Allow targeting a self-hosted Koina server

[BioGeek]

Problem

The Koina-backed features build their client with no server argument:

model = koinapy.Koina(self.intensity_model_name)          # fragment_match.py
model = koinapy.Koina(self.prosit_intensity_model_name)   # chimeric.py
koina_model = koinapy.Koina(self.irt_model_name)          # retention_time.py

so every intensity and iRT prediction goes to the public endpoint at koina.wilhelmlab.org, and there is no configuration hook to change it. That makes bulk work impractical.

Change

Adds koina.server_url and koina.ssl, defaulting to the public endpoint, so behaviour is unchanged for anyone not self-hosting:

winnow diagnose-calibration \
    koina.server_url=localhost:8500 \
    koina.ssl=false \
    dataset.spectrum_path_or_directory=data/spectra.mgf \
    dataset.predictions_path=data/preds.csv

• FragmentMatchFeatures, ChimericFeatures and RetentionTimeFeature take koina_server_url / koina_ssl and pass them to koinapy.Koina, falling back to a new DEFAULT_KOINA_SERVER_URL.
• ProbabilityCalibrator.apply_koina_server_overrides sets them on restored features, mirroring the existing apply_koina_model_input_overrides. With a pretrained calibrator the features come from the checkpoint, not from calibrator.yaml, so config wiring alone would have no effect. It means the pretrained general model can be used against a local server without retraining.
• apply_koina_intensity_config applies it where it already applies the model-input overrides, so every command reading the koina block picks it up with no CLI changes.
• calibrator.yaml interpolates the keys for the training path.

ssl=false is required because a self-hosted Triton serves gRPC without TLS while the public endpoint requires it, so the two settings have to travel together.

Tests

• tests/configs/test_koina_config.py — the shipped config defaults to the public endpoint, every feature naming a Koina model also names a server, and the interpolations are the expected ${koina.*} references.
• tests/calibration/test_calibrator.py — apply_koina_server_overrides retargets a Koina feature, is a no-op when given neither value, accepts one value without clobbering the other, and skips features that do not call Koina.
• tests/calibration/features/test_koina_server.py — all three feature classes default to no server, store a self-hosted one, and can be retargeted by assignment after construction.

Docs

docs/configuration.md gains a "Self-hosting Koina" section with the overrides, why ssl must be disabled locally, and a note that the settings apply to checkpoint-restored features too. The Koina config reference lists the new keys.