Fix collection extent schema

[hrodmn]

update_collection_extents() was unaware that collection_extent was already creating the "extent" key in the collection properties json, so we wound up with a redundant "extent" key around the outside. The solution is to return the only the extent contents in the collection_extent and consistently set the key outside of collection_extent.

We are also adding a few tests to make sure the update_collection_extent flag is working as expected.

Resolves #274