Right now the --notebook-dir flag only sets the saving directory, but kernels still start wherever the notebook process was started. For consistency, if the notebook dir flag was given, it should also apply to the kernel directories, otherwise it's a bit useless, and makes it clumsy to run isolated servers configured with directories for their own profiles.
This is easy but I think we should make it a blocker for 0.13 so that there's at least some consistent mechanism for mild user isolation out of the box.
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