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Cleanup Dockerfile and add some comments for why some files and folders are...

Andersen Pinckney requested to merge development into master

Cleanup Dockerfile and add some comments for why some files and folders are removed. Remove defaults for some ARGS to enforce that they are passed in from the yaml file. Add CODESONAR args to the yaml file. Extend usage of CODESONAR_HOME in the Dockerfile so that some hardcoded paths are no longer so.

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UNCLASSIFIED - NO CUI