vcftools: force new version

Override alpha/beta versioning for new release.
hotspot 4.0.0 (new formula)

Closes #739.
hotspot: add test to caveats
Migrate dotwrp, qrupdate, slicot to homebrew-science
octave 3.8.1: optional GUI & JIT
Fix for odd mkoctfile dependency issues
X11/TeX fixes