Google closure depswriter.py --root_with_prefix, what is prefix and root for?

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I went through sample in https://developers.google.com/closure/library/docs/depswriter and many readins on another related question in depswriter.py complains 'The command line is too long'

After housr of googling, and meddling with sample code from google web, I still do not understand what the --root_with_prefix is for.

$ closure-library/closure/bin/build/depswriter.py --root_with_prefix="myproject ../../myproject" > myproject-deps.js

why must myproject be specified as prefix, and ../../myproject as root? I can only guess a relationship between base.js and the dependencies file is specified as ../../myproject. I cant understand the relationship between prefix and the rest. Appreciate any help, and sorry for being obtuse if this is so obvious for some. I did google for explanation but failed to find any explanation that I can understand.

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