doc(architecture): update layer descriptions and configuration relationships

- Add cross-cutting nature section to Configuration Layer
- Update design principles to better describe Configuration inference
- Rename 'Configuration' to 'Execution Preparation' in Execution Layer
- Update CLAUDE.md file with improved guidelines

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: shntnu

CLAUDE.md

@@ -9,12 +9,16 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 - Test: `pytest`
 - Single test: `pytest path/to/test_file.py::test_function_name`
 - Lint Python: `ruff`
+- Package with setuptools: `python -m pip install -e .`
 
 ## Code Style
 ### Python
 - Snake_case for variables/functions, PascalCase for classes
 - Imports: stdlib → third-party → local (grouped with blank lines)
 - Consistent type annotations for all functions
-- 4-space indentation, ~88 char line limit
+- 4-space indentation, 80-88 char line limit
 - NumPy-style docstrings with triple double-quotes
 - Prefer returning typed objects over raising exceptions
+- Prefer pathlib for file operations
+- Use click for CLI interfaces
+- Docstrings required for modules and public functions

docs/architecture/00_architecture_overview.md

@@ -64,7 +64,7 @@ Note: The Configuration Layer (in `/starrynight/experiments/`) provides paramete
 - **Separation of concerns**: Each layer has distinct responsibilities
 - **Progressive composition**: Build complex pipelines from simple components
 - **Containerized execution**: Run code in reproducible environments
-- **Configuration inference**: Minimize manual configuration through smart defaults
+- **Configuration inference**: The Configuration Layer provides adaptive parameters across all other layers through smart defaults and data-driven inference
 
 ## Layer Overview
 

docs/architecture/05_execution_layer.md

@@ -8,7 +8,7 @@ The execution layer in StarryNight defines how modules and pipelines are execute
 
 The execution layer serves several critical purposes in the StarryNight architecture:
 
-1. **Configuration** - Setting up modules with appropriate parameters
+1. **Execution Preparation** - Preparing configured pipelines for runtime
 2. **Instantiation** - Creating configured module instances
 3. **Backend Selection** - Choosing appropriate execution backends
 4. **Execution Control** - Initiating and monitoring pipeline execution

docs/architecture/06_configuration_layer.md

@@ -4,6 +4,18 @@
 
 The configuration layer in StarryNight consists of two interconnected systems: experiment configuration, which manages experiment-specific parameters and infers settings from data, and module configuration, which connects these parameters with module specifications. Together, these systems enable automatic setup of complex pipelines with minimal manual input, creating a bridge between user-provided parameters and the detailed configuration needed for pipeline execution.
 
+## Cross-Cutting Nature
+
+Unlike the other five layers which operate in a primarily sequential flow, the Configuration Layer functions as a dimensional plane that intersects with all layers. It provides contextual intelligence and adaptive parameters throughout the system:
+
+- With **Algorithm Layer**: Provides parameters that influence algorithm behavior
+- With **CLI Layer**: Supplies default values and validation rules for command parameters
+- With **Module Layer**: Transforms high-level experiment parameters into detailed specifications
+- With **Pipeline Layer**: Influences how modules are composed and connected
+- With **Execution Layer**: Controls runtime behavior and resource allocation
+
+This cross-cutting nature allows the Configuration Layer to maintain state across layer boundaries and adapt the system to specific experimental contexts without changing the core architecture.
+
 ## Purpose
 
 The configuration layer in StarryNight serves several critical purposes: