fix(cli): dedupe MCP servers in project trust approval prompt (#3342)

Closes #2374

---

The startup project MCP approval prompt was listing servers once per
config file rather than once per server name. The downstream loader
already deduplicates via `merge_mcp_configs` (later configs override
earlier ones), so the prompt was inconsistent with what actually got
loaded — most noticeably for users of `rulesync`, which generates
`.deepagents/.mcp.json` alongside the project's root `.mcp.json`.

`_check_mcp_project_trust` now runs the loaded project configs through
`merge_mcp_configs` before extracting server summaries, so each server
name appears exactly once in the prompt and the displayed entry matches
the one that will be loaded.

---------

Co-authored-by: open-swe[bot] <open-swe@users.noreply.github.com>
Co-authored-by: Mason Daugherty <61371264+mdrxy@users.noreply.github.com>
Co-authored-by: Mason Daugherty <github@mdrxy.com>

libs/cli/deepagents_cli/main.py

@@ -1457,6 +1457,7 @@ def _check_mcp_project_trust(*, trust_flag: bool = False) -> bool | None:
         discover_mcp_configs,
         extract_project_server_summaries,
         load_mcp_config_lenient,
+        merge_mcp_configs,
     )
     from deepagents_cli.project_utils import ProjectContext
 
@@ -1470,12 +1471,17 @@ def _check_mcp_project_trust(*, trust_flag: bool = False) -> bool | None:
     if not project_configs:
         return None
 
-    # Collect all servers (stdio + remote) across project configs
-    all_servers: list[tuple[str, str, str]] = []
-    for path in project_configs:
-        cfg = load_mcp_config_lenient(path)
-        if cfg is not None:
-            all_servers.extend(extract_project_server_summaries(cfg))
+    # Merge configs by server name (last wins, matching the loader) so that
+    # a server defined in multiple project configs (for example,
+    # `.deepagents/.mcp.json` and higher-precedence `.mcp.json`) only shows
+    # up once in the prompt.
+    loaded_configs = [
+        cfg
+        for cfg in (load_mcp_config_lenient(path) for path in project_configs)
+        if cfg is not None
+    ]
+    merged_config = merge_mcp_configs(loaded_configs)
+    all_servers = extract_project_server_summaries(merged_config)
 
