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repository: Fix SetFullPath writing multiple entries

Patrick Steinhardt requested to merge pks-set-full-path-fix into master

The new SetFullPath() RPC uses git.Config.Add() to write the path into the gitconfig, which internally uses git config --add. What this does is to amend the config entry to the gitconfig while keeping all old entries, effectively turning the config entry into a multivar.

Fix this by invoking git-config(1) directly without the --add flag. To guard against the case where the key already is a multivar, this also adds the --replace-all flag such that we remove all multivars.

Changelog: fixed

Part of #1774 (closed)

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