Added info about filesystem, tools and git as procedures

procedures/version_control/reasoning.md

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+# Version Control
+
+Version control is essential for SIA's self-improvement capabilities.
+It provides a way to track changes, revert to previous states when necessary, and maintain a coherent evolution of the codebase.
+This document outlines the git workflow designed specifically for SIA's unique development model, where the agent itself is the primary developer.
+
+## Core Principles
+
+The git workflow for SIA is designed around several key principles:
+
+- **Simplicity**: Since SIA is the sole developer, complex branching strategies designed for human teams are unnecessary
+- **Traceability**: Every change should be traceable to its purpose and the reasoning behind it
+- **Stability**: The master branch should always be in a working state
+- **Recoverability**: It should always be possible to revert to a known good state
+- **Security**: Git credentials must be handled securely to protect repository access
+
+## Branching Strategy
+
+### Branch Structure
+
+SIA uses a simple branching strategy with two types of branches:
+
+- **master**: The main branch containing stable, production-ready code
+- **feature/{timestamp}_{description}**: Temporary branches for implementing specific improvements
+
+This minimal approach is appropriate because:
+- There is only one developer (SIA itself)
+- Changes are typically focused on specific, well-defined improvements
+- There's no need for parallel development streams
+- Simplicity reduces the cognitive load on the agent
+
+### Branch Naming
+
+Feature branches follow a consistent naming convention:
+```
+feature/{YYYYMMDD}_{brief_description}
+```
+
+For example:
+```
+feature/20250115_improve_context_management
+feature/20250203_add_email_tool
+```
+
+This convention:
+- Makes it easy to identify when a branch was created
+- Provides a clear indication of the branch's purpose
+- Creates a chronological ordering when listing branches
+- Avoids potential naming conflicts
+
+## Commit Strategy
+
+### Commit Frequency
+
+SIA should commit changes before running tests.
+This ensures that crashes of the core system can be traced back to a specific change.
+
+### Commit Messages
+
+Commit messages should follow a structured format:
+
+```
+{type}: {concise description}
+
+{detailed explanation of changes and reasoning}
+
+{reference to any relevant issues or test results}
+```
+
+Where `{type}` is one of:
+- `core`: for changes on the core system
+- `procedure`: for changes on procedures
+- `test`: for changes on tests
+- `tool`: for changes on tools
+- `training`: for changes on training data
+- `web`: for changes on the web interface
+
+This structure:
+- Makes it easy to understand the purpose of each commit
+- Provides context for future review
+- Creates a useful and navigable history
+
+### Merge Strategy
+
+The `--no-ff` flag creates a merge commit even for fast-forward merges, maintaining a clear record of the feature's development and completion.
+
+## Credential Management
+
+### Credential Storage
+
+Git credentials are stored in the environment, not in the filesystem.
+This ensures that credentials are not exposed in the iteration log.
+Info about the repository and relevant environment variables is stored in `/root/data/environment/sia_repo.md`.