XNAT-2900: Fixed issues where relative paths weren't resolved properly in non-root XNAT deployments.
XNAT-2896: Fixed issue with -l option, refactored a fair amount of code to un-purpose -l for input function.

xnatdataclient changes correspond to changeset https://bitbucket.org/nrg/xnatdataclient/commits/ca7d91a473cdc910bd1aa00519df72b4c2d8357c