Added info about filesystem, tools and git as procedures

procedures/tool_management/reasoning.md

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+# Tool Management
+
+SIA uses and creates tools to extend its capabilities.
+A tool in the SIA context refers to a clearly packaged software component that provides specific functionality.
+This document outlines how tools are structured, managed, and developed.
+All tools reside in the `/root/sia/tools/` directory and are part of the main git repository.
+
+## Typical patterns
+
+Tools in SIA follow these established patterns:
+
+- **Independence**: Each tool functions as a standalone component with clear boundaries
+- **Python**: The preferred language for tools is Python
+- **Installation**: The Dockerfile and bootstrap script intall all tools in the directory using `pip install -e`
+- **Documentation**: Each tool has a README.md file that provides requirements, usage instructions and documentation
+- **Modification**: Tools can be modified by SIA as part of its self-improvement process
+- **Procedures**: Tools are created to support procedures
+- **Training**: No separate training data is maintained, this is included in the procedure training
+
+## Tool Directory Structure
+
+Each tool follows a consistent structure:
+
+```
+tools/
+└── tool_name/
+    ├── README.md           # Documentation
+    ├── requirements.txt    # Tool-specific dependencies
+    ├── setup.py            # Installation configuration
+    ├── tool_name/          # Main package code
+    │   └── __init__.py
+    ├── bin/                # Command-line executables
+    │   └── tool_command
+    └── test/               # Tool-specific tests
+        └── test_tool.py
+```