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fix(core): potential edge-case issue with versions and generateFiles
This is a little bit of a shot in the dark, looking to solve an issue reported on Slack (https://kubernetes.slack.com/archives/CKM7CP8P9/p1614599864049600), but it's in any case a sane thing to do. Basically we now ensure that a new tree scan is performed after manipulating files in a particular module path.
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