How can I interact with the windows CMD in real time inside matlab GUI/APP

This may end up being the wrong question, but here goes.

I would like to send a command to the command line, wait for a response and then interact with the command line again from matlab.

At the moment I pass files to a program succesfully using the system() command and I can get a program to start using system(['start ',fullfile('{location of program}'.exe)]).

What I want to do is now ssh to somewhere which will need a password, enter that password interactively, and be able to move around and list files and folders interactively inside of my matlab app. Because I can't do this bit, I can't describe the likely problems I will have next, but for the experts I will list what i want to do next and they may be able to help ahead of time.

Ultimately I am running a program wrSPICE on my computer which I can run in a parallel for loop. It became obvious that since each simulation is independent that I can do this in parallel very easily, including analysing the data from a separate instance of matlab which just checks to see if the data folder has grown and then gets the new data and analyses it. What I now want to do is run loads of simulations from an app where the purpose of the app is to perform a number of pre-simulation checks and calculations, then copy the necesary .m files through an ssh connection to another computer, tell the big computer to run the simulation, then run the analysis code and control the analysis, then copy the analysed data to some place on my pc such that I can plot it.

I accept that this is not the best way to ask a question and if there are any answers I can change the question to be more precise