Fix links to the code.

docs/matlab-to-eigen.html

@@ -312,6 +312,6 @@
     <a href="http://eigen.tuxfamily.org/dox/AsciiQuickReference.txt">Eigen's
     "ASCII Quick Reference" with MATLAB translations</a>
     <br>
-    <a href="./tutorial.html">IGL Lib Tutorial</a>
+    <a href="./tutorial/chapter-1/">IGL Lib Tutorial</a>
   </body>
 </html>

docs/tutorial/chapter-1.md

@@ -152,15 +152,15 @@ Similarly, a mesh can be written in an OBJ file using:
 igl::writeOBJ("cube.obj",V,F);
 ```
 
-[Example 101](101_FileIO/main.cpp) contains a simple mesh
+[Example 101]({{ repo_url }}/tutorial/101_FileIO/main.cpp) contains a simple mesh
 converter from OFF to OBJ format.
 
 ## Visualizing surfaces
 
 Libigl provides an glfw-based OpenGL 3.2 viewer to visualize surfaces, their
 properties and additional debugging information.
 
-The following code ([Example 102](102_DrawMesh/main.cpp)) is a basic skeleton
+The following code ([Example 102]({{ repo_url }}/tutorial/102_DrawMesh/main.cpp)) is a basic skeleton
 for all the examples that will be used in the tutorial.
 It is a standalone application that loads a mesh and uses the viewer to
 render it.
@@ -189,9 +189,9 @@ The function `set_mesh` copies the mesh into the viewer.
 Additional properties can be plotted on the mesh (as we will see later),
 and it is possible to extend the viewer with standard OpenGL code.
 Please see the documentation in
-[Viewer.h](../include/igl/opengl/glfw/Viewer.h) for more details.
+[Viewer.h]({{ repo_url }}/include/igl/opengl/glfw/Viewer.h) for more details.
 
-![([Example 102](102_DrawMesh/main.cpp)) loads and draws a mesh.](images/102_DrawMesh.png)
+![([Example 102]({{ repo_url }}/tutorial/102_DrawMesh/main.cpp)) loads and draws a mesh.](images/102_DrawMesh.png)
 
 ## Interaction with keyboard and mouse
 
@@ -210,7 +210,7 @@ bool (*callback_key_up)(Viewer& viewer, unsigned char key, int modifiers);
 ```
 
 A keyboard callback can be used to visualize multiple meshes or different
-stages of an algorithm, as demonstrated in [Example 103](103_Events/main.cpp), where
+stages of an algorithm, as demonstrated in [Example 103]({{ repo_url }}/tutorial/103_Events/main.cpp), where
 the keyboard callback changes the visualized mesh depending on the key pressed:
 
 ```cpp
@@ -247,7 +247,7 @@ control the camera directly in your code.
 
 The viewer can be extended using plugins, which are classes that implements all
 the viewer's callbacks. See the
-[Viewer_plugin](../include/igl/opengl/glfw/ViewerPlugin.h) for more details.
+[Viewer_plugin]({{ repo_url }}/include/igl/opengl/glfw/ViewerPlugin.h) for more details.
 
 ## Scalar field visualization
 
@@ -268,7 +268,7 @@ scalar function is converted to colors using a color transfer function, which
 maps a scalar value between 0 and 1 to a color. A simple example of a scalar
 field defined on a surface is the z coordinate of each point, which can be
 extract from our mesh representation by taking the last column of `V`
-([Example 104](104_Colors/main.cpp)). The function `igl::jet` can be used to
+([Example 104]({{ repo_url }}/tutorial/104_Colors/main.cpp)). The function `igl::jet` can be used to
 convert it to colors:
 
 ```cpp
@@ -279,7 +279,7 @@ igl::jet(Z,true,C);
 The first row extracts the third column from `V` (the z coordinate of each
 vertex) and the second calls a libigl functions that converts a scalar field to colors. The second parameter of jet normalizes the scalar field to lie between 0 and 1 before applying the transfer function.
 
-![([Example 104](104_Colors/main.cpp)) igl::jet converts a scalar field to a color field.](images/104_Colors.png)
+![([Example 104]({{ repo_url }}/tutorial/104_Colors/main.cpp)) igl::jet converts a scalar field to a color field.](images/104_Colors.png)
 
 `igl::jet` is an example of a standard function in libigl: it takes simple
 types and can be easily reused for many different tasks.  Not committing to
@@ -307,7 +307,7 @@ viewer.data().add_label(p,str);
 
 Draws a label containing the string str at the position p, which is a vector of length 3.
 
