Update documentation

.gitignore

 build/build_SWE_*
 build/SWE_*
 
+documentation/doxy/
+
 *.pyc
 .sconsign.dblite
 *~

documentation/SWE.doxy

@@ -458,7 +458,7 @@ SORT_GROUP_NAMES       = NO
 # Note: This option applies only to the class list, not to the
 # alphabetical list.
 
-SORT_BY_SCOPE_NAME     = NO
+SORT_BY_SCOPE_NAME     = YES
 
 # The GENERATE_TODOLIST tag can be used to enable (YES) or
 # disable (NO) the todo list. This list is created by putting \todo
@@ -603,7 +603,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = . ../src ../src/examples ../src/scenarios ../src/solvers ../src/tools
+INPUT                  = .      \
+                         ../src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -626,7 +627,7 @@ FILE_PATTERNS          = *.txt *.h *.hh *.hpp *.cpp *.cu
 # should be searched for input files as well. Possible values are YES and NO.
 # If left blank NO is used.
 
-RECURSIVE              = NO
+RECURSIVE              = YES
 
 # The EXCLUDE tag can be used to specify files and/or directories that should
 # excluded from the INPUT source files. This way you can easily exclude a

documentation/mainpage.txt

@@ -156,7 +156,7 @@ We will model three different situations:
 To implement the boundary conditions, the class \texttt{SWE\_Block} contains an 
 array of four enum variables, \texttt{boundary[4]} (for left/right/bottom/top 
 boundary), that can take the values 
-\texttt{OUTFLOW}, \texttt{WALL}, and \texttt{CONNECT}.
+<code>OUTFLOW</code>, <code>WALL</code>, and <code>CONNECT</code>.
 
 
 \subsection multblocks Multiple Blocks
@@ -165,6 +165,8 @@ Via the connect boundary condition, it is also possible to connect several
 Cartesian grid blocks to build a more complicated domain. Figure \ref{fig:connect} 
 illustrates the exchange of ghost values for two connected blocks.
 
+\image html connect.gif
+\latexonly
 \begin{figure}
 \begin{center}
   \includegraphics[width=0.8\textwidth]{pics/connect.pdf}
@@ -172,10 +174,11 @@ illustrates the exchange of ghost values for two connected blocks.
 \caption{Exchange of values in ghost layers between two connected \texttt{SWE\_Block}s.}
 \label{fig:connect}
 \end{figure}
+\endlatexonly
 
-To store the neighbour block in case of a \texttt{CONNECT} boundary, \texttt{SWE\_Block} 
-contains a further array of four pointers, \texttt{neighbour[4]} (for left/right/bottom/top 
-boundary), that will store a pointer to the connected adjacent \texttt{SWE\_Block}.
+To store the neighbour block in case of a <code>CONNECT</code> boundary, <code>SWE_Block</code> 
+contains a further array of four pointers, <code>neighbour[4]</code> (for left/right/bottom/top 
+boundary), that will store a pointer to the connected adjacent <code>SWE_Block</code>.
 
 The respective block approach can also be exploited for parallelisation: 
 the different blocks would then be assigned to the available processors