Update code to work with gitlab_git 3

Gemfile

Gemfile.lock

app/controllers/projects/blame_controller.rb

app/controllers/projects/blob_controller.rb

app/controllers/projects/raw_controller.rb

app/controllers/projects/refs_controller.rb

app/controllers/projects/tree_controller.rb

app/helpers/blobs_helper.rb

app/helpers/tree_helper.rb

app/models/repository.rb

app/models/tree.rb

app/views/projects/commits/_diffs.html.haml

app/views/projects/tree/_tree.html.haml

config/initializers/5_backend.rb

lib/extracts_path.rb