catalog: Replaced "Index.java" for File.type=TYPE_INDEX
catalog: Fixed index attributes and indexation file location.
catalog: Fixed modify study uri.
catalog: some work in sample and annotations entities
catalog: Added new job state: PREPARED. A prepared job will be submited to the SGEManager by the daemon.
catalog: Implemented file deletion. New states "deleting" and "deleted".
catalog: two JUnit rules added
Merge branch 'feature/catalog' of https://github.com/j-coll/opencga into feature/catalog
catalog: some tests code clean up
catalog: JUnit tests and samples works done