README for the Doxygen documentation and Quick Start Manual updated.

docu/doxygen/doxygen-config/README.txt → docu/doxygen/doxygen-config/README.md

-How to create the Doxygen documentation locally:
+How to create the Doxygen documentation
+---------------------------------------
 
-1. Copy the config template:
-   cp doxygen1.8.1-config-template.txt my_doxygen1.8.1-config.txt
+1. Copy the config template:  
+   `cp doxygen1.8.1-config-template.txt my_doxygen1.8.1-config.txt`
 
-2. Edit my_doxygen1.8.1-config.txt:
+2. Edit my_doxygen1.8.1-config.txt:  
    Search for "Revision xxxx", and replace xxxx with the current
-   revision number.
+   revision number  
+   (execute `./rev_id.sh` in the runs directory to find out).  
    Search for "/home/username/Documents/sicopolis/src", and replace
    this by the actual path of the src directory. 
 
-3. Run the command
-   doxygen my_doxygen1.8.1-config.txt
-   (requires Doxygen version 1.8.1 or later).
-   This creates the html documentation in doxygen/html.
+3. Execute the command
+   `doxygen my_doxygen1.8.1-config.txt`
+   (requires Doxygen version 1.8.1 or later).  
+   This creates the html documentation in doxygen/html.  
    Main file: index.html.
 
-4. Documentation as PDF (optional):
-   Go to doxygen/latex and run make (requires LaTeX).
+4. Documentation as PDF (optional):  
+   Go to doxygen/latex and execute `make` (requires LaTeX).  
    This creates the file refman.pdf.

docu/quick_start/SICOPOLIS_V5dev_Quick_Start.tex

@@ -404,7 +404,7 @@ Subdirectory \textbf{quick\_start}:\\
 
 \item
 Subdirectory \textbf{doxygen}: documentation to be created by Doxygen\\
-(optional, see doxygen-config/README.txt).
+(optional, see doxygen-config/README.md).
 
 \begin{itemize}