Add --prune to EdkRepo cache update

[ashedesimone]

Add --prune to the git fetch command when running cache update as a separate --prune option in EdkRepo cli

This is to resolve a cases where the repo cache can't be updated to the latest content. The fetch will fail due to conflicts in branches. In this case using the --prune command will remove potentially conflicting entries before fetching the new entries.

It is suggested that this is not done by default since this may cause references to be removed that are needed for other projects.