What to do about differing JSON input and output formats?

[jamesaoverton]

On the OBO Slack a user pointed out that we handle ".json" extension differently for input and output. We are interpreting input JSON as JSON-LD https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java#L392 while the output JSON is OBOGraphs JSON https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java#L1714.

I'm not sure what to do about this. At the very least we need better documentation -- maybe a section of the docs on formats.