@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.2

package/CLAUDE.md

@@ -0,0 +1,376 @@
+# Developer Protocol
+
+**Server:** @cyanheads/interpro-mcp-server
+**Version:** 0.1.2
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.15`
+**Engines:** Bun ≥1.4.0, Node ≥24.0.0
+**MCP SDK:** `@modelcontextprotocol/server` ^2.3.1
+**Zod:** ^4.6.7
+
+> **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.
+
+---
+
+## What's Next?
+
+When the user asks what's next or needs direction, suggest options based on the current project state. Common next steps:
+
+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.
+
+---
+
+## Core Rules
+
+- **Keep gitignored planning notes under `docs/` private.** Exclude them from git, npm, bundles, Docker images, and every other distribution surface, and never reference them from public docs.
+- **Editing agents never commit, tag, push, or publish.** They hand verified working-tree changes to the orchestrator.
+- **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.
+
+---
+
+## Patterns
+
+### Tool
+
+Abridged from `src/mcp-server/tools/definitions/interpro-get-entry.tool.ts`. All six tools share this shape: a service call through `service.begin(ctx)`, `ctx.enrich` for notices, a per-tool `errors` contract, and the shared `formatInterpro` formatter.
+
+```ts
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { formatInterpro } from '@/services/interpro/format.js';
+import { getInterproService } from '@/services/interpro/interpro-service.js';
+import { resolveEntry } from '@/services/interpro/routing.js';
+
+export const interproGetEntry = tool('interpro_get_entry', {
+  title: 'InterPro entry metadata',
+  description: 'Retrieve one InterPro or member-database entry, including description, hierarchy, …',
+  annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+  auth: ['tool:interpro_get_entry:read'],
+  input: z.object({
+    accession: AccessionSchema.describe('InterPro or member-database entry accession, such as IPR011615 or PF00870; no URL syntax.'),
+    sourceDatabase: optionalString(SourceDatabaseSchema).describe('Database slug; inferred from standard accession prefixes when omitted.'),
+    includeThumbnail: z.boolean().default(false).describe('Include each Wikipedia thumbnail image …'),
+  }),
+  output: z.object({ accession: z.string().describe('…'), entry: EntryMetadataSchema.describe('…'), /* … */ }),
+  enrichment: { notice: z.string().optional().describe('Omitted Wikipedia thumbnail size and how to include it.') },
+  errors: [
+    { reason: 'entry_not_found', code: JsonRpcErrorCode.NotFound, when: '…', retryable: false,
+      recovery: 'Call interpro_search_entries in the correct database, or interpro_list_reference with topic accession_patterns.',
+      thrownBy: 'service' },
+    ...UPSTREAM_ERRORS,
+  ],
+
+  async handler(input, ctx) {
+    const target = resolveEntry(input.accession, input.sourceDatabase);
+    const service = getInterproService();
+    const response = await service.request(
+      service.begin(ctx),
+      ['entry', target.sourceDatabase, target.accession],
+      {},
+      detailSchema(EntryMetadataSchema),
+      { missing: { reason: 'entry_not_found', ...target } },
+    );
+    // …project thumbnails, ctx.enrich.notice(…)
+    return { ...target, entry: response.data.metadata, url: '…', sourceUrl: response.sourceUrl };
+  },
+
+  // format() populates content[] — the twin of structuredContent. Different clients
+  // read different surfaces, so both must carry the same data; the lint step checks
+  // that every `output` field appears in the rendered text.
+  format: formatInterpro,
+});
+```
+
+There are no resources or prompts and no server-specific environment variables: the InterPro API is keyless. Search/member pages clamp positive integer limits to 100, discovery to 50, with default 20 and composed notices. GO filters require the InterPro source; member recovery follows `member_databases` or `integratedInto`. Discovery requests native `extra_fields.is_fragment` on every page, binds only explicit `isFragment` selections to cursor scope, and preserves unknown status. Entry detail alone adds readable `descriptionText` through the `htmlparser2` streaming tokenizer while preserving raw descriptions and annotation flags.
+
+### Server identity and instructions
+
+`src/index.ts` passes `name` and `title` as the bare `interpro-mcp-server` and server-level `instructions` sent on every `initialize`:
+
+```ts
+await createApp({
+  name: 'interpro-mcp-server',
+  title: 'interpro-mcp-server',
+  tools: [/* six definitions */],
+  sessionMode: 'stateless',
+  setup() { initInterproService(); },
+  teardown() { disposeInterproService(); },
+  instructions: '…',
+});
+```
+
+`sessionMode` declares the HTTP session posture in `src/` instead of leaving it to a deployment's `MCP_SESSION_MODE`, which still wins whenever it carries a meaningful value (an empty string and an unsubstituted `${…}` placeholder read as unset and fall through to the option). `teardown()` is the `setup()` counterpart; it runs after the transport stops and before the logger closes, on every shutdown path.
+
+---
+
+## Context
+
+Handlers receive a unified `ctx` object. Key properties:
+
+| Property | Description |
+|:---------|:------------|
+| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
+| `ctx.enrich` | Success-path agent context (empty-result notices, query echo, pagination totals) — `ctx.enrich(...)` or `.notice()` / `.total()` / `.echo()` / `.truncated()`. Reaches `structuredContent` and `content[]`; lands only when the definition declares an `enrichment` block (no-op otherwise). |
+| `ctx.fail` | Throws a typed failure for a reason declared in the tool's `errors` contract. |
+| `ctx.signal` | `AbortSignal` for cancellation; the service composes it with its per-call deadline. |
+| `ctx.requestId` | Request ID — the one every log record of the call carries and its error envelope returns as `data.requestId`. |
+| `ctx.tenantId` | Tenant ID from JWT; `'default'` for stdio or HTTP with auth off. |
+
+---
+
+## Errors
+
+Handlers throw — the framework catches, classifies, and formats.
