feat(§03): 实现 MCP Server 核心 - Storage/Service/Tool/MCP Protocol Layers

**Storage Layer:**
- Database 类（aiosqlite + WAL + 并发保护）
- WikiPage 数据模型
- fix_dirty_states 恢复机制
- FTS5 全文搜索支持
- 完整的 SQLite 表结构

**Service Layer:**
- CacheService（LRU 缓存 + TTL + 大小限制）
- QueryService（查询服务）
- ParserService（Markdown 解析）
- IndexerService（索引服务）
- GraphService（链接图服务）

**Tool Layer (8 个 MCP Tools):**
- wiki_query - FTS5 全文搜索 + 标签过滤
- memory_bridge - 按工具来源浏览
- wiki_status - 索引状态
- wiki_lint - 健康审计
- cross_linker - 缺失链接发现
- tag_taxonomy - 标签一致性
- wiki_synthesize - 跨概念综合分析
- daily_update - 日常维护 + hot.md 生成

**MCP Protocol Layer:**
- MCP 协议解析和封装
- 工具注册和路由
- 错误处理和日志
- stdio 模式支持

**配置和部署:**
- requirements.txt
- config.example.yaml
- ecosystem.config.cjs (PM2)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

mcp_server/__init__.py

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+"""
+MCP Server - Wiki MCP Server
+
+混合架构 Wiki 系统的 MCP Server 实现。
+"""
+
+__version__ = "1.0.0"

mcp_server/main.py

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+"""
+MCP Server - Wiki MCP Server 主入口
+
+实现 MCP 协议解析、工具注册和路由。
+
+参考设计文档：第 2.1 节
+"""
+
+import asyncio
+import json
+import logging
+import sys
+from typing import Any, Callable, Dict, Optional
+from pathlib import Path
+
+# MCP SDK
+try:
+    from mcp.server.models import InitializationOptions
+    from mcp.server import Server, NotificationOptions
+    from mcp.types import Tool, TextContent
+    MCP_AVAILABLE = True
+except ImportError:
+    MCP_AVAILABLE = False
+    logger = logging.getLogger(__name__)
+    logger.warning("MCP SDK not available, using mock implementation")
+
+# 本地模块
+from .storage import Database, fix_dirty_states
+from .services import CacheService, QueryService, ParserService, IndexerService, GraphService
+from .tools import (
+    WikiQueryTool, MemoryBridgeTool, WikiStatusTool,
+    WikiLintTool, CrossLinkerTool, TagTaxonomyTool,
+    WikiSynthesizeTool, DailyUpdateTool
+)
+
+# 配置
+DEFAULT_WIKI_VAULT = "/Volumes/KnowledgeBase/wiki-vault"
+DEFAULT_INDEX_PATH = "~/.sanguo-llmwiki/index.db"
+DEFAULT_LOG_LEVEL = "INFO"
+
+# 配置日志
+logging.basicConfig(
+    level=getattr(logging, DEFAULT_LOG_LEVEL),
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+)
+logger = logging.getLogger(__name__)
+
+
+class MCPServer:
+    """MCP 服务器封装类"""
+
+    def __init__(self, wiki_vault_path: str, index_path: str):
+        self.wiki_vault_path = wiki_vault_path
+        self.index_path = index_path
+        self.db: Optional[Database] = None
+        self.tools: Dict[str, Callable] = {}
+        self.tool_schemas: Dict[str, dict] = {}
+
+        # 如果 MCP SDK 可用，创建 Server 实例
+        if MCP_AVAILABLE:
+            self.server = Server("wiki-mcp")
+            self._setup_handlers()
+        else:
+            self.server = None
+            logger.warning("Running in mock mode (MCP SDK not available)")
+
+    async def initialize(self) -> None:
+        """初始化数据库和服务"""
+        logger.info("Initializing Wiki MCP Server...")
+
+        # 初始化数据库
+        self.db = Database(self.index_path)
+        await self.db.connect()
+
+        # 恢复脏状态
+        await fix_dirty_states(self.db)
+
+        # 初始化服务
+        self.cache = CacheService(max_size=1000)
+        self.query_service = QueryService(self.db, self.cache)
+        self.parser_service = ParserService()
+        self.indexer_service = IndexerService(self.db, self.parser_service, self.wiki_vault_path)
+        self.graph_service = GraphService(self.db)
+
+        # 初始化工具
+        self._init_tools()
+
+        logger.info("Wiki MCP Server initialized")
+
+    def _init_tools(self) -> None:
+        """初始化所有工具"""
+        wiki_query = WikiQueryTool(self.query_service)
+        memory_bridge = MemoryBridgeTool(self.query_service)
+        wiki_status = WikiStatusTool(self.query_service, self.indexer_service, self.graph_service)
+        wiki_lint = WikiLintTool(self.parser_service, self.query_service, self.graph_service)
+        cross_linker = CrossLinkerTool(self.graph_service)
+        tag_taxonomy = TagTaxonomyTool(self.query_service)
+        wiki_synthesize = WikiSynthesizeTool(self.query_service, self.graph_service)
+        daily_update = DailyUpdateTool(self.query_service, self.indexer_service)
+
+        # 注册工具
+        self.tools = {
+            "wiki_query": wiki_query.handle,
+            "memory_bridge": memory_bridge.handle,
+            "wiki_status": wiki_status.handle,
+            "wiki_lint": wiki_lint.handle,
+            "cross_linker": cross_linker.handle,
+            "tag_taxonomy": tag_taxonomy.handle,
+            "wiki_synthesize": wiki_synthesize.handle,
+            "daily_update": daily_update.handle
+        }
+
+        # 注册工具 schema
+        self.tool_schemas = {
+            "wiki_query": wiki_query.get_schema(),
+            "memory_bridge": memory_bridge.get_schema(),
+            "wiki_status": wiki_status.get_schema(),
+            "wiki_lint": wiki_lint.get_schema(),
+            "cross_linker": cross_linker.get_schema(),
+            "tag_taxonomy": tag_taxonomy.get_schema(),
+            "wiki_synthesize": wiki_synthesize.get_schema(),
+            "daily_update": daily_update.get_schema()
+        }
+
+        logger.info(f"Registered {len(self.tools)} tools")
+
+    def _setup_handlers(self) -> None:
+        """设置 MCP 处理器"""
+        if not self.server:
+            return
+
+        @self.server.list_tools()
+        async def list_tools() -> list[Tool]:
+            """列出所有可用工具"""
+            return [
+                Tool(
+                    name=schema["name"],
+                    description=schema["description"],
+                    inputSchema=schema["inputSchema"]
+                )
+                for schema in self.tool_schemas.values()
+            ]
+
+        @self.server.call_tool()
+        async def call_tool(name: str, arguments: dict) -> list[TextContent]:
+            """调用工具"""
+            if name not in self.tools:
+                raise ValueError(f"Unknown tool: {name}")
+
+            try:
+                result = await self.tools[name](**arguments)
+                return [TextContent(type="text", text=json.dumps(result, ensure_ascii=False, indent=2))]
+            except Exception as e:
+                logger.error(f"Error calling tool {name}: {e}")
+                return [TextContent(type="text", text=json.dumps({
+                    "success": False,
+                    "error": str(e)
+                }, ensure_ascii=False))]
+
+    async def run(self) -> None:
+        """运行 MCP 服务器"""
+        if not self.server:
+            logger.error("MCP Server not available (MCP SDK not installed)")
+            return
+
+        # 运行服务器
+        async with self.server.stdio_stdio() as (read_stream, write_stream):
+            await self.server.run(
+                read_stream,
+                write_stream,
+                InitializationOptions(
+                    server_name="wiki-mcp",
+                    server_version="1.0.0",
+                    capabilities=self.server.get_capabilities(
+                        notification_options=NotificationOptions(),
+                        experimental_capabilities={}
+                    )
+                )
+            )
+
+    async def close(self) -> None:
+        """关闭服务器"""
+        if self.db:
+            await self.db.close()
+            logger.info("Database connection closed")
+
+
+async def main():
+    """主入口"""
+    import os
+
+    # 从环境变量读取配置
+    wiki_vault_path = os.environ.get("WIKI_VAULT_PATH", DEFAULT_WIKI_VAULT)
+    index_path = os.path.expanduser(os.environ.get("WIKI_INDEX_PATH", DEFAULT_INDEX_PATH))
+    log_level = os.environ.get("LOG_LEVEL", DEFAULT_LOG_LEVEL)
+
+    # 设置日志级别
+    logging.getLogger().setLevel(getattr(logging, log_level))
+
+    # 检查 wiki vault 路径
+    if not Path(wiki_vault_path).exists():
+        logger.error(f"Wiki vault path does not exist: {wiki_vault_path}")
+        sys.exit(1)
+
+    # 创建并运行服务器
+    server = MCPServer(wiki_vault_path, index_path)
+
+    try:
+        await server.initialize()
+        await server.run()
+    except KeyboardInterrupt:
+        logger.info("Interrupted by user")
+    finally:
+        await server.close()
+
+
+if __name__ == "__main__":
+    asyncio.run(main())

mcp_server/services/__init__.py

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+"""
+Service Layer - 服务层
+
+提供各种服务：缓存、查询、索引、解析、图服务。
+"""
+
+from .cache import CacheService
+from .query import QueryService
+from .parser import ParserService
+from .indexer import IndexerService
+from .graph import GraphService
+
+__all__ = [
+    "CacheService",
+    "QueryService",
+    "ParserService",
+    "IndexerService",
+    "GraphService"
+]

