Cleanup of project director, updating documentation

Cleaned up out of date scripts.
Updated readme
fixed line ending
Update README.md
Cleaned up documentation, fixed convergence issue

Cleaned up the documentation of the code
Fixed issue with convergence
Merge branch 'cleanup' of github.com:rzlee/bayes-detect into cleanup
Removed extra comment
Merge remote-tracking branch 'upstream/master' into fix
Merge pull request #21 from rzlee/fix

Fix