Permission Denied: `--NotebookApp.notebook_dir` vs `--FileContentsManager.root_dir`

### Bug description
`--NotebookApp.notebook_dir` vs `--FileContentsManager.root_dir` getting permission denied.

#### Expected behaviour
The git operation should occur in `--NotebookApp.notebook_dir`

#### Actual behaviour
The git operation is happening in `--FileContentsManager.root_dir` is passed to starting the JupyterLab instance.
Based on PR #71 and associated issues I found relating to that it seems that it was desired to have the starting directory be the `--NotebookApp.notebook_dir`, but in my environment, I have `notebook_dir` set as $HOME, but `--FileContentsManager.root_dir=/glade` set because that's common root for our shared filesystems, but for demonstrations `root_dir` could be set to `/home`

### How to reproduce

A minimum jupyterhub installation inside a VM that has the following configuration arguments and the user home directory being `/home/$USER`:
```
c.Spawner.args.append('--FileContentsManager.root_dir="/home"')
c.Spawner.args.append('--NotebookApp.notebook_dir="~"')
```
### Your personal set up

- OS:
OpenSUSE 15.3
- Version(s):
```
# jupyterhub --version
2.2.2

# python --version
Python 3.9.12
```
- Full environment

```
# packages in environment at /ncar/usr/jupyterhub.hpc.ucar.edu/test:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
aiofiles 0.7.0 pypi_0 pypi
aiohttp 3.8.1 py39h3811e60_0 conda-forge
aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge
alembic 1.7.7 pyhd8ed1ab_0 conda-forge
aniso8601 7.0.0 pypi_0 pypi
ansimarkup 1.5.0 pypi_0 pypi
anyio 3.5.0 py39hf3d152e_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h7f8727e_0
asttokens 2.0.5 pyhd3eb1b0_0
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
async_generator 1.10 py_0 conda-forge
asyncssh 2.10.0 pypi_0 pypi
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
batchspawner 1.1.1.dev0 pypi_0 pypi
beautifulsoup4 4.10.0 pyh06a4308_0
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.4 py_1 conda-forge
bokeh 2.4.2 py39hf3d152e_0 conda-forge
brotli 1.0.9 he6710b0_2
brotlipy 0.7.0 py39h3811e60_1003 conda-forge
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.3.18 h06a4308_0
certifi 2021.10.8 py39h06a4308_2
certipy 0.1.3 py_0 conda-forge
cffi 1.15.0 py39h4bc2ebd_0 conda-forge
cfgv 3.3.1 pyhd8ed1ab_0 conda-forge
chardet 4.0.0 py39hf3d152e_2 conda-forge
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.1.0 py39hf3d152e_0 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
conda 4.12.0 py39h06a4308_0
conda-package-handling 1.8.0 py39hb9d737c_0 conda-forge
configurable-http-proxy 4.5.1 node17_h7e777a6_1 conda-forge
coverage 6.3.2 py39hb9d737c_1 conda-forge
cryptography 36.0.2 py39hd97740a_0 conda-forge
curl 7.82.0 h7bff187_0 conda-forge
cycler 0.11.0 pyhd3eb1b0_0
cylc-ext 0.1.1 pypi_0 pypi
cylc-flow 8.0rc2 pypi_0 pypi
cylc-uiserver 1.0.1 pypi_0 pypi
cytoolz 0.11.2 py39h3811e60_1 conda-forge
dask 2022.3.0 pyhd8ed1ab_0 conda-forge
dask-core 2022.3.0 pyhd8ed1ab_0 conda-forge
dask-labextension 5.2.0 pyhd8ed1ab_0 conda-forge
dask_labextension 5.2.0 hd8ed1ab_0 conda-forge
dataclasses 0.8 pyh6d0b6a4_7
debugpy 1.5.1 py39h295c915_0
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
distlib 0.3.4 pyhd8ed1ab_0 conda-forge
distributed 2022.3.0 pyhd8ed1ab_0 conda-forge
elastic-transport 8.1.0 pypi_0 pypi
elasticsearch 8.1.1 pypi_0 pypi
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd3eb1b0_0
filelock 3.6.0 pyhd8ed1ab_0 conda-forge
flake8 4.0.1 pyhd8ed1ab_2 conda-forge
flit-core 3.6.0 pyhd3eb1b0_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.10.4 h0708190_1 conda-forge
frozenlist 1.2.0 py39h7f8727e_0
fsspec 2022.2.0 pyhd8ed1ab_0 conda-forge
future 0.18.2 py39h06a4308_1
gettext 0.21.0 hf68c758_0
giflib 5.2.1 h7b6447c_0
gitdb 4.0.7 pyhd3eb1b0_0
gitpython 3.1.27 pyhd8ed1ab_0 conda-forge
graphene 2.1.9 pypi_0 pypi
graphene-tornado 2.6.1 pypi_0 pypi
