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I have the same problem and I believe it is due to #4426. From what I understand, that commit sets the kernel's cwd to the directory where the server is started and now the configuration variable notebook_dir is useless. I used to start a server in a project's directory using a profile and now I have to do cd /path/to/Project && ipython notebook.
Which is super annoying, I don't know where this came from, but it is a change in behavior that if planned should be announced on ML I suppose.
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