Modernize the geometry stack

[tomyun]

Summary

• remove unused runtime and test dependencies, and use ColorTypes directly for RGBA
• migrate pot meshing to the Meshing 0.7 array API
• update GeometryBasics to 0.5, MeshIO to 0.5, and Makie to 0.24
• preserve root vertex colors with the GeometryBasics 0.5 mesh API
• require Julia 1.12 and Distributions 0.25
• add focused regression coverage for pot geometry, root colors, Makie figure construction, and STL round trips

Compatibility notes

A fresh resolution selects GeometryBasics 0.5.11, Makie 0.24.13, MeshIO 0.5.3, and Meshing 0.7.0 together.

Gadfly remains a transitive dependency of Cropbox, but it does not block this geometry stack. Colors 0.12 and ColorTypes 0.11 remain transitively constrained by Cropbox → Interact → CSSUtil, so CropRootBox now uses ColorTypes directly without forcing an incompatible Colors update.

Supersedes #13, #14, #15, #16, and #17.

Validation

• Julia 1.12.6
• fresh, Manifest-free dependency resolution
• julia --project=. --depwarn=error -e 'using Pkg; Pkg.instantiate(); Pkg.test()'
• 17/17 tests passed
• git diff --check origin/main...HEAD
• GitHub Actions passed on current stable Julia for macOS, Ubuntu, and Windows, including coverage upload

The experimental macOS nightly job reaches Julia 1.14-dev and fails in transitive Interpolations 0.15 and JuliaInterpreter before CropRootBox tests run. It remains non-blocking and is outside this PR's geometry-stack changes.

The docs environment resolves GLMakie 0.13.13 with Makie 0.24.13. A full local docs build was not completed because GLMakie's own precompile workload segfaults in GLFW monitor discovery on macOS; the existing Linux/Xvfb docs workflow is unchanged by this PR.

[codecov]

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

Thanks for integrating Codecov - We've got you covered ☂️