Add post-processing script to remove intersecting branches from PLY files

[Copilot]

Tree branch generation often produces intersecting geometry. This adds a post-processing script that detects and removes smaller intersecting branches from PLY output files.

Changes

• New script: lpy_treesim/tree_generation/remove_intersecting_branches.py

  • Parses PLY files, grouping vertices/faces by color (each branch has unique color)
  • Detects intersections via AABB tests between branch meshes
  • Removes lower-priority branch (Trunk > Branch > TertiaryBranch > Spur); falls back to volume comparison
  • Updates metadata JSON to reflect removed branches

• Documentation: Added usage section to README

Usage

python -m lpy_treesim.tree_generation.remove_intersecting_branches \
    --ply dataset/lpy_UFO_00000.ply \
    --metadata dataset/lpy_UFO_00000_metadata.json \
    --output cleaned.ply \
    --verbose

Original prompt

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This section details on the original issue you should resolve

<issue_title>Intersection of tertiary and secondary branches</issue_title>
<issue_description>When branches grow they often intersect with each other. Write a post-processing script that removes the smaller intersecting branch by going through the output ply file</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Intersection of tertiary and secondary branches #3

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