added link to configuration page to manual install
added ordered lists to instructions and cleaned up redundant text
fixed ordered list to show proper numbering
moved reference links to index page and removed reference.txt
moved dependencies into complete install
moved dependencies into complete install
update dev install ubuntu in readme

Updated instructions so that it works with a sh file in a clena ubuntu
12.04 x64 environment
Merge pull request #1214 from GuidoS/master

update dev install ubuntu in readme