09_git.ipynb: Add tests for commands and fix them

Added tests for `sparse_clone()`, `_repo_name_to_out_path()`, and
`commit_graph()`.  When analysing results one bug and one mis-feature
were corrected in the `repo_generate_adjlist()` function:

* with subprocess.run() we don't need to and should not to
  quote the '--format' option value (the bug created spurious
  quote characters in generated adjacency list file),

* all references include pull requests; use all branches instead

For easier testing, `commit_graph()` function now sets the 'name'
attribute of the generated NetworkX `DiGraph` object.

While at it, noticed that to_hdf() method for DataFrames requires
'tables' Python package (PyTables) to be installed.

Warning: this commit includes spurious changes caused by difference in
timing, date of modification of a file, and in existence of particular
directories.

Author: jnareb