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Refactor JSON output to prevent concurrency bugs

Vicentini Filippo requested to merge github/fork/femtobit/output into master

Created by: femtobit

The JSON output bug fixed by #64 was caused because converting an ObsManager to JSON performs an MPI reduction and thus has to be called from all processes, while in the first version of my code it was only called by rank 0.

This PR adds a few changes to the output code to make errors like this less likely.

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