How to include executable in deployed application

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Hi,
I want to deploy an application which calls a third-party .exe by system('') command. For non deployed, Matlab finds the executable if it is on Matlab Path.
However, when I want to call the executable from a deployed version of the application, system cant find it, although I included it with the app and I'm calling it with ctfroot().
Investigating the issue, I found the folder containing the executable to be located within the folder "C:\Progra...\mrcCache\nameOfAppli". This is a subfolder of ctfroot.
Is there a way to call the executable, or to get this folder's name, other than debugging with windows explorer and hoping that things won't change?

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