Hello here, and thanks for the great work on Jupyter!

Recently I have developed Jupytext, a contents manager for Jupyter, and I would now like to configure Jupyter to use Jupytext' contents manager when Jupytext is installed.

The contents manager works well when I install a etc/jupyter/jupyter_notebook_config.json file with content

{
  "NotebookApp": {
    "contents_manager_class": "jupytext.TextFileContentsManager"
  }
}

But I would much prefer to use the json diff configuration files, and write the same content into etc/jupyter/jupyter_notebook_config.d/jupytext.json. Yet, only the NotebookApp.nbserver_extensions part of these diff files are actually loaded by Jupyter (cf. the code).

I have therefore developed a server extension that replaces the contents manager. What I like in this approach is that the user can choose to enable or disable the server extension with e.g. jupyter serverextension disable jupytext.

But unfortunately, the server extension is loaded a bit too late, and I have to re-run a few of the initialization step of the NotebookApp (code). It works in simple cases, but in others it does not - cf. mwouts/jupytext#185. May I ask therefore if you have a recommendation on how to best offer a defaut (and removable) configuration that activates Jupytext's contents manager?