Rewrite of run_GUI and run_CMD

[MaximeBaudette]

I'm not very familiar with MatLab programming, but I think both interface can be rebuild around common core functions that both interface should use.
This way we could ensure a better maintenance of the code.

Also It seems that run_cmd is implemented in such a way that the user should modify the script for setting the parameters of his choice. I don't really like that and think it should be implemented in such way that everything is put in argument (using objects defining the plugins parameter)

[MaximeBaudette]

From @lvanfretti

It is very important we have all examples with scripts.

Indeed, in the current implementation there is no real CLI in rapid, but scripts can be prepared to directly interact with the core and run the toolbox's algorithms.

In a first stage we can update all examples with a script to run them.
In a further evolution we should implement a CLI with public methods (that would also be used in the GUI), and deprecate the direct interaction with the core.

[MaximeBaudette]

I added an issue to track that we add a script in each example #29

[janlav]

rapid() can be called with an object or an struct with properties/fields that conforms to that a RaPIdObject.

A suggestion is that we rename/remove run_rapid_cmd.m (rename it to rapid_scripting_template.m or something).

Can we create a detailed checklist for this issue?