Project Ara is staying with Google's Android team

In his announcement post about the deal, Google CEO Larry Page said that "Lenovo intends to keep Motorola’s distinct brand identity", which seems to indicate that the Moto X, Moto G, and Moto Maker will all continue to function as is; and, Motorola won't suddenly be abandoning its near-stock Android software philosophy. As far as Project Ara, Motorola's modular phone initiative, that is not part of this deal and will be staying with Google's Android team.

On a conference call with reporters, Lenovo said that the deal only includes Motorola's devices division, and not the Advanced Technology and Projects group. The Advanced Technology and Projects group is about 100 people strong and led by former DARPA director Regina Dugan, and is the group directly responsible for Project Ara, security tattoos, and biotech sensors. 

Reportedly, the plan is for Google to scale Project Ara with the full backing of Google's own resources, which should prove to accelerate the project quite a bit. 

source: The Verge