1. A method for generating a virtual desktop for a virtual machine to be displayed at a client computing device, the method comprising: booting the virtual desktop from a virtual disk comprised of a base disk image and a user delta disk image that receives all disk writes to the virtual disk; for a selected application to be provided to a user of the virtual desktop, allocating disk space on the virtual disk for one or more files associated with the selected application, the allocating comprising generating and storing on the user delta disk image meta data that indicates one or more locations on the virtual disk at which the one or more files are to be stored; shutting down the virtual desktop after the allocating of the disk space; while the virtual desktop is shut down, maintaining the meta data on the user delta disk; and recomposing the virtual disk by linking the base disk image, an application delta disk image, and the user delta disk image, the user delta disk image configured to receive all disk writes to the composed virtual disk, the application delta disk image including the one or more files associated with the selected application, and the recomposing comprising copying the meta data from the user delta disk image to the application delta disk image and modifying the meta data of the application delta disk image and the user delta disk image so that the one or more files associated with the selected application are mapped to the disk space allocated for the one or more files associated with the selected application and read requests to the virtual disk for the one or more files are satisfied with data from the one or more files associated with the application on the application delta disk image.