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JGit only supports 2 of the 3 server-side hooks. https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks#Server-Side-Hooks The "update" hook is called once per updated branch and can reject changes to any one branch, while still allowing them for others. It takes three arguments: branchName, oldSha1, newSha1. For now, I only expect you to put it in the missing features list. It's probably not high priority for you, but it took a lot of searching through other people's code to figure-out that it really wasn't my fault that the hook wasn't working.
marking as enhancement request
*** Bug 493721 has been marked as a duplicate of this bug. ***