Merge pull request #62 from CHLNDDEV/reorganization

Reorganization of files.

Author: keith roberts

Example_1_NZ.m renamed to Examples/Example_1_NZ.m

@@ -4,16 +4,6 @@
 ## IMPORTANT NOTE:
 This is the default and recommended `PROJECTION` branch. Please use it unless you otherwise require legacy (`MASTER` branch) or the absolute newest features (`DEV` branch). 
 
-## `DISCLAIMER: `
-The boundary of the meshing domain must be a polygon (first point equals the last and non-self intersecting) but it does not need to be simplified. Read the user guide for more information about the inputs.
-
-<p align="center">
-  <img src = "VizGilgo.png"> &nbsp &nbsp &nbsp &nbsp
-  <img src = "Example1.png"> &nbsp &nbsp &nbsp &nbsp
-  <img src = "nesting.png"> &nbsp &nbsp &nbsp &nbsp
-  <img src = "ResoNA.png"> &nbsp &nbsp &nbsp &nbsp
-  <img src = "Globalocean.jpg"> &nbsp &nbsp &nbsp &nbsp
-</p>
 OceanMesh2D is a set of user-friendly MATLAB functions to generate two-dimensional (2D) unstructured meshes for coastal ocean circulation problems. These meshes are based on a variety of feature driven geometric and bathymetric mesh size functions, which are generated according to user-defined parameters. Mesh generation is achieved through a force-balance algorithm combined with a number of topological improvement strategies aimed at improving the worst case triangle quality. The software embeds the mesh generation process into an object-orientated framework that contains pre- and post-processing workflows, which makes mesh generation flexible, reproducible, and script-able. 
 
 ## `Code framework` 
@@ -36,12 +26,12 @@ Download the data for the following examples [here](https://drive.google.com/ope
 
 in addition to [here](http://www.soest.hawaii.edu/pwessel/gshhg/gshhg-shp-2.3.7.zip) for the GSHHG ESRI shapefile and here: "ftp://topex.ucsd.edu/pub/srtm15_plus/SRTM15+V2.nc" for the latest SRTM15_PLUS global topobathy DEM.
 ```
-Featured in  ┌╼ Example_1_NZ.m   %<- A simple mesh around South Island New Zealand that uses GSHHS shoreline. 
-user guide   ├── Example_2_NY.m   %<- A high-resolution mesh around the New York/Manhattan area that uses a DEM created from LiDAR data.  
-             └── Example_3_ECGC.m %<- Builds a mesh for the western North Atlantic with a local high-resolution nest around New York
-Featured in         ┌╼ Example_4_PRVI.m %<- Builds a mesh for the western North Atlantic with three high-resolution nests around Peurto Rico and US Virgin Islands
-Geoscientific Model ├── Example_5_JBAY.m %<- An extremely high-fidelity (15-m) mesh from LiDAR data around Jamaica Bay with CFL-limiting.
-Development paper[1]└── Example_6_GBAY.m %<- An example of the polyline/thalweg mesh size function along the Houston Ship Channel. 
+Featured in  ┌╼ Examples/Example_1_NZ.m   %<- A simple mesh around South Island New Zealand that uses GSHHS shoreline. 
+user guide   ├── Examples/Example_2_NY.m   %<- A high-resolution mesh around the New York/Manhattan area that uses a DEM created from LiDAR data.  
+             └── Examples/Example_3_ECGC.m %<- Builds a mesh for the western North Atlantic with a local high-resolution nest around New York
+Featured in         ┌╼ Examples/Example_4_PRVI.m %<- Builds a mesh for the western North Atlantic with three high-resolution nests around Peurto Rico and US Virgin Islands
+Geoscientific Model ├── Examples/Example_5_JBAY.m %<- An extremely high-fidelity (15-m) mesh from LiDAR data around Jamaica Bay with CFL-limiting.
+Development paper[1]└── Examples/Example_6_GBAY.m %<- An example of the polyline/thalweg mesh size function along the Houston Ship Channel. 
 
 ```
 
@@ -51,7 +41,7 @@ All pull requests are tested with Jenkins on a local host. However, to ensure th
 
 ## `References!`
 
-If you make use of `OceanMesh2D` please include a reference to the following:
+If you make use of `OceanMesh2D` please include a reference to [1], and to any of [2]-[4] if pertinent:
 ```
 
 [1] - Roberts, K. J., Pringle, W. J., and Westerink, J. J., 2019. 
@@ -65,7 +55,17 @@ If you make use of `OceanMesh2D` please include a reference to the following:
 [4] - Roberts, Keith J., Pringle W.J., Westerink J. J. Contreras, M.T., Wirasaet, D., 2019. 
       On the automatic and a priori design of unstructured mesh resolution for coastal ocean circulation models, 
       Ocean Modelling, 144, 101509. https://doi.org/10.1016/j.ocemod.2019.101509
+      
+```
 
+## `DISCLAIMER: `
+The boundary of the meshing domain must be a polygon (first point equals the last and non-self intersecting) but it does not need to be simplified. Read the user guide for more information about the inputs.
 
-
-```
+## `GALLERY: `
+<p align="center">
+  <img src = "imgs/VizGilgo.png"> &nbsp &nbsp &nbsp &nbsp
+  <img src = "imgs/Example1.png"> &nbsp &nbsp &nbsp &nbsp
+  <img src = "imgs/nesting.png"> &nbsp &nbsp &nbsp &nbsp
+  <img src = "imgs/ResoNA.png"> &nbsp &nbsp &nbsp &nbsp
+  <img src = "imgs/Globalocean.jpg"> &nbsp &nbsp &nbsp &nbsp
+</p>