Improve option initialization in traj. analysis.

Improve option initialization in traj. analysis.

All methods that add options to an options object now take an externally
provided options object.  This both simplifies the calling code,
allowing them to control the lifetime of the objects, as well as the
implementing code, since they no longer need to have an internal options
object just for the purpose of returning it.  With the old interface, it
was also impossible to get a reference to the options object more than
once; with the new, the caller has much more flexibility.

Change-Id: I8a2e539fa5abefe696a26919b8591691a1cccc61