mcp_server/services/cache.py

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+"""
+Service Layer - CacheService（缓存服务）
+
+使用 LRU 缓存 + TTL 过期策略，防止内存泄漏。
+
+参考设计文档：第 2.3 节
+"""
+
+import asyncio
+import time
+from collections import OrderedDict
+from typing import Optional, Any
+import fnmatch
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class CacheService:
+    """缓存服务 - LRU 缓存 + TTL 过期"""
+
+    def __init__(self, max_size: int = 1000):
+        self.cache: OrderedDict[str, tuple] = OrderedDict()  # key -> (value, expire_time)
+        self.max_size = max_size
+        self.lock = asyncio.Lock()
+
+    async def get(self, key: str) -> Optional[Any]:
+        """获取缓存值（异步，带锁）"""
+        async with self.lock:
+            if key not in self.cache:
+                return None
+
+            value, expire_time = self.cache[key]
+
+            # 检查是否过期
+            if expire_time and time.time() > expire_time:
+                del self.cache[key]
+                logger.debug(f"Cache expired: {key}")
+                return None
+
+            # LRU: 移到末尾
+            self.cache.move_to_end(key)
+            return value
+
+    async def set(self, key: str, value: Any, ttl: int = 3600) -> None:
+        """设置缓存值（异步，带锁）"""
+        async with self.lock:
+            expire_time = time.time() + ttl if ttl else None
+
+            # 如果缓存已满，删除最旧的条目
+            if len(self.cache) >= self.max_size and key not in self.cache:
+                self.cache.popitem(last=False)  # FIFO 删除
+                logger.debug(f"Cache full, evicted oldest entry")
+
+            self.cache[key] = (value, expire_time)
+            self.cache.move_to_end(key)
+            logger.debug(f"Cache set: {key} (TTL={ttl}s)")
+
+    async def invalidate(self, pattern: str) -> int:
+        """按模式清除缓存（支持 * 通配符）"""
+        async with self.lock:
+            if pattern == "*":
+                count = len(self.cache)
+                self.cache.clear()
+                logger.info(f"Cache cleared: {count} entries")
+                return count
+
+            keys_to_delete = [k for k in self.cache.keys() if fnmatch.fnmatch(k, pattern)]
+            for key in keys_to_delete:
+                del self.cache[key]
+            logger.info(f"Cache invalidated: {len(keys_to_delete)} entries matching '{pattern}'")
+            return len(keys_to_delete)
+
+    async def get_stats(self) -> dict:
+        """获取缓存统计信息"""
+        async with self.lock:
+            now = time.time()
+            expired_count = sum(1 for _, expire_time in self.cache.values() if expire_time and now > expire_time)
+
+            return {
+                "size": len(self.cache),
+                "max_size": self.max_size,
+                "expired_count": expired_count,
+                "utilization": len(self.cache) / self.max_size if self.max_size > 0 else 0
+            }
+
+    async def clear(self) -> None:
+        """清空缓存"""
+        async with self.lock:
+            self.cache.clear()
+            logger.info("Cache cleared")

mcp_server/services/graph.py

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+"""
+Service Layer - GraphService（图服务）
+
+管理页面间的链接关系，查找孤立页面和缺失链接。
+
+参考设计文档：第 2.3 节
+"""
+
+import logging
+from typing import Set, List, Tuple
+from ..storage import Database
+
+logger = logging.getLogger(__name__)
+
+
+class GraphService:
+    """图服务 - 管理链接关系"""
+
+    def __init__(self, db: Database):
+        self.db = db
+
+    async def get_links(self, path: str) -> Set[str]:
+        """获取页面的出链"""
+        return await self.db.get_links(path)
+
+    async def get_backlinks(self, path: str) -> Set[str]:
+        """获取页面的反向链接"""
+        return await self.db.get_backlinks(path)
+
+    async def find_orphans(self) -> Set[str]:
+        """查找孤立页面（无反向链接）"""
+        all_pages = await self.db.get_all_pages()
+        orphans = set()
+
+        for page in all_pages:
+            backlinks = await self.db.get_backlinks(page.path)
+            if not backlinks and page.path != "index.md":
+                orphans.add(page.path)
+
+        return orphans
+
+    async def find_missing_links(self) -> List[Tuple[str, str]]:
+        """查找缺失的交叉引用"""
+        # 获取所有页面内容
+        all_pages = await self.db.get_all_pages()
+        page_paths = {page.path for page in all_pages}
+
+        # 获取所有链接关系
+        links_rows = await self.db.fetch_all("SELECT source, target FROM wiki_links")
+
+        missing = []
+        for source, target in links_rows:
+            if target not in page_paths:
+                missing.append((source, target))
+
+        return missing
+
+    async def get_link_graph(self) -> dict:
+        """获取完整的链接图"""
+        pages = await self.db.get_all_pages()
+        graph = {}
+
+        for page in pages:
+            links = await self.db.get_links(page.path)
+            backlinks = await self.db.get_backlinks(page.path)
+            graph[page.path] = {
+                "title": page.title,
+                "category": page.category,
+                "links": sorted(links),
+                "backlinks": sorted(backlinks),
+                "links_count": len(links),
+                "backlinks_count": len(backlinks)
+            }
+
+        return graph
+
+    async def get_highly_connected_pages(self, threshold: int = 5) -> List[dict]:
+        """获取高度连接的页面（入链 + 出链 >= threshold）"""
+        pages = await self.db.get_all_pages()
+        highly_connected = []
+
+        for page in pages:
+            links = await self.db.get_links(page.path)
+            backlinks = await self.db.get_backlinks(page.path)
+            total = len(links) + len(backlinks)
+
+            if total >= threshold:
+                highly_connected.append({
+                    "path": page.path,
+                    "title": page.title,
+                    "links_count": len(links),
+                    "backlinks_count": len(backlinks),
+                    "total_connections": total
+                })
+
+        return sorted(highly_connected, key=lambda x: x["total_connections"], reverse=True)
+
+    async def get_disconnected_components(self) -> List[Set[str]]:
+        """获取不连通的图分量（使用 BFS）"""
+        pages = await self.db.get_all_pages()
+        page_paths = {page.path for page in pages}
+
+        if not page_paths:
+            return []
+
+        visited = set()
+        components = []
+
+        for start_path in page_paths:
+            if start_path in visited:
+                continue
+
+            # BFS 构建连通分量
+            component = set()
+            queue = [start_path]
+
+            while queue:
+                current = queue.pop(0)
+                if current in visited:
+                    continue
+
+                visited.add(current)
+                component.add(current)
+
+                # 添加出链和入链
+                for link in await self.db.get_links(current):
+                    if link in page_paths and link not in visited:
+                        queue.append(link)
+                for backlink in await self.db.get_backlinks(current):
+                    if backlink in page_paths and backlink not in visited:
+                        queue.append(backlink)
+
+            components.append(component)
+
+        # 返回最大的分量以外的所有分量（即孤立的子图）
+        main_component = max(components, key=len)
+        return [c for c in components if c != main_component]

