Update test routing config to alleviate pydantic errors

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This PR attempts to resolve the GHA failures we're seeing with the master branch of t-route in the integration tests.

Changes

• Comments out the config parameters causing pydantic errors:
  • supernetwork_parameters -> geo_file_type
  • supernetwork_parameters -> level_pool -> reservoir_parameter_file
  • compute_parameters -> nexus_input_folder
  • compute_parameters -> next_file_pattern_filter

Checklist

• PR has an informative and human-readable title
• Changes are limited to a single goal (no scope creep)
• Code can be automatically merged (no conflicts)
• Code follows project standards (link if applicable)
• Passes all existing automated tests
• Any change in functionality is tested
• New functions are documented (with a description, list of inputs, and expected output)
• Placeholder code is flagged / future todos are captured in comments
• Project documentation has been updated (including the "Unreleased" section of the CHANGELOG)
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The current issue is a pydantic validation error + a dict default value issue. With the current routing config (in this PR), we get the AttributeError error:

C++ exception with description "AttributeError: 'NoneType' object has no attribute 'get'

At:
  /home/runner/work/ngen/ngen/.venv/lib/python3.10/site-packages/troute/HYFeaturesNetwork.py(30): read_geopkg
  /home/runner/work/ngen/ngen/.venv/lib/python3.10/site-packages/troute/HYFeaturesNetwork.py(140): read_geo_file
  /home/runner/work/ngen/ngen/.venv/lib/python3.10/site-packages/troute/HYFeaturesNetwork.py(233): __init__
  /home/runner/work/ngen/ngen/.venv/lib/python3.10/site-packages/nwm_routing/__main__.py(80): main_v04
" thrown in the test body.

This is because in read_geopkg, when those values are read, if they don't exist then the values default to None instead of {} -- however, a .get() call is immediately called on these, which doesn't exist for None.

If we add shims to the routing config that contain the defaults, then we get a ValidationError from pydantic:

C++ exception with description "ValidationError: 3 validation errors for Config
network_topology_parameters -> waterbody_parameters -> rfc
  extra fields not permitted (type=value_error.extra)
compute_parameters -> data_assimilation_parameters -> reservoir_da -> reservoir_persistence_usace
  extra fields not permitted (type=value_error.extra)
compute_parameters -> data_assimilation_parameters -> reservoir_da -> reservoir_persistence_usgs
  extra fields not permitted (type=value_error.extra)