Batch module split refactor

[yvette-carlisle]

Summary

• split MCP core tool routing into focused tool modules
• split trace compare analysis, provenance note types, docs internal types, and work continuity metrics into language-level modules
• kept behavior-preserving facades and explicit visibility boundaries

Validation

• After each split segment: RUSTC=/run/current-system/sw/bin/rustc cargo make fmt-rust && RUSTC=/run/current-system/sw/bin/rustc cargo make check
• Final branch diff: 31 files changed, 1593 insertions, 1416 deletions