When saving FileObjects as project settings (and system 
settings, maybe?) and restarting netbeans, the FileObject 
gets de-serialzed and placed in the SystemFileSystem, no 
matter where it originated.

The problem shows up when overriding SystemOption like 
this:

    public void writeExternal( ObjectOutput out )
        throws IOException
    {
        super.writeExternal(out);
        out.writeObject(getMyFileObject());
    }

    public void readExternal( ObjectInput in )
        throws IOException, ClassNotFoundException
    {
        super.readExternal(in);
        FileObjectWrapper fo = (FileObject)in.readObject();
        setMyFileObject(fo);
    }

I can work around the bug by changing this code to:

    public void writeExternal( ObjectOutput out )
        throws IOException
    {
        super.writeExternal(out);
        out.writeObject(new FileObjectWrapper
(getMyFileObject()));
    }

    public void readExternal( ObjectInput in )
        throws IOException, ClassNotFoundException
    {
        super.readExternal(in);
        FileObjectWrapper foWrapper = (FileObjectWrapper)
in.readObject();
        setMyFileObject(foWrapper.getFileObject());
    }
    
    protected static class FileObjectWrapper implements 
Serializable
    {
        FileObjectWrapper( FileObject fo )
        {
            m_sPath = fo.toString();
            try
            {
                m_fileSystem = fo.getFileSystem();
            }
            catch( FileStateInvalidException ex )
            {
                ex.printStackTrace();
            }
        }

        FileObject getFileObject()
        {
            if( m_fileSystem == null )
            {
                return null;
            }
            return m_fileSystem.findResource(m_sPath);
        }

        private String m_sPath;
        private FileSystem m_fileSystem;
    }