feat(native): sync yocto codes (#14243)

#### PR Dependency Tree


* **PR #14243** 👈

This tree was auto-generated by
[Charcoal](https://github.com/danerwilliams/charcoal)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Batch management API for coordinated document mutations and change
tracking.
* New document accessors (IDs, state snapshots, change/delete set
queries) and subscriber count.

* **Chores**
  * Upgraded Rust edition across packages to 2024.
  * Repository-wide formatting, stylistic cleanups and test adjustments.

* **Breaking Changes**
* Removed the Node native bindings package and its JS/TS declarations
and tests (no longer published/available).

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

tools/utils/src/workspace.gen.ts

@@ -1222,11 +1222,6 @@ export const PackageList = [
     name: '@affine/reader',
     workspaceDependencies: ['blocksuite/affine/all'],
   },
-  {
-    location: 'packages/common/y-octo/node',
-    name: '@y-octo/node',
-    workspaceDependencies: [],
-  },
   {
     location: 'packages/frontend/admin',
     name: '@affine/admin',
@@ -1572,7 +1567,6 @@ export type PackageName =
   | '@toeverything/infra'
   | '@affine/nbstore'
   | '@affine/reader'
-  | '@y-octo/node'
   | '@affine/admin'
   | '@affine/android'
   | '@affine/electron'