Include deprecated configuration properties in the reference documentation

[wilkinsona]

The current appendix for application properties filters out any properties that are deprecated so they don't appear. Auto-completion is still offered in an IDE but they're hidden in the reference docs. I think it would be useful to include deprecated properties in the docs somehow. A separate Deprecated Configuration Properties appendix perhaps.

[wilkinsona]

Re-opening as we don't want properties with error-level deprecation to be included.