CLI: make sure MCP server doesn't persist even after removal (#11602)

Co-authored-by: openhands <openhands@all-hands.dev>

openhands-cli/openhands_cli/tui/settings/store.py

@@ -45,9 +45,7 @@ class AgentStore:
                 system_message_suffix=f'You current working directory is: {WORK_DIR}',
             )
 
-            additional_mcp_config = self.load_mcp_configuration()
-            mcp_config: dict = agent.mcp_config.copy().get('mcpServers', {})
-            mcp_config.update(additional_mcp_config)
+            mcp_config: dict = self.load_mcp_configuration()
 
             # Update LLM metadata with current information
             agent_llm_metadata = get_llm_metadata(

openhands-cli/tests/settings/test_mcp_settings_reconciliation.py

@@ -0,0 +1,114 @@
+"""Minimal tests: mcp.json overrides persisted agent MCP servers."""
+
+import json
+from pathlib import Path
+from unittest.mock import patch
+import pytest
+from pydantic import SecretStr
+
+from openhands.sdk import Agent, LLM
+from openhands_cli.locations import MCP_CONFIG_FILE, AGENT_SETTINGS_PATH
+from openhands_cli.tui.settings.store import AgentStore
+
+
+# ---------------------- tiny helpers ----------------------
+
+def write_json(path: Path, obj: dict) -> None:
+    path.write_text(json.dumps(obj))
+
+
+def write_agent(root: Path, agent: Agent) -> None:
+    (root / AGENT_SETTINGS_PATH).write_text(
+        agent.model_dump_json(context={"expose_secrets": True})
+    )
+
+
+# ---------------------- fixtures ----------------------
+
+@pytest.fixture
+def persistence_dir(tmp_path, monkeypatch) -> Path:
+    # Create root dir and point AgentStore at it
+    root = tmp_path / "openhands"
+    root.mkdir()
+    monkeypatch.setattr("openhands_cli.tui.settings.store.PERSISTENCE_DIR", str(root))
+    return root
+
+
+@pytest.fixture
+def agent_store() -> AgentStore:
+    return AgentStore()
+
+
+# ---------------------- tests ----------------------
+
+@patch("openhands_cli.tui.settings.store.get_default_tools", return_value=[])
+@patch("openhands_cli.tui.settings.store.get_llm_metadata", return_value={})
+def test_load_overrides_persisted_mcp_with_mcp_json_file(
+    mock_meta,
+    mock_tools,
+    persistence_dir,
+    agent_store
+):
+    """If agent has MCP servers, mcp.json must replace them entirely."""
+    # Persist an agent that already contains MCP servers
+    persisted_agent = Agent(
+        llm=LLM(model="gpt-4", api_key=SecretStr("k"), usage_id="svc"),
+        tools=[],
+        mcp_config={
+            "mcpServers": {
+                "persistent_server": {"command": "python", "args": ["-m", "old_server"]}
+            }
+        },
+    )
+    write_agent(persistence_dir, persisted_agent)
+
+    # Create mcp.json with different servers (this must fully override)
+    write_json(
+        persistence_dir / MCP_CONFIG_FILE,
+        {
+            "mcpServers": {
+                "file_server": {"command": "uvx", "args": ["mcp-server-fetch"]}
+            }
+        },
+    )
+
+    loaded = agent_store.load()
+    assert loaded is not None
+    # Expect ONLY the MCP json file's config
+    assert loaded.mcp_config == {
+        "mcpServers": {
+            "file_server": {
+                "command": "uvx",
+                "args": ["mcp-server-fetch"],
+                "env": {},
+                "transport": "stdio",
+            }
+        }
+    }
+
+
+@patch("openhands_cli.tui.settings.store.get_default_tools", return_value=[])
+@patch("openhands_cli.tui.settings.store.get_llm_metadata", return_value={})
+def test_load_when_mcp_file_missing_ignores_persisted_mcp(
+    mock_meta,
+    mock_tools,
+    persistence_dir,
+    agent_store
+):
+    """If mcp.json is absent, loaded agent.mcp_config should be empty (persisted MCP ignored)."""
+    persisted_agent = Agent(
+        llm=LLM(model="gpt-4", api_key=SecretStr("k"), usage_id="svc"),
+        tools=[],
+        mcp_config={
+            "mcpServers": {
+                "persistent_server": {"command": "python", "args": ["-m", "old_server"]}
+            }
+        },
+    )
+    write_agent(persistence_dir, persisted_agent)
+
+    # No mcp.json created
+
+    loaded = agent_store.load()
+    assert loaded is not None
+    assert loaded.mcp_config == {}  # persisted MCP is ignored if file is missin