If we decide to revert #85, this will work as a "pseudo" non-persistent storage of sorts – which would affect files but not notebooks. The idea is that we can loop over files matching the supported file formats (CSV/TSV, PNG, JPEG) and delete them ourselves, despite JupyterLite's efforts to keep them stored persistently.
To be on the safe side, so as not to remove any useful files, I think we can also add a breaking change so that all the uploaded files in the EmFS are stored under, say, jupytereverywhere-files/ or jupytereverywhere-storage/ instead of in the root directory.
However, again, this is iff we revert #85 later on.