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Fix updating configs script and formatting in docs

Maria Mironova requested to merge mironova-patch-script into master

Fixes the script for updating configs to work with the different kinds of paths we can have ("relToExec", "relToCon" etc), mostly to work with the directory structure we usually have for module QC.

Additionally, some minor (formatting) fixes to the docs.

Also includes some fixes to the CmlBias scan script to make it nicer and pick paths correctly.

Edited by Maria Mironova

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