Add semantic distance matrix and tool clustering

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Summary

Build semantic distance matrix and clustering (SEARCH/WRITE/DESTRUCTIVE-style groups) to help developers understand large MCP catalogs and feed collision warnings.

Milestone

Milestone 9 — Semantic Intelligence

Suggested labels

enhancement, priority:p2, area:diff, research

Acceptance criteria

• Library API to compute pairwise similarity matrix for a snapshot’s tools
• Simple clustering into action families (documented heuristic or embedding-based)
• CLI or eval/audit section that surfaces top similar pairs and clusters
• Deterministic default; embeddings optional
• Tests with github-style fixture catalogs
• Performance note for N≥500 (may subsample or require flag)

Depends on

• Tool collision / confusability primitives