feat: add pattern reconciler for gene seeds

Author: AvaPrime

src/codessa_co_design/reconciliation/pattern_reconciler.py

@@ -0,0 +1,41 @@
+from __future__ import annotations
+
+from collections import defaultdict
+from typing import Any
+
+
+class PatternReconciler:
+    """P0 reconciler that groups gene seeds by category into simple pattern families."""
+
+    def reconcile(self, gene_seeds: list[dict[str, Any]]) -> list[dict[str, Any]]:
+        grouped: dict[str, list[dict[str, Any]]] = defaultdict(list)
+        for seed in gene_seeds:
+            grouped[seed["category"]].append(seed)
+
+        patterns: list[dict[str, Any]] = []
+        for category, seeds in grouped.items():
+            pattern_id = f"rp:{category}:1"
+            labels = [seed["label"] for seed in seeds]
+            confidences = [float(seed.get("confidence", 0.0)) for seed in seeds]
+            avg_confidence = sum(confidences) / len(confidences) if confidences else 0.0
+            source_observations: list[str] = []
+            for seed in seeds:
+                source_observations.extend(seed.get("source_observations", []))
+
+            patterns.append(
+                {
+                    "pattern_id": pattern_id,
+                    "category": category,
+                    "label": f"reconciled-{category}-pattern",
+                    "constituent_gene_seeds": [seed["gene_seed_id"] for seed in seeds],
+                    "source_observations": sorted(set(source_observations)),
+                    "reconciliation_note": f"Grouped {len(seeds)} gene seed(s) with shared category '{category}' into a P0 pattern family.",
+                    "conflict_resolved": False,
+                    "resolution_strategy": "group_by_category",
+                    "unified_intent": "; ".join(labels),
+                    "confidence": round(avg_confidence, 3),
+                    "tags": sorted({tag for seed in seeds for tag in seed.get("tags", [])}),
+                }
+            )
+
+        return sorted(patterns, key=lambda p: p["pattern_id"])