feat(cli): phentrieve config calibrate-thresholds subcommand

[berntpopp]

Summary

Add phentrieve config calibrate-thresholds to help users tune quality_threshold and margin_threshold after switching the retrieval embedding model.

Why

The CLI profiles + adaptive re-chunking work landing under #28 / #171 / #148 ships threshold defaults calibrated specifically for BioLORD-class biomedical encoders:

• chunk_retrieval_threshold = 0.7
• aggregated_term_confidence = 0.75
• adaptive_rechunking.quality_threshold = 0.55
• adaptive_rechunking.margin_threshold = 0.03

Users who switch to a different retrieval_model see different similarity-score distributions and need to retune. Today the user-guide tells them to "retune your thresholds" without telling them how. This subcommand closes that gap.

Proposed Behavior

phentrieve config calibrate-thresholds
phentrieve config calibrate-thresholds --benchmark-fixture tests/data/benchmarks/german/tiny_v1.json
phentrieve config calibrate-thresholds --model FremyCompany/BioLORD-2023-M --output suggested-profile.yaml

The command:

1. Loads the configured retrieval model (or the one passed via --model).
2. Runs it against a fixture benchmark (default: a small bundled set; user can pass --benchmark-fixture).
3. Computes per-encoder distributions of: top-1 similarity, top-1 minus top-2 margin, and aggregated-term confidence on hits and misses.
4. Suggests calibrated values for each threshold, written to stdout as a YAML profile snippet that can be pasted into phentrieve.yaml.
5. Reports the score distribution stats so the user understands where the suggestions came from.

Acceptance Criteria

• New phentrieve config calibrate-thresholds Typer command in phentrieve/cli/config_commands.py.
• Outputs a YAML snippet ready to paste into phentrieve.yaml profiles: section.
• Documented in docs/user-guide/configuration-profiles.md and docs/user-guide/adaptive-rechunking.md (cross-referenced).
• Smoke test on the German tiny benchmark fixture.
• Exit non-zero with a clear error if the configured model can't be loaded or the fixture is missing.

References

• Spec A: .planning/specs/2026-04-25-cli-profiles-default-resolution-spec.md Future work
• Spec B: .planning/specs/2026-04-25-adaptive-rechunking-spec.md Future work
• Encoder calibration warning in docs/user-guide/adaptive-rechunking.md (added by Plan B)