Rename id fields in JS API to be more foolproof

[Cormac Relf]

While I'm at it breaking compatibility in favour of usability, I might also kill the reuse of the field name "id" to refer to every different kind of ID. clusterId on a Cluster, refId on a Cite because it points to a Reference. Then you won't have so many accidents like earlier in this issue.

Originally posted by @cormacrelf in #117 (comment)