feat(server): add document write tools for mcp (#14245)

## Summary

This PR adds write capabilities to AFFiNE's MCP (Model Context Protocol)
integration, enabling external tools (Claude, GPT, etc.) to create and
modify documents programmatically.

**New MCP Tools:**
- `create_document` - Create new documents from markdown content
- `update_document` - Update document content using structural diffing
for minimal changes (preserves document history and enables real-time
collaboration)

**Implementation:**
- `markdown_to_ydoc.rs` - Converts markdown to AFFiNE-compatible y-octo
binary format
- `markdown_utils.rs` - Shared markdown parsing utilities (used by both
ydoc-to-md and md-to-ydoc)
- `update_ydoc.rs` - Structural diffing implementation for updating
existing documents
- `DocWriter` service - TypeScript service for document operations
- Exposes `markdownToDocBinary` and `updateDocBinary` via napi bindings

**Supported Markdown Elements:**
- Headings (H1-H6)
- Paragraphs
- Bullet lists and numbered lists
- Code blocks (with language detection)
- Blockquotes
- Horizontal dividers
- Todo items (checkboxes)

**y-octo Changes:**
This PR reverts the y-octo sync (ca2462f, a5b60cf) which introduced a
concurrency bug causing hangs when creating documents with many nested
block structures. It also ports the improved `get_node_index` binary
search fix from upstream that prevents divide-by-zero panics when
decoding documents.

## Test Results ✅

### Unit Tests (47/47 passing)

| Test Suite | Tests | Status |
|------------|-------|--------|
| markdown_to_ydoc | 16/16 | ✅ Pass |
| markdown_utils | 11/11 | ✅ Pass |
| update_ydoc | 13/13 | ✅ Pass |
| delta_markdown | 2/2 | ✅ Pass |
| affine (doc parser) | 5/5 | ✅ Pass |

### End-to-End MCP Testing ✅

Tested against local AFFiNE server with real MCP client requests:

| Tool | Result | Notes |
|------|--------|-------|
| `tools/list` | ✅ Pass | Returns all 5 tools with correct schemas |
| `create_document` | ✅ Pass | Successfully created test documents |
| `update_document` | ✅ Pass | Successfully updated documents with
structural diffing |
| `read_document` | ✅ Pass | Existing tool, works correctly |
| `keyword_search` | ✅ Pass | Existing tool, works correctly |

**E2E Test Details:**
- Started local AFFiNE server with PostgreSQL, Redis, and Manticore
- Created test user and workspace via seed/GraphQL
- Verified MCP endpoint at `/api/workspaces/:workspaceId/mcp`
- Tested JSON-RPC calls with proper SSE streaming
- Confirmed documents are stored and indexed correctly (verified via
server logs)

## Test Plan
- [x] All Rust unit tests pass (47 tests)
- [x] Native bindings build successfully (release mode)
- [x] Document creation via MCP works end-to-end
- [x] Document update via MCP works end-to-end
- [x] CodeRabbit feedback addressed
- [ ] Integration testing with Claude/GPT MCP clients

Closes #14161

---

**Requested by:** @realies  
**Key guidance from:** @darkskygit (use y-octo instead of yjs for memory
efficiency)

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

* **New Features**
* Create documents from Markdown: generate new documents directly from
Markdown content with automatic title extraction
* Update documents with Markdown: modify existing documents using
Markdown as the source with automatic diff calculation for efficient
updates
* Copilot integration: new tools for document creation and updates
through Copilot's interface

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

packages/backend/native/index.d.ts

@@ -4,6 +4,20 @@ export declare class Tokenizer {
   count(content: string, allowedSpecial?: Array<string> | undefined | null): number
 }
 
