catalog: Added uri to study and uriScheme to file.

CatalogManager.shareFile will be unsupported in this version
Merge branch 'feature/catalog' of https://github.com/j-coll/opencga into feature/catalog

Conflicts:
	opencga-catalog/opencga-catalog-core/src/main/java/org/opencb/opencga/catalog/core/db/CatalogMongoDBAdaptor.java
catalog: minor fixes.