Building igl statically and moving to the dep scripts

Fixing dep build script on Windows and removing some warnings.

Use bundled igl by default.

Not building with the dependency scripts if not explicitly stated. This way, it will stay in
Fix the libigl patch to include C source files in header only mode.

src/libigl/igl/covariance_scatter_matrix.h

@@ -0,0 +1,38 @@
+// This file is part of libigl, a simple c++ geometry processing library.
+// 
+// Copyright (C) 2013 Alec Jacobson <alecjacobson@gmail.com>
+// 
+// This Source Code Form is subject to the terms of the Mozilla Public License 
+// v. 2.0. If a copy of the MPL was not distributed with this file, You can 
+// obtain one at http://mozilla.org/MPL/2.0/.
+#ifndef IGL_COVARIANCE_SCATTER_MATRIX_H
+#define IGL_COVARIANCE_SCATTER_MATRIX_H
+
+#include "igl_inline.h"
+#include "ARAPEnergyType.h"
+#include <Eigen/Dense>
+#include <Eigen/Sparse>
+ 
+namespace igl
+{
+  // Construct the covariance scatter matrix for a given arap energy
+  // Inputs:
+  //   V  #V by Vdim list of initial domain positions
+  //   F  #F by 3 list of triangle indices into V
+  //   energy  ARAPEnergyType enum value defining which energy is being used.
+  //     See ARAPEnergyType.h for valid options and explanations.
+  // Outputs:
+  //   CSM dim*#V/#F by dim*#V sparse matrix containing special laplacians along
+  //     the diagonal so that when multiplied by V gives covariance matrix
+  //     elements, can be used to speed up covariance matrix computation
+  IGL_INLINE void covariance_scatter_matrix(
+    const Eigen::MatrixXd & V, 
+    const Eigen::MatrixXi & F,
+    const ARAPEnergyType energy,
+    Eigen::SparseMatrix<double>& CSM);
+}
+
+#ifndef IGL_STATIC_LIBRARY
+#include "covariance_scatter_matrix.cpp"
+#endif
+#endif