better support for Clang

previously we only set the flags we wanted when CC/CXX=gnu compilers.
the same flags work for clang.
bundle samtools 0.1.19 rather than requiring it externally
remove build-common as a submodule NOTE:

this commit will not compile. the next commit will re-add build-common
as a subtree
Squashed 'build-common/' content from commit 72dadf7

git-subtree-dir: build-common
git-subtree-split: 72dadf78c9d55e8b472acf23081375d1d7808218
Merge commit '9024457cc8b1b54e665ad323019c7f90b7802105' as 'build-common'
Merge pull request #1 from genome/pkg

dependency bundling to ease packaging woes
Create an initial Readme.md
Update formatting for installation command