ConfigManager should not write out default values found in the .d directory #3485
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This is a followup of #3116.
When the config manager reads the
.json+.d/*.jsonfiles, all the data gets merged into one dict. When writted out again, everything ends on in the root.jsonfile. Here I remove all entries that are already present in the.d/*.jsonfiles.For instance, when installing ipyvolume, you end up with the file
{prefix}/etc/jupyter/nbconfig/notebook.d/ipyvolume.json. If you now runjupyter nbextension ...for anything, all the data from theipyvolume.jsonfile ends up in{prefix}/etc/jupyter/nbconfig/notebook.d. Uninstalling ipyvolume will never clean this up, so it will always stay around. This is now avoided by this PR.