Fix armada object can override values by --set
Fix armada object can override values by --set

This PS fix to override values by --set option.
Now values come from --set are overriden on self.documents object.
But self.manifest object don't know what happens.
So need to update self.manifest object after override.

Change-Id: I714224788b4b6bd3da3508982821c59b5cff4a42

att-comdev/armada,att-comdev/armada