1. A system for organization of files during a software development process, comprising: a computer including a processor and storage medium; a split directory structure stored on the computer, for use in deploying a software application, said split directory structure further comprising a source folder that stores source files for use with or as part of the software application, and a corresponding output folder that stores compiled versions of the source files for use with or as part of the software application, wherein the output folder is generated during the build process, and includes a build file which includes a list of path mappings from physical file locations to virtual file locations, and wherein the split directory is accessed as a virtual file that provides an abstraction over the source and output folders, so that the folders appear as a single application; and wherein subsequently, during deployment of the software application, the system determines the presence of the build file in the output folder, parses the list of path mappings included therein, maps virtual file locations specified in the source directory to physical file locations according to the path mappings, and deploys the application by making requests to the virtual file including retrieving source files and compiled versions of the sources files as required from the physical locations according to the path mappings.