Fixes #3742
This PR replaces the bit-packed encoding with a flat list of entries, each containing:

layerId: The unique ID of the layer.
depth: The nesting depth (0 = root).
isLastInParent: Whether this is the last child in its parent (for efficient UI rendering).

This format is:
-More compact than a tree/bti-packed, but still human-readable and easy to debug.
-Easier to serialize/deserialize using standard serde and class-transformer pipelines.
-Faster to process in the frontend, as it avoids recursion and allows for simple, index-based hierarchy reconstruction.

Tests
Added Rust unit tests:
-test_serialize_root_empty_document
-test_serialize_root_flat_structure
-test_serialize_root_excludes_collapsed_children