Adding the notebooks directory

[amjjbonvin]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Haddock3 version has been incremented in pyproject.toml
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Added HADDOCK3-antibody-antigen.ipynb jupyter notebook and README.md file

Related Issue

#1367

[amjjbonvin]

Checked if mybinder.org would be an option to be added to the README file, but it does not seem to have allocated resources (a problem already reported by the BioBB team of BioExcel).

Currently installating haddock3 from a repo clone with pip install . - might switch to pip install haddock3 once the 2025.9.0 version (or higher) will be available on pypi

[rvhonorato]

As I said in the now closed without a reason previous pr #1360:

The latest changes have tied the execution of this notebook to a git clone which is very error prone and likely to make the notebook unstable.

and

Fix the version here to make sure this tutorial will not break in the future

[amjjbonvin]

OK - changed it already - but we can only test live once we will make a new release for version 2025.9.3 (which should be this pull request)