Update method `git-bundle` doesn't remove deleted files if `rsync` method was used before

[Ma27]

Given a batou deployment:

• update_method set to rsync for the environment we're deploying
• a directory foo exists with a file bar exists in it. The change is checked in.
• running ./batou deploy env makes it appear on the target host in ~s-service/deployment/foo.
• Remove the directory foo from your local checkout and commit the change.
• Set update_method to git-bundle for the environment to deploy (and commit).
• ./batou deploy env doesn't remove foo now.

Related AppOps ticket: FC-37992