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_ORGANIZATION_SUMMARY.md

@@ -0,0 +1,65 @@
+# Project Root Directory Organization
+
+## Changes Made
+
+### Files Moved from Root to Subdirectories:
+
+#### 📁 project-config/
+- `pyproject.toml` - Python project configuration
+- `requirements.txt` - Python dependencies  
+- `poetry.lock` - Dependency lock file
+- `.gitignore` - Git ignore rules
+- `.deployment_progress` - Deployment tracking
+- `=26.0` - Version marker
+
+#### 📁 documentation/
+- `README.md` - Main project documentation
+- `SETUP.md` - Setup instructions
+- `PYTHON_VERSION_STATUS.md` - Python compatibility
+- `AITBC1_TEST_COMMANDS.md` - Testing commands
+- `AITBC1_UPDATED_COMMANDS.md` - Updated commands
+
+#### 📁 security/
+- `SECURITY_VULNERABILITY_REPORT.md` - Security analysis
+- `SECURITY_FIXES_SUMMARY.md` - Security fixes summary
+
+#### 📁 backup-config/
+- `aitbc-cli.backup` - Backup of old CLI wrapper
+
+### Files Remaining in Root:
+- `LICENSE` - Project license (essential)
+- `README.md` - New root README with structure guide
+- `aitbc-cli` - CLI symlink (essential)
+- All directories (apps/, cli/, scripts/, etc.)
+
+### Scripts Updated:
+- `scripts/setup.sh` - Updated requirements.txt path
+- `scripts/dependency-management/update-dependencies.sh` - Updated pyproject.toml path
+- All scripts updated via `scripts/maintenance/update-file-references.sh`
+
+## Benefits:
+1. **Cleaner Root**: Only essential files at root level
+2. **Better Organization**: Logical grouping of configuration files
+3. **Easier Maintenance**: Related files grouped together
+4. **Clearer Structure**: New README explains organization
+5. **Preserved Functionality**: All references updated
+
+## Root Directory Structure:
+```
+/opt/aitbc/
+├── LICENSE                    # Essential
+├── README.md                  # Essential (new)
+├── aitbc-cli                  # Essential (symlink)
+├── aitbc/                     # Core package
+├── apps/                      # Applications
+├── cli/                       # CLI implementation
+├── scripts/                   # Automation scripts
+├── project-config/            # Configuration files
+├── documentation/             # User docs
+├── security/                  # Security reports
+├── backup-config/             # Backups
+└── [other directories...]     # Unchanged
+```
+
+---
+**Status**: Root directory organized ✅