Replace deprecated "show" calls with "setVisible".

Most of these changes are pretty straightforward; I simply replaced calls to the deprecated `show` methods with `setVisible(true)`.

However, for the following classes, I removed the overridden (and deprecated) `show` methods, added `setVisible` methods, and adjusted code that called the old show methods:

`ucar.unidata.idv.ui.BundleTree`

`ucar.visad.display.AnimationPropertiesDialog`

The change to AnimationPropertiesDialog will only call `updateTimeline` if the dialog is to be made visible. This seemed to be in line with how `updateTimeline` is used…but I figured it was worth mentioning.

The only remaining call to a deprecated `show` method should be the one within `ucar.unidata.ui.IndependentWindow` at line 95. I left it because IndependentWindow is only ever used as an import in IdvWindow…maybe it can be removed? FWIW it seems to be an older version of `ucar.nc2.ui.widget.IndependentWindow`.