fix: suppress legacy warnings in machine JSON paths

harness/tests/test_qdrant_cli_commands.py

@@ -61,6 +61,18 @@ embeddings:
     return cfg
 
 
+def _legacy_qdrant_runtime_config(tmp_path: Path) -> Path:
+    cfg = _qdrant_runtime_config(tmp_path)
+    text = cfg.read_text()
+    text = text.replace(
+        "dwh:\n  type: postgres_direct\n  connection: {database: analytics, schema: mart, user: reader, password: secret}\n",
+        "database: {database: analytics, schema: mart, user: reader, password: secret}\n",
+    )
+    text = text.replace("roots:\n", "paths:\n")
+    cfg.write_text(text)
+    return cfg
+
+
 def _write_schema_artifacts(tmp_path: Path) -> None:
     (tmp_path / "artifacts" / "mschema").mkdir(parents=True, exist_ok=True)
     (tmp_path / "artifacts" / "mschema" / "physical.yaml").write_text(
@@ -252,3 +264,33 @@ def test_vector_index_schema_human_missing_config_has_original_error(tmp_path):
     assert response.exit_code == 1
     assert response.output
     assert "ERRORE:" in response.output
+
+
+def test_vector_index_schema_json_legacy_config_has_no_stderr_on_success(monkeypatch, tmp_path):
+    cfg = _legacy_qdrant_runtime_config(tmp_path)
+    _write_schema_artifacts(tmp_path)
+    store = _FakeVectorStore()
+    monkeypatch.setattr("tht.adapters.factory.build_vector_store", lambda cfg, require_write: store)
+    monkeypatch.setattr("tht.cli.vector_cmd.make_embedder", lambda _: _FakeEmbedder())
+
+    response = CliRunner().invoke(app, ["vector", "index-schema", "--json", "-c", str(cfg)])
+
+    assert response.exit_code == 0, response.output
+    assert response.stderr == ""
+    assert response.stdout.count("\n") == 1
+    assert json.loads(response.stdout)["status"] == "succeeded"
+
+
+def test_vector_index_schema_json_legacy_config_has_no_stderr_on_failure(tmp_path):
+    cfg = _legacy_qdrant_runtime_config(tmp_path)
+    _write_schema_artifacts(tmp_path)
+    (tmp_path / "artifacts" / "mschema" / "physical.yaml").unlink()
+
+    response = CliRunner().invoke(app, ["vector", "index-schema", "--json", "-c", str(cfg)])
+
+    assert response.exit_code == 1
+    assert response.stderr == ""
+    assert response.stdout.count("\n") == 1
+    assert json.loads(response.stdout) == {
+        "status": "failed", "code": "physical_schema_missing"
+    }

harness/tests/test_schema_fk_annotations.py

@@ -241,6 +241,7 @@ def test_suggest_fks_json_is_single_deterministic_document_without_writing(tmp_p
         app, ["schema", "suggest-fks", "--json", "-c", str(cfg), "--from-sql", str(staged)]
     )
     assert response.exit_code == 0, response.output
+    assert response.stderr == ""
     assert response.stdout.count("\n") == 1
     payload = json.loads(response.stdout)
     assert payload["status"] == "succeeded"
@@ -261,6 +262,7 @@ def test_suggest_fks_json_failure_is_safe_and_single_document(tmp_path):
     (tmp_path / "artifacts" / "mschema" / "physical.yaml").unlink()
     response = CliRunner().invoke(app, ["schema", "suggest-fks", "--json", "-c", str(cfg)])
     assert response.exit_code != 0
+    assert response.stderr == ""
     assert response.stdout.count("\n") == 1
     payload = json.loads(response.stdout)
     assert payload == {"status": "failed", "code": "physical_schema_missing"}
@@ -276,6 +278,7 @@ def test_schema_check_json_reports_orphan_count_without_prose(tmp_path):
     )
     response = CliRunner().invoke(app, ["schema", "check", "--json", "-c", str(cfg)])
     assert response.exit_code == 3
+    assert response.stderr == ""
     assert response.stdout.count("\n") == 1
     assert json.loads(response.stdout) == {
         "status": "failed", "code": "annotation_orphans", "orphan_count": 1,
@@ -327,11 +330,14 @@ def test_schema_check_json_success_and_reviewed_annotations_are_preserved(tmp_pa
 
     check = CliRunner().invoke(app, ["schema", "check", "--json", "-c", str(cfg)])
     assert check.exit_code == 0, check.output
+    assert check.stderr == ""
+    assert check.stdout.count("\n") == 1
     assert json.loads(check.stdout) == {
         "status": "succeeded", "code": "ok", "orphan_count": 0, "orphans": []
     }
     suggest = CliRunner().invoke(app, ["schema", "suggest-fks", "--json", "-c", str(cfg)])
     assert suggest.exit_code == 0, suggest.output
+    assert suggest.stderr == ""
     assert json.loads(suggest.stdout)["candidate_count"] == 0
     assert annotations_path.read_text() == before
 

harness/tht/cli/schema_cmd.py

@@ -1,5 +1,6 @@
 # ruff: noqa: BLE001, S110, B008
 import logging
+import warnings
 from pathlib import Path
 from typing import TypedDict
 
@@ -143,6 +144,15 @@ def _schema_json(payload: dict) -> None:
 
 
 def _machine_config(config: Path):
+    # Legacy resource keys remain accepted, but their deprecation warning is not part of
+    # the JSON machine contract.  Keep this filter scoped to this call so human commands
+    # (and unrelated warnings/errors) retain their existing behavior.
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message=r"^DEPRECATION: legacy workspace resource keys are deprecated;",
+            category=FutureWarning,
+        )
         try:
             return load_config(config)
         except ConfigError: