Fix examples and acoustics API

[akeeste]

This PR makes a few fixes to the documentation:

• github Actions copies the example correctly. Currently they are not appearing, e.g. https://mhkit-software.github.io/MHKiT/river_example.ipynb and https://mhkit-software.github.io/MHKiT/mhkit-matlab/river_example.html
• fixes a minor formatting issue in the acoustics API
• fix minor path in .gitignore
• update make.bat and Make paths for consistent local builds

[akeeste]

@ssolson This PR is ready for review. I tried forcing the docs.yml file to use make clean and make html for total consistency with the local builds, but it caused an error with the ``.nojekyll` file and it was unclear why this was happening. But now the Actions Workflow copies the example files and they should load in our live pages