docs: reorganize project structure and update root README

Project Organization:
- Moved configuration files to project-config/ directory
- Moved documentation files to documentation/ directory
- Moved security reports to security/ directory
- Moved backup files to backup-config/ directory
- Created PROJECT_ORGANIZATION_SUMMARY.md documenting changes
- Updated all script references to new file locations

Root README Simplification:
- Replaced 715-line detailed README with 95-line structure guide

project-config/README.md

@@ -0,0 +1,47 @@
+# Project Configuration
+
+This directory contains all project configuration files.
+
+## Files
+
+- `pyproject.toml` - Python project configuration with build system, dependencies, and metadata
+- `requirements.txt` - Python dependencies list
+- `poetry.lock` - Dependency lock file for reproducible builds
+- `.gitignore` - Git ignore patterns for the project
+- `.deployment_progress` - Tracks deployment progress and status
+
+## Usage
+
+### Installing Dependencies
+
+```bash
+# Using pip
+pip install -r requirements.txt
+
+# Using poetry (if available)
+poetry install
+```
+
+### Project Configuration
+
+The `pyproject.toml` file contains:
+- Project metadata (name, version, description)
+- Build system configuration
+- Dependency specifications
+- Tool configurations (black, ruff, mypy, etc.)
+
+### Git Configuration
+
+The `.gitignore` file excludes:
+- Python cache files
+- Virtual environments
+- IDE files
+- Build artifacts
+- Log files
+- Temporary files
+
+## Notes
+
+- Configuration files are kept separate from source code for better organization
+- The project uses modern Python packaging standards (PEP 517/518)
+- Dependencies are pinned for reproducible builds