mcp_server/services/indexer.py

@@ -0,0 +1,226 @@
+"""
+Service Layer - IndexerService（索引服务）
+
+管理 wiki 页面索引，支持增量更新和全量重建。
+
+参考设计文档：第 2.3 节
+"""
+
+import logging
+import asyncio
+from pathlib import Path
+from typing import List, Set, Optional
+from datetime import datetime
+from ..storage import Database, WikiPage, compute_content_hash
+from .parser import ParserService
+
+logger = logging.getLogger(__name__)
+
+
+class IndexerService:
+    """索引服务 - 管理页面索引"""
+
+    def __init__(self, db: Database, parser: ParserService, wiki_vault_path: str):
+        self.db = db
+        self.parser = parser
+        self.wiki_vault_path = Path(wiki_vault_path)
+        self._lock = asyncio.Lock()
+
+    async def index_page(self, page_path: str) -> Optional[WikiPage]:
+        """索引单个页面"""
+        try:
+            full_path = self.wiki_vault_path / page_path
+
+            # 读取文件内容
+            with open(full_path, 'r', encoding='utf-8') as f:
+                content = f.read()
+
+            # 解析页面
+            parsed = self.parser.parse_wiki_page(page_path, content)
+
+            # 计算内容哈希
+            content_hash = compute_content_hash(content)
+
+            # 检查是否需要更新
+            stored_hash = await self.db.get_page_hash(page_path)
+            if stored_hash == content_hash:
+                logger.debug(f"Page unchanged, skipping: {page_path}")
+                return None
+
+            # 创建 WikiPage 对象
+            page = WikiPage(
+                path=parsed["path"],
+                title=parsed["title"],
+                category=parsed["category"],
+                tags=parsed["tags"],
+                summary=parsed["summary"],
+                content_hash=content_hash,
+                lifecycle="draft",  # 默认为 draft，后续可通过 wiki_lint 提升
+                source_tool=parsed["source_tool"],
+                created_at=parsed["created_at"],
+                updated_at=parsed["updated_at"],
+                indexed_at=parsed["indexed_at"]
+            )
+
+            # 更新数据库
+            await self.db.upsert_page(page)
+
+            # 更新 FTS5 索引
+            await self.db.update_fts_content(
+                page_path,
+                page.title,
+                content,
+                page.summary
+            )
+
+            # 更新链接关系
+            await self.db.delete_links(page_path)
+            for link in parsed.get("links", []):
+                await self.db.upsert_link(page_path, link)
+
+            # 更新标签
+            for tag in page.tags:
+                await self.db.upsert_tag(tag)
+
+            logger.info(f"Indexed page: {page_path}")
+            return page
+
+        except Exception as e:
+            logger.error(f"Failed to index page {page_path}: {e}")
+            return None
+
+    async def index_batch(self, page_paths: List[str]) -> dict:
+        """批量索引页面"""
+        results = {
+            "success": 0,
+            "failed": 0,
+            "skipped": 0,
+            "pages": []
+        }
+
+        for page_path in page_paths:
+            try:
+                page = await self.index_page(page_path)
+                if page:
+                    results["success"] += 1
+                    results["pages"].append(page_path)
+                else:
+                    results["skipped"] += 1
+            except Exception as e:
+                logger.error(f"Failed to index {page_path}: {e}")
+                results["failed"] += 1
+
+        return results
+
+    async def get_dirty_pages(self) -> List[str]:
+        """获取需要重新索引的页面（增量更新）"""
+        all_pages = self.scan_wiki_vault()
+        dirty_pages = []
+
+        for page_path in all_pages:
+            full_path = self.wiki_vault_path / page_path
+            try:
+                with open(full_path, 'r', encoding='utf-8') as f:
+                    content = f.read()
+                current_hash = compute_content_hash(content)
+                stored_hash = await self.db.get_page_hash(page_path)
+                if stored_hash != current_hash:
+                    dirty_pages.append(page_path)
+            except Exception as e:
+                logger.warning(f"Failed to check {page_path}: {e}")
+
+        return dirty_pages
+
+    async def incremental_update(self) -> dict:
+        """增量更新索引 - 只处理变化的页面"""
+        logger.info("Starting incremental update...")
+
+        async with self._lock:
+            # 1. 获取所有 wiki 页面
+            all_pages = self.scan_wiki_vault()
+
+            # 2. 检查每个页面的哈希
+            for page_path in all_pages:
+                try:
+                    full_path = self.wiki_vault_path / page_path
+                    with open(full_path, 'r', encoding='utf-8') as f:
+                        content = f.read()
+                    current_hash = compute_content_hash(content)
+                    stored_hash = await self.db.get_page_hash(page_path)
+
+                    if stored_hash != current_hash:
+                        await self.index_page(page_path)
+                except Exception as e:
+                    logger.error(f"Failed to update {page_path}: {e}")
+
+            # 3. 处理删除的页面
+            indexed_paths = await self.db.get_all_indexed_paths()
+            for path in indexed_paths:
+                if path not in all_pages:
+                    await self.db.delete_page(path)
+                    await self.db.delete_fts_content(path)
+                    logger.info(f"Deleted from index: {path}")
+
+        # 更新元数据
+        await self.db.set_meta("last_incremental_update", datetime.now().isoformat())
+
+        stats = await self.db.get_stats()
+        logger.info(f"Incremental update completed: {stats}")
+        return stats
+
+    async def rebuild_index(self) -> dict:
+        """全量重建索引"""
+        logger.info("Starting full index rebuild...")
+
+        async with self._lock:
+            # 清空现有索引
+            await self.db.execute("DELETE FROM wiki_pages")
+            await self.db.execute("DELETE FROM wiki_content")
+            await self.db.execute("DELETE FROM wiki_fts")
+            await self.db.execute("DELETE FROM wiki_links")
+            await self.db.execute("DELETE FROM wiki_tags")
+            await self.db.execute("DELETE FROM wiki_page_tags")
+            logger.info("Cleared existing index")
+
+            # 扫描并索引所有页面
+            all_pages = self.scan_wiki_vault()
+            results = await self.index_batch(all_pages)
+
+        # 更新元数据
+        await self.db.set_meta("last_full_reindex", datetime.now().isoformat())
+
+        stats = await self.db.get_stats()
+        logger.info(f"Full rebuild completed: {stats}")
+        return {"results": results, "stats": stats}
+
+    def scan_wiki_vault(self) -> List[str]:
+        """扫描 wiki vault，返回所有 .md 文件的相对路径"""
+        if not self.wiki_vault_path.exists():
+            logger.error(f"Wiki vault path does not exist: {self.wiki_vault_path}")
+            return []
+
+        markdown_files = list(self.wiki_vault_path.rglob("*.md"))
+        relative_paths = []
+
+        for md_file in markdown_files:
+            try:
+                relative_path = md_file.relative_to(self.wiki_vault_path).as_posix()
+                relative_paths.append(relative_path)
+            except ValueError:
+                logger.warning(f"Failed to get relative path for: {md_file}")
+
+        return sorted(relative_paths)
+
+    async def get_index_status(self) -> dict:
+        """获取索引状态"""
+        stats = await self.db.get_stats()
+        dirty_pages = await self.get_dirty_pages()
+
+        return {
+            "total_pages": stats.get("total_pages", 0),
+            "total_links": stats.get("total_links", 0),
+            "total_tags": stats.get("total_tags", 0),
+            "last_indexed": stats.get("last_indexed"),
+            "dirty_pages": len(dirty_pages),
+            "dirty_page_list": dirty_pages[:10]  # 只返回前 10 个
+        }

mcp_server/services/parser.py

@@ -0,0 +1,239 @@
+"""
+Service Layer - ParserService（解析服务）
+
+解析 Markdown 文件，提取 frontmatter、链接、标签等。
+
+参考设计文档：第 2.3 节
+"""
+
+import re
+import logging
+import json
+from typing import List, Dict, Optional, Tuple
+from datetime import datetime
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+
+class ParserService:
+    """解析服务 - 解析 Markdown 文件"""
+
+    # Frontmatter 正则
+    FRONTMATTER_PATTERN = re.compile(r'^---\s*\n(.*?)\n---\s*\n', re.DOTALL)
+
+    # Wikilink 正则
+    WIKILINK_PATTERN = re.compile(r'\[\[([^\]|]+)(?:\|[^\]]+)?\]\]')
+
+    # Tag 正则（frontmatter 中的 tags 字段）
+    TAG_PATTERN = re.compile(r'tags:\s*\[(.*?)\]')
+
+    def parse_frontmatter(self, content: str) -> Dict:
+        """
+        解析 frontmatter
+
+        返回格式：
+        {
+            "name": "...",
+            "description": "...",
+            "metadata": {...},
+            "custom": {...}  # 自定义字段
+        }
+        """
+        frontmatter = {}
+        match = self.FRONTMATTER_PATTERN.match(content)
+
+        if match:
+            yaml_content = match.group(1)
+            # 简单解析（对于复杂情况，应该使用 PyYAML）
+            for line in yaml_content.split('\n'):
+                if ':' in line:
+                    key, value = line.split(':', 1)
+                    key = key.strip()
+                    value = value.strip()
+                    frontmatter[key] = value
+
+        return frontmatter
+
+    def extract_links(self, content: str) -> List[str]:
+        """
+        提取所有 [[wikilinks]]
+
+        返回链接目标列表（去重）
+        """
+        links = self.WIKILINK_PATTERN.findall(content)
+        return list(set(links))
+
+    def extract_tags(self, content: str) -> List[str]:
+        """
+        从 frontmatter 中提取标签
+
+        支持：
+        - tags: ["tag1", "tag2"]
+        - tags: [tag1, tag2]
+        """
+        tags = []
+        match = self.TAG_PATTERN.search(content)
+
+        if match:
+            tag_content = match.group(1)
+            # 尝试 JSON 解析
+            try:
+                tags = json.loads(f"[{tag_content}]")
+            except:
+                # 简单逗号分隔
+                tags = [t.strip().strip('"\'') for t in tag_content.split(',')]
+
+        return tags
+
+    def extract_title(self, content: str) -> str:
+        """
+        提取标题（优先级：frontmatter > 第一个 # 标题）
+
+        返回标题或空字符串
+        """
+        # 先检查 frontmatter
+        frontmatter = self.parse_frontmatter(content)
+        if "title" in frontmatter:
+            return frontmatter["title"]
+
+        # 检查第一个 # 标题
+        lines = content.split('\n')
+        for line in lines:
+            line = line.strip()
+            if line.startswith('#'):
+                # 移除 # 符号和空格
+                title = re.sub(r'^#+\s*', '', line)
+                return title
+
+        return ""
+
+    def extract_summary(self, content: str, max_length: int = 200) -> str:
+        """
+        提取摘要（优先级：frontmatter description > 第一段文字）
+
+        限制在 max_length 字符内
+        """
+        # 先检查 frontmatter
+        frontmatter = self.parse_frontmatter(content)
+        if "description" in frontmatter:
+            return frontmatter["description"][:max_length]
+
+        # 移除 frontmatter 和代码块
+        content_without_frontmatter = self.FRONTMATTER_PATTERN.sub('', content)
+        content_without_code = re.sub(r'```.*?```', '', content_without_frontmatter, flags=re.DOTALL)
+
+        # 获取第一段
+        lines = content_without_code.strip().split('\n\n')
+        for paragraph in lines:
+            paragraph = paragraph.strip()
+            if paragraph and not paragraph.startswith('#'):
+                # 移除 Markdown 格式
+                clean_paragraph = re.sub(r'[*_`#\[\]]', '', paragraph)
+                if clean_paragraph:
+                    return clean_paragraph[:max_length]
+
+        return ""
+
+    def infer_category(self, path: str) -> str:
+        """
+        从路径推断分类
+
+        例如：practices/xxx.md -> practices
+        """
+        path_obj = Path(path)
+        if path_obj.parent.name:
+            return path_obj.parent.name
+        return "uncategorized"
+
+    def infer_source_tool(self, content: str) -> str:
+        """
+        从内容推断来源工具
+
+        检查 frontmatter 中的特定字段：
+        - source_tool: claude/web_reader/gitea/other
+        """
+        frontmatter = self.parse_frontmatter(content)
+        return frontmatter.get("source_tool", "other")
+
+    def validate_page(self, path: str, content: str) -> List[str]:
+        """
+        验证页面，返回问题列表
+
+        检查：
+        - 是否有标题
+        - 是否有摘要
+        - 是否有分类
+        - frontmatter 是否有效
+        """
+        issues = []
+
+        # 检查标题
+        title = self.extract_title(content)
+        if not title:
+            issues.append("Missing title")
+
+        # 检查摘要
+        summary = self.extract_summary(content)
+        if not summary:
+            issues.append("Missing summary")
+
+        # 检查分类
+        category = self.infer_category(path)
+        if category == "uncategorized":
+            issues.append("Uncategorized page")
+
+        # 检查 frontmatter
+        frontmatter = self.parse_frontmatter(content)
+        if not frontmatter:
+            issues.append("Missing or invalid frontmatter")
+
+        return issues
+
+    def parse_wiki_page(self, path: str, content: str, created_at: Optional[str] = None, updated_at: Optional[str] = None) -> Dict:
+        """
+        完整解析 wiki 页面，返回结构化数据
+
+        返回格式与 WikiPage 兼容
+        """
+        title = self.extract_title(content)
+        summary = self.extract_summary(content)
+        category = self.infer_category(path)
+        tags = self.extract_tags(content)
+        source_tool = self.infer_source_tool(content)
+        links = self.extract_links(content)
+
+        now = datetime.now().isoformat()
+
+        return {
+            "path": path,
+            "title": title,
+            "category": category,
+            "tags": tags,
+            "summary": summary,
+            "links": links,
+            "source_tool": source_tool,
+            "created_at": created_at or now,
+            "updated_at": updated_at or now,
+            "indexed_at": now
+        }
+
+    def format_wikilink(self, path: str, title: Optional[str] = None) -> str:
+        """
+        格式化 wikilink
+
+        如果提供 title，使用 [[path|title]] 格式
+        否则使用 [[path]] 格式
+        """
+        if title:
+            return f"[[{path}|{title}]]"
+        return f"[[{path}]]"
+
+    def resolve_wikilink_path(self, link: str, current_path: str) -> str:
+        """
+        解析相对 wikilink 路径
+
+        例如：在 practices/a.md 中的 [[../concepts/x]] 解析为 concepts/x
+        """
+        # TODO: 实现相对路径解析
+        return link

