refactor: move CLI to top-level and clean up configs

.gitignore

@@ -5,4 +5,7 @@
 *.egg-info
 *.db*
 .DS_Store
-__pycache__
+__pycache__
+kaizen_data
+demo/workdir/.claude/
+.claude

AGENTS.md

@@ -25,10 +25,10 @@ Kaizen is a Python library and service which enables AI agents to improve throug
 │   └── claudecode
 ├── kaizen (Primary Source Root)
 │   ├── backend (Entity Database Backend implementations, primarily vector databases)
+│   ├── cli (A CLI wrapper over the native Python client)
 │   ├── config (All configurations which are derived from environment variables or instantiated as an object)
 │   ├── db (A sqlite database for when vector databases are a poor fit for the data)
 │   ├── frontend (Interfaces to interact with the backend)
-│   │   ├── cli (A CLI wrapper over the native Python client)
 │   │   ├── client (A native Python client which thinly wraps the configured backend)
 │   │   └── mcp (An MCP server implementing some high-level methods useful for AI agents)
 │   ├── llm (All code that prompts an LLM)
@@ -64,4 +64,5 @@ pre-commit install
 ## Coding Standards
 - Use Ruff for linting and formatting (configured in pyproject.toml)
 - Run pre-commit hooks before committing
-- All new features need tests (unit + e2e where applicable)
+- All new features need tests (unit + e2e where applicable)
+- Use uv to run Python commands, including pip.

README_phoenix_sync.md

@@ -32,20 +32,20 @@ No additional dependencies required - uses only stdlib for Phoenix API calls.
 
 ```bash
 # Basic sync with defaults
-uv run python -m kaizen.frontend.cli.cli sync phoenix
+uv run python -m kaizen.cli.cli sync phoenix
 
 # Custom Phoenix URL and namespace
-uv run python -m kaizen.frontend.cli.cli sync phoenix \
+uv run python -m kaizen.cli.cli sync phoenix \
   --url http://phoenix.example.com:6006 \
   --namespace my_namespace
 
 # Fetch more spans and include errors
-uv run python -m kaizen.frontend.cli.cli sync phoenix \
+uv run python -m kaizen.cli.cli sync phoenix \
   --limit 500 \
   --include-errors
 
 # Full options
-uv run python -m kaizen.frontend.cli.cli sync phoenix \
+uv run python -m kaizen.cli.cli sync phoenix \
   --url http://localhost:6006 \
   --namespace production \
   --project my_project \
@@ -145,7 +145,7 @@ Two entity types are stored:
 
 ```bash
 # Sync every hour
-0 * * * * cd /path/to/kaizen && uv run python -m kaizen.frontend.cli.cli sync phoenix --limit 100
+0 * * * * cd /path/to/kaizen && uv run python -m kaizen.cli.cli sync phoenix --limit 100
 ```
 
 ### Systemd Timer
@@ -158,7 +158,7 @@ Description=Kaizen Phoenix Sync
 [Service]
 Type=oneshot
 WorkingDirectory=/path/to/kaizen
-ExecStart=/path/to/uv run python -m kaizen.frontend.cli.cli sync phoenix
+ExecStart=/path/to/uv run python -m kaizen.cli.cli sync phoenix
 Environment=PHOENIX_URL=http://localhost:6006
 Environment=KAIZEN_NAMESPACE_ID=production
 ```

pyproject.toml

@@ -31,7 +31,7 @@ examples = [
 ]
 
 [project.scripts]
-kaizen = "kaizen.frontend.cli.cli:app"
+kaizen = "kaizen.cli.cli:app"
 
 [dependency-groups]
 dev = [

tests/unit/test_cli.py

@@ -6,7 +6,7 @@
 import pytest
 from typer.testing import CliRunner
 
-from kaizen.frontend.cli.cli import app
+from kaizen.cli.cli import app
 from kaizen.schema.core import Namespace, RecordedEntity
 from kaizen.schema.conflict_resolution import EntityUpdate
 from kaizen.schema.exceptions import (
@@ -22,7 +22,7 @@
 @pytest.fixture
 def mock_client():
     """Create a mock KaizenClient."""
-    with patch("kaizen.frontend.cli.cli.get_client") as mock_get_client:
+    with patch("kaizen.cli.cli.get_client") as mock_get_client:
         client = MagicMock()
         mock_get_client.return_value = client
         yield client