Update README

Remove --remote from the submodule recommendations.
Travis: move doxygen updates to it's own script
Travis: move boost-build to /Users/carneiro/build
Travis: move GCC to it's own script
Travis: move CLANG to it's own script
Travis: move BOOST to it's own script
Merge pull request #100 from broadinstitute/mc_travis_updates

Travis: overhaul script to call out to scripts #64
ref/alt alleles