Properly initialize the local repo in CLI's clone so that it gets properly closed afterwards.

The CLI Clone command was calling InitOp directly instead of cli.getOrCreateRepository().
As a result, there's no Repository instance reference inside the GeoGIT instance, and
hence GeoGIT.close() does not properly closes the databases, leading to the program exiting
without closing the db, which may lead to unsaved objects.
Merge pull request #537 from groldan/master

Properly initialize the local repo in CLI's clone