Fix duplicate layer test which used /etc

Fix duplicate layer test which used /etc

The ImplicitLayers.DuplicateLayers test requires there to be two separate
files on the file system, located in different paths. To accomplish that, the
test writes a file to /etc and another to the default location. By default,
that is typically /usr/local/share. If the project is configured to set /etc
as that default location, only one file will be written.

The fix is to move the duplicate file from /etc to the default home directory,
since that is configured from inside the tests itself. This does change the
order the layers are found in, so the logic of the test had to be flipped.