Added a shell script for documentation generation.

tools/doc/doxygen.sh

+#run Doxygen
+
+doxygen doxygen.cfg 1>&- 2>&-;
+
+#fix it using the perl script
+
+perl fix.pl 1>&- 2>&-;
+
+#filter docwarnings.log and make a file called warnings.log to only contain warnings
+
+grep "Warning" <docwarnings.log >warnings.log;