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Currently, running vc-update in my Emacs runs git pull. Is there a way to customize it so that it runs something different like git pull --prune? Is it even advisable to do that?

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Looking at the source of vc-update and vc-git-pull (the function that is called by vc-update when using a git backend), there doesn't seem to be a straightforward way to permanently customize the pull command that gets run (short of redefining vc-git-pull).

However, a quick look at the documentation for vc-update (via C-h f vc-update RET) tells you:

[...] On a distributed version control system, this runs a "pull" operation to update the current branch, prompting for an argument list if required. Optional prefix ARG forces a prompt.

In other words, if you want to alter the pull command that vc-update uses, just prefix the call with C-u. You'll get a prompt that says:

Git pull command: git pull

You can then append --prune and hit RET.

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