What is NOT done yet:
- OpenGL context of QOpenGLWindow must be made
  active before calling any GL function in scene.cc. The wrong
  GL context is active otherwise.
- cmake polishing
- final grepping for QT4 leftovers

changes:

-GetPrincipalAxes in Vec3List
 Results with Eigen3 have been verified with 10 randomly picked pdb structures.
 Differences only occur with changing signs of the vectors.

-CalcPrincipalAxis in BoundingBox
 No difference in algorithm, the SelfAdjointEigenSolver no lives in
 Eigenvalues. Does in principal the same thing as the function above,
 just using different functionality.

-SVD superposer
 Unit tests still run through with the changes introduced for Eigen3
 and also manual testing seems to work well.

-CartoonRenderer
 Principal axes calculation for rendering helices as cylinders had to be
 adapted. Rendering looks exactly the same...

-SuperposeFrames
 Not yet tested...

ToDo:
numeric.h and levenberg_marquardt.h in the img/alg module have to be
ported. This will be done in the next few days.

OpenMM library

run cmake with -DENABLE_MM=1
if you can successfully compile, check out the examples in the
modules/mol/mm/examples directory

fixed lddt compilation on Windows
removed DLLEXPORTS from pdbsize.cc

Refactored FindEigen.cmake to adhere to cmake guidelines
Adapted master CMakeLists.txt to changes in find modules

Substitutes DEBIAN_STYLE_LIBEXEC flag and manages location and name of lib and libexec folders on Debian/Ubuntu-based systems

fix master CMakeLists.txt to only add -Wno-attributes for newer compilers (not all older compilers have that option)

added skeleton for Linux deployment with CPack

added CPack configuration to create complete bundle dmg on OSX with "make package"

relative paths

RuleBased conop is an experimental new interface for processing
structures in the conop module. The class exposes a single method
Process with takes care of the complete conop procedure. There are
still a few methods missing, they will be added shortly.

The Transform class was moved from the mol module to the geom module. A typedef
was put into the mol namespace in C++, and a similar alias was put into the
mol python module, with an added deprecation warning.