Porting to AMatrix

These are the steps to be taken in order to migrate from ublas dense matrix and vectors to AMatrix:

• Replacing the ublas_interface.h with amatrix_interface.h
• Changing resize(size) of vector to resize(size, false) which not preserve the previous data
• Replacing the boost::numeric::ublas::vector with DenseVector
• Replacing the boost::numeric::ublas::bounded_matrix with DenseMatrix