updates and proper tagging for dox

README.md

@@ -1,8 +1,8 @@
-[![Build Status](https://travis-ci.org/OpenWaterAnalytics/EPANET.svg?branch=dev-2.1)](https://travis-ci.org/OpenWaterAnalytics/EPANET)
-
-EPANET
+EPANET {#epanet-readme}
 ======
 
+[![Build Status](https://travis-ci.org/OpenWaterAnalytics/EPANET.svg?branch=dev-2.1)](https://travis-ci.org/OpenWaterAnalytics/EPANET)
+
 The EPANET Library is a pressurized pipe network hydraulic and water quality analysis toolkit written in C. 
 
 __Note:__ This repository is not affiliated with, or endorsed by, the USEPA. For the "official" release of EPANET (2.00.12 UI and Toolkit) please go to the [EPA's GitHub repo](https://github.com/USEPA/Water-Distribution-Network-Model) or [the USEPA website](http://www2.epa.gov/water-research/epanet). It is also not the graphical user interface version. This is the hydraulic and water quality solver engine.

ReleaseNotes2_1.md

@@ -1,4 +1,5 @@
-#Release Notes for EPANET 2.1
+Release Notes for EPANET 2.1 {#release_2_1}
+============================
 
 The last update to the EPANET engine was "Build 2.00.12" in February of 2008. Since that time, a community effort to update and extend the open-source code has emerged. This group has made a number of bug-fixes and API additions that help to improve the EPANET engine for everyone. Version 2.1 is now released after 8.5 years.
 

doc/doxyfile

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 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../ \
-                         ../include \
+INPUT                  = ../include \
                          ../src \
-                         ../doc
+                         ../doc \
+                         ../
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses