[test] File: test for reusability of file handles

This test currently fails, because shared_ptr count does not seem to
reach zero, groups are therefore not cleaned up and this then later
on confuses the hdf5 library somehow. Details are not clear yet, needs
further investigation. See also Github issue #214
File: nullify the shared_ptr on close()

This fixes the symptoms of issue #214 for now, the root of the evil still
is unkown.
Merge pull request #216 from gicmo/file_issue

Test and fix File reusability issues