Merging the ac-refac branch into master will bring in all the calibration related work from the last several years. Most of the development work was done on the calib branch, but this was not kept up-to-date with the master branch. The ac-refac branch started from calib and then refactored all the new calibration code (sensitivity analysis, Mads optimization, associated workflow tools and documentation) with these goals in mind:

1. Remove redundancy: during development some of the files were more or duplicated but with different names.
2. Clean up namespaces: in the course of development names of functions, files, modules etc were not always reflective of their purpose or location in the broader structure.
3. Streamline end user workflow: make the command line interfaces, config files, and plotting interfaces more standardized and easier to use.