app: Added variant-index command. Added stoage.mongo configuration file.
app: Dependency problem fixed. Excluded apache.commons.codec in opencga-app from opencga-lib

opencb.commons.utils.CryptoUtils uses commons.codec version 1.7, and opencga-lib had the same dependency with version 1.3.
Merge branch 'feature/refactoring' of https://github.com/opencb/opencga into feature/refactoring