fix: preserve species roles through confirmation

tests/unit/test_intent_species_roles.py

@@ -1,3 +1,6 @@
+import pytest
+
+from gfa_core.mas.agents.intent_v2 import IntentAgentV2
 from gfa_core.mas.utils.intent_parser import (
     parse_explicit_species_role_mentions,
     parse_gene_family_scope_selection,
@@ -30,3 +33,58 @@ def test_explicit_role_parser_keeps_unassigned_mentions_separate() -> None:
         "comparativeSpecies": [],
         "unassigned": ["Ppy"],
     }
+
+
+@pytest.mark.parametrize("species", ["Gm", "Br", "Pt", "Sb"])
+def test_scope_parser_preserves_species_supported_by_legacy_intent(species: str) -> None:
+    scope = parse_gene_family_scope_selection(f"分析 {species} 的 SPL 基因家族")
+
+    assert scope["targetSpecies"] == [species]
+
+
+def test_scope_parser_accepts_explicit_role_bound_custom_species_code() -> None:
+    scope = parse_gene_family_scope_selection("目标物种 Sv；参考物种 At")
+
+    assert scope["targetSpecies"] == ["Sv"]
+    assert scope["referenceSpecies"] == ["At"]
+
+
+def test_scope_parser_does_not_treat_gene_family_as_species() -> None:
+    scope = parse_gene_family_scope_selection("目标物种 Ft；分析 SPL 基因家族")
+
+    assert scope["targetSpecies"] == ["Ft"]
+
+
+def test_scope_parser_does_not_bind_custom_code_to_generic_goal_word() -> None:
+    scope = parse_gene_family_scope_selection("分析目标 SPL 基因家族")
+
+    assert scope["targetSpecies"] == []
+
+
+def test_intent_validation_keeps_confirmed_target_and_reference_separate() -> None:
+    agent = object.__new__(IntentAgentV2)
+
+    intent = agent._validate_intent(
+        {"gene_family": "SPL", "stages": ["identify"], "params": {}},
+        (
+            "请按照你规划的步骤来帮我执行\n"
+            "已确认上下文：基因家族 SPL；目标物种 Ft；参考物种 At。"
+        ),
+    )
+
+    assert intent["target_species"] == ["Ft"]
+    assert intent["reference_species"] == ["At"]
+    assert intent["species"] == "Ft"
+
+
+def test_intent_validation_preserves_unlabelled_multi_target_request() -> None:
+    agent = object.__new__(IntentAgentV2)
+
+    intent = agent._validate_intent(
+        {"gene_family": "SPL", "stages": ["identify"], "params": {}},
+        "分析 Ft 和 Os 的 SPL 基因家族",
+    )
+
+    assert intent["target_species"] == ["Ft", "Os"]
+    assert intent["reference_species"] == []
+    assert intent["species"] == "Multi"

tests/unit/test_subfamily_prediction_plan.py

@@ -426,6 +426,64 @@ def test_confirmed_multi_species_roles_remain_separate(monkeypatch):
     assert resolved["classification_species"] == ["Ft", "Ppy"]
 
 
+def test_confirmation_ack_normalizes_structured_role_drift(monkeypatch):
+    main = _load_vue3_main()
+    monkeypatch.setattr(
+        main,
+        "_confirmed_config_species_scope",
+        lambda _job_id: {
+            "targetSpecies": ["Ft"],
+            "referenceSpecies": ["At"],
+            "comparativeSpecies": [],
+        },
+    )
+
+    resolved = main._reconcile_confirmed_gene_family_species(
+        "job-confirmed-ack",
+        "是",
+        {
+            "gene_family": "SPL",
+            "stages": ["identify"],
+            "target_species": ["Ft", "At"],
+            "params": {"targetSpecies": ["Ft", "At"]},
+        },
+    )
+
+    assert resolved["conflicts"] == []
+    assert resolved["target_species"] == ["Ft"]
+    assert resolved["reference_species"] == ["At"]
+
+
+def test_unassigned_reference_species_analysis_request_remains_blocked(monkeypatch):
+    main = _load_vue3_main()
+    monkeypatch.setattr(
+        main,
+        "_confirmed_config_species_scope",
+        lambda _job_id: {
+            "targetSpecies": ["Ft"],
+            "referenceSpecies": ["At"],
+            "comparativeSpecies": [],
+        },
+    )
+
+    resolved = main._reconcile_confirmed_gene_family_species(
+        "job-unassigned-reference",
+        "分析 At 的 SPL 基因家族",
+        {
+            "gene_family": "SPL",
+            "stages": ["identify"],
+            "target_species": ["At"],
+            "params": {"targetSpecies": ["At"]},
+        },
+    )
+
+    assert any(
+        conflict["code"] == "analysis_target_config_role_conflict"
+        and conflict["species"] == "At"
+        for conflict in resolved["conflicts"]
+    )
+
+
 def test_confirmed_config_duplicate_roles_are_blocked(monkeypatch):
     main = _load_vue3_main()
     monkeypatch.setattr(