pep8 fixes for setup.py

as reported by flake8
syntax highlighting for shell commands in sphinx
Update to changes in libgit2 concerning refs

Two methods have been drop:

- Repository.packall_references
- Reference.reload

The unit tests have been commented until we wrap the new reference
database from libgit2.
Merge remote-tracking branch 'esc/pep8/setup.py'
Merge remote-tracking branch 'esc/refactor/install_docs'