Harmonise "model" variable names

[zouter]

Right now the first argument of most dynwrap functions can be:

• model
• traj
• object
• trajectory

Possible solutions:

• All to object/model
• Object/model if it is not a trajectory, traj/trajectory if it is a trajectory

Any preference @rcannood ?

[zouter]

Forgot to mention:

• dataset (for infer_trajectory)

[zouter]

I propose the following:

If a wrapper contains a trajectory, use trajectory
Otherwise use dataset

This makes the most sense in the two main dynwrap use cases: creating a trajectory and working with it (i.e. adding a root or calculating a dimensionality reduction), and creating a dataset and working with it (i.e. adding prior information or running a TI method)

This proposal is in branch renamefactorisation

[zouter]

To enhance consistency, I added "common" parameters to the dynwrap object. See 4438600

[zouter]

Fixed by #125