Strip notebook outputs and add nbstripout pre-commit hook

[zfergus]

Summary

• Adds the nbstripout pre-commit hook so notebook output cells (execution counts, embedded plot JSON/images) no longer get committed on every re-run.
• Strips existing output from all 13 tracked notebooks to match what the hook now enforces.

Output-heavy notebooks were bloating diffs and repo size for no rendering benefit — several embed Plotly figures (application/vnd.plotly.v1+json) with no image/png/text/html fallback, which GitHub's notebook viewer doesn't render anyway.

Test plan

• pre-commit run nbstripout --all-files runs clean (no further changes) after this PR
• Contributors run pre-commit install locally so the hook applies to future commits

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

This PR standardizes Jupyter notebooks by clearing execution artifacts (outputs/execution counts) and adds a pre-commit hook to keep notebooks stripped going forward.

Changes:

• Added nbstripout to pre-commit hooks.
• Cleared notebook cell outputs and set execution_count to null across multiple notebooks.
• Removed some non-essential notebook metadata fields (e.g., orig_nbformat) and adjusted cell metadata/IDs in places.

Reviewed changes

Copilot reviewed 7 out of 14 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
notebooks/tangent_basis_grad.ipynb	Clears execution artifacts; also rewrites cell IDs to numeric strings.
notebooks/physical_barrier.ipynb	Clears outputs/execution counts; removes some cell metadata and notebook-level fields.
notebooks/ee_mollifier_shape_derivative.ipynb	Clears outputs/execution counts.
notebooks/distances.ipynb	Clears outputs/execution counts; removes orig_nbformat.
notebooks/closest_point_grad.ipynb	Clears outputs/execution counts; removes orig_nbformat.
notebooks/area_weights.ipynb	Clears outputs/execution counts; removes orig_nbformat.
notebooks/adhesion.ipynb	Clears outputs/execution counts and large embedded outputs.
.pre-commit-config.yaml	Adds nbstripout hook to enforce stripping notebooks on commit.

Comments suppressed due to low confidence (1)

notebooks/physical_barrier.ipynb:1

• This change drops existing cell metadata (previously included scrolled: true). If the goal is purely to strip execution artifacts, avoid removing UI/authoring metadata because it can change how the notebook is presented when opened. Consider adjusting the notebook-cleaning workflow (or nbstripout configuration) to only clear outputs and execution counts while preserving cell metadata fields.

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