[BUG] Incremental scan does not populate graph tables (only full scan does)

[Wolfvin]

Discovered during #8 verification

PR #24 (graph data model) populates graph_nodes + graph_edges only during full scan. Incremental scan (scan --incremental) skips graph population entirely, so the graph tables become stale after incremental scans.

Reproduction

codelens scan /workspace                  # graph: {nodes: N, edges: M} populated
codelens scan /workspace --incremental    # graph field absent, tables NOT updated
# trace --use-graph now returns stale data

Expected

Incremental scan should update graph tables for changed files only:

1. Detect changed files (existing incremental logic)
2. Delete graph_nodes + graph_edges where file IN (changed_files)
3. Re-parse changed files, INSERT new nodes + edges
4. This keeps graph in sync without full re-population

Workaround (current)

Run codelens scan (full) after incremental scans to refresh graph. Or use trace --no-graph to force flat backend.

Priority

Medium — not blocking Phase 1 (full scan works), but agents using --incremental (the recommended post-edit workflow) will have stale graph data. Should be fixed before Phase 1 is declared done.

Related

• Implemented in PR feat(graph): true graph data model (nodes + edges) — closes #8 #24 (closes [ARCH] Replace flat registry with true graph data model (nodes + edges) #8)
• Phase 1 roadmap: [ROADMAP] Phase 1 — Solidify (Pure Python, no Rust yet) #21