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Consolidate dataset stop methods and test for issue #2000 (#2001)

* Consolidate dataset stop methods and test for issue #2000

* Try reverting to see if warped vrt tests will fail

* Undo previous commit

* Make WarpedVRT safer

We're only calling GDALClose now if reference counts are 0 and
insisting that the dataset passed to WarpedVRT be opened in
read-only mode.

Resolves #2000

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