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build-system: always update module config files if requested

Merged build-system: always update module config files if requested
cherry-pick-d00b776e into 1.1.22
Merged gsell requested to merge cherry-pick-d00b776e into 1.1.22

(cherry picked from commit d00b776e)

Co-authored-by: Achim Gsell achim.gsell@psi.ch

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