-These functions are demonstrate in [Example 105](105_Overlays/main.cpp) where
+These functions are demonstrate in [Example 105]({{ repo_url }}/tutorial/105_Overlays/main.cpp) where
 the bounding box of a mesh is plotted using lines and points.
 Using matrices to encode the mesh and its attributes allows to write short and
 efficient code for many operations, avoiding to write for loops. For example,
@@ -318,14 +318,14 @@ Eigen::Vector3d m = V.colwise().minCoeff();
 Eigen::Vector3d M = V.colwise().maxCoeff();
 ```
 
-![([Example 105](105_Overlays/main.cpp)) The bounding box of a mesh is shown using overlays.](images/105_Overlays.png)
+![([Example 105]({{ repo_url }}/tutorial/105_Overlays/main.cpp)) The bounding box of a mesh is shown using overlays.](images/105_Overlays.png)
 
 ## Viewer Menu
 
 As of latest version, the viewer uses a new menu and completely replaces
 [AntTweakBar](http://anttweakbar.sourceforge.net/doc/) and
 [nanogui](https://github.com/wjakob/nanogui) with [Dear ImGui](https://github.com/ocornut/imgui). To extend the default menu of the
-viewer and to expose more user defined variables you have to implement a custom interface, as in [Example 106](106_ViewerMenu/main.cpp):
+viewer and to expose more user defined variables you have to implement a custom interface, as in [Example 106]({{ repo_url }}/tutorial/106_ViewerMenu/main.cpp):
 ```cpp
 // Add content to the default menu window
 menu.callback_draw_viewer_menu = [&]()
@@ -405,7 +405,7 @@ menu.callback_draw_custom_window = [&]()
 };
 ```
 
-![([Example 106](106_ViewerMenu/main.cpp)) The UI of the viewer can be easily customized.](images/106_ViewerMenu.png)
+![([Example 106]({{ repo_url }}/tutorial/106_ViewerMenu/main.cpp)) The UI of the viewer can be easily customized.](images/106_ViewerMenu.png)
 
 ## Multiple Meshes
 
@@ -417,4 +417,4 @@ field. By default it his is set to `0`, so in the typical case of a single mesh
 `viewer.data()` returns the `igl::ViewerData` corresponding to the one
 and only mesh.
 
-![([Example 107](107_MultipleMeshes/main.cpp)) The `igl::opengl::glfw::Viewer` can render multiple meshes, each with its own attributes like colors.](images/multiple-meshes.png)
+![([Example 107]({{ repo_url }}/tutorial/107_MultipleMeshes/main.cpp)) The `igl::opengl::glfw::Viewer` can render multiple meshes, each with its own attributes like colors.](images/multiple-meshes.png)

docs/tutorial/chapter-2.md

@@ -8,7 +8,7 @@ coloring routines of our viewer.
 ## Normals
 Surface normals are a basic quantity necessary for rendering a surface. There
 are a variety of ways to compute and store normals on a triangle mesh. [Example
-201](201_Normals/main.cpp) demonstrates how to compute and visualize normals
+201]({{ repo_url }}/tutorial/201_Normals/main.cpp) demonstrates how to compute and visualize normals
 with libigl.
 
 ### Per-face
@@ -87,7 +87,7 @@ where $N(i)$ are the triangles incident on vertex $i$ and $θ_{ij}$ is the angle
 at vertex $i$ in triangle $j$ [^meyer_2003].
 
 Just like the continuous analog, our discrete Gaussian curvature reveals
-elliptic, hyperbolic and parabolic vertices on the domain, as demonstrated in [Example 202](202_GaussianCurvature/main.cpp).
+elliptic, hyperbolic and parabolic vertices on the domain, as demonstrated in [Example 202]({{ repo_url }}/tutorial/202_GaussianCurvature/main.cpp).
 
 ![The `GaussianCurvature` example computes discrete Gaussian curvature and visualizes it in pseudocolor.](images/bumpy-gaussian-curvature.jpg)
 
@@ -132,7 +132,7 @@ Alternatively, a robust method for determining principal curvatures is via
 quadric fitting [^panozzo_2010]. In the neighborhood around every vertex, a
 best-fit quadric is found and principal curvature values and directions are
 analytically computed on this quadric ([Example
-203](203_curvatureDirections/main.cpp)).
+203]({{ repo_url }}/tutorial/203_curvatureDirections/main.cpp)).
 
 ![The `CurvatureDirections` example computes principal curvatures via quadric fitting and visualizes mean curvature in pseudocolor and principal directions with a cross field.](images/fertility-principal-curvature.jpg)
 
@@ -166,7 +166,7 @@ where $\mathbf{f}$ is $n\times 1$ and $\mathbf{G}$ is an $md\times n$ sparse
 matrix. This matrix $\mathbf{G}$ can be derived geometrically, e.g.
 ch. 2[^jacobson_thesis_2013].
 Libigl's `grad` function computes $\mathbf{G}$ for
-triangle and tetrahedral meshes ([Example 204](204_Gradient/main.cpp)):
+triangle and tetrahedral meshes ([Example 204]({{ repo_url }}/tutorial/204_Gradient/main.cpp)):
 
 ![The `Gradient` example computes gradients of an input function on a mesh and visualizes the vector field.](images/cheburashka-gradient.jpg)
 
@@ -239,7 +239,7 @@ book" FEM construction which involves many (small) matrix inversions, cf.
 [^sharf_2007].
 
 The operator applied to mesh vertex positions amounts to smoothing by _flowing_
-the surface along the mean curvature normal direction ([Example 205](205_Laplacian/main.cpp)). Note that this is equivalent to minimizing surface area.
+the surface along the mean curvature normal direction ([Example 205]({{ repo_url }}/tutorial/205_Laplacian/main.cpp)). Note that this is equivalent to minimizing surface area.
 
 ![The `Laplacian` example computes conformalized mean curvature flow using the cotangent Laplacian [^kazhdan_2012].](images/cow-curvature-flow.jpg)
 
@@ -305,7 +305,7 @@ Eigen::VectorXd d;
 igl::exact_geodesic(V,F,VS,FS,VT,FT,d);
 ```
 
