Move graph module from lib or vendor directory to app directory.

Because not autoloading lib directory at development mode.
Fix the commits are not ordered commiter date.

It is fixed that the date label of network graph is broken.
Finding free space from the way near commit which is downward
It improves detecting an overlap of a line
A tip is made slanting.
Commits are arranged below their first parent.
Show gravatar icon on tooltip.
Fix spinach errors.
Add some tests for network graph
Merge pull request #3109 from hiroponz/improve-network-graph

Improve network graph