Replace MinIO with S3-compatible storage and reorganize project structure

- Switch from MinIO to boto3 for S3-compatible object storage (Cloudflare R2)
- Rename storage config vars from R2_* to generic S3_*
- Organize root directory: docs/, tools/, output/, Archive/{audio,results}/
- Output transcriptions to output/ directory
- Add transcribe_legacy.py, transcribe_all.py, and docs

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitignore

@@ -34,3 +34,7 @@ Desktop.ini
 
 # Output
 output/
+Archive/
+
+# Tools
+tools/