Method and apparatus for factory-installing directories with long filenames while maintaining proper references to the short filename equivalents thereof are described. During a development stage, a determination is made whether any files or directories with long filenames were created by an application installed on a development system for developing an installation package for the application. If so, the development system is queried for the short filenames associated with these long filenames. The development system then creates a factory-install package for the application in which all short filename references to these long filename files and directories are programmatically replaced with tokens that are unique to each long filename. The factory-install package is then uploaded to a factory server. Subsequently, during a factory-installation stage, the factory-install package is downloaded to a built-to-order ("BTO") system and, as the package is installed on the BTO system, the instances of all tokens are dynamically replaced with the equivalent short filenames.