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The recommended way of doing it at this point is to create an IPython profile and set the working directory for the notebooks there. In IPython 2.0+ the setting is:
c.NotebookApp.notebook_dir='path/to/working/dir'
In the file ipython_notebook_config.py in the profile directory (you can look up how to create profiles in the ipython docs).
When you set the command, simply add --profile=profilename (obviously changing the profile name as appropriate).
At the moment there isn't a way to dynamically set the working directory when you start the server, but I could look into adding this. So far the idea has been to rely as much as possible on existing mechanisms in IPython for doing things and so avoid having to maintain too much custom code. What I am considering is adding a wizard for creating and managing ipython profiles to make it easier to switch between them. (Following the philosophy of using the desktop interface to do things you can't easily do with the existing NB server)
When starting a server, the working directory appears to be something completely arbitrary. I would be nice to be able to set it explicitly.
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