server: Added some include/exclude
server: Fixed QueryOptions construction for OpenCGAWSserver.
server: Added http post method for study creation. #25
Merge branch 'feature/catalog' into feature/refactoring

Conflicts:
	opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java
	opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java
catalog: CreateFolder bugfix. Overwrote when folder already exists.
server-post: createStudyPOST now uses all fields. #25
server-post: createFilePOST implemented. #25
server-post: createFilePOST and createStudyPOST return one QueryResult per element. #25
catalog: Added generic CatalogException.
Merge branch 'feature/http-post-methods' into feature/catalog

Conflicts:
	opencga-catalog/src/main/java/org/opencb/opencga/catalog/CatalogManager.java
	opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/CatalogDBAdaptor.java
	opencga-server/src/main/java/org/opencb/opencga/server/FileWSServer.java
	opencga-server/src/main/java/org/opencb/opencga/server/StudyWSServer.java
catalog: Type migration from "final static String" values to single Enum

New enums created:
File.Format
File.Type
File.Bioformat
File.Status

Job.Status
Job.Type

User.Role
catalog: Metadata bean modified. Only one counter for all IDs.
catalog: Created new StudyCollection. Studies moved.
catalog: Added create and read sample methods.
catalog: Added some sample annotation methods and validators.
catalog: Added CatalogManager some Sample, Variable and Annotation methods.
catalog: Added parameter QueryOptions to CatalogManager methods. Resolves #28
catalog: Some methods implemented. Minnor changes.
catalog: Minnor changes
catalog: some attributes renamed