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Thanks for the clear repro. I opened PR #974 to fix this.

The fix preserves root dependency specifiers from npm package-lock.json entries, so the existing drift checker can now see when package.json has moved from @raycast/api to @vicinae/api. With that, aube install --lockfile-only should re-resolve instead of reporting the stale lockfile as fresh, and aube install --frozen-lockfile should fail on the mismatch.

I also added regression coverage for the reported case.

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