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A file with .json extension briefly appeared on my workspace while I was saving my new MDL file created in R. Why?

This is due to the fact that the R->MDL conversion is done via the JSON format. It is also related to the automatic refresh of the Project Explorer view. This refresh occurs periodically, so it may occur exactly at the moment when the '.json' file is written and so it would become visible. The bottom line is that it will not cause any problems and if it is seen it will shortly be replaced with the '.mdl' equivalent model.