Verified.

The problem is the FileObject handling code in 
Project.knowsObject(Object object) :

   if (object instanceof FileObject) {
      try {
          objFS = ((FileObject) object).getFileSystem ();
      } catch (FileStateInvalidException e) {
          objFS = null;
      }

      if (objFS == filesystem) {

HelloWorld's FileSystem is not the project file system,
but ExLocalFileSystem (my root directory, /.)  

What's more, when I have multiple projects open, all the
source files report the same ExLocalFileSystem, not each
of their own ProjectFileSystems. 

So, the FileObject recognition code needs to get enhanced.
One quick fix is to do
  DataObject.find(fileobject)
and look for the DataObject (that works) but DataObject.find
may be slow (I've never looked at the implementation so
I don't know).

Alternatively, perhaps we have a quick way to check the
project contents using filesets?

One more note: while projectObject.getProject() works,
Project.find(projectObject) returns null. Probably not a big
deal.

1. Semantics of Project.find and Project.findAll has been changed
according to issue #27189 (see details there). Basicaly, the
Project.findAll method should be used to get the list of projects
containing file. This method accept both DataObjects and FileObjects,
when DO is passed in the methods operates on primary file of that DO.

2. Project.find(ProjectObject) returns the same as
ProjectObject.getProject()

Verified

As described in
http://www.netbeans.org/servlets/ReadMsg?msgId=619519&listName=nbdiscuss the
current work on projects prototype has been stopped.

Marking issue as CLOSED.