Broken projects search on dashboard

Convert branch-graph.js to branch-graph.js.coffee

API: system hook request functions and documentation updated

Refactor network graph

Added system hooks link to doc index

* updated system hooks documentation and code comments
* fixed access to system hooks if no user given resulting in a `500 Server Error`
* added tests

Fix API return codes

Conflicts:
	doc/api/projects.md
	spec/requests/api/projects_spec.rb

Capistrano deploy example

Autofocus to username input (LDAP login).

* Network::Commit
** Removing unnecessary accessors.
** Removing add_refs methods.
* Network::Graph
** Removing unnecessary accessors.
** The 3 times loop of commits don't need.