The refactoring in 4e28e1d3ff incorrectly switched a check for
`if args.from_git` into `if NEW_ZULIP_MERGE_BASE`, which is
incorrect -- the merge-base is always defined, it may just match the
version. This led to errors when installing from tarball, without a
git repo.
Since the run_hooks command was already set up to take a `--from-git`
argument, but was ignoring it, pass down that flag from
upgrade-zulip-stage-3 when necessary, and swap the run_hooks logic
back to basing the version-resolution logic on that flag.
