v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks

216 implanted events in 22 synthetic GSA samples (4 replicates per kind x fraction x
size; reference model from 30 other samples): constitutional DEL/DUP 16/16 at 5-20 Mb,
mosaic loss/gain/CN-LOH at 15 % / 5 Mb 12/12.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/pipeline/cn.py

@@ -88,9 +88,10 @@ def run_build_model(
     n_ref = 0
     if reference_gtcs is not None:
         from simurg.cn.model import reference_stats
+        from simurg.formats.discovery import discover_gtcs
         from simurg.formats.gtc import read_gtc
 
-        paths = sorted(reference_gtcs.rglob("*.gtc"))
+        paths = sorted(discover_gtcs(reference_gtcs).values())  # E_NO_INPUT when there is none
         if len(paths) > max_reference:
             idx = np.random.default_rng(42).choice(len(paths), max_reference, replace=False)
             paths = [paths[i] for i in sorted(idx)]