Added a page on how to generate doxygen docs

docs/Readme.md

  * [Limitations & Common Issues](Limitations-and-Common-Issues.md)
  
 ## API Docs
- * [C#](html/annotated.html)
- 	* [Academy](html/classAcademy.html)
-	* [Agent](html/classAgent.html)
-	* [Decision](html/interfaceDecision.html)
-	* [Monitor](html/classMonitor.html)
- * Python (coming soon)
-
-## Python API
+ * [API Reference](API-Reference.md)
  * [How to use the Python API](Python-API.md)

docs/API-Reference.md

+# API Reference
+
+Our developer-facing C# classes (Academy, Agent, Decision and 
+Monitor) have been documented to be compatabile with 
+[Doxygen](http://www.stack.nl/~dimitri/doxygen/) for auto-generating HTML 
+documentation.
+
+To generate the API reference, 
+[download Doxygen](http://www.stack.nl/~dimitri/doxygen/download.html) and run
+the following command within the `docs/` directory:
+
+    doxygen ml-agents.conf
+
+`ml-agents.conf` is a configuration file that includes the classes
+that have been properly formatted. The generated HTML files will be placed
+in the `html/` subdirectory. Open `index.html` within that subdirectory to 
+navigate to the API reference home. Note that `html/` is already included in 
+the repository's `.gitignore` file.
+
+In the near future, we aim to expand our documentation
+to include all the Unity C# classes and Python API.