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Debugging user input in a consistently running application

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IntelliJ IDE Spring BSD
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SO having some issues with trying to debug a program that I'm using, and wondered if anyone could help me out.

The current environment is I'm running Cassandra (v2), using cqlsh (v3) that comes with it. I'm making changes to some of it's functionality, and then using cqlsh to test commands to see if my changes are working as intended, or if not what the input looks like as I step through the program.
I start up a debugging session (either in eclipse of IntelJ, doesn't really matter), firing up the server code to accept connections/input.
I then load up cqlsh, and specify the keyspace that I want to use. This seems to work fine.
I then execute a line of cql to test my changes via command line. What I expect to see is the command line entry being caught by the debugger in my IDE, where I can see how the input is handled by my code changes. What I'm seeing is nothing happening at all, as if no command was submitted.

So my questions would be the following:

1) SHould I see anything in my debugging IDE when executing commands as described above?
2) If not, how would you debug a server based application that has this configuration, especially in the realm of handling user input?
3) If so, what settings should I check to see if I have set correctly, or what processes should be followed to view and debug said submissions?

I figure there has to be a better way then having 50,000 System.out.println() all over the place (assuming they'd even work), or at least, I hope there is.

Thanks for anyone that reads this. Any questions (which I'm sure there may be since I'm probably not using the right descriptors) please ask away.
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