Prune and document application.yml

[mark-dce]

• [ ] remove any settings in application.yml that are not used by the application
• [ ] document the remaining settings in the wiki

[mark-dce]

TODO:

1. go through application.yml, for each item, search for the item in the code - it it doesn't exist, remove it from the sample file
2. for remaining items, add a short comment to the sample file clarifying how the value is used