Hi,
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How can I make the connection secure? Is there a way to setup SSH, SSL, or other means?
You can connect to MySQL server using SSH and SSL. Please refer SQLyog's help documentation here: http://static.webyog.com/docs/SQLyog/#SSH_Tunneling_SQLyog_MySQL_Client.html and http://static.webyog.com/docs/SQLyog/#SSL_encryption_SQLyog_MySQL_Client.html
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Can I control the port on which SJA works? say 443 or 22?
We can't clearly understand what you are exactly referring to? If you want SJA to connect to any specific port while making SSH connection, Yes you can mention that particular port number where SSH server is listening. If you want SJA's MySQL client to connect to MySQL server using user defined port, that can't be done.
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Can I define multiple databases in the XML configuration file?
No, while synchronizing databases you can't define multiple databases in single job file. You will have to create multiple job files for synchronizing each database and you can execute them in one go by scheduling batch script.
Regards,
Shubhansh