perf(topology): bound Sigma work on large graphs

[Marsu6996]

Draft / stacked PR

Do not merge before #67 through #70. This branch is stacked on those fixes, so the GitHub diff includes dependency commits until they land. It will then be rebased onto main to leave only the bounded Sigma topology work.

Problem

The exact native average-shortest-path kernel materializes an N x N float64
distance matrix. A Sigma observation computed it for the observed graph and
three random references, while compute_topology_snapshot also repeated work
already returned by fast_sigma. The snapshot then ran exact betweenness
centrality solely to count the top ten percent of nodes, even though that count
is fixed by definition.

Solution

• preserve the exact APSL path through 2,500 nodes;
• above that threshold, sample 512 deterministic source nodes and run SciPy's
  sparse unweighted Dijkstra in batches of 32;
• reuse fast_sigma's observed Sigma, clustering, and path-length result in
  the topology snapshot;
• compute the rich-club size ratio directly as ceil(0.10 * N) / N, without a
  discarded exact centrality ranking.

Guarantees and scope

Small and frozen fixtures keep exact native parity. Large-graph APSL becomes a
deterministic estimator; retrieval, embeddings, and HNSW ranking are untouched.
The helper continues to operate on the largest connected component, matching
the existing Sigma contract.

Validation

• exact-boundary, deterministic sampling, bounded-batch, path-graph accuracy,
  single-pass snapshot, and centrality-cold tests;
• a large encrypted-store snapshot completed the full topology calculation in
  seconds without an N x N allocation or an exact centrality call;
• a 512-source run differed from a 2,048-source reference by less than 0.2% on
  that snapshot;
• exhaustive default-suite result recorded on the final stacked tip.

Designed by Marsu — Refined by Codex.

Public CI result

The cumulative macOS correctness gate is fully green: 5,130 passed, 113 skipped, 107 deselected, and 4 xfailed in 1:16:17. The universal2 wheel and secret scan also pass.