feat(investigation): preserve cumulative reference graphs
Accumulate investigation paths and preserve failed attempts across rounds. Keep graph annotations separate from execution state, synchronize the API contract, and consolidate documentation.
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# Missing API Endpoints
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> Historical endpoint inventory. Counts and missing-route claims describe the original scan, not the current API. Check [API rules](../docs/api-style.md) and [the generated contract](../contracts/server-v1.openapi.json) before planning changes.
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- Legacy endpoints checked: 392
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- Current endpoints found: 401
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- Missing endpoints: 17
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