XDA Forum Member WugFresh has built a Nexus 7 toolkit. The toolkit provides a wide range of functions but right under one program. You can now flash ROMs, installs apps and fixes permissions. The toolkit is also able to restore and backup ROMs. One can also Unlock the device and root it and also doubles up as a lock kit. This is a pretty solid toolkit in my opinion and the only one so far for the Nexus 7 device. Download the toolkit here.
Source XDA thread