CLI query mode returns empty results despite successful indexing

[jsyrjala]

Summary

All graph query tools (get_architecture, search_graph, get_graph_schema, get_code_snippet) return empty results when used via CLI mode, even though indexing succeeds and list_projects shows correct node/edge counts.

Reproduction

# 1. Index succeeds — 3174 nodes, 8682 edges
codebase-memory-mcp cli index_repository '{"repo_path": "/path/to/project"}'
# Output: {"project":"...","status":"indexed","nodes":3174,"edges":8682}

# 2. list_projects confirms data exists
codebase-memory-mcp cli list_projects '{}'
# Output: {"projects":[{"name":"...","nodes":3174,"edges":8682,"size_bytes":10420224}]}

# 3. All queries return empty
codebase-memory-mcp cli get_architecture '{"repo_path": "/path/to/project", "aspects": ["all"]}'
# Output: {"total_nodes":0,"total_edges":0,"node_labels":[],"edge_types":[]}

codebase-memory-mcp cli search_graph '{"repo_path": "/path/to/project", "label": "Function", "name_pattern": "Finalize"}'
# Output: {"total":0,"results":[],"has_more":false}

codebase-memory-mcp cli get_graph_schema '{"repo_path": "/path/to/project"}'
# Output: {"node_labels":[],"edge_types":[]}

Environment

• OS: macOS (Apple Silicon)
• Binary: codebase-memory-mcp installed at ~/.local/bin/
• Also configured as MCP server in ~/.claude/.mcp.json

Analysis

list_projects works because it reads metadata, not the graph. The graph DB handle appears not to be opened for reads in CLI query mode — only the metadata store is accessible. Indexing writes succeed, suggesting the graph DB is created correctly but not reconnected for subsequent CLI invocations.

This may be a session/connection lifecycle issue where the CLI opens the DB for writes during indexing but doesn't reopen it for read queries.