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It could be helpful to number or order the files according to the modeling steps (and make key files (like bayesian_cognitive_modeling.md) more visible at the start. This would make it easier to follow the intended workflow and understand how the individual files fit together.
The code is clear, but more detailed comments explaining what each block does would guide the reader through why things are done. It would also make it easier to do further research if needed.
Regarding this, I really like seeing the relevant research paper names in the files. If possible, showing directory to external sources such as lecture slides could also be helpful.
Listing alternative modeling options in the explanation comment of functional forms implemented in the model (at the start of the file), possibly linking to further explanations could turn this tutorial more into a tool to see which versions of models could be done rather than a single implementation example.
If the figures had descriptive titles or short explanations on what they showed more explicitly, I think they could be interpreted quicker.
Adding simple visualisation blocks within the code (maybe as extra comments) could be helpful in improving intuition for what the model is doing.
some ideas to improve clarity and usability.