separated glob translation code into util namespace

Fixed numerous conversion bugs
documented util
removed unused decl
removed excess whitespace
moved testable functions from indexing to doc-prep
moved rest of document formatting functions to doc-prep
extracted irods calling logic into repo

The repo namespace was created to encapsulate the irods calling logic.
separated testable doc prep logic from indexing logic
documented the doc-prep namespace.
documented the indexing namespace.
documented the repo namespace.
documented the curation namespace.