feat(cli): add orphans command to show entities without relations

Adds a new `basic-memory orphans` CLI command that identifies entities
with no incoming or outgoing connections in the knowledge graph, helping
users discover isolated notes that haven't been linked into their knowledge base.

Changes:
- EntityRepository.find_without_relations(): efficient SQL EXISTS subquery
- GET /v2/projects/{id}/knowledge/orphans API endpoint
- OrphanEntitiesResponse schema (entities list + total count)
- KnowledgeClient.get_orphans() typed API client method
- `basic-memory orphans` CLI command with table and --json output
- Tests for repository method, API endpoint, and CLI command

Closes #762

Co-authored-by: Paul Hernandez <phernandez@users.noreply.github.com>
Signed-off-by: claude[bot] <41898282+claude[bot]@users.noreply.github.com>

tests/cli/test_orphans_command.py

@@ -0,0 +1,112 @@
+"""Tests for the 'basic-memory orphans' CLI command."""
+
+import json
+from contextlib import asynccontextmanager
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pytest
+from typer.testing import CliRunner
+
+from basic_memory.cli.main import app as cli_app
+
+# Register the orphans command on the shared app.
+import basic_memory.cli.commands.orphans as orphans_cmd  # noqa: F401
+
+runner = CliRunner()
+
+_MOCK_PROJECT_ITEM = MagicMock()
+_MOCK_PROJECT_ITEM.name = "test-project"
+_MOCK_PROJECT_ITEM.external_id = "11111111-1111-1111-1111-111111111111"
+
+_ORPHAN_ENTITIES = [
+    {
+        "external_id": "aaaa-1111",
+        "title": "Isolated Note",
+        "file_path": "notes/isolated.md",
+        "note_type": "note",
+    },
+    {
+        "external_id": "bbbb-2222",
+        "title": "Dangling Spec",
+        "file_path": "specs/dangling.md",
+        "note_type": "spec",
+    },
+]
+
+
+def _mock_config_manager():
+    mock_cm = MagicMock()
+    mock_cm.default_project = "test-project"
+    return mock_cm
+
+
+@asynccontextmanager
+async def _fake_get_client(project_name=None):
+    yield MagicMock()
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_json_output(mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls):
+    """bm orphans --json outputs a JSON array of entity objects."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+
+    mock_knowledge_instance = AsyncMock()
+    mock_knowledge_instance.get_orphans.return_value = _ORPHAN_ENTITIES
+    mock_knowledge_cls.return_value = mock_knowledge_instance
+
+    result = runner.invoke(cli_app, ["orphans", "--json"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    start = result.output.index("[")
+    data = json.loads(result.output[start:])
+    assert len(data) == 2
+    titles = {e["title"] for e in data}
+    assert "Isolated Note" in titles
+    assert "Dangling Spec" in titles
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_table_output(mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls):
+    """bm orphans (default) renders a Rich table with titles and paths."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+
+    mock_knowledge_instance = AsyncMock()
+    mock_knowledge_instance.get_orphans.return_value = _ORPHAN_ENTITIES
+    mock_knowledge_cls.return_value = mock_knowledge_instance
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    assert "Isolated Note" in result.output
+    assert "Dangling Spec" in result.output
+    assert "notes/isolated.md" in result.output
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_no_results(mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls):
+    """bm orphans prints a success message when no orphans are found."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+
+    mock_knowledge_instance = AsyncMock()
+    mock_knowledge_instance.get_orphans.return_value = []
+    mock_knowledge_cls.return_value = mock_knowledge_instance
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    assert "No orphan entities" in result.output