graphql-core 2.3.2 pypi_0 pypi
graphql-relay 2.0.1 pypi_0 pypi
graphql-ws 0.4.4 pypi_0 pypi
greenlet 1.1.2 py39he80948d_1 conda-forge
heapdict 1.0.1 py_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
identify 2.4.12 pyhd8ed1ab_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.3 py39hf3d152e_0 conda-forge
importlib_resources 5.2.0 pyhd3eb1b0_1
invoke 1.7.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.10.0 py39hef51801_0 conda-forge
ipython 8.2.0 py39hf3d152e_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.7.0 pyhd8ed1ab_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 py39hf3d152e_0 conda-forge
jinja2 2.11.3 pypi_0 pypi
jpeg 9e h7f98852_0 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter-packaging 0.12.0 pyhd8ed1ab_0 conda-forge
jupyter-resource-usage 0.6.1 pyhd8ed1ab_0 conda-forge
jupyter-server-mathjax 0.2.5 pyhc268e32_0 conda-forge
jupyter-server-proxy 3.2.1 pyhd8ed1ab_0 conda-forge
jupyter_client 7.2.0 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.2 py39hf3d152e_0 conda-forge
jupyter_server 1.15.6 pyhd8ed1ab_1 conda-forge
jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge
jupyterhub 2.2.2 hd8ed1ab_0 conda-forge
jupyterhub-base 2.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab 3.3.2 pyhd8ed1ab_0 conda-forge
jupyterlab-git 0.36.0 pyhd8ed1ab_0 conda-forge
jupyterlab-latex 3.1.0 pypi_0 pypi
jupyterlab-mathjax3 4.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab-ncar-menu 0.1.1 pypi_0 pypi
jupyterlab-nvdashboard 0.6.0 pyhd8ed1ab_0 conda-forge
jupyterlab-recents 3.0.1 pyhd8ed1ab_0 conda-forge
jupyterlab-server 2.10.3 pypi_0 pypi
jupyterlab-sublime 0.4.1 pypi_0 pypi
jupyterlab-variableinspector 3.0.9 pyhd8ed1ab_0 conda-forge
jupyterlab_code_formatter 1.4.10 pyhd8ed1ab_1 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.1.0 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.0 py39hf939315_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libarchive 3.5.2 hccf745f_1 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.82.0 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_14 conda-forge
libgfortran-ng 11.2.0 h69a702a_14 conda-forge
libgfortran5 11.2.0 h5c6108e_14 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 11.2.0 h1d223b6_14 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libmamba 0.22.1 h9c208ef_0 conda-forge
libmambapy 0.22.1 py39h3216e65_0 conda-forge
libmemcached 1.0.18 h17b2bb4_1003 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsolv 0.7.20 h4ff587b_0
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.43.0 h7f98852_0 conda-forge
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h1bed415_1
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h7b6447c_2
mako 1.2.0 pyhd8ed1ab_0 conda-forge
mamba 0.22.1 py39hfa8f2c8_0 conda-forge
markdown 3.1.1 pypi_0 pypi
markupsafe 2.0.1 pypi_0 pypi
matplotlib-base 3.5.1 py39h2fa2bec_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
metomi-isodatetime 1!2.0.2 pypi_0 pypi
mistune 0.8.4 py39h3811e60_1005 conda-forge
mock 4.0.3 py39hf3d152e_2 conda-forge
msgpack-python 1.0.3 py39h1a9c180_0 conda-forge
multidict 6.0.2 py39h3811e60_0 conda-forge
munkres 1.1.4 py_0
nb_conda_kernels 2.3.1 py39hf3d152e_1 conda-forge
nbclassic 0.3.7 pyhd8ed1ab_0 conda-forge
nbclient 0.5.13 pyhd8ed1ab_0 conda-forge
nbconvert 5.6.1 pypi_0 pypi
nbconvert-pandoc 6.4.5 pyhd8ed1ab_1 conda-forge
nbdime 3.1.1 pyhd8ed1ab_0 conda-forge
nbformat 5.2.0 pyhd8ed1ab_0 conda-forge
nbgitpuller 1.1.0 pyhd8ed1ab_0 conda-forge
nbviewer 1.0.1+265.gd9c5da7 pypi_0 pypi
ncurses 6.3 h9c3ff4c_0 conda-forge
nest-asyncio 1.5.4 pyhd8ed1ab_0 conda-forge
newrelic 7.6.0.173 py39hb9d737c_0 conda-forge
nodeenv 1.6.0 pyhd8ed1ab_0 conda-forge
nodejs 17.8.0 h784f1fd_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.4.10 pyha770c72_0 conda-forge
notebook-shim 0.1.0 pyhd8ed1ab_0 conda-forge
numpy 1.22.3 py39h18676bf_0 conda-forge