mcp_server/services/query.py

@@ -0,0 +1,120 @@
+"""
+Service Layer - QueryService（查询服务）
+
+负责所有查询逻辑，包括 FTS5 全文搜索、标签搜索、页面查询等。
+
+参考设计文档：第 2.3 节
+"""
+
+import logging
+from typing import List, Set, Optional
+from ..storage import Database, WikiPage
+from .cache import CacheService
+
+logger = logging.getLogger(__name__)
+
+
+class QueryService:
+    """查询服务 - 负责所有查询逻辑"""
+
+    def __init__(self, db: Database, cache: CacheService):
+        self.db = db
+        self.cache = cache
+
+    async def search(self, query: str, limit: int = 10) -> List[WikiPage]:
+        """FTS5 全文搜索"""
+        # 1. 检查缓存
+        cache_key = f"search:{query}:{limit}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            logger.debug(f"Cache hit for search: {query}")
+            return cached
+
+        # 2. FTS5 搜索
+        results = await self.db.fts_search(query, limit)
+
+        # 3. 缓存结果
+        await self.cache.set(cache_key, results, ttl=3600)
+
+        return results
+
+    async def search_by_tags(self, tags: List[str]) -> List[WikiPage]:
+        """按标签搜索"""
+        cache_key = f"tags:{','.join(tags)}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        results = await self.db.search_by_tags(tags)
+        await self.cache.set(cache_key, results, ttl=3600)
+        return results
+
+    async def search_by_source_tool(self, tool_name: str, limit: int = 50) -> List[WikiPage]:
+        """按来源工具搜索（memory_bridge 使用）"""
+        cache_key = f"tool:{tool_name}:{limit}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        results = await self.db.search_by_source_tool(tool_name, limit)
+        await self.cache.set(cache_key, results, ttl=1800)  # 30 分钟 TTL
+        return results
+
+    async def get_page(self, path: str) -> Optional[WikiPage]:
+        """获取单个页面"""
+        cache_key = f"page:{path}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        page = await self.db.get_page(path)
+        if page:
+            await self.cache.set(cache_key, page, ttl=3600)
+        return page
+
+    async def get_links(self, path: str) -> Set[str]:
+        """获取页面的出链"""
+        cache_key = f"links:{path}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        links = await self.db.get_links(path)
+        await self.cache.set(cache_key, links, ttl=3600)
+        return links
+
+    async def get_backlinks(self, path: str) -> Set[str]:
+        """获取页面的反向链接"""
+        cache_key = f"backlinks:{path}"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        backlinks = await self.db.get_backlinks(path)
+        await self.cache.set(cache_key, backlinks, ttl=3600)
+        return backlinks
+
+    async def find_orphans(self) -> Set[str]:
+        """查找孤立页面（无反向链接）"""
+        cache_key = "orphans"
+        cached = await self.cache.get(cache_key)
+        if cached:
+            return cached
+
+        all_pages = await self.db.get_all_pages()
+        orphans = set()
+        for page in all_pages:
+            backlinks = await self.db.get_backlinks(page.path)
+            if not backlinks and page.path != "index.md":
+                orphans.add(page.path)
+
+        await self.cache.set(cache_key, orphans, ttl=1800)
+        return orphans
+
+    async def get_stats(self) -> dict:
+        """获取索引统计信息"""
+        return await self.db.get_stats()
+
+    async def invalidate_cache(self, pattern: str = "*") -> int:
+        """使缓存失效"""
+        return await self.cache.invalidate(pattern)

mcp_server/storage/__init__.py

@@ -0,0 +1,14 @@
+"""
+Storage Layer - 数据存储层
+
+提供数据库访问和缓存功能。
+"""
+
+from .database import Database, WikiPage, fix_dirty_states, compute_content_hash
+
+__all__ = [
+    "Database",
+    "WikiPage",
+    "fix_dirty_states",
+    "compute_content_hash"
+]

