Update old references to SwissTPH/openmalaria. Ran `find . | grep "\.md$" | xargs sed -i "s/SwissTPH\/openmalaria/OpenMalaria-org\/openmalaria/g"`.
Updated XmlEntoVector (markdown)
Changed most anchors to github-syntax
fixed relative code.google.com-style links by removing .md-extension
Migrating wiki contents from Google Code