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Do Unix programs typically expect their caller to have already opened the std io files?
They're typically opened by the shell (the command-line environment) before any programs are invoked. Then, the descriptors are inherited each time a new process is created. So, normally the only time a Unix program would open them is to override the default behavior.
So the JVM is created in my job's memory, but as independent threads that communicate by pipes, semaphores, shared memory, common files, something else?
Typically threads communicate using shared memory, and synchronize the memory using mutexes. But, you could certainly write code that uses pipes, common files, sockets, etc... Depends on what the programmer decided when he wrote the code.
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