Remove sqlite_metadata, package_checksum_type, and metadata_checksum_type from the API after verifying that bindings won't break

[dralley]

Support for generating sqlite metadata was removed in #3328, and support for specifying metadata and package checksum types independently was deprecated in #3342 / #2480

However these fields were not removed from the API due to some concern around how the API bindings would react - we've had some reports that older versions of the client bindings might always send certain fields even if the user isn't using them. In such a case, any removals from the API might be breaking, despite lack of use of the features removed.