Add class GitFile

It contains logic for file and directory
retrieval on git/lib level.
Introduce service object RepositoryFile

It contains the logic for file and directory
retrieval on model level.
Refactor files action of FilesController

Make use of RepositoryFile and GitFile.

Use InheritedResources for FilesController
and simplify files action (will be renamed later).
Improve routing

Only routes for existing files and ontologies are considered.
adjust tests, fix implementation
rename files action to show
fix empty repository error
remove unnecessary comment
remove collection method
comment on inclusions/extension
put default branch into config file
remove unnecessary begin block
use reduce instead of select + map
remove begin block
simplify content method
improve implementation of grouped_entries
remove unneeded attr_reader
remove unneeded method