FIX replace np.atleast_2d with new utils.array2d

doc/developers/index.rst

sklearn/cluster/_feature_agglomeration.py

sklearn/covariance/empirical_covariance_.py

sklearn/covariance/shrunk_covariance_.py

sklearn/covariance/tests/test_covariance.py

sklearn/datasets/samples_generator.py

sklearn/decomposition/dict_learning.py

sklearn/decomposition/fastica_.py

sklearn/decomposition/pca.py

sklearn/feature_extraction/image.py

sklearn/feature_selection/univariate_selection.py

sklearn/gaussian_process/gaussian_process.py

sklearn/linear_model/base.py

sklearn/linear_model/least_angle.py

sklearn/linear_model/omp.py

sklearn/manifold/locally_linear.py

sklearn/naive_bayes.py

sklearn/neighbors/ball_tree.c

sklearn/neighbors/ball_tree.pyx

sklearn/svm/base.py