Documentation added to QCD for formula and references.
QCD.bib added for references in QCD class.
README.md.in is deprecated and will be removed. README.md now read in
bibconversion.pl and not generated. The "Bibliography" section should be
kept as is in README.md. Doxygen autolinking being used for this.
1. README.md is now used as source and not generated.
2. Bibliography linking is done by Doxygen autolink generation.
3. Bugs in .bib conversion fixed.
Merge origin/master