feat: complete migration to SCIP-based code indexing architecture

**Major Architecture Overhaul:**
- Migrate from language-specific analyzers to unified SCIP protobuf system
- Implement industry-standard SCIP (Source Code Intelligence Protocol) format
- Replace 8 separate language analyzers with single SCIP-based approach

**Core SCIP Infrastructure:**
- Add comprehensive SCIP core components (symbol_manager, position_calculator, reference_resolver, moniker_manager)
- Implement two-phase SCIP analysis: symbol collection → reference resolution
- Create unified index management with index_provider and unified_index_manager
- Add SCIP-compliant symbol ID generation with cross-file reference support

**Enhanced Strategy System:**
- Refactor all language strategies (Python, Java, JavaScript, Objective-C) to SCIP compliance
- Add external symbol extraction and dependency tracking capabilities
- Implement proper SCIP symbol roles and syntax kind classification
- Add robust encoding detection and error handling

**Dependency Updates:**
- Replace tree-sitter-languages with pathspec for improved file filtering
- Add comprehensive dependency list (watchdog, protobuf, tree-sitter components)
- Ensure consistent cross-platform dependency resolution

**Technical Improvements:**
- Add SCIPSymbolAnalyzer to replace legacy query tools
- Implement detailed logging throughout SCIP indexing pipeline
- Add symbol analysis tools and inspection scripts
- Update sample projects for multilingual testing

This establishes a robust, industry-standard foundation for accurate code
intelligence with proper SCIP compliance and improved performance.

Author: johnhuang316

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "tree-sitter-typescript>=0.20.0",
     "tree-sitter-java>=0.20.0",
     "tree-sitter-c>=0.20.0",
-    "tree-sitter-languages>=1.10.2",
+    "pathspec>=0.12.1",
 ]
 
 [project.urls]

requirements.txt

@@ -1 +1,9 @@
 mcp>=0.3.0
+watchdog>=3.0.0
+protobuf>=4.21.0
+tree-sitter>=0.20.0
+tree-sitter-javascript>=0.20.0
+tree-sitter-typescript>=0.20.0
+tree-sitter-java>=0.20.0
+tree-sitter-c>=0.20.0
+pathspec>=0.12.1

src/code_index_mcp/indexing/index_provider.py

@@ -0,0 +1,150 @@
+"""
+索引提供者接口定义
+
+定义所有索引访问的标准接口，确保不同实现的一致性。
+"""
+
+from typing import List, Optional, Dict, Any, Protocol
+from dataclasses import dataclass
+
+
+@dataclass
+class SymbolInfo:
+    """符号信息标准数据结构"""
+    name: str
+    kind: str  # 'class', 'function', 'method', 'variable', etc.
+    location: Dict[str, int]  # {'line': int, 'column': int}
+    scope: str
+    documentation: List[str]
+
+
+# Define FileInfo here to avoid circular imports
+@dataclass
+class FileInfo:
+    """文件信息标准数据结构"""
+    relative_path: str
+    language: str
+    absolute_path: str
+    
+    def __hash__(self):
+        return hash(self.relative_path)
+    
+    def __eq__(self, other):
+        if isinstance(other, FileInfo):
+            return self.relative_path == other.relative_path
+        return False
+
+
+@dataclass
+class IndexMetadata:
+    """索引元数据标准结构"""
+    version: str
+    format_type: str
+    created_at: float
+    last_updated: float
+    file_count: int
+    project_root: str
+    tool_version: str
+
+
+class IIndexProvider(Protocol):
+    """
+    索引提供者标准接口
+    
+    所有索引实现都必须遵循这个接口，确保一致的访问方式。
+    """
+    
+    def get_file_list(self) -> List[FileInfo]:
+        """
+        获取所有索引文件列表
+        
+        Returns:
+            文件信息列表
+        """
+        ...
+    
+    def get_file_info(self, file_path: str) -> Optional[FileInfo]:
+        """
+        获取特定文件信息
+        
+        Args:
+            file_path: 文件相对路径
+            
+        Returns:
+            文件信息，如果文件不在索引中则返回None
+        """
+        ...
+    
+    def query_symbols(self, file_path: str) -> List[SymbolInfo]:
+        """
+        查询文件中的符号信息
+        
+        Args:
+            file_path: 文件相对路径
+            
+        Returns:
+            符号信息列表
+        """
+        ...
+    
+    def search_files(self, pattern: str) -> List[FileInfo]:
+        """
+        按模式搜索文件
+        
+        Args:
+            pattern: glob模式或正则表达式
+            
+        Returns:
+            匹配的文件列表
+        """
+        ...
+    
+    def get_metadata(self) -> IndexMetadata:
+        """
+        获取索引元数据
+        
+        Returns:
+            索引元数据信息
+        """
+        ...
+    
+    def is_available(self) -> bool:
+        """
+        检查索引是否可用
+        
+        Returns:
+            True if index is available and functional
+        """
+        ...
+
+
+class IIndexManager(Protocol):
+    """
+    索引管理器接口
+    
+    定义索引生命周期管理的标准接口。
+    """
+    
+    def initialize(self) -> bool:
+        """初始化索引管理器"""
+        ...
+    
+    def get_provider(self) -> Optional[IIndexProvider]:
+        """获取当前活跃的索引提供者"""
+        ...
+    
+    def refresh_index(self, force: bool = False) -> bool:
+        """刷新索引"""
+        ...
+    
+    def save_index(self) -> bool:
+        """保存索引状态"""
+        ...
+    
+    def clear_index(self) -> None:
+        """清理索引状态"""
+        ...
+    
+    def get_index_status(self) -> Dict[str, Any]:
+        """获取索引状态信息"""
+        ...