some comments fixed, small fix for windows OSes and some other things fixed
-rw-r--r-- 8931 .gitattributes
-rw-r--r-- 29 .gitignore
-rw-r--r-- 55478 Doxyfile
drwxr-xr-x - application
drwxr-xr-x - db
drwxr-xr-x - devel
drwxr-xr-x - docs
drwxr-xr-x - inc
-rw-r--r-- 4751 index.php
-rwxr-xr-x 132 rebuild_doc.sh
drwxr-xr-x - templates