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Own endpoint identity and per-edge kind knowledge in one parsed reference representation. Preserve exact same-artifact coordinates and cross-artifact name uncertainty, including generated and nonunique procedure labels. Use exact multiplicity-preserving sparse compatibility flow instead of positional/greedy pairing or a quadratic adjacency matrix. Share the native coordinate parser with call paths and remove the superseded projections. Validate public MCP comparison/reconstruction outcomes, independent tiny permutation oracles, dense matching and advertised JSON Schemas. Fixes #4210 Fixes #5131 Co-authored-by: Henglie <ebhenglie@gmail.com>