Rewrite options such that they can be constructed without the commandline parser

Closes #36

See merge request !126

Add tests for Stokes DG on quadrilaterals

See merge request !123

PEP8

See merge request !125

Stokes on quadrilaterals (with diagonal_jacobian transformation)

Closes #69

See merge request !116

Update UFL to 2016.2

Closes #68

See merge request !124

Update submodules

See merge request !122

We avoid the bug by not applying the transformation and casting the
result of jacobianInverseTransposed to a FieldMatrix. This way we do
not exploit the diagonal structure of the Transformation. Should get
fixed in the near future.