feat(server): improve doc gc (#15363)

#### PR Dependency Tree


* **PR #15363** 👈

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

* **Bug Fixes**
* Improved validation of workspace roots and document projections, with
clearer failures for malformed or incomplete data.
  * Improved document reference rebuilding and cleanup reliability.
* Updated document update merging to better handle invalid binary data.

* **Performance**
* Avoided unnecessary document reconstruction when no updates are
pending.

* **Tests**
* Updated coverage for malformed workspace roots and document snapshot
parsing.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Cargo.toml

@@ -16,7 +16,7 @@ resolver = "3"
   [workspace.dependencies]
   aes-gcm = "0.10"
   affine_common = { path = "./packages/common/native" }
-  affine_doc_loader = "0.1.3"
+  affine_doc_loader = "0.1.4"
   affine_importer = "0.1.2"
   affine_nbstore = { path = "./packages/frontend/native/nbstore" }
   affine_preview = { version = "0.1.0", default-features = false }
@@ -114,7 +114,7 @@ resolver = "3"
     "Win32_UI_Shell_PropertiesSystem",
   ] }
   windows-core = { version = "0.61" }
-  y-octo = "0.0.3"
+  y-octo = "0.1.0"
   zip = "8.6"
 
 [profile.dev.package.sqlx-macros]