mcp_server/storage/database.py

@@ -0,0 +1,531 @@
+"""
+Storage Layer - Database 类
+
+使用 aiosqlite 实现真正的异步支持，配合 WAL 模式和并发保护。
+
+参考设计文档：第 2.4 节
+"""
+
+import aiosqlite
+import asyncio
+import logging
+import time
+from typing import List, Tuple, Dict, Set, Optional, Any
+from datetime import datetime
+from dataclasses import dataclass, asdict
+import hashlib
+import json
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class WikiPage:
+    """Wiki 页面模型"""
+    path: str
+    title: str
+    category: str
+    tags: List[str]
+    summary: str
+    content_hash: str
+    lifecycle: str
+    source_tool: str
+    created_at: str
+    updated_at: str
+    indexed_at: str
+
+    def is_stale(self, days: int = 90) -> bool:
+        """检查页面是否过期"""
+        updated = datetime.fromisoformat(self.updated_at)
+        return (datetime.now() - updated).days > days
+
+    def to_dict(self) -> dict:
+        """转换为字典"""
+        return asdict(self)
+
+
+class Database:
+    """SQLite 数据库封装，使用 aiosqlite 实现真正的异步支持"""
+
+    def __init__(self, path: str):
+        self.path = path
+        self._conn: Optional[aiosqlite.Connection] = None
+        self._lock = asyncio.Lock()
+
+    async def connect(self) -> None:
+        """建立连接，启用 WAL 模式和并发保护"""
+        logger.info(f"Connecting to database: {self.path}")
+        self._conn = await aiosqlite.connect(self.path)
+
+        # 启用 WAL 模式提升并发性能
+        await self._conn.execute("PRAGMA journal_mode=WAL")
+        await self._conn.execute("PRAGMA busy_timeout=10000")  # 10s
+        await self._conn.execute("PRAGMA synchronous=NORMAL")
+        await self._conn.commit()
+
+        # 创建表结构
+        await self._create_tables()
+
+        logger.info("Database connected and initialized")
+
+    async def _create_tables(self) -> None:
+        """创建所有表结构"""
+
+        # 页面索引表
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_pages (
+                path TEXT PRIMARY KEY,
+                title TEXT NOT NULL,
+                category TEXT,
+                tags TEXT,
+                summary TEXT,
+                content_hash TEXT NOT NULL,
+                lifecycle TEXT DEFAULT 'draft',
+                source_tool TEXT DEFAULT 'other',
+                created_at TIMESTAMP,
+                updated_at TIMESTAMP,
+                indexed_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+            )
+        """)
+
+        # 索引
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_pages_category ON wiki_pages(category)")
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_pages_lifecycle ON wiki_pages(lifecycle)")
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_pages_updated ON wiki_pages(updated_at)")
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_pages_source_tool ON wiki_pages(source_tool)")
+
+        # 内容表（FTS5 外部内容表）- 必须先创建
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_content (
+                path TEXT PRIMARY KEY,
+                content TEXT NOT NULL
+            )
+        """)
+
+        # FTS5 全文搜索表
+        await self._conn.execute("""
+            CREATE VIRTUAL TABLE IF NOT EXISTS wiki_fts USING fts5(
+                path UNINDEXED,
+                title,
+                content,
+                summary,
+                content=wiki_content,
+                content_rowid=rowid,
+                tokenize = 'porter unicode61'
+            )
+        """)
+
+        # 链接关系表
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_links (
+                source TEXT NOT NULL,
+                target TEXT NOT NULL,
+                created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+                PRIMARY KEY (source, target)
+            )
+        """)
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_links_target ON wiki_links(target)")
+
+        # 标签索引表
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_tags (
+                tag TEXT PRIMARY KEY,
+                count INTEGER DEFAULT 0,
+                updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+            )
+        """)
+
+        # 页面-标签关联表
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_page_tags (
+                path TEXT NOT NULL,
+                tag TEXT NOT NULL,
+                PRIMARY KEY (path, tag),
+                FOREIGN KEY (path) REFERENCES wiki_pages(path) ON DELETE CASCADE,
+                FOREIGN KEY (tag) REFERENCES wiki_tags(tag) ON DELETE CASCADE
+            )
+        """)
+        await self._conn.execute("CREATE INDEX IF NOT EXISTS idx_page_tags_tag ON wiki_page_tags(tag)")
+
+        # 索引元数据表
+        await self._conn.execute("""
+            CREATE TABLE IF NOT EXISTS wiki_meta (
+                key TEXT PRIMARY KEY,
+                value TEXT,
+                updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+            )
+        """)
+
+        await self._conn.commit()
+
+    async def execute(self, sql: str, params: tuple = ()) -> aiosqlite.Cursor:
+        """执行 SQL（带写入锁）"""
+        async with self._lock:
+            cursor = await self._conn.execute(sql, params)
+            await self._conn.commit()
+            return cursor
+
+    async def execute_with_retry(self, sql: str, params: tuple = (), max_retries: int = 2) -> aiosqlite.Cursor:
+        """带重试的数据库操作（指数退避）"""
+        for attempt in range(max_retries):
+            try:
+                return await self.execute(sql, params)
+            except aiosqlite.OperationalError as e:
+                if "database is locked" in str(e) and attempt < max_retries - 1:
+                    wait_time = 0.1 * (2 ** attempt)
+                    logger.warning(f"Database locked, retrying in {wait_time}s (attempt {attempt + 1}/{max_retries})")
+                    await asyncio.sleep(wait_time)
+                    continue
+                raise
+
+    async def fetch_all(self, sql: str, params: tuple = ()) -> List[Tuple]:
+        """查询所有结果（读操作无需锁，WAL 自动处理）"""
+        cursor = await self._conn.execute(sql, params)
+        return await cursor.fetchall()
+
+    async def fetch_one(self, sql: str, params: tuple = ()) -> Optional[Tuple]:
+        """查询单个结果"""
+        rows = await self.fetch_all(sql, params)
+        return rows[0] if rows else None
+
+    # === 页面操作 ===
+
+    async def get_page(self, path: str) -> Optional[WikiPage]:
+        """获取单个页面"""
+        row = await self.fetch_one(
+            "SELECT path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at FROM wiki_pages WHERE path = ?",
+            (path,)
+        )
+        if not row:
+            return None
+
+        return WikiPage(
+            path=row[0],
+            title=row[1],
+            category=row[2],
+            tags=json.loads(row[3]) if row[3] else [],
+            summary=row[4],
+            content_hash=row[5],
+            lifecycle=row[6],
+            source_tool=row[7],
+            created_at=row[8],
+            updated_at=row[9],
+            indexed_at=row[10]
+        )
+
+    async def get_all_pages(self) -> List[WikiPage]:
+        """获取所有页面"""
+        rows = await self.fetch_all(
+            "SELECT path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at FROM wiki_pages"
+        )
+        return [
+            WikiPage(
+                path=row[0],
+                title=row[1],
+                category=row[2],
+                tags=json.loads(row[3]) if row[3] else [],
+                summary=row[4],
+                content_hash=row[5],
+                lifecycle=row[6],
+                source_tool=row[7],
+                created_at=row[8],
+                updated_at=row[9],
+                indexed_at=row[10]
+            )
+            for row in rows
+        ]
+
+    async def get_page_hash(self, path: str) -> Optional[str]:
+        """获取页面内容哈希"""
+        row = await self.fetch_one("SELECT content_hash FROM wiki_pages WHERE path = ?", (path,))
+        return row[0] if row else None
+
+    async def upsert_page(self, page: WikiPage) -> None:
+        """插入或更新页面"""
+        await self.execute_with_retry("""
+            INSERT INTO wiki_pages (path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at)
+            VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+            ON CONFLICT(path) DO UPDATE SET
+                title = excluded.title,
+                category = excluded.category,
+                tags = excluded.tags,
+                summary = excluded.summary,
+                content_hash = excluded.content_hash,
+                lifecycle = excluded.lifecycle,
+                source_tool = excluded.source_tool,
+                updated_at = excluded.updated_at,
+                indexed_at = excluded.indexed_at
+        """, (
+            page.path, page.title, page.category, json.dumps(page.tags),
+            page.summary, page.content_hash, page.lifecycle, page.source_tool,
+            page.created_at, page.updated_at, page.indexed_at
+        ))
+
+    async def delete_page(self, path: str) -> None:
+        """删除页面（级联删除相关数据）"""
+        await self.execute_with_retry("DELETE FROM wiki_pages WHERE path = ?", (path,))
+
+    async def get_all_indexed_paths(self) -> Set[str]:
+        """获取所有已索引的页面路径"""
+        rows = await self.fetch_all("SELECT path FROM wiki_pages")
+        return {row[0] for row in rows}
+
+    # === FTS5 搜索 ===
+
+    async def fts_search(self, query: str, limit: int = 10) -> List[WikiPage]:
+        """FTS5 全文搜索"""
+        # 先从 FTS5 获取匹配的路径
+        fts_rows = await self.fetch_all(
+            "SELECT path FROM wiki_fts WHERE wiki_fts MATCH ? ORDER BY rank LIMIT ?",
+            (query, limit)
+        )
+        paths = [row[0] for row in fts_rows]
+
+        if not paths:
+            return []
+
+        # 从 wiki_pages 获取完整数据
+        placeholders = ','.join('?' * len(paths))
+        rows = await self.fetch_all(
+            f"SELECT path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at FROM wiki_pages WHERE path IN ({placeholders})",
+            paths
+        )
+
+        return [
+            WikiPage(
+                path=row[0],
+                title=row[1],
+                category=row[2],
+                tags=json.loads(row[3]) if row[3] else [],
+                summary=row[4],
+                content_hash=row[5],
+                lifecycle=row[6],
+                source_tool=row[7],
+                created_at=row[8],
+                updated_at=row[9],
+                indexed_at=row[10]
+            )
+            for row in rows
+        ]
+
+    async def search_by_tags(self, tags: List[str]) -> List[WikiPage]:
+        """按标签搜索"""
+        if not tags:
+            return []
+
+        placeholders = ','.join('?' * len(tags))
+        rows = await self.fetch_all(
+            f"SELECT DISTINCT p.path, p.title, p.category, p.tags, p.summary, p.content_hash, p.lifecycle, p.source_tool, p.created_at, p.updated_at, p.indexed_at FROM wiki_pages p JOIN wiki_page_tags pt ON p.path = pt.path WHERE pt.tag IN ({placeholders})",
+            tags
+        )
+
+        return [
+            WikiPage(
+                path=row[0],
+                title=row[1],
+                category=row[2],
+                tags=json.loads(row[3]) if row[3] else [],
+                summary=row[4],
+                content_hash=row[5],
+                lifecycle=row[6],
+                source_tool=row[7],
+                created_at=row[8],
+                updated_at=row[9],
+                indexed_at=row[10]
+            )
+            for row in rows
+        ]
+
+    async def search_by_source_tool(self, tool_name: str, limit: int = 50) -> List[WikiPage]:
+        """按来源工具搜索（memory_bridge 使用）"""
+        rows = await self.fetch_all(
+            "SELECT path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at FROM wiki_pages WHERE source_tool = ? ORDER BY updated_at DESC LIMIT ?",
+            (tool_name, limit)
+        )
+
+        return [
+            WikiPage(
+                path=row[0],
+                title=row[1],
+                category=row[2],
+                tags=json.loads(row[3]) if row[3] else [],
+                summary=row[4],
+                content_hash=row[5],
+                lifecycle=row[6],
+                source_tool=row[7],
+                created_at=row[8],
+                updated_at=row[9],
+                indexed_at=row[10]
+            )
+            for row in rows
+        ]
+
+    # === 链接操作 ===
+
+    async def get_links(self, path: str) -> Set[str]:
+        """获取页面的出链"""
+        rows = await self.fetch_all("SELECT target FROM wiki_links WHERE source = ?", (path,))
+        return {row[0] for row in rows}
+
+    async def get_backlinks(self, path: str) -> Set[str]:
+        """获取页面的反向链接"""
+        rows = await self.fetch_all("SELECT source FROM wiki_links WHERE target = ?", (path,))
+        return {row[0] for row in rows}
+
+    async def upsert_link(self, source: str, target: str) -> None:
+        """插入或更新链接"""
+        await self.execute_with_retry(
+            "INSERT INTO wiki_links (source, target) VALUES (?, ?) ON CONFLICT(source, target) DO NOTHING",
+            (source, target)
+        )
+
+    async def delete_links(self, path: str) -> None:
+        """删除页面的所有链接"""
+        await self.execute_with_retry("DELETE FROM wiki_links WHERE source = ?", (path,))
+
+    # === 标签操作 ===
+
+    async def upsert_tag(self, tag: str, count: int = 1) -> None:
+        """插入或更新标签"""
+        await self.execute_with_retry(
+            "INSERT INTO wiki_tags (tag, count) VALUES (?, ?) ON CONFLICT(tag) DO UPDATE SET count = count + excluded.count",
+            (tag, count)
+        )
+
+    async def get_all_tags(self) -> Dict[str, int]:
+        """获取所有标签"""
+        rows = await self.fetch_all("SELECT tag, count FROM wiki_tags")
+        return {row[0]: row[1] for row in rows}
+
+    # === 元数据操作 ===
+
+    async def get_meta(self, key: str, default: str = "") -> str:
+        """获取元数据"""
+        row = await self.fetch_one("SELECT value FROM wiki_meta WHERE key = ?", (key,))
+        return row[0] if row else default
+
+    async def set_meta(self, key: str, value: str) -> None:
+        """设置元数据"""
+        await self.execute_with_retry(
+            "INSERT INTO wiki_meta (key, value) VALUES (?, ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value",
+            (key, value)
+        )
+
+    # === FTS5 内容更新 ===
+
+    async def update_fts_content(self, path: str, title: str, content: str, summary: str) -> None:
+        """更新 FTS5 内容"""
+        # 先更新内容表
+        await self.execute_with_retry(
+            "INSERT INTO wiki_content (path, content) VALUES (?, ?) ON CONFLICT(path) DO UPDATE SET content = excluded.content",
+            (path, content)
+        )
+
+        # 再更新 FTS5 表（会自动从内容表同步）
+        await self.execute_with_retry(
+            "INSERT INTO wiki_fts (path, title, summary) VALUES (?, ?, ?) ON CONFLICT(path) DO UPDATE SET title = excluded.title, summary = excluded.summary",
+            (path, title, summary)
+        )
+
+    async def delete_fts_content(self, path: str) -> None:
+        """删除 FTS5 内容"""
+        await self.execute_with_retry("DELETE FROM wiki_content WHERE path = ?", (path,))
+        await self.execute_with_retry("DELETE FROM wiki_fts WHERE path = ?", (path,))
+
+    # === 状态查询 ===
+
+    async def get_stats(self) -> Dict[str, Any]:
+        """获取索引统计信息"""
+        page_count = await self.fetch_one("SELECT COUNT(*) FROM wiki_pages")
+        link_count = await self.fetch_one("SELECT COUNT(*) FROM wiki_links")
+        tag_count = await self.fetch_one("SELECT COUNT(*) FROM wiki_tags")
+        last_indexed = await self.fetch_one("SELECT MAX(indexed_at) FROM wiki_pages")
+
+        return {
+            "total_pages": page_count[0] if page_count else 0,
+            "total_links": link_count[0] if link_count else 0,
+            "total_tags": tag_count[0] if tag_count else 0,
+            "last_indexed": last_indexed[0] if last_indexed and last_indexed[0] else None
+        }
+
+    async def get_recent_pages(self, days: int = 7, limit: int = 50) -> List[WikiPage]:
+        """获取最近更新的页面"""
+        rows = await self.fetch_all(
+            "SELECT path, title, category, tags, summary, content_hash, lifecycle, source_tool, created_at, updated_at, indexed_at FROM wiki_pages WHERE updated_at >= datetime('now', '-' || ? || ' days') ORDER BY updated_at DESC LIMIT ?",
+            (str(days), limit)
+        )
+
+        return [
+            WikiPage(
+                path=row[0],
+                title=row[1],
+                category=row[2],
+                tags=json.loads(row[3]) if row[3] else [],
+                summary=row[4],
+                content_hash=row[5],
+                lifecycle=row[6],
+                source_tool=row[7],
+                created_at=row[8],
+                updated_at=row[9],
+                indexed_at=row[10]
+            )
+            for row in rows
+        ]
+
+    async def get_new_tags(self, days: int = 7) -> List[Tuple[str, str]]:
+        """获取新增标签"""
+        rows = await self.fetch_all(
+            "SELECT tag, updated_at FROM wiki_tags WHERE updated_at >= datetime('now', '-' || ? || ' days') ORDER BY updated_at DESC",
+            (str(days),)
+        )
+        return list(rows)
+
+    # === 完整性检查 ===
+
+    async def check_integrity(self) -> bool:
+        """检查数据库完整性"""
+        try:
+            result = await self.fetch_one("PRAGMA integrity_check")
+            if result and result[0] == "ok":
+                return True
+            logger.warning(f"Database integrity check failed: {result}")
+            return False
+        except Exception as e:
+            logger.error(f"Integrity check error: {e}")
+            return False
+
+    # === 关闭连接 ===
+
+    async def close(self) -> None:
+        """关闭连接"""
+        if self._conn:
+            await self._conn.close()
+            self._conn = None
+            logger.info("Database connection closed")
+
+
+async def fix_dirty_states(db: Database) -> None:
+    """启动时清理可能的脏状态"""
+    logger.info("Checking for dirty states...")
+
+    try:
+        # 1. 检查 WAL 文件是否损坏
+        if db._conn:
+            await db._conn.execute("PRAGMA wal_checkpoint(PASSIVE)")
+            await db._conn.commit()
+
+        # 2. 检查数据库完整性
+        if not await db.check_integrity():
+            raise Exception("Database integrity check failed")
+
+        logger.info("No dirty states found, database is healthy")
+
+    except Exception as e:
+        logger.warning(f"Dirty states detected, attempting recovery: {e}")
+        # TODO: 实现自动重建逻辑
+        # await rebuild_index(db)
+
+
+def compute_content_hash(content: str) -> str:
+    """计算内容 MD5 哈希"""
+    return hashlib.md5(content.encode('utf-8')).hexdigest()

