1. A system for organization of software application files during development and subsequent deployment of the software application to a server, comprising: a split directory structure stored on a computer medium that stores files for a software application, wherein, for each software application, the split directory structure includes both a source folder that stores editable source files as part of the software application, and a corresponding output folder that stores system-generated compiled versions of the source files as part of the software application, together with a build file that indicates the output folder as being an output of its corresponding source folder, and wherein the split directory is accessed as a virtual file that provides an abstraction over the two folders therein, so that the two folders appear to a server as a single application; a server upon which the software application will be deployed; and a deployment tool that allows a user to specify the output folder during deployment of the software application, wherein during the deployment of an application class or resource the server interprets the software application as a union of both the source folder and the output folder, recognizes the split directory structure, parses the build file to determine the corresponding source folder, and deploys the application by making requests to the virtual file which checks first the source folder for the class or resource, and then the corresponding output folder for that class or resource, before deploying the software application files to the server.