refactor: 移除图索引功能，修复内存泄露，优化嵌入生成

主要更改:

1. 移除图索引功能 (graph indexing)
   - 删除 graph_analyzer.py 及相关迁移文件
   - 移除 CLI 的 graph 命令和 --enrich 标志
   - 清理 chain_search.py 中的图查询方法 (370行)
   - 删除相关测试文件

2. 修复嵌入生成内存问题
   - 重构 generate_embeddings.py 使用流式批处理
   - 改用 embedding_manager 的内存安全实现
   - 文件从 548 行精简到 259 行 (52.7% 减少)

3. 修复内存泄露
   - chain_search.py: quick_search 使用 with 语句管理 ChainSearchEngine
   - embedding_manager.py: 使用 with 语句管理 VectorStore
   - vector_store.py: 添加暴力搜索内存警告

4. 代码清理
   - 移除 Symbol 模型的 token_count 和 symbol_type 字段
   - 清理相关测试用例

测试: 760 passed, 7 skipped

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

codex-lens/src/codexlens/storage/sqlite_store.py

@@ -10,7 +10,7 @@ from dataclasses import asdict
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional, Tuple
 
-from codexlens.entities import CodeRelationship, IndexedFile, SearchResult, Symbol
+from codexlens.entities import IndexedFile, SearchResult, Symbol
 from codexlens.errors import StorageError
 
 
@@ -420,167 +420,6 @@ class SQLiteStore:
             }
 
 
-    def add_relationships(self, file_path: str | Path, relationships: List[CodeRelationship]) -> None:
-        """Store code relationships for a file.
-
-        Args:
-            file_path: Path to the file containing the relationships
-            relationships: List of CodeRelationship objects to store
-        """
-        if not relationships:
-            return
-
-        with self._lock:
-            conn = self._get_connection()
-            resolved_path = str(Path(file_path).resolve())
-
-            # Get file_id
-            row = conn.execute("SELECT id FROM files WHERE path=?", (resolved_path,)).fetchone()
-            if not row:
-                raise StorageError(f"File not found in index: {file_path}")
-            file_id = int(row["id"])
-
-            # Delete existing relationships for symbols in this file
-            conn.execute(
-                """
-                DELETE FROM code_relationships
-                WHERE source_symbol_id IN (
-                    SELECT id FROM symbols WHERE file_id=?
-                )
-                """,
-                (file_id,)
-            )
-
-            # Insert new relationships
-            relationship_rows = []
-            for rel in relationships:
-                # Find source symbol ID
-                symbol_row = conn.execute(
-                    """
-                    SELECT id FROM symbols
-                    WHERE file_id=? AND name=? AND start_line <= ? AND end_line >= ?
-                    ORDER BY (end_line - start_line) ASC
-                    LIMIT 1
-                    """,
-                    (file_id, rel.source_symbol, rel.source_line, rel.source_line)
-                ).fetchone()
-
-                if symbol_row:
-                    source_symbol_id = int(symbol_row["id"])
-                    relationship_rows.append((
-                        source_symbol_id,
-                        rel.target_symbol,
-                        rel.relationship_type,
-                        rel.source_line,
-                        rel.target_file
-                    ))
-
-            if relationship_rows:
-                conn.executemany(
-                    """
-                    INSERT INTO code_relationships(
-                        source_symbol_id, target_qualified_name, relationship_type,
-                        source_line, target_file
-                    )
-                    VALUES(?, ?, ?, ?, ?)
-                    """,
-                    relationship_rows
-                )
-            conn.commit()
-
-    def query_relationships_by_target(
-        self, target_name: str, *, limit: int = 100
-    ) -> List[Dict[str, Any]]:
-        """Query relationships by target symbol name (find all callers).
-
-        Args:
-            target_name: Name of the target symbol
-            limit: Maximum number of results
-
-        Returns:
-            List of dicts containing relationship info with file paths and line numbers
-        """
-        with self._lock:
-            conn = self._get_connection()
-            rows = conn.execute(
-                """
-                SELECT
-                    s.name AS source_symbol,
-                    r.target_qualified_name,
-                    r.relationship_type,
-                    r.source_line,
-                    f.full_path AS source_file,
-                    r.target_file
-                FROM code_relationships r
-                JOIN symbols s ON r.source_symbol_id = s.id
-                JOIN files f ON s.file_id = f.id
-                WHERE r.target_qualified_name = ?
-                ORDER BY f.full_path, r.source_line
-                LIMIT ?
-                """,
-                (target_name, limit)
-            ).fetchall()
-
-            return [
-                {
-                    "source_symbol": row["source_symbol"],
-                    "target_symbol": row["target_qualified_name"],
-                    "relationship_type": row["relationship_type"],
-                    "source_line": row["source_line"],
-                    "source_file": row["source_file"],
-                    "target_file": row["target_file"],
-                }
-                for row in rows
-            ]
-
-    def query_relationships_by_source(
-        self, source_symbol: str, source_file: str | Path, *, limit: int = 100
-    ) -> List[Dict[str, Any]]:
-        """Query relationships by source symbol (find what a symbol calls).
-
-        Args:
-            source_symbol: Name of the source symbol
-            source_file: File path containing the source symbol
-            limit: Maximum number of results
-
-        Returns:
-            List of dicts containing relationship info
-        """
-        with self._lock:
-            conn = self._get_connection()
-            resolved_path = str(Path(source_file).resolve())
-
-            rows = conn.execute(
-                """
-                SELECT
-                    s.name AS source_symbol,
-                    r.target_qualified_name,
-                    r.relationship_type,
-                    r.source_line,
-                    f.path AS source_file,
-                    r.target_file
-                FROM code_relationships r
-                JOIN symbols s ON r.source_symbol_id = s.id
-                JOIN files f ON s.file_id = f.id
-                WHERE s.name = ? AND f.path = ?
-                ORDER BY r.source_line
-                LIMIT ?
-                """,
-                (source_symbol, resolved_path, limit)
-            ).fetchall()
-
-            return [
-                {
-                    "source_symbol": row["source_symbol"],
-                    "target_symbol": row["target_qualified_name"],
-                    "relationship_type": row["relationship_type"],
-                    "source_line": row["source_line"],
-                    "source_file": row["source_file"],
-                    "target_file": row["target_file"],
-                }
-                for row in rows
-            ]
-
     def _connect(self) -> sqlite3.Connection:
         """Legacy method for backward compatibility."""
         return self._get_connection()