Adds an opt-in --timing flag that prints per-stage wall-clock timings to stderr so
slow stages are visible on large corpora. extract reports detect / AST extract /
semantic extract / build / cluster / analyze / export (and write on --no-cluster);
cluster-only reports load / cluster / analyze / label / report / export; both end
with a total. A small _StageTimer helper uses monotonic perf_counter.
Off by default and stderr-only, so default output and machine-read stdout/graph.json
are byte-identical (the extract arg loop already swallows unknown flags). Added a
regression test asserting the lines appear with --timing and are absent without it.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>