mcp_server/tools/__init__.py

@@ -0,0 +1,25 @@
+"""
+Tool Layer - 工具层
+
+提供所有 MCP Tools。
+"""
+
+from .wiki_query import WikiQueryTool
+from .memory_bridge import MemoryBridgeTool
+from .wiki_status import WikiStatusTool
+from .wiki_lint import WikiLintTool
+from .cross_linker import CrossLinkerTool
+from .tag_taxonomy import TagTaxonomyTool
+from .wiki_synthesize import WikiSynthesizeTool
+from .daily_update import DailyUpdateTool
+
+__all__ = [
+    "WikiQueryTool",
+    "MemoryBridgeTool",
+    "WikiStatusTool",
+    "WikiLintTool",
+    "CrossLinkerTool",
+    "TagTaxonomyTool",
+    "WikiSynthesizeTool",
+    "DailyUpdateTool"
+]

mcp_server/tools/cross_linker.py

@@ -0,0 +1,87 @@
+"""
+Tool Layer - cross_linker 工具
+
+扫描 wiki，自动发现缺失的交叉引用。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any, List
+from ..services import GraphService
+
+logger = logging.getLogger(__name__)
+
+
+class CrossLinkerTool:
+    """cross_linker 工具实现"""
+
+    def __init__(self, graph_service: GraphService):
+        self.graph_service = graph_service
+
+    async def handle(self, path: str = "", dry_run: bool = True) -> Dict[str, Any]:
+        """
+        扫描 wiki，发现缺失的交叉引用
+
+        Args:
+            path: 指定路径（空字符串表示全部）
+            dry_run: 是否为模拟运行（不实际修改）
+
+        Returns:
+            {
+                "missing_links": [
+                    {
+                        "source": "practices/a.md",
+                        "target": "concepts/x",
+                        "suggestion": "Consider creating [[concepts/x]]"
+                    }
+                ],
+                "total": 12,
+                "dry_run": true
+            }
+        """
+        # 获取缺失的链接
+        all_missing = await self.graph_service.find_missing_links()
+
+        # 过滤指定路径
+        if path:
+            missing_links = [(s, t) for s, t in all_missing if s == path or t == path]
+        else:
+            missing_links = all_missing
+
+        # 格式化结果
+        missing_links_formatted = []
+        for source, target in missing_links:
+            missing_links_formatted.append({
+                "source": source,
+                "target": target,
+                "suggestion": f"Consider creating [[{target}]] or updating the link in [[{source}]]"
+            })
+
+        return {
+            "missing_links": missing_links_formatted[:50],  # 最多返回 50 条
+            "total": len(missing_links),
+            "dry_run": dry_run
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "cross_linker",
+            "description": "扫描 wiki，自动发现缺失的交叉引用",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "path": {
+                        "type": "string",
+                        "default": "",
+                        "description": "指定路径（空字符串表示全部）"
+                    },
+                    "dry_run": {
+                        "type": "boolean",
+                        "default": True,
+                        "description": "是否为模拟运行（不实际修改）"
+                    }
+                }
+            }
+        }

mcp_server/tools/daily_update.py

@@ -0,0 +1,105 @@
+"""
+Tool Layer - daily_update 工具
+
+日常维护（检查源新鲜度、更新 index、重新生成 hot.md）。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any
+from datetime import datetime
+from pathlib import Path
+from ..services import QueryService, IndexerService
+
+logger = logging.getLogger(__name__)
+
+
+class DailyUpdateTool:
+    """daily_update 工具实现"""
+
+    def __init__(self, query_service: QueryService, indexer_service: IndexerService):
+        self.query_service = query_service
+        self.indexer_service = indexer_service
+
+    async def handle(self) -> Dict[str, Any]:
+        """
+        日常维护
+
+        Returns:
+            {
+                "updated": 5,
+                "new": 2,
+                "hot_md_generated": true,
+                "index_status": {...}
+            }
+        """
+        # 1. 增量更新索引
+        index_status = await self.indexer_service.incremental_update()
+
+        # 2. 获取最近更新的页面
+        recent_pages = await self.query_service.db.get_recent_pages(days=7, limit=20)
+
+        # 3. 获取新增标签
+        new_tags = await self.query_service.db.get_new_tags(days=7)
+
+        # 4. 查找孤立页面
+        from ..services import GraphService
+        graph_service = GraphService(self.query_service.db)
+        orphans = await graph_service.find_orphans()
+
+        # 5. 生成 hot.md
+        hot_md_generated = await self._generate_hot_md(recent_pages, new_tags, orphans)
+
+        return {
+            "updated": len(recent_pages),
+            "new": len(new_tags),
+            "hot_md_generated": hot_md_generated,
+            "index_status": index_status
+        }
+
+    async def _generate_hot_md(self, recent_pages, new_tags, orphans) -> bool:
+        """生成热点文件"""
+        try:
+            # 确定 hot.md 保存路径
+            vault_path = Path(self.query_service.db.path).parent.parent / "wiki-vault"
+            hot_path = vault_path / "hot.md"
+
+            # 格式化内容
+            content = f"""# Wiki Hot - {datetime.now().strftime('%Y-%m-%d')}
+
+## 最近更新（7 天内）
+
+"""
+            for page in recent_pages[:10]:
+                content += f"- [[{page.path}|{page.title}]] - {page.updated_at}\n"
+
+            content += "\n## 新增标签（7 天内）\n\n"
+            for tag, updated_at in new_tags[:10]:
+                content += f"- `{tag}` - {updated_at}\n"
+
+            content += "\n## 待链接页面（孤立页面）\n\n"
+            for orphan in sorted(list(orphans))[:10]:
+                content += f"- [[{orphan}]]\n"
+
+            # 写入文件
+            with open(hot_path, 'w', encoding='utf-8') as f:
+                f.write(content)
+
+            logger.info(f"Generated hot.md: {hot_path}")
+            return True
+
+        except Exception as e:
+            logger.error(f"Failed to generate hot.md: {e}")
+            return False
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "daily_update",
+            "description": "日常维护（检查源新鲜度、更新 index、重新生成 hot.md）",
+            "inputSchema": {
+                "type": "object",
+                "properties": {}
+            }
+        }