oauthlib 3.2.0 pyhd8ed1ab_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1n h7f8727e_0
packaging 21.3 pyhd8ed1ab_0 conda-forge
pamela 1.0.0 py_0 conda-forge
pandas 1.4.1 py39hde0f152_0 conda-forge
pandoc 2.17.1.1 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 0.12.6 pyhd8ed1ab_0 conda-forge
param 1.12.0 pyh6c4a22f_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.0.1 py39hae2aec6_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge
pre-commit 2.17.0 py39hf3d152e_0 conda-forge
prometheus_client 0.13.1 pyhd8ed1ab_0 conda-forge
promise 2.3 pypi_0 pypi
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
protobuf 3.19.4 pypi_0 pypi
psutil 5.9.0 py39h3811e60_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd3eb1b0_0
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycodestyle 2.8.0 pyhd8ed1ab_0 conda-forge
pycosat 0.6.3 py39h3811e60_1009 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 pyhd3eb1b0_0
pycurl 7.45.1 py39hd73adbb_0 conda-forge
pydantic 1.9.0 py39h3811e60_0 conda-forge
pyflakes 2.4.0 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.3.0 pyhd8ed1ab_1 conda-forge
pylibmc 1.6.1 py39h3811e60_4 conda-forge
pynvml 11.4.1 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py39h3811e60_0 conda-forge
pysocks 1.7.1 py39hf3d152e_4 conda-forge
python 3.9.12 h9a8a25e_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-editor 1.0.4 py_0 conda-forge
python-json-logger 2.0.1 pyh9f0ad1d_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyuv 1.4.0 pypi_0 pypi
pyviz_comms 2.1.0 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py39h3811e60_3 conda-forge
pyzmq 22.3.0 py39h37b5a0c_1 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
reproc 14.2.4 h295c915_1
reproc-cpp 14.2.4 h295c915_1
requests 2.27.1 pyhd8ed1ab_0 conda-forge
rich 12.0.1 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.17.21 py39h3811e60_0 conda-forge
ruamel.yaml.clib 0.2.6 py39h3811e60_0 conda-forge
ruamel_yaml 0.15.80 py39h3811e60_1006 conda-forge
rx 1.6.1 pypi_0 pypi
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 61.2.0 py39hf3d152e_1 conda-forge
simpervisor 0.4 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
sniffio 1.2.0 py39hf3d152e_2 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.1 pyhd3eb1b0_0
sqlalchemy 1.4.32 py39hb9d737c_0 conda-forge
sqlite 3.37.1 h4ff8645_0 conda-forge
sshspawner 0.1.0 pypi_0 pypi
stack_data 0.2.0 pyhd3eb1b0_0
statsd 3.3.0 py_0 conda-forge
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
terminado 0.13.3 py39hf3d152e_0 conda-forge
testpath 0.6.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 1.2.2 pyhd3eb1b0_0
tomlkit 0.10.1 pyha770c72_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39h3811e60_2 conda-forge
tqdm 4.63.1 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing 3.10.0.0 py39h06a4308_0
typing-extensions 4.1.1 hd8ed1ab_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
ukkonen 1.0.1 py39h1a9c180_1 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
urwid 2.1.2 pypi_0 pypi
virtualenv 20.14.0 py39hf3d152e_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.3.2 pyhd8ed1ab_0 conda-forge
werkzeug 0.12.2 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 3.6.0 py39hf3d152e_0 conda-forge
wrapspawner 1.0.1 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.6.3 he1b5a44_4 conda-forge
yarl 1.7.2 py39h3811e60_1 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zict 2.1.0 pyhd8ed1ab_0 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
```

- Configuration
A basic configuration with the two lines mentioned above:
```python
c.Spawner.args.append('--FileContentsManager.root_dir="/home"')
c.Spawner.args.append('--NotebookApp.notebook_dir="~"')
```

- Logs

```
$ git clone --depth 1 --branch CSG_tutorial -- https://github.com/dphow/GPU_workshop /home/GPU_workshop
fatal: could not create work tree dir '/home/GPU_workshop': Permission denied
```