BatchedMesh: Fix index and attribute updates in the optimize method

[querielo]

Description

Fix buffer sync issues in BatchedMesh.prototype.optimize() that caused incorrect rendering after repacking. The method now:

• Marks the index buffer as dirty after in-place reordering.
• Marks moved vertex attributes as dirty after in-place copies.
• Flags _visibilityChanged so draw ranges and visibility-dependent state get refreshed.

When optimize() compacts geometry ranges, it mutates the underlying typed arrays via copyWithin. However, without setting needsUpdate = true, WebGL/WebGPU buffers aren’t re-uploaded, resulting in stale GPU data and visible artifacts, especially after sequences like add/delete/optimize.

Also, _visibilityChanged must be set to ensure the next render pass rebuilds multi-draw ranges and respects updated starts/counts after repacking.

[github-actions]

📦 Bundle size

Full ESM build, minified and gzipped.

	Before	After	Diff
WebGL	355.14 86.33	355.14 86.33	+0 B +0 B
WebGPU	609.62 170.99	609.62 170.99	+0 B +0 B
WebGPU Nodes	608.23 170.72	608.23 170.72	+0 B +0 B

🌳 Bundle size after tree-shaking

Minimal build including a renderer, camera, empty scene, and dependencies.

	Before	After	Diff
WebGL	486.77 121.07	486.77 121.07	+0 B +0 B
WebGPU	678.47 186.28	678.47 186.28	+0 B +0 B
WebGPU Nodes	620.47 169.54	620.47 169.54	+0 B +0 B

[Copilot]

Pull Request Overview

This PR adds necessary update flags to the optimize() method in BatchedMesh to ensure geometry data changes are properly synchronized with the GPU. The changes address a bug where optimized geometry buffers were not being marked for update.

• Adds needsUpdate = true flags for index and attribute buffer updates during optimization
• Sets _visibilityChanged = true to trigger re-rendering after geometry reorganization

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