Sorry. This was a false alarm.
It turns out that I was anticipating a new installation into /Applications.
However I had a prior installation in username/Downloads so that got updated 
instead.

J

> On 18 Sep 2016, at 22:22, Jonathan Mitchell <li...@mugginsoft.com> wrote:
> 
> Hi
> 
> I have a MacOS package that installs into /Applications on 10.11.
> On 10.12 it appears to install into the user’s Downloads folder.
> 
> Is this change related to the new feature in MacOS 12 to encapsulate 
> downloaded apps into a read only container?
> 
> Thanks
> 
> J
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