-![[Example 206](206_GeodesicDistance/main.cpp) allows to interactively pick the source vertex and displays the distance using a periodic color pattern.](images/geodesicdistance.jpg)
+![[Example 206]({{ repo_url }}/tutorial/206_GeodesicDistance/main.cpp) allows to interactively pick the source vertex and displays the distance using a periodic color pattern.](images/geodesicdistance.jpg)
 
 ## References
 

docs/tutorial/chapter-3.md

@@ -17,7 +17,7 @@ If `A` is a $m \times n$ matrix and `R` is a $j$-long list of row-indices
 (between 1 and $m$) and `C` is a $k$-long list of column-indices, then as a
 result `B` will be a $j \times k$ matrix drawing elements from `A` according to
 `R` and `C`. In libigl, the same functionality is provided by the `slice`
-function ([Example 301](301_Slice/main.cpp)):
+function ([Example 301]({{ repo_url }}/tutorial/301_Slice/main.cpp)):
 
 ```cpp
 VectorXi R,C;
@@ -82,7 +82,7 @@ where again `I` reveals the index of sort so that it can be reproduced with
 
 Analogous functions are available in libigl for: `max`, `min`, and `unique`.
 
-![The example `Sort` shows how to use `igl::sortrows` to pseudocolor triangles according to their barycenters' sorted order ([Example 302](302_Sort/main.cpp)).](images/decimated-knight-sort-color.jpg)
+![The example `Sort` shows how to use `igl::sortrows` to pseudocolor triangles according to their barycenters' sorted order ([Example 302]({{ repo_url }}/tutorial/302_Sort/main.cpp)).](images/decimated-knight-sort-color.jpg)
 
 
 ### Other Matlab-style functions
@@ -202,7 +202,7 @@ this solution is not very general.
 With array slicing no explicit sort is needed. Instead we can _slice-out_
 submatrix blocks ($\mathbf{L}_{in,in}$, $\mathbf{L}_{in,b}$, etc.) and follow
 the linear algebra above directly. Then we can slice the solution _into_ the
-rows of `Z` corresponding to the interior vertices ([Example 303](303_LaplaceEquation/main.cpp)).
+rows of `Z` corresponding to the interior vertices ([Example 303]({{ repo_url }}/tutorial/303_LaplaceEquation/main.cpp)).
 
 ![The `LaplaceEquation` example solves a Laplace equation with Dirichlet boundary conditions.](images/camelhead-laplace-equation.jpg)
 
@@ -351,7 +351,7 @@ difference from the straight quadratic _minimization_ system, is that this
 saddle problem system will not be positive definite. Thus, we must use a
 different factorization technique (LDLT rather than LLT): libigl's
 `min_quad_with_fixed_precompute` automatically chooses the correct solver in
-the presence of linear equality constraints ([Example 304](304_LinearEqualityConstraints/main.cpp)).
+the presence of linear equality constraints ([Example 304]({{ repo_url }}/tutorial/304_LinearEqualityConstraints/main.cpp)).
 
 ![The example `LinearEqualityConstraints` first solves with just fixed value constraints (left: 1 and -1 on the left hand and foot respectively), then solves with an additional linear equality constraint (right: points on right hand and foot constrained to be equal).](images/cheburashka-biharmonic-leq.jpg)
 
@@ -397,7 +397,7 @@ igl::active_set_params as;
 igl::active_set(Q,B,b,bc,Aeq,Beq,Aieq,Bieq,lx,ux,as,Z);
 ```
 
