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.
API: system hooks API functions and documentation updated

* updated system hooks documentation and code comments
* fixed access to system hooks if no user given resulting in a `500 Server Error`
* added tests
Merge branch 'master' into api/system_hooks_adjustments
Added system hooks link to doc index
Merge pull request #3173 from m4tthumphrey/patch-1

Added system hooks link to doc index
fix event relative date being cached
better logo images for header
Replace current Wiki system with Gollum Wikis.

This commit replaces the old database backed Wiki system with the
excellent Gollum git based Wiki system.

The UI has been updated to allow for utilizing the extra features
that Gollum provides. Specifically:

* Edit page now allows you to choose the content format.
* Edit page allows you to provide a commit message for the change.
* History page now shows Format, Commit Message, and Commit Hash.
* A new Git Access page has been added with the Wiki Repo URL.
* The default page has been changed to Home from Index to match
the Gollum standard.

The old Wiki model has been left in tact to provide for the
development of a migration script that will move all content stored
in the old Wiki system into new Gollum Wikis.
Merge pull request #3169 from hiroponz/refactor-network-graph

Refactor network graph
Move groups and teams to tabs on dashboard. Remember tab with cookie
Group and team rss is valid now
add coveralls.io to travis builds
fixed travis env, added coverage badge