[NeurIPS Rebuttal] Codebase Polish, API Simplification, and GNN Bug Fix

[Jiaqing-ASU]

Context:
Addressing Reviewer z8Q2's comments regarding the codebase and open-source standards for the NeurIPS rebuttal.

Action Items:

• Fix GNN 2-node bug (Reviewer z8Q2 - Q17): Fix the aggressive default noise-filtering threshold that collapsed the smaller persistence bars, ensuring the un-filtered topological structure is accurately plotted.
• API Design Update (Reviewer z8Q2 - Q18): Simplify the compute() API so users only need to provide a standard loss criterion (removing the confusion around scalar_function).
• Documentation & Tests: Ensure comprehensive docstrings, unit tests, and explanatory markdown texts are added to the example notebooks to meet open-source standards.

[rostyhn]

I think the compute fn can stay as is. It can't be simplified any more than it is without adding many layers of indirection. I'll work on adding more documentation that explains why it is implemented the way it is.

[rostyhn]

Also documentation and tests are already there. Will add a code coverage counter and clean up the notebooks.