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fix: Do not override user pinned versions with pnpm (#10635)
Any user defined (package.json / NpmPackage-annotation) versions will not be overridden by based on the platform versions (versions.json file). This means that the users will have to remember to also remove their pins after those are not needed anymore or they will stay on using old versions, which is the same as with Maven overrides. Fixes #9793
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