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1. Add something to the project, for example a Java package 2. Add something again - the initial wizard panel (Select File or Folder) will show two directories whose name starts with "Project Home" - that's unintuitive. The users usually think of "home" as a unique entity. I suggest changing the name to something different, such as "Project Root Directory" (or something shorter).
The file chooser isn't complete yet, but it will be based on JFileChooser and will not display the list of 'prefered' or 'known' locations, it will display the contents of all disks and preselect the location (folder) which user selected last time. Thus there will be no need to label special nodes in either way.
The mechanism for adding things into the project is now completely different, so agreed that this is invalid.