Add an active-overlay graph comparator to the incremental benchmark harness and use it as the structural gate for incremental_overlay rows. Canonical/noop/exact/containment rows continue to use canonical graph equality.
This caught the same-stem File-node collision that answer-level MCP oracles missed, and the follow-up route-handler benchmark now passes with active_overlay_graph.equal=true.
Validation: uv run python -m py_compile scripts/benchmark-incremental-speed.py; /private/tmp/cbm-pan87-active-graph-route-handler-mcp-after-file-qn-20260704T.json passed with 1842 ms incremental vs 22607 ms fresh full, 12.27x speedup.
Signed-off-by: Andrew Hundt <ATHundt@gmail.com>
Andrew Hundt
74db5187f6