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Does Automatic branch managements "Deleted branches" option and "Inactive branches" option remove the branch from GIT?

If I enable these 2 options, when they run will they just remove the plan branches from Bamboo but leave the underlying branch that is in GIT or will it delete both? If it's both how can I just remove the one in Bamboo?

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No, Bamboo does not remove branches from remote vcs. It only remove the sub-plan (a.k.a plan branch) that refers to vcs branch.

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