Ensure dependency management configs can be updated

[IanWoodard]

Currently, the git configs used for dependency management can't easily be updated for already installed dependencies because they are only set at install. Ideally, if we change these down the line, they should take effect even if we already installed dependencies. There are a few ways to solve this problem:

• Version the installed dependencies via a nested folder structure where we use /v1/dependencies to signify the version installed. We could then bump that version if/when we change the configs to ensure we re-install the dependencies if we change the git config.
• Instead of setting the git config directly, we could pass it with every git command we run. This would enable us to not have to worry about what config we may have used in the past since it will always use whatever it is currently configured to.