Add 2.0 support for cert.py tests

I've updated config.json to set the version to be 2.0.
The changes to the open remote window test were forced due to an API change which removed getRunningApps.
The fxos_appgen version change is required to generate files for 2.0.

I've filed Bug 1053246 to track some crashes on the Flame which seem to be related to the voice and data window properties. I'm working around this in the webapi tests as a crash there prevents getting results. I think this is also causing two individual permissions tests to timeout, but I'm not doing a workaround there, as it is possible to get results for the remainder of the permissions.
Can you peg the marionette version? The client may signficantly change in subsequent packages, so pegging the version makes sure this works