Also, is there a way to exclude a directory from being included in the current project namespace.

OsCommerce, for instance, contains files, variables, and object with the same name in /admin irectory and /include directory. So when I open the index.php file in the root folder and use 'open file at cursor', it opens the file in the admin directory instead of one in the include directory . Similar variable conflict occurs in code explorer; when I try to find the declaration of a function/class/variable, it opens the declaration in admin directory. Is there a way I can exclude admin from being excluded unless I need it.

You may put word "admin" in to the list of directories to hide. See Hide Directories in the project properties.
Code Insight won't access php files in 'hidden' directories.
Similarly you may create 2nd project with hidden "include" and work with either of them according to your needs.