upgrade-zulip-from-git: init, then add remote.

30457ecd02 removed the `--mirror` from
initial clones, but did not add back `--bare`, which `--mirror`
implies.  This leads to `/srv/zulip.git` having a working tree in it,
with a `/srv/zulip.git/.git` directory.

This is mostly harmless, and since the bug was recent, not worth
introducing additional complexity into the upgrade process to handle.

Calling `git clone --bare`, however, would clone the refs into
`refs/heads/`, not the `refs/remotes/origin/` we want.  Instead, use
`git init --bare`, followed by `git remote add origin`.  The remote
will be fetched by the usual `git fetch --all --prune` which is below.

scripts/lib/upgrade-zulip-from-git

@@ -60,11 +60,15 @@ try:
 
     # Populate LOCAL_GIT_CACHE_DIR with both the requested remote and zulip/zulip.
     if not os.path.exists(LOCAL_GIT_CACHE_DIR):
-        logging.info("Cloning the repository")
+        logging.info("Making local repository cache")
         subprocess.check_call(
-            ["git", "clone", "-q", remote_url, LOCAL_GIT_CACHE_DIR],
+            ["git", "init", "--bare", "-q", LOCAL_GIT_CACHE_DIR],
             stdout=subprocess.DEVNULL,
         )
+        subprocess.check_call(
+            ["git", "remote", "add", "origin", remote_url],
+            cwd=LOCAL_GIT_CACHE_DIR,
+        )
 
     if os.stat(LOCAL_GIT_CACHE_DIR).st_uid == 0:
         subprocess.check_call(["chown", "-R", "zulip:zulip", LOCAL_GIT_CACHE_DIR])