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 -->

Cargo.lock

@@ -43,8 +43,10 @@ dependencies = [
  "criterion",
  "docx-parser",
  "infer",
+ "nanoid",
  "path-ext",
  "pdf-extract",
+ "pulldown-cmark",
  "rand 0.9.2",
  "rayon",
  "readability",
@@ -1793,6 +1795,15 @@ dependencies = [
  "version_check",
 ]
 
+[[package]]
+name = "getopts"
+version = "0.2.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cfe4fbac503b8d1f88e6676011885f34b7174f46e59956bba534ba83abded4df"
+dependencies = [
+ "unicode-width",
+]
+
 [[package]]
 name = "getrandom"
 version = "0.2.16"
@@ -3474,10 +3485,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1e8bbe1a966bd2f362681a44f6edce3c2310ac21e4d5067a6e7ec396297a6ea0"
 dependencies = [
  "bitflags 2.10.0",
+ "getopts",
  "memchr",
+ "pulldown-cmark-escape",
  "unicase",
 ]
 
+[[package]]
+name = "pulldown-cmark-escape"
+version = "0.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "007d8adb5ddab6f8e3f491ac63566a7d5002cc7ed73901f72057943fa71ae1ae"
+
 [[package]]
 name = "quick-error"
 version = "1.2.3"
@@ -5161,6 +5180,12 @@ version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f6ccf251212114b54433ec949fd6a7841275f9ada20dddd2f29e9ceea4501493"
 
+[[package]]
+name = "unicode-width"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b4ac048d71ede7ee76d585517add45da530660ef4390e49b098733c6e897f254"
+
 [[package]]
 name = "uniffi"
 version = "0.29.5"