refactor: split mcp/tools/repo.rs into domain submodules#70
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- Split 730-line src/mcp/tools/repo.rs into repo/{scan,health,sync,index,query_repos,nl_query}.rs
- Keep repo.rs as a thin re-export module (~100 lines)
- Preserve existing behavior, tests, and public API paths
- Update T11 invariant exception list and AGENTS.md to include repo/nl_query.rs
- Mark repo.rs split as resolved in KNOWN_ISSUES.md
- Update McpToolEnum variant count 68 -> 71 in KNOWN_ISSUES.md
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This PR splits the 730-line repository management tool file into focused domain submodules.