fix: address PR review feedback and fix CI test failures

- Revert default transport to streamable-http (not a breaking change)
- Extract AVAILABLE_APPS constant to server/__init__.py (DRY)
- Wrap get_stdio_mcp ValueError in click.ClickException for clean errors
- Fix test_stdio.py: call _reload_config() so dynaconf sees env changes
- Use lazy %-style logging in stdio.py
- Add private API comments in test assertions
- Derive --enable-app CLI choices from AVAILABLE_APPS
- README: show explicit --transport stdio in uvx examples

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

tests/test_cli.py

@@ -108,8 +108,6 @@ def test_cli_options_set_environment_variables(runner, clean_env, monkeypatch):
     _ = runner.invoke(
         run,
         [
-            "--transport",
-            "streamable-http",
             "--nextcloud-host",
             "https://test.example.com",
             "--nextcloud-username",
@@ -166,8 +164,6 @@ def test_cli_options_override_environment_variables(runner, monkeypatch):
     _ = runner.invoke(
         run,
         [
-            "--transport",
-            "streamable-http",
             "--nextcloud-host",
             "https://from-cli.example.com",
             "--nextcloud-username",
@@ -218,7 +214,7 @@ def test_environment_variables_used_when_cli_not_provided(runner, monkeypatch):
     monkeypatch.setattr("nextcloud_mcp_server.cli.get_app", mock_get_app)
 
     # Don't provide any CLI options - should use env vars
-    _ = runner.invoke(run, ["--transport", "streamable-http"])
+    _ = runner.invoke(run, [])
 
     # Verify env vars were used
     assert captured_env["NEXTCLOUD_HOST"] == "https://from-env.example.com"
@@ -250,7 +246,7 @@ def test_default_values(runner, clean_env, monkeypatch):
     monkeypatch.setattr("nextcloud_mcp_server.cli.get_app", mock_get_app)
 
     # Don't provide CLI options or env vars - should use defaults
-    _ = runner.invoke(run, ["--transport", "streamable-http"])
+    _ = runner.invoke(run, [])
 
     # Verify default values
     assert captured_env["NEXTCLOUD_OIDC_SCOPES"] == (
@@ -282,14 +278,12 @@ def test_oauth_token_type_case_normalization(runner, clean_env, monkeypatch):
     monkeypatch.setattr("nextcloud_mcp_server.cli.get_app", mock_get_app)
 
     # Test uppercase JWT
-    runner.invoke(run, ["--transport", "streamable-http", "--oauth-token-type", "JWT"])
+    runner.invoke(run, ["--oauth-token-type", "JWT"])
     assert captured_env["NEXTCLOUD_OIDC_TOKEN_TYPE"] in ["JWT", "jwt"]
 
     # Test mixed case Bearer
     captured_env.clear()
-    runner.invoke(
-        run, ["--transport", "streamable-http", "--oauth-token-type", "Bearer"]
-    )
+    runner.invoke(run, ["--oauth-token-type", "Bearer"])
     assert captured_env["NEXTCLOUD_OIDC_TOKEN_TYPE"] in ["Bearer", "bearer"]
 
 

tests/unit/test_stdio.py

@@ -3,6 +3,7 @@
 import pytest
 from mcp.server.fastmcp import FastMCP
 
+from nextcloud_mcp_server.config import _reload_config
 from nextcloud_mcp_server.config_validators import AuthMode
 from nextcloud_mcp_server.stdio import get_stdio_mcp
 
@@ -13,6 +14,9 @@ def single_user_env(monkeypatch):
     monkeypatch.setenv("NEXTCLOUD_HOST", "https://cloud.example.com")
     monkeypatch.setenv("NEXTCLOUD_USERNAME", "admin")
     monkeypatch.setenv("NEXTCLOUD_PASSWORD", "secret")
+    # Ensure multi-user mode is off (may leak from other tests)
+    monkeypatch.delenv("ENABLE_MULTI_USER_BASIC_AUTH", raising=False)
+    _reload_config()
 
 
 @pytest.mark.unit
@@ -48,6 +52,7 @@ def test_get_stdio_mcp_rejects_non_single_user_mode(monkeypatch):
 def test_get_stdio_mcp_registers_all_apps_by_default(single_user_env):
     """All app tool groups are registered when no filter is specified."""
     mcp = get_stdio_mcp()
+    # NOTE: _tool_manager is a FastMCP internal; may break on SDK upgrades
     tools = mcp._tool_manager.list_tools()
     tool_names = {t.name for t in tools}
 
@@ -68,6 +73,7 @@ def test_get_stdio_mcp_registers_all_apps_by_default(single_user_env):
 def test_get_stdio_mcp_respects_enabled_apps(single_user_env):
     """Only specified apps have their tools registered."""
     mcp = get_stdio_mcp(enabled_apps=["notes"])
+    # NOTE: _tool_manager is a FastMCP internal; may break on SDK upgrades
     tools = mcp._tool_manager.list_tools()
     tool_names = {t.name for t in tools}
 
@@ -81,6 +87,7 @@ def test_get_stdio_mcp_respects_enabled_apps(single_user_env):
 def test_get_stdio_mcp_no_semantic_tools(single_user_env):
     """Semantic search tools are never registered in stdio mode."""
     mcp = get_stdio_mcp()
+    # NOTE: _tool_manager is a FastMCP internal; may break on SDK upgrades
     tools = mcp._tool_manager.list_tools()
     tool_names = {t.name for t in tools}
 
@@ -92,5 +99,6 @@ def test_get_stdio_mcp_no_semantic_tools(single_user_env):
 def test_get_stdio_mcp_registers_capabilities_resource(single_user_env):
     """The nc://capabilities resource is registered."""
     mcp = get_stdio_mcp()
+    # NOTE: _resource_manager._resources is a FastMCP internal; may break on SDK upgrades
     resources = mcp._resource_manager._resources
     assert "nc://capabilities" in resources