Replace PyYAML with ruamel, add ability to save yaml

When we first setup daiquiri i inadvertantly though that ruamel provided the yaml package, but this is actually provided by PyYAML. We require ruamel in deps to be consistent with bliss, but something somewhere else does provide PyYAML as its available in the environment, hence the confusion.

This PR fully replaces any PyYAML deps with ruamel, and also allows us to save yaml back out (as ruamel preserves comments)

Initially pulled from !439 (closed)