Fix trailing whitespace and line endings

[dlm]

Currently there are a lot of files that have trailing white space and some files use CRLF others use LF for line endings. Both can become an easy and frustrating place for errors. A few things that we can do to resolve and make developing easier for others:

• LF vs. CLRF can be fixed with: https://help.github.com/articles/dealing-with-line-endings/
• Remove trailing whitespace
• add Rproj file to ease config