Fix test_ensure_cloned and JWT tests

This is two changes in one since they both fix breakage due to
external dep changes:

Git no longer allows file urls in submodules by default, but one
of our unit tests relied on that behavior (in order to verify that
we can clone repos with submodules).  Run the submodule add command
in the test with a flag which allows file urls.

Pin PyJWT <2.6.0

2.6.0 causes the following error:

2022-10-20 15:58:04,800 cherrypy.error.140001002710128   ERROR    [req: 86efa7775e88473a9e9d5e54f0c83050] [20/Oct/2022:15:58:04] HTTP
Traceback (most recent call last):
  File "/home/corvus/git/zuul/zuul/.tox/py310/lib/python3.10/site-packages/cherrypy/_cprequest.py", line 638, in respond
    self._do_respond(path_info)
  File "/home/corvus/git/zuul/zuul/.tox/py310/lib/python3.10/site-packages/cherrypy/_cprequest.py", line 702, in _do_respond
    response.finalize()
  File "/home/corvus/git/zuul/zuul/.tox/py310/lib/python3.10/site-packages/cherrypy/_cprequest.py", line 901, in finalize
    content = self.collapse_body()
  File "/home/corvus/git/zuul/zuul/.tox/py310/lib/python3.10/site-packages/cherrypy/_cprequest.py", line 859, in collapse_body
    new_body = b''.join(self.body)
  File "/home/corvus/git/zuul/zuul/.tox/py310/lib/python3.10/site-packages/cherrypy/_json.py", line 24, in encode
    for chunk in _encode(value):
  File "/usr/lib/python3.10/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/usr/lib/python3.10/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/usr/lib/python3.10/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/usr/lib/python3.10/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type ImmatureSignatureError is not JSON serializable

Change-Id: I2e345f24ea0a62ce8d9dbe1c066438f194e7075c

requirements.txt

@@ -23,7 +23,7 @@ alembic
 cryptography>=1.6
 cachecontrol<0.12.7
 cachetools
-pyjwt>=2.0.0,<3.0
+pyjwt>=2.0.0,<2.6.0
 iso8601
 psutil
 fb-re2>=1.0.6

tests/unit/test_merger_repo.py

@@ -71,8 +71,11 @@ class TestMergerRepo(ZuulTestCase):
 
         # Forge a repo having a submodule
         parent_repo = git.Repo(parent_path)
-        parent_repo.git.submodule('add', os.path.join(
-            self.upstream_root, 'org/project2'), 'subdir')
+        parent_repo.git(c='protocol.file.allow=always').submodule(
+            'add',
+            os.path.join(self.upstream_root, 'org/project2'),
+            'subdir')
+
         parent_repo.index.commit('Adding project2 as a submodule in subdir')
         # git 1.7.8 changed .git from being a directory to a file pointing
         # to the parent repository /.git/modules/*