This is absolutely normal and part of how PDT provides Code Assist in PHP projects.
Basically PHP Language Library contains what you can find in the PHP documentation. When you call a core function e.g.
preg_replace() it will provide Code Assist, like autocompletion and showing you which arguments the function takes. It's just a bunch of Interfaces for core features, SPL containing phpdoc generated from the documentation.
The PHP Include Path resembles your
include_path in PHP, in that you can refer to stuff outside your project, e.g. PEAR or a common folder containing shared PHP classes, which are then recognized by Eclipe's Code Assist.
is just a hierarchy view of your global namespace, similar to how you can unfold a php file and see its hierarchy directly from the explorer.