SCHEMA-201. Fixes command-line tools.

 - Fixes findbugs warnings (unable to understand setup/run/cleanup workflow).
 - Get rid of BaseTool.parseURI.
 - Fixes various NPEs in CLI tool.

Signed-off-by: Aaron Feldstein <afeldstein@wibidata.com>
SCHEMA-201. Changed to use InternalKijiError.
over the shoulder: Daisy
SCHEMA-205. Fix NPE when creating 1-region table.

Signed-off-by: Christophe Taton <taton@wibidata.com>