Added gage references for CAMELS, gages-3000, and gages-II

[taddyb]

Issue Addressed

Updated the streamflow_datasets/ folder to be called references/ and added more CSV files with MERIT COMID references. These CSV files are:

• camels_670.csv
  • for the camels dataset
• gages_3000.csv
  • for GAGES-3000
• GAGES-II.csv
• for GAGES-II

additionally, I checked to see if engine/ still works, and updated docs.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Code cleanup/refactor
• Documentation update

Other (please specify):

Checklist

• Branch is up to date with master
• Updated tests or added new tests
• Tests & pre-commit hooks pass
• Updated documentation (if applicable)
• Code follows established style and conventions

[taddyb]

Changes

---

Gage Reference Data — Added reference CSV files for benchmarking streamflow observations:

• references/gage_info/GAGES-II.csv (8,946 gages)
• references/gage_info/camels_670.csv (670 gages)
• references/gage_info/gages_3000.csv (3,212 gages)
• references/gage_info/README.md documenting the datasets
• references/README.md for the top-level references directory
• Moved streamflow_datasets/ content into references/ (deleted old streamflow_datasets/README.md)

Deprecated ddr_engine.hydrofabric removal — Deleted the old engine/src/ddr_engine/hydrofabric/ package (v2_2 adjacency/gages_adjacency modules) and updated all imports to use ddr_engine.lynker_hydrofabric:

• tests/engine/hydrofabric/test_adjacency.py
• tests/engine/hydrofabric/test_gages_adjacency.py
• engine/scripts/build_hydrofabric_v2.2_matrices.py

pyproject.toml consolidation — Simplified dependency groups:

• Merged cpu, tests, docs, jupyter groups into a single dev group
• Removed [project.optional-dependencies] section in favor of [dependency-groups]
• Relaxed cupy-cuda12x pin from ==13.6.0 to >=13.6.0
• Updated default-groups from ["cpu", "tests", "dev"] to ["dev"]

Docs — Added docs/references.md and minor updates to existing docs (datasets.md, engine/, startup.md, gpu.md, index.md).

Other — Added NOTICE.txt, minor README.md and benchmarks/ config/pyproject tweaks.

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