Installing with --sys-prefix inside virtualenv created with --system-site-packages breaks

[MBlistein]

Hey,
love this package, unfortunately it is giving me some head-aches during installation.

I have installed all jupyter-related things as debian packages. Next, I created a virtual environment for this package only (virtualenv was created with --system-site-packages to access outside packages) and proceeded to install it:
jupyter contrib nbextension install --sys-prefix
I chose the --sys-prefix option to keep the installation contained to the environment. The installation runs fine until:

[I 16:23:26 InstallContribNbextensionsApp] Installing jupyter_contrib_nbextensions items to config in /etc/jupyter
Enabling: jupyter_nbextensions_configurator
- Writing config: /etc/jupyter
Traceback (most recent call last):
  File "/home/my_user/.venvs/jupyter/bin/jupyter-contrib", line 10, in <module>
    sys.exit(main())
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 266, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_core/application.py", line 50, in start
    super(JupyterContribApp, self).start()
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 255, in start
    self.subapp.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/application.py", line 231, in start
    super(ContribNbextensionsApp, self).start()
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 255, in start
    self.subapp.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/application.py", line 180, in start
    toggle_install_config(self._toggle_value, **kwargs)
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/install.py", line 97, in toggle_install_config
    configurator_app.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_nbextensions_configurator/application.py", line 66, in start
    'jupyter_nbextensions_configurator')
  File "/usr/lib/python3/dist-packages/notebook/serverextensions.py", line 202, in toggle_server_extension_python
    self.toggle_server_extension(module)
  File "/usr/lib/python3/dist-packages/notebook/serverextensions.py", line 185, in toggle_server_extension
    sys_prefix=self.sys_prefix, logger=self.log)
  File "/usr/lib/python3/dist-packages/notebook/serverextensions.py", line 74, in toggle_serverextension_python
    cm.update("jupyter_notebook_config", cfg)
  File "/usr/lib/python3/dist-packages/traitlets/config/manager.py", line 87, in update
    self.set(section_name, data)
  File "/usr/lib/python3/dist-packages/traitlets/config/manager.py", line 74, in set
    f = io.open(filename, 'w', encoding='utf-8')
PermissionError: [Errno 13] Permission denied: '/etc/jupyter/jupyter_notebook_config.json'

Installing without --sys-prefix fails also:

[I 16:23:44 InstallContribNbextensionsApp] Installing /home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/nbextensions/addbefore -> addbefore
Traceback (most recent call last):
  File "/home/my_user/.venvs/jupyter/bin/jupyter-contrib", line 10, in <module>
    sys.exit(main())
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 266, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_core/application.py", line 50, in start
    super(JupyterContribApp, self).start()
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 255, in start
    self.subapp.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/application.py", line 231, in start
    super(ContribNbextensionsApp, self).start()
  File "/usr/lib/python3/dist-packages/jupyter_core/application.py", line 255, in start
    self.subapp.start()
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/application.py", line 178, in start
    toggle_install_files(self._toggle_value, **kwargs_files)
  File "/home/my_user/.venvs/jupyter/lib/python3.6/site-packages/jupyter_contrib_nbextensions/install.py", line 75, in toggle_install_files
    mod.__name__, overwrite=overwrite, symlink=symlink, **kwargs)
  File "/usr/lib/python3/dist-packages/notebook/nbextensions.py", line 225, in install_nbextension_python
    destination=dest, logger=logger
  File "/usr/lib/python3/dist-packages/notebook/nbextensions.py", line 126, in install_nbextension
    ensure_dir_exists(nbext)
  File "/usr/lib/python3/dist-packages/ipython_genutils/path.py", line 167, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/home/my_user/.venvs/jupyter/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/home/my_user/.venvs/jupyter/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/usr/local/share/jupyter'

Installation via --user works, but then I have files in home/local. Is there a user error somewhere or is this a bug?