[yordis]

• Agents were sent to fix the wrong thing when a storyboard entry had an observer but no read model, because the finding said the entry was missing entirely.
• The offline link check failed after pnpm install on links inside dependencies we do not own.
• Integration tests failed on OrbStack until people discovered they had to export DOCKER_HOST by hand.
• docs: PR titles kept failing the title check; the allowed types live in the shared action, so contributors need to know to use chore(docs):.
• Agents naturally pass entity and batch payloads as JSON objects, and having to double-encode them as strings caused avoidable call failures.

Closes #96
Closes #87
Closes #86
Closes #84
Refs #88

---

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PR Summary

Low Risk
Changes are mostly validation copy, MCP input parsing (backward-compatible strings), link-check exclusions, and local Docker test setup; no auth or persistence behavior changes beyond more precise warning metadata.

Overview
This PR tightens developer and agent ergonomics around validation messaging, CI/dev setup, docs, and MCP JSON arguments.

Storyboard validation refines STORYBOARD_MISSING_ENTRY: instead of always saying the entry is missing, warnings now distinguish no entry, empty entry, missing read model, or missing observer, with matching subject_field paths (entry, entry.read_model, entry.observer).

MCP mutations accept entity_json and request_json as either a JSON object or a JSON-encoded string via a new JsonPayload type; handlers normalize with to_json_text() before size checks and proto parsing. Schemas, unit tests, and an integration test cover the object form; repair docs note the same for batch_mutate_json.

Tooling/docs: lychee skips node_modules/; the Rust test mise task sets DOCKER_HOST from the active Docker context when unset; AGENTS.md documents SemConv PR titles (chore(docs): not docs:).

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Cursor Bugbot has reviewed your changes using default effort and found 1 potential issue.

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📥 Commits

Reviewing files that changed from the base of the PR and between f97cd1a and 579ed3b.

📒 Files selected for processing: 8

• .config/lychee.toml
• .config/mise/tasks/github/workflows/ci/rust-test
• AGENTS.md
• docs/how-to/repair-validation-findings.md
• rsworkspace/crates/trogon-atlas-mcp/src/server.rs
• rsworkspace/crates/trogon-atlas-mcp/src/tools.rs
• rsworkspace/crates/trogon-atlas-mcp/tests/operation_id_mcp_integration.rs
• rsworkspace/crates/trogon-atlas-server/src/validation.rs

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