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.
Alglib: numerical analysis and data processing library

Closes #1177.
getdp: Update sha1.

Closes #1300.
Sundials: update url.

The official Sundials site requires registration and doesn't provide
a direct download link any more.
Arpack: Use MPI compilers.

Closes #1294.
masurca 2.2.1: conflicts with jellyfish, parallel
cuba 4.0

Closes #1305.
netcdf: update fortran resource to 4.4.1

Closes #1301.
Armadillo 4.500.0

Closes #1310.
ASL: version 20141024.

Closes #1309.
blis: new formula

BLIS - BLAS-like Library Instantiation Software

BLIS is a software framework for instantiating
high-performance BLAS-like dense linear algebra libraries.

The formula currently requires a "--with-configuration" option to
specify the framework configuration and raises an error if this option
is not specified.

Signed-off-by: Kevin Locke <kevin@kevinlocke.name>

Closes #1097.
Superlu_dist 3.3 (new formula)

Distributed version of SuperLU

Closes #1296.
sga 0.10.13: Install sga-align and sga-joinedpe
sga 0.10.13: Do not install Makefile Makefile.in