Improve documentation on the distinction between a (synced) JSONDict and a dict

[csadorf]

We need to clarify that the synchronized JSONDict data structure underlying for example a Job.statepoint or a Job.document is similar to, but not the same as a Python dict. This is especially important when it comes to the conversion to a dict and subsequent manipulation which can lead to some confusion as demonstrated in this issue.

I suggest to add highly visible warnings and links to respective sections wherever we introduce the data structure.