[AIDA-72] Export INDEXDIR, otherwise maven and indexer.Indexer will not see it.
[AIDA-72] rely on 'cp --parents' to create staging directory structure.
[AIDA-72] log all messages to log file.
[AIDA-72] single function creates all required directories.
Merge branch 'master' into AIDA-113-patient-metadata-in-reports
[AIDA-113] Rename Sex to Gender.
[AIDA-113] Html reports contain patient's age and gender.