mcp_server/tools/memory_bridge.py

@@ -0,0 +1,112 @@
+"""
+Tool Layer - memory_bridge 工具
+
+按 AI 工具来源浏览和对比 wiki 知识。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any, Optional
+from datetime import datetime
+from ..services import QueryService
+
+logger = logging.getLogger(__name__)
+
+
+class MemoryBridgeTool:
+    """memory_bridge 工具实现"""
+
+    def __init__(self, query_service: QueryService):
+        self.query_service = query_service
+
+    async def handle(self, tool_name: str = "claude", date_range: str = "") -> Dict[str, Any]:
+        """
+        按 AI 工具来源浏览和对比 wiki 知识
+
+        Args:
+            tool_name: AI 工具名称（claude/web_reader/gitea/other）
+            date_range: 日期范围（如 "2024-01-01:2024-12-31" 或空字符串表示不限）
+
+        Returns:
+            {
+                "entries": [
+                    {
+                        "path": "practices/moziplus-orchestration.md",
+                        "title": "moziplus 编排实践",
+                        "summary": "...",
+                        "updated_at": "2024-06-15T10:30:00",
+                        "relevance_score": 0.85
+                    }
+                ],
+                "total": 12,
+                "tool_name": "claude",
+                "date_range": "2024-01-01:2024-12-31"
+            }
+        """
+        # 按工具来源搜索
+        pages = await self.query_service.search_by_source_tool(tool_name, limit=100)
+
+        # 按日期范围过滤
+        if date_range:
+            try:
+                start_str, end_str = date_range.split(":")
+                start_date = datetime.fromisoformat(start_str)
+                end_date = datetime.fromisoformat(end_str)
+
+                filtered = []
+                for page in pages:
+                    updated = datetime.fromisoformat(page.updated_at)
+                    if start_date <= updated <= end_date:
+                        filtered.append(page)
+                pages = filtered
+            except Exception as e:
+                logger.warning(f"Invalid date_range format '{date_range}': {e}")
+
+        # 格式化结果
+        entries = []
+        for page in pages:
+            # 计算相关性分数（基于摘要长度和更新时间）
+            recency_days = (datetime.now() - datetime.fromisoformat(page.updated_at)).days
+            relevance_score = max(0.1, 1.0 - recency_days / 365)  # 简单衰减
+
+            entries.append({
+                "path": page.path,
+                "title": page.title,
+                "summary": page.summary,
+                "updated_at": page.updated_at,
+                "relevance_score": round(relevance_score, 2)
+            })
+
+        # 按相关性排序
+        entries.sort(key=lambda x: x["relevance_score"], reverse=True)
+
+        return {
+            "entries": entries[:50],  # 最多返回 50 条
+            "total": len(entries),
+            "tool_name": tool_name,
+            "date_range": date_range
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "memory_bridge",
+            "description": "按 AI 工具来源浏览和对比 wiki 知识",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "tool_name": {
+                        "type": "string",
+                        "default": "claude",
+                        "description": "AI 工具名称（claude/web_reader/gitea/other）",
+                        "enum": ["claude", "web_reader", "gitea", "other"]
+                    },
+                    "date_range": {
+                        "type": "string",
+                        "default": "",
+                        "description": "日期范围，格式：YYYY-MM-DD:YYYY-MM-DD"
+                    }
+                }
+            }
+        }

mcp_server/tools/tag_taxonomy.py

@@ -0,0 +1,117 @@
+"""
+Tool Layer - tag_taxonomy 工具
+
+用受控词表强制标签一致性。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any, List, Set
+from ..services import QueryService
+
+logger = logging.getLogger(__name__)
+
+
+class TagTaxonomyTool:
+    """tag_taxonomy 工具实现"""
+
+    # 受控词表（可配置）
+    CONTROLLED_VOCABULARY: Set[str] = {
+        # 分类
+        "practices", "concepts", "entities", "projects", "skills", "references",
+        # 技术栈
+        "python", "typescript", "rust", "go", "swift",
+        # 领域
+        "ai", "ml", "database", "web", "mobile", "devops",
+        # 团队
+        "sanguo", "moziplus", "bitnet",
+        # 通用
+        "tutorial", "reference", "guide", "example", "draft"
+    }
+
+    def __init__(self, query_service: QueryService):
+        self.query_service = query_service
+
+    async def handle(self, path: str = "", enforce: bool = False) -> Dict[str, Any]:
+        """
+        用受控词表强制标签一致性
+
+        Args:
+            path: 指定路径（空字符串表示全部）
+            enforce: 是否强制修正（否则仅报告）
+
+        Returns:
+            {
+                "conflicts": [
+                    {
+                        "path": "practices/example.md",
+                        "invalid_tags": ["CustomTag"],
+                        "suggested_tags": ["practices"]
+                    }
+                ],
+                "total_conflicts": 5,
+                "enforced": false
+            }
+        """
+        conflicts = []
+
+        # 获取所有标签
+        all_tags = await self.query_service.db.get_all_tags()
+
+        # 检查非受控标签
+        invalid_tags = set(all_tags.keys()) - self.CONTROLLED_VOCABULARY
+
+        if invalid_tags:
+            # 获取使用这些标签的页面
+            for tag in invalid_tags:
+                tag_pages = await self.query_service.search_by_tags([tag])
+
+                for page in tag_pages:
+                    page_tags = set(page.tags) & invalid_tags
+
+                    if page_tags:
+                        # 推断修正建议（基于页面分类）
+                        suggested_tags = [page.category] if page.category else []
+
+                        conflicts.append({
+                            "path": page.path,
+                            "invalid_tags": list(page_tags),
+                            "suggested_tags": suggested_tags
+                        })
+
+                        if enforce and path and page.path == path:
+                            # TODO: 实际修正标签
+                            pass
+
+        return {
+            "conflicts": conflicts[:50],
+            "total_conflicts": len(conflicts),
+            "enforced": enforce
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "tag_taxonomy",
+            "description": "用受控词表强制标签一致性",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "path": {
+                        "type": "string",
+                        "default": "",
+                        "description": "指定路径（空字符串表示全部）"
+                    },
+                    "enforce": {
+                        "type": "boolean",
+                        "default": False,
+                        "description": "是否强制修正（否则仅报告）"
+                    }
+                }
+            }
+        }
+
+    def get_controlled_vocabulary(self) -> List[str]:
+        """获取当前受控词表"""
+        return sorted(list(self.CONTROLLED_VOCABULARY))

mcp_server/tools/wiki_lint.py

@@ -0,0 +1,164 @@
+"""
+Tool Layer - wiki_lint 工具
+
+审计 wiki 健康（格式、链接、frontmatter 规范）。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any, List
+from ..services import ParserService, QueryService, GraphService
+
+logger = logging.getLogger(__name__)
+
+
+class WikiLintTool:
+    """wiki_lint 工具实现"""
+
+    def __init__(self, parser: ParserService, query_service: QueryService, graph_service: GraphService):
+        self.parser = parser
+        self.query_service = query_service
+        self.graph_service = graph_service
+
+    async def handle(self, path: str = "", level: str = "basic") -> Dict[str, Any]:
+        """
+        审计 wiki 健康
+
+        Args:
+            path: 指定路径（空字符串表示全部）
+            level: 检查级别（basic/strict）
+
+        Returns:
+            {
+                "issues": [
+                    {
+                        "path": "practices/example.md",
+                        "type": "missing_title",
+                        "message": "Missing title",
+                        "severity": "warning"
+                    }
+                ],
+                "fixes": [
+                    {
+                        "path": "practices/example.md",
+                        "action": "add_title",
+                        "suggestion": "# Example Page"
+                    }
+                ],
+                "summary": {
+                    "total_issues": 5,
+                    "critical": 0,
+                    "warning": 5,
+                    "info": 0
+                }
+            }
+        """
+        issues = []
+        fixes = []
+
+        # 获取所有页面或指定页面
+        if path:
+            pages = [await self.query_service.get_page(path)]
+        else:
+            pages = await self.query_service.db.get_all_pages()
+
+        summary = {"critical": 0, "warning": 0, "info": 0}
+
+        for page in pages:
+            # 读取内容
+            try:
+                from pathlib import Path
+                vault_path = Path(self.query_service.db.path).parent.parent / "wiki-vault"
+                full_path = vault_path / page.path
+                with open(full_path, 'r', encoding='utf-8') as f:
+                    content = f.read()
+            except Exception as e:
+                issues.append({
+                    "path": page.path,
+                    "type": "file_error",
+                    "message": f"Failed to read file: {e}",
+                    "severity": "critical"
+                })
+                summary["critical"] += 1
+                continue
+
+            # 验证页面
+            validation_issues = self.parser.validate_page(page.path, content)
+
+            for issue in validation_issues:
+                severity = "warning" if "Missing" in issue else "info"
+                issues.append({
+                    "path": page.path,
+                    "type": issue.lower().replace(" ", "_"),
+                    "message": issue,
+                    "severity": severity
+                })
+                summary[severity] += 1
+
+                # 生成修复建议
+                if "Missing title" in issue:
+                    title = self.parser.extract_title(content)
+                    if not title:
+                        title = page.path.replace(".md", "").replace("-", " ").replace("_", " ").title()
+                    fixes.append({
+                        "path": page.path,
+                        "action": "add_title",
+                        "suggestion": f"# {title}"
+                    })
+
+        # strict 模式额外检查
+        if level == "strict":
+            # 检查孤立页面
+            orphans = await self.graph_service.find_orphans()
+            for orphan in orphans:
+                issues.append({
+                    "path": orphan,
+                    "type": "orphan",
+                    "message": "No backlinks found",
+                    "severity": "info"
+                })
+                summary["info"] += 1
+
+            # 检查缺失链接
+            missing_links = await self.graph_service.find_missing_links()
+            for source, target in missing_links[:10]:
+                issues.append({
+                    "path": source,
+                    "type": "broken_link",
+                    "message": f"Link to non-existent page: {target}",
+                    "severity": "warning"
+                })
+                summary["warning"] += 1
+
+        return {
+            "issues": issues,
+            "fixes": fixes,
+            "summary": {
+                "total_issues": len(issues),
+                **summary
+            }
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "wiki_lint",
+            "description": "审计 wiki 健康（格式、链接、frontmatter 规范）",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "path": {
+                        "type": "string",
+                        "default": "",
+                        "description": "指定路径（空字符串表示全部）"
+                    },
+                    "level": {
+                        "type": "string",
+                        "default": "basic",
+                        "enum": ["basic", "strict"],
+                        "description": "检查级别"
+                    }
+                }
+            }
+        }

