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Make changes persistent

Vladimír Višňovský requested to merge persist into master

Everything that user changes (new files, file changes, file deletes, etc...) should be reflected after restarting of the instance. Deletion will not be made persistent for default files - files that are in git repo will not be affected by deletion. For example if one deletes .ipynb main notebook, by resetting instance, the default notebook will appear.

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