refactor: reorganize podman directory structure

Organize podman/ directory into logical subdirectories:

New structure:
- docs/          - ML_TOOLS_GUIDE.md, jupyter_workflow.md
- configs/       - environment*.yml, security_policy.json
- containers/    - *.dockerfile, *.podfile
- scripts/       - *.sh, *.py (secure_runner, cli_integration, etc.)
- jupyter/       - jupyter_cookie_secret (flattened from jupyter_runtime/runtime/)
- workspace/     - Example projects (cleaned of temp files)

Cleaned workspace:
- Removed .DS_Store, mlflow.db, cache/
- Removed duplicate cli_integration.py

Removed unnecessary nesting:
- Flattened jupyter_runtime/runtime/ to just jupyter/

Improves maintainability by grouping files by purpose and eliminating root directory clutter.

podman/workspace/cli_integration.py

@@ -1,8 +0,0 @@
-# CLI-Jupyter Integration Helper
-import subprocess
-import os
-def sync_project(project_path):
-    """Sync project using CLI"""
-    cmd = ["../cli/zig-out/bin/ml", "sync", project_path, "--queue"]
-    result = subprocess.run(cmd, capture_output=True, text=True)
-    return result.returncode == 0