Refactor: replace "render :json = graph.to_json" to view template(show.json.erb).

Because model shouldn't know about view logic.
Refactor: grouping parent and their space by including array.
Refactor: rename module and class names.

* Module: Graph -> Network
* Class: JsonBuilder -> Graph
Refactor: clean up models.

* Network::Commit
** Removing unnecessary accessors.
** Removing add_refs methods.
* Network::Graph
** Removing unnecessary accessors.
** The 3 times loop of commits don't need.
Refacor: removing the times array, because that is same with @commits array.
Refactor: change the map hash from a local variable to private variable.
Refactor: Removing the duplicated code.
Refactor: Removing a if statement, because the nil value is already removed in the view template.
better logo images for header
Merge pull request #3169 from hiroponz/refactor-network-graph

Refactor network graph