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

scripts/dependency-management/update-dependencies.sh

@@ -41,7 +41,7 @@ backup_requirements() {
     
     # Backup all requirements files
     find . -name "requirements*.txt" -not -path "./venv/*" -exec cp {} "$backup_dir/" \;
-    find . -name "pyproject.toml" -not -path "./venv/*" -exec cp {} "$backup_dir/" \;
+    find . -name "pyproject.toml" -not -path "./venv/*" -not -path "./project-config/*" -exec cp {} "$backup_dir/" \;
     
     log_success "Backup created in $backup_dir"
 }