different ecommerce engine, for example) that is not on the master site and that will only apply to the slave site. Would this work?

I'm also trying to figure out if I am limited to the extensions found at www.jms2win.com/en/list-of-extensions, or can I install any extra extensions I want on any slave site?

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(you said)

"You can uninstall extensions in the slave site or use the JMS tool menu to install extensions..." (but it is still not clear if you mean it is only possible to install extensions that have already been installed on the master site.)

The concept of JMS is to share the same joomla application including all the extension.
Therefore ALL the extension must be installed in the master website to allow the slave sites using them. It is NOT possible to install an extension in a slave site that is NOT present in the master.

In general, we explain that the master website should be considered as a library or a repository where all the extension are installed. In addition we recommend to not put any data in the master. This is just a warehouse (a library, a repository).

To make an extension (mainly a component) working, you need the application (php code) and the data (DB). The JMS tools allow creating the require DBs tables used by the extension (as the PHP code is already present in the master).

When an extension is not defined in the JMS tool, the only method to create the MySQL tables required by the extension is to re-install the extension in the slave site.

I hope this is more clear.

Things are much clearer now, thank you!

It is the last thing you said that I need to be sure I understand... It sounds like not every extension must be defined in JMS (I'm assuming the only ones that can be defined are on this list: www.jms2win.com/en/list-of-extensions). So I can install any extension I want on the master, whether it's on this list or not, correct? I don't mind re-installing it manually again on slave sites, I just don't want to be limited to this list of extensions (or this will not work at all... since there are many extensions that I need to use that are not on that list.)

When we defining the extension in the JMS tools, this mean that we define the list of MySQL tables that are used by this extension to allow its re-installatino from a central point.

Otherwise, you have have to go in the slave site to re-install it from the back-end and let the extension create its specific tables.

So the installation can be performed via the JMS tool or from the back-end slave site.