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I usually interact with the shell, but I prefer to have the items on the desktop organized. Is there a command or a scripting interface to organize the desktop?

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It's not entirely clear what your question is. However, if it is that you want to be able to "organise desktop icons" (i.e. into a grid) from the command-line then this will likely depend on what flavour and version of Ubuntu you are using, because they use different managers.

There is a similar question here with no answer. However, there is quite a lot of discussion here with some very good answers, including a custom-made perl script that appears to do exactly that.

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