Just like in the title; I have a remote server and I want to access it from inside Eclipse.


Why do I have to set the local directory for the server? Somebody please tell me how to do this!
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You have to set a directory because the server is supposed to be local. You could have a mount(or mapping in windows) on a remote server but the process of the JVM running Glassfish would run locally again.
If you just want to debug:
Enable debugging in the administration console of Glassfish and restart the domain.
Attach to the Glassfish debug port with Eclipse | Debug Configurations… | Remote Java Application.