     if not all_servers:
         return None

libs/cli/tests/unit_tests/test_main.py

@@ -921,3 +921,177 @@ class TestThreadsListCwdArgparse:
         """`--cwd /some/path` stores the literal value as-is."""
         ns = self._parse(["threads", "list", "--cwd", "/some/path"])
         assert ns.cwd == "/some/path"
+
+
+class TestCheckMcpProjectTrustDedupe:
+    """Regression tests for the project MCP approval prompt deduplication.
+
+    When the same server name appears in multiple project-level configs
+    (e.g. both `.mcp.json` and `.deepagents/.mcp.json`), the approval
+    prompt must list it once — not once per file.
+    """
+
+    def _write_config(self, path: Path, servers: dict[str, Any]) -> None:
+        import json
+
+        path.parent.mkdir(parents=True, exist_ok=True)
+        path.write_text(json.dumps({"mcpServers": servers}), encoding="utf-8")
+
+    def _deny_project_mcp(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        monkeypatch.chdir(tmp_path)
+        monkeypatch.setattr(
+            "deepagents_cli.mcp_trust.is_project_mcp_trusted",
+            lambda *_a, **_k: False,
+        )
+        monkeypatch.setattr("builtins.input", lambda _prompt="": "n")
+
+    def _captured_prompt(self, capsys: pytest.CaptureFixture[str]) -> str:
+        captured = capsys.readouterr()
+        return captured.out + captured.err
+
+    def test_duplicate_server_across_configs_listed_once(
+        self,
+        tmp_path: Path,
+        monkeypatch: pytest.MonkeyPatch,
+        capsys: pytest.CaptureFixture[str],
+    ) -> None:
+        """A server defined in both project configs appears once in the prompt."""
+        from deepagents_cli.main import _check_mcp_project_trust
+
+        server = {
+            "fs": {
+                "command": "uvx",
+                "args": ["mcp-server-filesystem", "/tmp"],
+            }
+        }
+        self._write_config(tmp_path / ".mcp.json", server)
+        self._write_config(tmp_path / ".deepagents" / ".mcp.json", server)
+
+        self._deny_project_mcp(tmp_path, monkeypatch)
+
+        result = _check_mcp_project_trust(trust_flag=False)
+
+        assert result is False
+        combined = self._captured_prompt(capsys)
+        assert combined.count('  "fs" (stdio):') == 1, combined
+
+    def test_duplicate_server_across_configs_uses_project_root_definition(
+        self,
+        tmp_path: Path,
+        monkeypatch: pytest.MonkeyPatch,
+        capsys: pytest.CaptureFixture[str],
+    ) -> None:
+        """The higher-precedence project-root config wins for duplicate names."""
+        from deepagents_cli.main import _check_mcp_project_trust
+
+        self._write_config(
+            tmp_path / ".deepagents" / ".mcp.json",
+            {"fs": {"command": "npx", "args": ["subdir-server", "/subdir"]}},
+        )
+        self._write_config(
+            tmp_path / ".mcp.json",
+            {"fs": {"command": "uvx", "args": ["root-server", "/root"]}},
+        )
+
+        self._deny_project_mcp(tmp_path, monkeypatch)
+
+        result = _check_mcp_project_trust(trust_flag=False)
+
+        assert result is False
+        combined = self._captured_prompt(capsys)
+        assert combined.count('  "fs" (stdio):') == 1, combined
+        assert '  "fs" (stdio):  uvx root-server /root' in combined
+        assert "subdir-server" not in combined
+
+    def test_duplicate_remote_server_across_configs_listed_once(
+        self,
+        tmp_path: Path,
+        monkeypatch: pytest.MonkeyPatch,
+        capsys: pytest.CaptureFixture[str],
+    ) -> None:
+        """Duplicate remote servers are deduped the same way as stdio servers."""
+        from deepagents_cli.main import _check_mcp_project_trust
+
+        self._write_config(
+            tmp_path / ".deepagents" / ".mcp.json",
+            {
+                "remote": {
+                    "type": "http",
+                    "url": "https://subdir.example.com/mcp",
+                }
+            },
+        )
+        self._write_config(
+            tmp_path / ".mcp.json",
+            {
+                "remote": {
+                    "type": "http",
+                    "url": "https://root.example.com/mcp",
+                }
+            },
+        )
+
+        self._deny_project_mcp(tmp_path, monkeypatch)
+
+        result = _check_mcp_project_trust(trust_flag=False)
+
+        assert result is False
+        combined = self._captured_prompt(capsys)
+        assert combined.count('  "remote" (http):') == 1, combined
+        assert '  "remote" (http):  https://root.example.com/mcp' in combined
+        assert "subdir.example.com" not in combined
+
+    def test_invalid_project_config_does_not_block_valid_config(
+        self,
+        tmp_path: Path,
+        monkeypatch: pytest.MonkeyPatch,
+        capsys: pytest.CaptureFixture[str],
+    ) -> None:
+        """Malformed project configs are skipped while valid configs still prompt."""
+        from deepagents_cli.main import _check_mcp_project_trust
+
+        invalid = tmp_path / ".deepagents" / ".mcp.json"
+        invalid.parent.mkdir(parents=True, exist_ok=True)
+        invalid.write_text("{not json", encoding="utf-8")
+        self._write_config(
+            tmp_path / ".mcp.json",
+            {"fs": {"command": "uvx", "args": ["root-server", "/root"]}},
+        )
+
+        self._deny_project_mcp(tmp_path, monkeypatch)
+
+        result = _check_mcp_project_trust(trust_flag=False)
+
+        assert result is False
+        combined = self._captured_prompt(capsys)
+        assert combined.count('  "fs" (stdio):') == 1, combined
+        assert '  "fs" (stdio):  uvx root-server /root' in combined
+
+    def test_distinct_servers_across_configs_all_listed(
+        self,
+        tmp_path: Path,
+        monkeypatch: pytest.MonkeyPatch,
+        capsys: pytest.CaptureFixture[str],
+    ) -> None:
+        """Different servers from different project configs are all shown."""
+        from deepagents_cli.main import _check_mcp_project_trust
+
+        self._write_config(
+            tmp_path / ".mcp.json",
+            {"alpha": {"command": "uvx", "args": ["alpha"]}},
+        )
+        self._write_config(
+            tmp_path / ".deepagents" / ".mcp.json",
+            {"beta": {"command": "uvx", "args": ["beta"]}},
+        )
+
+        self._deny_project_mcp(tmp_path, monkeypatch)
+
+        result = _check_mcp_project_trust(trust_flag=False)
+
+        assert result is False
+        combined = self._captured_prompt(capsys)
+        assert combined.count('  "alpha" (stdio):') == 1, combined
+        assert combined.count('  "beta" (stdio):') == 1, combined