1) YES you can try install extension using ioncube but if you have problem as they encode their extension, it will not be possible to deliver any pathces
2) NO as I have not defined any ioncube application.
If you want to send me this extension I could try identify the DB tables that could require sharing. This is not an easy task to identify such information as they are encrypted
3) To provide a JMS tools replication for the ioncube application, you have first to send me this extension by email to let me analyze it.
This is extension dependent and you can alreadry try yourself the installation in a master and a slave site. If you test it yourself, this will reply to your questions.
If you are able to install this ioncube extension in a master and re-install it in a slave with succes, this will reply to your question no 2.
Of your test is successful, you can send me the extension to let me add the definition for the JMS tools.
As I don't have the extension that you want to install, I can not reply.
All I can tell you is that encrypted application may have a risk to not working and that you have to test it yourself.
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