Clean up files from repo, add cleanup script, correct configure.ac

[eddelbuettel]

Here is a first PR that

• removes a number of files that should not be in a source repo (compare with many other on GitHub) such as output from configure or compilation
• adds a file cleanup which removes such files when running R CMD build and alike (see Writing R Extensions)
• correct configure.ac to reference the correct location for src/Makevars