The new pybind11 bindings require at least Eigen-3.2.7. Travis and Ubuntu 14.04 only include Eigen-3.2.2, so let's include Eigen as a submodule.
Unfortunately Eigen uses Mercurial and no official git mirror exists, so I've cloned Eigen's mercurial repo and added it at patrikhuber/eigen.git at version tag 3.3.3.

The submodule is the current master, which is exactly v1.2.2.
The removed local copy is v1.1.1.

Files saved with the old version seem to be readable with the new version. (apart from the fact that we've now changed to Eigen, which makes it incompatible to the old models.)

This contains a NNLS solver, which we use to solve for the blendshape coefficients.

Submodule points at release tag 0.9.8.3