I set to autocomplete everything, but limit the scope to include files. The problem is that with that setting the variables and such from include files are not autocompleted. When I uncheck the option I get the autocomplete for everything in the project. How do I get the PHP IDE to behave the way it suggests it will work? Is this a bug or a feature? I use version 5.0 build 5025.

could you please provide a sample that will replicate the problem?

Check your PM.

Did anyone have a chance to look at this?

sure, we'll look at this in next few days, after we get build 5026 released.