Updated Quick Start guide in README

Closes #68
Fix README
Mentioned Hadoop from README Quick Start
Adjusted README heading levels
small README fix
Moved velocity templates under the right package
Code clean up and warning fixes
Moved images for wiki to gh-pages branch
Cleaned up log messages (Closes #58)
Merge #71 and #70
Added commons-collections to POM
Merge branch 'master' of https://github.com/semihsalihoglu/graft
Upstream merge.
Adding missed index.html to last commit and upstream merge