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You can use Eclipse or any Java IDE to debug the cloudstack systemVM services as described below:
Then you can connect to agent in ssvm, based on the ip address based on on eth1 or eth2, and port 8787
Or if the above steps sound too complicated, you can debug the systemvm resource locally using the cloudstack codebase:
For example, There is unit test code, called, LocalNfsSecondaryStorageResourceTest, you can mock the commands send to resource, then test it locally, but the requirement is that your local machine needs to be able to mount nfs(Both Linux/Mac works, Windows can't). I'd prefer unit test, as it's easier to test/debug/fix.