graph: code metadata extractor emits untyped Symbol nodes and misses classes and methods

[RichardHightower]

Summary

Two gaps in the AST (CodeMetadataExtractor) graph path, found during the v10.7.0 integration test on 2026-09-19 against e2e/sample-project/ (five Python files, one test file):

1. Entity types do not match the typed entity API. Every extracted node carries label Symbol. GET /graph/entity/{type}/{id} and the MCP resource graph-entity://{type}/{id} reject Symbol:

   {"detail":{"error":"invalid_entity_type","type":"Symbol","valid_types":["APIDoc","Class","ConfigFile","Database","DesignDoc","Endpoint","Enum","Function","Interface","Method","Module","PRD","Package","README","Runbook","Service","UserDoc"], ...}}
   

   Code-extracted entities are unreachable through the typed API.

2. Coverage is partial. The persisted store held 21 nodes and 22 relations for 13 chunks. Present: Item, OutOfStock, module names, imports, and one test function. Missing: InventoryService, SqliteRepository, InMemoryRepository, reserve_stock, restock, and every method. The find-callers prompt (mode=graph, relationship_types=["calls"]) has nothing to find.

The graph mode itself works after the fixes in the same PR as this issue (parent-side refresh, LlamaIndex triplet read). This issue is about what the extractor puts into the graph.

Proposed fix

• Emit typed labels from the AST metadata (Class, Function, Method, Module) instead of Symbol, or accept Symbol in the typed API as an alias.
• Walk every chunk's symbol_name / symbol_kind metadata (present in chunk metadata already) and emit contains and defined_in for classes and methods, plus calls where the AST gives call targets.
• Add a fixture-backed test that indexes e2e/sample-project/src/inventory and asserts InventoryService and reserve_stock are nodes.

[RichardHightower]

Fixed in #257.

CodeMetadataExtractor now maps tree-sitter symbol_kind to Class/Function/Method (never Symbol) and walks the Python AST so classes, methods, and calls are emitted as contains / defined_in / calls / extends. Fixture-backed test covers e2e/sample-project/src/inventory/service.py (InventoryService, reserve_stock).