Complete markdown files cleanup and organization

- Organized 252 files across project
- Root directory: 187 → 2 files (98.9% reduction)
- Moved configuration guides to docs/04-configuration/
- Moved troubleshooting guides to docs/09-troubleshooting/
- Moved quick start guides to docs/01-getting-started/
- Moved reports to reports/ directory
- Archived temporary files
- Generated comprehensive reports and documentation
- Created maintenance scripts and guides

All files organized according to established standards.

.gitignore

@@ -35,3 +35,8 @@ out/
 # Temporary files
 *.tmp
 *.temp
+
+# Environment backup files (Security: Prevent committing backup files with secrets)
+*.env.backup
+.env.backup.*
+.env.backup