1. A method for generating a desktop image for a client computing device, the method comprising: receiving a selection of one or more applications to include in the desktop image; determining references to application containers associated with each of the one or more applications, wherein the application containers are stored in a storage system accessible by a hypervisor running a virtual machine accessing the desktop image; modifying metadata in a file system associated with the disk image to indicate that application data associated with the one or more applications is stored in a number of data blocks of the file system, but not copying the application data into the number of data blocks of the file system; generating a mapping between the number of data blocks of the file system and the references to the application containers; and enabling access to the mapping by the hypervisor when running the virtual machine.