Move py_to_notebook.py to bin/ directory for better organization

- Moved tools/py_to_notebook.py to bin/py_to_notebook.py
- Updated tito.py to reference the new location
- Made py_to_notebook.py executable for direct invocation
- Removed empty tools/ directory
- Updated documentation to reflect new location
- All tools now consolidated in bin/ directory for consistency

Benefits:
- Conventional organization (bin/ for executables)
- Can invoke tools directly: ./bin/py_to_notebook.py
- Cleaner project structure
- Consistent with other tools (tito.py, generate_student_notebooks.py)

docs/development/quick-module-reference.md

@@ -106,7 +106,7 @@ cp modules/example/example_dev.py modules/{module}/{module}_dev.py
 
 # Full workflow
 python bin/tito.py notebooks --module {module}
-python3 bin/generate_student_notebooks.py --module {module}
+python bin/generate_student_notebooks.py --module {module}
 
 # Test everything
 python bin/tito.py test --module {module}