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Allow repartition to change on restart

Peter W. Draper requested to merge restart-repartition into master

Attempt to address #801 (closed).

As part of these changes a new file used_parameters.yml.<stepno> is written on any restart. If any parameters have changed with respect to the original values used when the application was first run, they will be written to this file.

Edited by Peter W. Draper

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