The most central classes in the last release are all the Manager classes.
They are all defined and initialized in the ManagerController class.
Every "module" in Phex has its own Manager class.
Regarding your question how Phex connects: The triggering of outgoing connections happens in the HostManager.doAutoConnectCheck() method. Incoming connection are accepted in the OIOServer class.
Please ask if you need any more guidance..
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