Silent index degradation — status:"indexed" but only ~500 nodes for 72k LOC Rust codebase

[nguiaSoren]

Title: Silent index degradation — status:"indexed" but only ~500 nodes for 72k LOC Rust codebase

Version: codebase-memory-mcp 0.6.0
Platform: macOS (Apple Silicon)
Project size: 72k LOC, 9 Rust files (single Cargo project)

Symptom

index_repository(mode="full") returns status:"indexed" but produces only ~500 nodes and ~500 edges for a 72k LOC Rust codebase. Expected ~5,000–10,000+ symbol nodes based on comparable smaller projects.

The status:"ready" / status:"indexed" response is misleading — the rebuild silently fails on something but reports success.

Reproduction

1. Kill any existing codebase-memory-mcp processes:
   ps aux | grep codebase-memory then kill <PID>
2. Delete cached index:
   rm ~/.local/share/codebase-memory-mcp/Users-soren-Desktop-new_simulator.db
3. Verify directory is empty of project cache
4. Restart Claude Code (spawns fresh MCP server process)
5. In Claude Code: index_repository(mode="full")
6. Run index_status — shows ~500 nodes / ~500 edges, status:"indexed"

Multiple fresh rebuilds produce the same low node count (469/462, 540/531, 572/555 across attempts).

Comparison with healthy project

Same machine, same MCP server binary:

• X project (~6k LOC): 6,436 nodes / 10,308 edges, 14 MB .db file ✓ healthy
• Y project (72k LOC): ~500 nodes / ~500 edges, 2 MB .db file ✗ degraded

The 2 MB file size is suspiciously exactly 2 × 1024 × 1024 bytes — suggests the database is being truncated or capped at a fixed boundary.

Known-symbol verification

search_graph(name_pattern="apply_knight_hero_effects") returns 0 results.

This function exists at src/hero_system.rs (verified via grep). Should be indexed as a function symbol but is missing from the graph.

Workaround

Direct file reads + grep work fine. The bug appears specific to the graph-based query path (search_graph, trace_path).

Diagnostic information requested

Happy to provide:

• Sample file from the codebase that may be triggering the issue (if I can isolate which file)
• Full index_repository output
• Any debug logging the indexer emits