+/**
+ * Adds a document ID to the workspace root doc's meta.pages array.
+ * This registers the document in the workspace so it appears in the UI.
+ *
+ * # Arguments
+ * * `root_doc_bin` - The current root doc binary (workspaceId doc)
+ * * `doc_id` - The document ID to add
+ * * `title` - Optional title for the document
+ *
+ * # Returns
+ * A Buffer containing the y-octo update binary to apply to the root doc
+ */
+export declare function addDocToRootDoc(rootDocBin: Buffer, docId: string, title?: string | undefined | null): Buffer
+
 export const AFFINE_PRO_LICENSE_AES_KEY: string | undefined | null
 
 export const AFFINE_PRO_PUBLIC_KEY: string | undefined | null
@@ -19,6 +33,18 @@ export declare function getMime(input: Uint8Array): string
 
 export declare function htmlSanitize(input: string): string
 
+/**
+ * Converts markdown content to AFFiNE-compatible y-octo document binary.
+ *
+ * # Arguments
+ * * `markdown` - The markdown content to convert
+ * * `doc_id` - The document ID to use for the y-octo doc
+ *
+ * # Returns
+ * A Buffer containing the y-octo document update binary
+ */
+export declare function markdownToDocBinary(markdown: string, docId: string): Buffer
+
 /**
  * Merge updates in form like `Y.applyUpdate(doc, update)` way and return the
  * result binary.
@@ -77,4 +103,18 @@ export declare function parseWorkspaceDoc(docBin: Buffer): NativeWorkspaceDocCon
 
 export declare function readAllDocIdsFromRootDoc(docBin: Buffer, includeTrash?: boolean | undefined | null): Array<string>
 
+/**
+ * Updates an existing document with new markdown content.
+ * Uses structural and text-level diffing to apply minimal changes.
+ *
+ * # Arguments
+ * * `existing_binary` - The current document binary
+ * * `new_markdown` - The new markdown content to apply
+ * * `doc_id` - The document ID
+ *
+ * # Returns
+ * A Buffer containing only the delta (changes) as a y-octo update binary
+ */
+export declare function updateDocWithMarkdown(existingBinary: Buffer, newMarkdown: string, docId: string): Buffer
+
 export declare function verifyChallengeResponse(response: string, bits: number, resource: string): Promise<boolean>

packages/backend/native/src/doc.rs

@@ -132,3 +132,52 @@ pub fn read_all_doc_ids_from_root_doc(doc_bin: Buffer, include_trash: Option<boo
     .map_err(|e| Error::new(Status::GenericFailure, e.to_string()))?;
   Ok(result)
 }
+
+/// Converts markdown content to AFFiNE-compatible y-octo document binary.
+///
+/// # Arguments
+/// * `markdown` - The markdown content to convert
+/// * `doc_id` - The document ID to use for the y-octo doc
+///
+/// # Returns
+/// A Buffer containing the y-octo document update binary
+#[napi]
+pub fn markdown_to_doc_binary(markdown: String, doc_id: String) -> Result<Buffer> {
+  let result =
+    doc_parser::markdown_to_ydoc(&markdown, &doc_id).map_err(|e| Error::new(Status::GenericFailure, e.to_string()))?;
+  Ok(Buffer::from(result))
+}
+
+/// Updates an existing document with new markdown content.
+/// Uses structural and text-level diffing to apply minimal changes.
+///
+/// # Arguments
+/// * `existing_binary` - The current document binary
+/// * `new_markdown` - The new markdown content to apply
+/// * `doc_id` - The document ID
+///
+/// # Returns
+/// A Buffer containing only the delta (changes) as a y-octo update binary
+#[napi]
+pub fn update_doc_with_markdown(existing_binary: Buffer, new_markdown: String, doc_id: String) -> Result<Buffer> {
+  let result = doc_parser::update_ydoc(&existing_binary, &new_markdown, &doc_id)
+    .map_err(|e| Error::new(Status::GenericFailure, e.to_string()))?;
+  Ok(Buffer::from(result))
+}
+
+/// Adds a document ID to the workspace root doc's meta.pages array.
+/// This registers the document in the workspace so it appears in the UI.
+///
+/// # Arguments
+/// * `root_doc_bin` - The current root doc binary (workspaceId doc)
+/// * `doc_id` - The document ID to add
+/// * `title` - Optional title for the document
+///
+/// # Returns
+/// A Buffer containing the y-octo update binary to apply to the root doc
+#[napi]
+pub fn add_doc_to_root_doc(root_doc_bin: Buffer, doc_id: String, title: Option<String>) -> Result<Buffer> {
+  let result = doc_parser::add_doc_to_root_doc(root_doc_bin.into(), &doc_id, title.as_deref())
+    .map_err(|e| Error::new(Status::GenericFailure, e.to_string()))?;
+  Ok(Buffer::from(result))
+}