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operations: Reimplement UserUpdateSubmodule without git2go

John Cai requested to merge jc-submodule-in-git into master

Updating a submodule is simply updating the oid of the commit at the path. We can do this by manually rewriting trees and writing a new commit. If we implement it this way, we don't need to rely on Git2Go.

fixes: #4577 (closed)

Edited by John Cai

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