When I'm in Code Explorer looking at the classes using the ProjectTree view (build 3338) it incorrectly displays the name of certain classes i.e.
[-] Class.1_container.php
|- require_once foo
[-] class 1_container extends base_container
|- method baz
|- method bar
[-] Class.1_container.php
|- require_once bar
[-] class 2_container extends base_container
|- method rey
|- method rop
|- method rar
|
Even though the class information is correct, it incorrectly names the class file the same as the one above it, and tries to access the class above it for the methods if you explore the code from the code explorer. In the above example the second Class.1_container.php is actually named Class.2_container.php.