You can ship other files, however the deploytool requires that they be subfolders of your application. They can't be just anywhere you want. That's why I don't use deploytool. You can use a third party installation package builder to put your files where you want and they don't have to be on the MATLAB search path. However, when you go to access them, you must use the full path where you expect them to be. If you leave off the folder in your filename when you use something like load() or xlsread(), then it will search only the search path and won't find your special folder. That's why you need to specify the full path name, which, of course, is an excellent idea in any case.