Fix NEE flat-file var read; registry overlay hygiene; min_year default

[zhongwangwei]

Summary

Three fixes from a debugging session on the persistent Net_Ecosystem_Exchange evaluation error (plus related cleanups).

1. NEE flat-file variable resolution (the actual bug)

Preprocessing correctly derives NEE from f_respc/f_assim and relabels the saved variable to the evaluation item (Net_Ecosystem_Exchange) for output-label correctness. But the flat file is named with the config varname (f_respc), and downstream readers hard-indexed ds[sim_varname] → xarray No variable named 'f_respc'. Variables on the dataset include ['Net_Ecosystem_Exchange', 'time', 'lat', 'lon'].

• Add util.names.select_data_array(ds, *names): resolve by name (case-insensitive), else fall back to the sole data variable (flat files have exactly one).
• Use it in runner/masking.py (the preprocess crash), core/evaluation.py (grid scoring), and all 7 core/_comparison_*.py modules.
• Write-side relabel to the item is intentional and unchanged.

2. Registry overlay hygiene — openbench registry diff|prune

A legacy full-snapshot ~/.openbench overlay silently shadows bundled catalog fixes (this is why the CLARA albedo unit fix didn't take effect until the overlay was reset). New tooling:

• Classify overlay entries: redundant / stale full-copy / delta / custom.
• registry prune re-sparses behavior-preservingly (drops redundant, minimizes stale full-copies; merged registry identical before/after).
• Throttled, silent-when-clean startup notice; suppress via OPENBENCH_NO_REGISTRY_CHECK.

3. min_year_threshold default → 1

schema + loader default 3 → 1 (matches GUI/smoke); init now writes 1 for every project span.

Testing

• New: tests/test_flat_var_resolution.py (reproduces the exact error + end-to-end masking read), tests/test_registry_overlay_audit.py.
• Updated test_cli_stubs.py, test_config/test_schema.py for the new defaults/command.
• Full suite: 1532 passed, 5 skipped. ruff clean.

Remote sync note

After pulling + reinstalling on the HPC, run openbench registry prune once to un-shadow the bundled catalog (the remote ~/.openbench overlay is separate).