Migrated documentation directory to doc. README updated. Error fixes. Moved make options to doc/include.am

doc/generate_documentation.sh

@@ -0,0 +1,66 @@
+#!/bin/sh
+
+command -v g++
+if [ $? -ne "0" ]; then
+echo "Please install g++"
+exit 1
+fi
+
+command -v cmake
+if [ $? -ne "0" ]; then
+echo "Please install cmake"
+exit 1
+fi
+
+command -v git
+if [ $? -ne "0" ]; then
+echo "Please install git"
+exit 1
+fi
+
+command -v make
+if [ $? -ne "0" ]; then
+echo "Please install make"
+exit 1
+fi
+
+if [ ! -e "build/bin/doxygen" ]; then
+mkdir -p build
+cd build
+echo "cloning doxygen 1.8.13..."
+git clone https://github.com/doxygen/doxygen --branch Release_1_8_13
+cmake -G "Unix Makefiles" doxygen/
+make
+cd ..
+fi
+
+if [ $1 = "-html" ] || [ $1 = "-all" ]; then
+#HTML GENERATION
+cp -r formats/html/* ./
+echo "generating html..."
+build/bin/doxygen Doxyfile
+cp html_changes/search/* html/search/
+cp html_changes/*.css html/
+cp html_changes/*.js html/
+rm footer.html header.html
+rm -rf html_changes
+rm mainpage.dox
+rm Doxyfile
+echo "finished generating html..."
+echo "To view the html files use a browser to open the index.html file located at doc/html/index.html"
+fi
+
+#PDF GENERATION
+if [ $1 = "-pdf" ] || [ $1 = "-all" ]; then
+cp -r formats/pdf/* ./
+echo "generating pdf..."
+build/bin/doxygen Doxyfile
+cd latex/
+make
+mv refman.pdf ../
+cd ..
+rm -rf latex/
+rm Doxyfile
+rm header.tex
+echo "finished generating pdf..."
+fi