How to preserve a directory structure when packaging an app

I created an app that includes a number of subdirectories. Some of these subdirectories contain shell scripts (no *.m extension) which are being invoked by some of the Matlab source files. However, the app package tool does not pick up the non-Matlab files. How can I force the package tool to include all files in all directories?

[Jayaram Theegala]

You can manually add the shell scripts that are not being picked by the dependency analyzer by clicking on the "+" icon under section "Files required for your application to run" in your project window or you can use the "-a" flag to the mcc command to add the files you need.