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This is definitely a worthwhile project. It always seems to me that the merits of the desktop metaphor are oversold when I consider how much time I've spent on locating and placing windows where I can see them, often with minimal help from the operating system. It would be great on Linux, having identified the active processes, to match these to the windows from which they have been invoked. There must be scope for using dependency to link the location of windows to content in useful ways (e.g. assembling all the windows with certain content within a particular display for instance) or iconifying all the windows relating to the use of a particular application. As it is, I mislay half finished emails and file edits because I'm distracted by an interruption. That said, you can now get a lot of help towards this model-building exercise from Karl King's drawScout, I think, so it will be important to look for new features that your model can offer over and above that. (I'm incidentally not sure what use you expect to make of Donald in model-building in this context, though there may be a role for this.)

A good subsidiary objective - creating a customised window management feature to deal with the eden modelling scenario (especially e.g. for use in conjunction with teaching a class of students in CS101, where the size of text displayed in input and output and the positions of windows is an issue!) Of course, ideally it would be good to be able to incorporate utilities like text editors in the display itself, and this probably lies beyond the scope of what can easily be achieved using tkeden at present. If you want to do an experiment of this nature, you could use Edward Yung's original text editor in a prototype however (see texteditorYung1987). You might also wish (e.g. in your conclusion) to discuss the window management problem in the context of an even ambitious objective: that of modelling yet more of the operating system using EM principles and tools.

Need to take a little more care with English:

'a software' -> software
'role in human computing' is odd, since 'human computing' is not a term used outside EM - perhaps you mean 'role in human computer interaction'?
'If a desktop is cluttered, how can .... ' needs a '?' at the end