I have just update aptana into the 3.6 version but I have lost all connections that I had in my projects. Also, making new projects just won't show the connections row anymore.
I have received an answer in the ticket system of Aptana. In order to see the connections again you have to change the project format from PHP or anything that you have activated into Web. Only that. It doesn't make a lot of sense, but that's how it works now.
To change that you have to go to properties of the project -> project natures and check only Web and make it primary. All the rest of natures must be unchecked.