Remove unneeded python dependencies for R2D2 and replace with python dependencies from r2d2-client

[ericlingerfelt]

Is your feature request related to a problem? Please describe.
R2D2 V3 will only require the end user to apply the new r2d2-client module. This module has a much shorter python dependency list that V2. I inspected EWOK and SIMOBS to make sure we didn't remove anything they needed.

The new r2d2-client uses the following dependencies.

Package            Version
------------------ -----------
boto3              1.35.74
botocore           1.35.74
certifi            2024.8.30
charset-normalizer 3.4.0
idna               3.10
jmespath           1.0.1
pip                23.2.1
python-dateutil    2.9.0.post0
PyYAML             6.0.2
r2d2               3.0.0
requests           2.32.3
s3transfer         0.10.4
setuptools         65.5.0
six                1.16.0
urllib3            2.2.3

The current r2d2@develop installation uses the following dependencies.

Package                Version
---------------------- -----------
boto3                  1.35.76
botocore               1.35.76
certifi                2024.8.30
cftime                 1.6.4.post1
gitdb                  4.0.11
GitPython              3.1.43
jmespath               1.0.1
mysql-connector-python 8.2.0
netCDF4                1.7.2
numpy                  2.1.3
pip                    24.2
protobuf               4.21.12
python-dateutil        2.9.0.post0
PyYAML                 6.0.2
r2d2                   2.4.0
s3transfer             0.10.4
six                    1.17.0
smmap                  5.0.1
solo                   1.3.0
urllib3                2.2.3

Dependencies to remove (not needed by r2d2-client, ewok, or simobs)

Package                Version
---------------------- -----------
mysql-connector-python 8.2.0
protobuf               4.21.12

Dependencies to add (needed by r2d2-client)

Package            Version
------------------ -----------
charset-normalizer 3.4.0
idna               3.10
requests           2.32.3
s3transfer         0.10.4

[ericlingerfelt]

@ericlingerfelt, Why do we need s3transfer?

[stiggy87]

I think we can just update the r2d2 package.py for everything we need for the new r2d2, when it is ready.