Fix git_submodule_sync and add new config helper
This fixes `git_submodule_sync` to correctly update the remote URL of the default branch of the submodule along with the URL in the parent repository config (i.e. match core Git's behavior). Also move some useful helper logic from the submodule code into a shared config API `git_config__update_entry` that can either set or delete an entry with constraints like not overwriting or not creating a new entry. I used that helper to update a couple other places in the code.
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