clustal-w: bump clang, use double quotes

Closes #1281.
edirect: update sha1
root: general cleanup

Closes #1283.
octave: build gnuplot with Qt

Fixes #1275.
CONTRIBUTING: update core doc links
README: migrate from core wiki
mrbayes 3.2.3

MrBayes is updated to version 3.2.3 on SourceForge
https://sourceforge.net/projects/mrbayes/files/mrbayes/3.2.3/

Closes #1288.