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It might be actually a bug, because when I do gt log, I can see that currentbranch is built on top of baseBranch. But in the log there are repeated commits in the currentBranch which are already in baseBranch. And the new commits are not propagated upstack.

hmm. @Jacob Gold for what could be going on here! a quick fyi - i would suggest using

gt stack restack

or

gt sr

to restack branches in your whole stack!