mcp_server/tools/wiki_query.py

@@ -0,0 +1,116 @@
+"""
+Tool Layer - wiki_query 工具
+
+基于 SQLite 索引查询 wiki，支持关键词（FTS5）和标签搜索。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import List, Dict, Any
+from ..services import QueryService
+
+logger = logging.getLogger(__name__)
+
+
+class WikiQueryTool:
+    """wiki_query 工具实现"""
+
+    def __init__(self, query_service: QueryService):
+        self.query_service = query_service
+
+    async def handle(self, query: str = "", tags: List[str] = None, limit: int = 10) -> Dict[str, Any]:
+        """
+        查询 wiki 页面
+
+        Args:
+            query: 查询关键词（FTS5 全文搜索）
+            tags: 标签过滤
+            limit: 返回数量限制
+
+        Returns:
+            {
+                "results": [
+                    {
+                        "path": "practices/moziplus-orchestration.md",
+                        "title": "moziplus 编排实践",
+                        "category": "practices",
+                        "tags": ["moziplus", "orchestration"],
+                        "summary": "...",
+                        "lifecycle": "verified",
+                        "updated_at": "2024-06-15T10:30:00",
+                        "wikilink": "[[practices/moziplus-orchestration.md|moziplus 编排实践]]"
+                    }
+                ],
+                "total": 5,
+                "query": "...",
+                "tags": [...]
+            }
+        """
+        if tags is None:
+            tags = []
+
+        results = []
+
+        # 组合查询
+        if query and tags:
+            # 先 FTS5 搜索，再标签过滤
+            fts_results = await self.query_service.search(query, limit * 2)
+            filtered = [r for r in fts_results if any(t in r.tags for t in tags)]
+            pages = filtered[:limit]
+        elif query:
+            # 仅 FTS5 搜索
+            pages = await self.query_service.search(query, limit)
+        elif tags:
+            # 仅标签搜索
+            pages = await self.query_service.search_by_tags(tags[:5])  # 限制标签数量
+            pages = pages[:limit]
+        else:
+            # 无查询条件，返回最近更新的页面
+            pages = []
+
+        # 格式化结果
+        for page in pages:
+            results.append({
+                "path": page.path,
+                "title": page.title,
+                "category": page.category,
+                "tags": page.tags,
+                "summary": page.summary,
+                "lifecycle": page.lifecycle,
+                "updated_at": page.updated_at,
+                "wikilink": f"[[{page.path}|{page.title}]]"
+            })
+
+        return {
+            "results": results,
+            "total": len(results),
+            "query": query,
+            "tags": tags
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "wiki_query",
+            "description": "查询 wiki 页面，支持关键词（FTS5）和标签搜索",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "query": {
+                        "type": "string",
+                        "description": "查询关键词（FTS5 全文搜索）"
+                    },
+                    "tags": {
+                        "type": "array",
+                        "items": {"type": "string"},
+                        "description": "标签过滤"
+                    },
+                    "limit": {
+                        "type": "integer",
+                        "default": 10,
+                        "description": "返回数量限制"
+                    }
+                }
+            }
+        }

mcp_server/tools/wiki_status.py

@@ -0,0 +1,75 @@
+"""
+Tool Layer - wiki_status 工具
+
+显示 wiki 当前状态（页面数、待处理项、增量差异）。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any
+from ..services import QueryService, IndexerService, GraphService
+
+logger = logging.getLogger(__name__)
+
+
+class WikiStatusTool:
+    """wiki_status 工具实现"""
+
+    def __init__(self, query_service: QueryService, indexer_service: IndexerService, graph_service: GraphService):
+        self.query_service = query_service
+        self.indexer_service = indexer_service
+        self.graph_service = graph_service
+
+    async def handle(self) -> Dict[str, Any]:
+        """
+        显示 wiki 当前状态
+
+        Returns:
+            {
+                "stats": {
+                    "total_pages": 1353,
+                    "total_links": 4200,
+                    "total_tags": 156,
+                    "last_indexed": "2024-06-26T10:30:00"
+                },
+                "orphans": ["path1", "path2"],
+                "orphans_count": 5,
+                "dirty_pages": 12,
+                "cache_stats": {
+                    "size": 100,
+                    "max_size": 1000,
+                    "utilization": 0.1
+                }
+            }
+        """
+        # 获取统计信息
+        stats = await self.query_service.get_stats()
+
+        # 获取孤立页面
+        orphans = await self.graph_service.find_orphans()
+
+        # 获取索引状态
+        index_status = await self.indexer_service.get_index_status()
+
+        # 获取缓存统计
+        cache_stats = await self.query_service.cache.get_stats()
+
+        return {
+            "stats": stats,
+            "orphans": sorted(list(orphans)),
+            "orphans_count": len(orphans),
+            "dirty_pages": index_status.get("dirty_pages", 0),
+            "cache_stats": cache_stats
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "wiki_status",
+            "description": "显示 wiki 当前状态（页面数、待处理项、增量差异）",
+            "inputSchema": {
+                "type": "object",
+                "properties": {}
+            }
+        }

mcp_server/tools/wiki_synthesize.py

@@ -0,0 +1,105 @@
+"""
+Tool Layer - wiki_synthesize 工具
+
+发现跨概念的综合分析机会，生成 synthesis 页面。
+
+参考设计文档：第 2.2 节
+"""
+
+import logging
+from typing import Dict, Any, List
+from ..services import QueryService, GraphService
+
+logger = logging.getLogger(__name__)
+
+
+class WikiSynthesizeTool:
+    """wiki_synthesize 工具实现"""
+
+    def __init__(self, query_service: QueryService, graph_service: GraphService):
+        self.query_service = query_service
+        self.graph_service = graph_service
+
+    async def handle(self, concepts: List[str] = None, threshold: float = 0.3) -> Dict[str, Any]:
+        """
+        发现跨概念的综合分析机会
+
+        Args:
+            concepts: 概念列表（空表示自动发现）
+            threshold: 相关性阈值
+
+        Returns:
+            {
+                "synthesis": [
+                    {
+                        "concept_a": "SQLite",
+                        "concept_b": "Concurrency",
+                        "common_references": ["page1", "page2"],
+                        "strength": 0.8,
+                        "suggestion": "Consider creating synthesis page: SQLite & Concurrency"
+                    }
+                ],
+                "total": 5
+            }
+        """
+        synthesis = []
+
+        # 如果未提供概念，自动发现高相关性概念
+        if not concepts:
+            # 获取高度连接的页面作为候选
+            highly_connected = await self.graph_service.get_highly_connected_pages(threshold=10)
+            concepts = [item["title"] for item in highly_connected[:10]]
+
+        # 分析概念间的关联
+        for i, concept_a in enumerate(concepts):
+            for concept_b in concepts[i + 1:]:
+                # 查找同时引用两个概念的页面
+                pages_a = await self.query_service.search(concept_a, limit=50)
+                pages_b = await self.query_service.search(concept_b, limit=50)
+
+                paths_a = {p.path for p in pages_a}
+                paths_b = {p.path for p in pages_b}
+
+                common = paths_a & paths_b
+
+                if len(common) >= 2:  # 至少 2 个共同引用
+                    strength = len(common) / max(len(paths_a), len(paths_b))
+
+                    if strength >= threshold:
+                        synthesis.append({
+                            "concept_a": concept_a,
+                            "concept_b": concept_b,
+                            "common_references": sorted(list(common)),
+                            "strength": round(strength, 2),
+                            "suggestion": f"Consider creating synthesis page: {concept_a} & {concept_b}"
+                        })
+
+        # 按关联强度排序
+        synthesis.sort(key=lambda x: x["strength"], reverse=True)
+
+        return {
+            "synthesis": synthesis[:20],
+            "total": len(synthesis)
+        }
+
+    def get_schema(self) -> dict:
+        """返回 MCP Tool schema"""
+        return {
+            "name": "wiki_synthesize",
+            "description": "发现跨概念的综合分析机会，生成 synthesis 页面",
+            "inputSchema": {
+                "type": "object",
+                "properties": {
+                    "concepts": {
+                        "type": "array",
+                        "items": {"type": "string"},
+                        "description": "概念列表（空表示自动发现）"
+                    },
+                    "threshold": {
+                        "type": "number",
+                        "default": 0.3,
+                        "description": "相关性阈值"
+                    }
+                }
+            }
+        }