pubmed-mcp-server: Instructions file for Codex

Agent Protocol

Server: @cyanheads/pubmed-mcp-server Version: 2.10.22 Framework: @cyanheads/mcp-ts-core ^0.13.15 Engines: Bun ≥1.4.0, Node ≥24.0.0

Read the framework docs first: node_modules/@cyanheads/mcp-ts-core/CLAUDE.md contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.

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What's Next?

When the user asks what to do next, what's left, or needs direction, suggest relevant options based on the current project state:

1. Re-run the setup skill — ensures CLAUDE.md, skills, structure, and metadata are populated and up to date with the current codebase
2. Run the design-mcp-server skill — if the tool/resource surface hasn't been mapped yet, work through domain design
3. Add tools/resources/prompts — scaffold new definitions using the add-tool, add-app-tool, add-resource, add-prompt skills
4. Add services — scaffold domain service integrations using the add-service skill
5. Add tests — scaffold tests for existing definitions using the add-test skill
6. Field-test definitions — exercise tools/resources/prompts with real inputs using the field-test skill, get a report of issues and pain points
7. Run devcheck — lint, format, typecheck, and security audit
8. Run the security-pass skill — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
9. Run the polish-docs-meta skill — finalize README, CHANGELOG, metadata, and agent protocol for shipping
10. Run the maintenance skill — investigate changelogs, adopt upstream changes, and sync skills after bun update --latest

Tailor suggestions to what's actually missing or stale — don't recite the full list every time.

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Core Rules

• Logic throws, framework catches. Tool/resource handlers are pure — throw on failure, no try/catch. Plain Error is fine; the framework catches, classifies, and formats. Use error factories (notFound(), validationError(), etc.) when the error code matters.
• Use ctx.log for request-scoped logging. No console calls.
• Use ctx.state for tenant-scoped storage. Never access persistence directly.
• Need input the caller didn't supply? return ctx.requestInput(...) and read ctx.inputs when the handler is re-entered. Never await for user input mid-handler.
• Secrets in env vars only — never hardcoded.
• Cut noise. Add only what earns its place: no speculative generality, no guards for states the framework already prevents (Zod-validated params, classified errors), no abstraction until a third caller proves it, no option nothing sets.
• Close the loop on issues. When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.