-![ [Example 305](305_QuadraticProgramming/main.cpp) uses an active set solver to optimize discrete biharmonic kernels [^rustamov_2011] at multiple scales .](images/cheburashka-multiscale-biharmonic-kernels.jpg)
+![ [Example 305]({{ repo_url }}/tutorial/305_QuadraticProgramming/main.cpp) uses an active set solver to optimize discrete biharmonic kernels [^rustamov_2011] at multiple scales .](images/cheburashka-multiscale-biharmonic-kernels.jpg)
 
 ## Eigen Decomposition
 
@@ -440,7 +440,7 @@ slowly changing functions over the mesh (e.g. [^hildebrandt_2011]). Modal
 analysis and model subspaces have been used frequently in real-time deformation
 (e.g. [^barbic_2005]).
 
-In [Example 306](306_EigenDecomposition/main.cpp)), the first 5 eigen vectors
+In [Example 306]({{ repo_url }}/tutorial/306_EigenDecomposition/main.cpp)), the first 5 eigen vectors
 of the discrete Laplace-Beltrami operator are computed and displayed in
 pseudo-color atop the beetle. Eigen vectors are computed using `igl::eigs`
 (mirroring MATLAB's `eigs`). The 5 eigen vectors are placed into the columns
@@ -455,7 +455,7 @@ Eigen::VectorXd S;
 igl::eigs(L,M,5,igl::EIGS_TYPE_SM,U,S);
 ```
 
-![([Example 306](306_EigenDecomposition/main.cpp)) Low frequency eigen vectors of the discrete Laplace-Beltrami operator vary smoothly and slowly over the _Beetle_.](images/beetle-eigen-decomposition.gif)
+![([Example 306]({{ repo_url }}/tutorial/306_EigenDecomposition/main.cpp)) Low frequency eigen vectors of the discrete Laplace-Beltrami operator vary smoothly and slowly over the _Beetle_.](images/beetle-eigen-decomposition.gif)
 
 ## References
 

docs/tutorial/chapter-4.md

@@ -91,7 +91,7 @@ igl::harmonic(V,F,b,D_bc,2,D);
 U = V+D;
 ```
 
-![The [BiharmonicDeformation](401_BiharmonicDeformation/main.cpp) example deforms a statue's head as a _biharmonic surface_ (top) and using a _biharmonic displacements_ (bottom).](images/max-biharmonic.jpg)
+![The [BiharmonicDeformation]({{ repo_url }}/tutorial/401_BiharmonicDeformation/main.cpp) example deforms a statue's head as a _biharmonic surface_ (top) and using a _biharmonic displacements_ (bottom).](images/max-biharmonic.jpg)
 
