Look into the feasibility of implementing a better mechanism to tie applications with multiple executables together

Look into the feasibility of implementing a better mechanism to tie applications with multiple executables together. Currently platforms such as Dos and Amazon can have an issue where the program will automatically define multiple executables as either multiple applications in Galaxy of as one with multiple executions available. Look into providing a better option to the user for interfacing with these programs. Suggested to look into seeing if tying the application id to the folder, to ensure it is the same, for these platforms which utilize folders as the root of the application along with any way to provide differentiation between the executables.