Not criticizing the authors approach, but the Jupyter+Git Problem was solved for a long time with Jupytext [1].

Jupytext will convert Notebooks (.ipynb) files to Markdown (md) and Python (py) 'on the fly' (while working in Notebooks).

- Markdown files can be added to git

- Python and .ipynb files are added to .gitignore

- Python files allow 'chained' import of notebooks (*.py verions), which allows to split larger notebooks into multiple smaller ones

This is my folder structure: .

├── notebooks

| ├── notebook1.ipynb # automatically generated from md

| └── notebook2.ipynb # automatically generated from md

├── md

| ├── notebook1.md # versioned in git

| └── notebook2.md # versioned in git

├── py

| ├──modules

| | ├──__init__.py # empty

| | └──tools.py # use for cross-project base tools

| ├──__init__.py # empty

| ├── notebook1.py # automatically generated from md

| └── notebook2.py # automatically generated from md

├──jupytext.toml

├──.git

└── README.md

See an example here [2]

Jupytext is mentioned as a 'potential' alternative. Re the "save" cell output: I usually produce html-files at the end of my notebooks (see the example), and add those either to git or auto-upload to an external webserver. The html is standalone and includes outputs, table of contents, and images (example [3]). I would advice against versioning all outputs (images) in git.

Very happy with this approach for a long time now. Jupytext increased my productivity by a hundred percent.

[1]: https://github.com/mwouts/jupytext

[2]: https://gitlab.vgiscience.de/ad/yfcc_gridagg

[3]: https://ad.vgiscience.org/tagmaps-mapnik-jupyter/01_mapnik-t...