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It should be possible to specify Include Path for PHP Project: List of directories, where to search for included files in addition to project's source root directory. Ability to set PHP Include path will appear in Project customizer as 'PHP Include Path' panel. It is not planned to appear in new project creation wizard.
See also http://saturn.czech.sun.com/wiki/view/Mythoughtphp61
Will not fix for NB 6.1. Depends on issue 124183
Now it's possible to add a folder to PHP Include Path. Reopening to mark as fixed/verified.
Marking as fixed.
Marking as verified.