 #### Relationship to "differential coordinates" and Laplacian surface editing
 Biharmonic functions (whether positions or displacements) are solutions to the
@@ -130,7 +130,7 @@ int k = 2;// or 1,3,4,...
 igl::harmonic(V,F,b,bc,k,Z);
 ```
 
-![The [PolyharmonicDeformation](402_PolyharmonicDeformation/main.cpp) example deforms a flat domain (left) into a bump as a solution to various $k$-harmonic PDEs.](images/bump-k-harmonic.jpg)
+![The [PolyharmonicDeformation]({{ repo_url }}/tutorial/402_PolyharmonicDeformation/main.cpp) example deforms a flat domain (left) into a bump as a solution to various $k$-harmonic PDEs.](images/bump-k-harmonic.jpg)
 
 ## Bounded biharmonic weights
 In computer animation, shape deformation is often referred to as "skinning".
@@ -191,7 +191,7 @@ parition of unity and encourage sparsity:
 This is a quadratic programming problem and libigl solves it using its active
 set solver or by calling out to [Mosek](http://www.mosek.com).
 
-![The example [BoundedBiharmonicWeights](403_BoundedBiharmonicWeights/main.cpp) computes weights for a tetrahedral mesh given a skeleton (top) and then animates a linear blend skinning deformation (bottom).](images/hand-bbw.jpg)
+![The example [BoundedBiharmonicWeights]({{ repo_url }}/tutorial/403_BoundedBiharmonicWeights/main.cpp) computes weights for a tetrahedral mesh given a skeleton (top) and then animates a linear blend skinning deformation (bottom).](images/hand-bbw.jpg)
 
 ## Dual quaternion skinning
 Even with high quality weights, linear blend skinning is limited. In
@@ -237,7 +237,7 @@ internally converts to the dual quaternion representation before blending:
 igl::dqs(V,W,vQ,vT,U);
 ```
 
-![The example [DualQuaternionSkinning](404_DualQuaternionSkinning/main.cpp) compares linear blend skinning (top) to dual quaternion skinning (bottom), highlighting LBS's candy wrapper effect (middle) and joint collapse (right).](images/arm-dqs.jpg)
+![The example [DualQuaternionSkinning]({{ repo_url }}/tutorial/404_DualQuaternionSkinning/main.cpp) compares linear blend skinning (top) to dual quaternion skinning (bottom), highlighting LBS's candy wrapper effect (middle) and joint collapse (right).](images/arm-dqs.jpg)
 
 ## As-rigid-as-possible
 
@@ -340,7 +340,7 @@ Libigl's implementation of as-rigid-as-possible deformation takes advantage of
 the highly optimized singular value decomposition code from McAdams et al.
 [^mcadams_2011] which leverages SSE intrinsics.
 
-![The example [AsRigidAsPossible](405_AsRigidAsPossible/main.cpp) deforms a surface as if it were made of an elastic material](images/decimated-knight-arap.jpg)
+![The example [AsRigidAsPossible]({{ repo_url }}/tutorial/405_AsRigidAsPossible/main.cpp) deforms a surface as if it were made of an elastic material](images/decimated-knight-arap.jpg)
 
 The concept of local rigidity will be revisited shortly in the context of
 surface parameterization.
@@ -447,7 +447,7 @@ biharmonic distance embedding.
 In this light, we can think of the "spokes+rims" style surface ARAP as a (slight and
 redundant) clustering of the per-triangle edge-sets.
 
-![The example [FastAutomaticSkinningTransformations](406_FastAutomaticSkinningTransformations/main.cpp) compares a full (slow) ARAP deformation on a detailed shape (left of middle), to ARAP with grouped rotation edge sets (right of middle), to the very fast subpsace method (right).](images/armadillo-fast.jpg)
+![The example [FastAutomaticSkinningTransformations]({{ repo_url }}/tutorial/406_FastAutomaticSkinningTransformations/main.cpp) compares a full (slow) ARAP deformation on a detailed shape (left of middle), to ARAP with grouped rotation edge sets (right of middle), to the very fast subpsace method (right).](images/armadillo-fast.jpg)
 
 ## Biharmonic Coordinates
 
@@ -528,7 +528,7 @@ handles):
 igl::biharmonic_coordinates(V,F,S,W);
 ```
 
-![([Example 407](407_BiharmonicCoordinates/main.cpp)) shows a physics simulation on a coarse orange mesh. The vertices of this mesh become control points for a biharmonic coordinates deformation of the blue high-resolution mesh.](images/octopus-biharmonic-coordinates-physics.gif)
+![([Example 407]({{ repo_url }}/tutorial/407_BiharmonicCoordinates/main.cpp)) shows a physics simulation on a coarse orange mesh. The vertices of this mesh become control points for a biharmonic coordinates deformation of the blue high-resolution mesh.](images/octopus-biharmonic-coordinates-physics.gif)
 
 ## References