There are a lot of great things in 5.6.

The only change that I'm sure of is searching the project files.

When searching a project for a term like 'log in' the result comes back with a long list of images (i.e., flower.jpg, tower.gif, etcetera). In the long list of images there isn't one .php page listed on the Search Results page.

What setting needs to be changed so the result will show only the PHP pages like the previous versions did?

you need to set File Masks input to for example *.php,*.html,*.inc
and make sure that file extensions of your images are included into the Picture type, see Tools->Settings->File Associations

Thanks Dmitri.