Add memory directory

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

apps/cli/run_subfamily_confirm.py

@@ -118,7 +118,7 @@ def _atomic_promote_pair(curated_id: Path, curated_pep: Path, final_id: Path, fi
     tmp_pep.write_text(curated_pep.read_text(encoding="utf-8", errors="ignore"), encoding="utf-8")
     tmp_ids = _read_id_list(tmp_id)
     tmp_fasta_ids = _read_fasta_ids(tmp_pep)
-    if tmp_ids != tmp_fasta_ids:
+    if sorted(tmp_ids) != sorted(tmp_fasta_ids):
         tmp_id.unlink(missing_ok=True)
         tmp_pep.unlink(missing_ok=True)
         raise RuntimeError(f"Temporary final member validation failed for {final_id.stem}")
@@ -160,7 +160,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
         if not curated_ids:
             raise ValueError(f"Curated member ID file is empty: {curated_id}")
         fasta_ids = _read_fasta_ids(curated_pep)
-        if curated_ids != fasta_ids:
+        if sorted(curated_ids) != sorted(fasta_ids):
             raise ValueError(
                 f"Curated member ID/FASTA mismatch for {member_prefix}: "
                 f"{len(curated_ids)} IDs vs {len(fasta_ids)} FASTA records"
@@ -179,7 +179,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
 
         promoted_ids = _read_id_list(final_id)
         promoted_fasta_ids = _read_fasta_ids(final_pep)
-        if promoted_ids != curated_ids or promoted_fasta_ids != curated_ids:
+        if sorted(promoted_ids) != sorted(curated_ids) or sorted(promoted_fasta_ids) != sorted(curated_ids):
             raise RuntimeError(f"Post-promotion final member validation failed for {member_prefix}")
         promotions.append({
             "prefix": member_prefix,