Integrate msckd

[arrenglover]

Will Maddern modified the modified sequential clustering, by adding a few of the TODO functionality plus modifying the Mahalanobis distance to use a nearest neighbour technique for speed-ups. This code should be integrated back in to the bowmsctrainer. The openMP changes might conflict with these changes and needs to be dealt with.

The files are present in the repository but not included in the project.

[kmactavish]

I also changed the Mahalanobis distance to the L2 norm (which is much faster) since the covariance matrix was hard-coded to identity (so there probably are conflicts...).