1. A method for generating a virtual desktop for a client computing device, the method comprising: receiving a user selection of one or more applications to include in the virtual desktop, the virtual desktop running in a virtual machine that includes a virtual disk and is executed in a physical computer system; determining references to application containers associated with each of the one or more applications, each of the application containers including one of the applications and application data associated therewith; generating metadata associated with the application data included in the application containers, the metadata indicating that data blocks containing the application data are reserved and not stored in the virtual disk, and are stored in the application containers; generating a mapping between the data blocks of the application data that are reserved in the virtual disk and the data blocks of the application data stored in the application containers; and enabling access to the mapping by the hypervisor when running the virtual desktop in the virtual machine.