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.
pep8 fixes for setup.py

as reported by flake8
syntax highlighting for shell commands in sphinx
the extension compiles to _pygit2.so, so ignore that too
fixed compiler warnings
fixed memory leaks in config.c

* Config does not need Repository pointer
    -> No need for cyclic garbage collecter support
* fixed several ref counter issues
* some refactorization