get_repository_stats MCP tool returns incorrect counts for indexed repo #682

Description

get_repository_stats (MCP tool) returns wrong counts for an indexed repository, even after a complete fresh re-index.

Steps to Reproduce

1. Index a large Python/Django project (~1400 Python files, ~29K functions, ~3800 classes)
2. Verify via cgc stats CLI that indexing completed:

   Files:    1892
   Functions: 29086
   Classes:   3797
   Modules:   1838
   

3. Call get_repository_stats MCP tool with the repo path

Expected Result

Stats matching (or close to) the CLI output.

Actual Result

{"files": 1, "functions": 0, "classes": 0, "modules": 16}

The Cypher query MATCH (f:File) WHERE f.path STARTS WITH '{repo_path}' RETURN count(f) correctly returns 1892, so the data is in Neo4j — the get_repository_stats tool query is broken.

Environment

• CGC version: 0.2.14 (also reproduced on 0.2.5 and 0.2.8)
• Database: Neo4j
• OS: Linux (Ubuntu/WSL2)