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NetBeans IDE Dev (Build 200612051900) 1.5.0_06; Java HotSpot(TM) Client VM 1.5.0_06-64 Mac OS X version 10.4.8 running on ppc en_US (nb); MacRoman Open Project and Create J2SE project actions offer the project path as /home/user_name/NetBeansProjects. While actions "Add Project" and "Add JAR/Folder" on Libraries node of J2se project offer default location /home/user_name/. Please set this to /home/user_name/NetBeansProjects to be consistent.
Probably specific to the filechooser impl (L&F, or standard vs. quickfilechooser vs. Soot Phengsy's dirchooser) - check to see if the project folder is selected. May not be fixable.
For 'Add Project' it already works this way and for 'Add JAR/Folder' it ends in home dir, which I think is more correct.