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Code already exists in the JGit implementation to evaluate the prune implementation that was included in JGit 3.3. Unfortunately, the JGit 3.3 prune removes more branches than command line git. Since that would give incompatible behavior between CliGit and JGit, and CliGit is the reference implementation, the JGit prune at fetch can't be enabled.
Refer to this submission which attempted to use JGit prune with JGit 3.5.2 and confirmed that it is still pruning too many branches.