Bump some of the npm dependencies.
Bump some other npm dependencies.
Fix the current URL references in the error messages.
Revert to using the 'clone' package for deep clones.

lodash's cloneDeep function doesn't deep clone functions, so it broke
some of the config stuff where mongo ObjectID functions were being
cloned. Some testing really needs to be added to the whole configuration
being loaded out of MongoDB area so this could be covered by tests.