Changed the log messages to write to standard error

git-svn-id: https://svn.code.sf.net/p/vcftools/code@888 19d466ce-640d-45be-954f-fad4d9839663
More tinkering with writing to standard error

git-svn-id: https://svn.code.sf.net/p/vcftools/code@889 19d466ce-640d-45be-954f-fad4d9839663
Edits to the website documentation and the man page documentation

git-svn-id: https://svn.code.sf.net/p/vcftools/code@890 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'