+
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive `ctx.fail(reason, …)` typed against the reason union. TypeScript catches typos at compile time, `data.reason` is auto-populated for observability, linter enforces conformance against the handler body. `recovery` is required (≥ 5 words, lint-validated) — the single source of truth for the agent's next move. The framework puts it on the wire whenever a failure carrying that `reason` arrives without a hint — a bare `ctx.fail('reason')` or a service throw with `data: { reason }` — as `data.recovery.hint`, mirrored into `content[]` text unless the message already contains it verbatim; override with an explicit `{ recovery: { hint: '...' } }` when dynamic runtime context matters. Every error envelope also carries `data.requestId`, the id the server's log records for that call carry, and `content[]` closes with `(reason … · request <id>)`. Mark an entry the service layer throws with `thrownBy: 'service'` so `error-contract-unthrown` skips it — lint-only metadata, nothing at runtime reads it. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
+
+```ts
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+
+errors: [
+  { reason: 'no_match', code: JsonRpcErrorCode.NotFound,
+    when: 'No item matched the query',
+    recovery: 'Broaden the query or check the spelling and try again.' },
+],
+async handler(input, ctx) {
+  const item = await db.find(input.id);
+  if (!item) throw ctx.fail('no_match', `No item ${input.id}`);
+  return item;
+}
+```
+
+**Declare contracts inline on each tool.** The contract is part of the tool's public surface — one file should give the full picture. Don't extract a shared `errors[]` constant; per-tool repetition is the intended cost of locality.
+
+**Fallback (no contract entry fits):** throw via factories or plain `Error`.
+
+```ts
+// Error factories — explicit code
+import { notFound, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+throw notFound('Item not found', { itemId });
+throw serviceUnavailable('API unavailable', { url }, { cause: err });
+
+// Plain Error — framework auto-classifies from message patterns
+throw new Error('Item not found');           // → NotFound
+throw new Error('Invalid query format');     // → ValidationError
+
+// McpError — when no factory exists for the code
+import { McpError, JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+throw new McpError(JsonRpcErrorCode.InitializationFailed, 'Connection failed', { pool: 'primary' });
+```
+
+See framework CLAUDE.md and the `api-errors` skill for the full auto-classification table, all available factories, and the contract reference.
+
+---
+
+## Structure
+
+```text
+src/
+  index.ts                              # createApp() entry point
+  services/
+    interpro/
+      interpro-service.ts               # Paced, cancellable request boundary (init/accessor pattern)
+      http-adapter.ts                   # node:https HTTP/1.1 transport with 204 handling
+      routing.ts                        # Accession → database routing, fixed-origin URL building
+      schemas.ts                        # Wire and output Zod schemas
+      cursors.ts                        # Opaque cursor envelopes
+      budget.ts                         # 100,000-byte response budget and whole-item fitting
+      relationships.ts                  # Clan relationship-graph slicing
+      reference.ts                      # Static vocabulary for interpro_list_reference
+      format.ts                         # Shared content[] formatter
+      description-text.ts               # Readable HTML fragment projection for entry detail
+      upstream-errors.ts                # Shared upstream error contract rows
+  mcp-server/
+    tools/definitions/
+      interpro-[name].tool.ts           # Six tool definitions
+tests/
+  services/                             # Service, adapter, and budget tests
+  tools/                                # Tool contract tests
+```
+
+---
+
+## Naming
+
+| What | Convention | Example |
+|:-----|:-----------|:--------|
+| Files | kebab-case with suffix | `interpro-get-entry.tool.ts` |
+| Tool/resource/prompt names | snake_case | `interpro_get_entry` |
+| Directories | kebab-case | `src/services/interpro/` |
+| Descriptions | Single string or template literal, no `+` concatenation | `'Search items by query and filter.'` |
+
+---
+
+## Skills
+
+Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool. `bun run list-skills` prints the full registry. The directory is deliberately not `skills/`: Claude Code and Codex auto-load a plugin's root `skills/`, so a server that ships `.claude-plugin/` or `.codex-plugin/` would hand these development skills to every agent that installs it. Keep `skills/` free for skills meant for those agents.
+
+**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). Skills then load as context without referencing `framework-skills/` paths. After framework updates, run the `maintenance` skill — Phase B re-syncs the agent directory.
+
+Available skills:
+
+| Skill | Purpose |
+|:------|:--------|
+| `setup` | Post-init project orientation |
+| `design-mcp-server` | Design tool surface, resources, and services for a new server |
+| `add-tool` | Scaffold a new tool definition |
+| `add-app-tool` | Scaffold an MCP App tool + paired UI resource |
+| `add-resource` | Scaffold a new resource definition |
+| `add-prompt` | Scaffold a new prompt definition |
+| `add-service` | Scaffold a new service integration |
+| `add-test` | Scaffold test file for a tool, resource, or service |
+| `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
+| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
+| `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
+| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
+| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
+| `git-wrapup` | Land working-tree changes as a commit stack — version bump, changelog, verify, commit by concern, release commit on top. No tag, no push to main; opens the release PR when the project declares release PR mode |
+| `release-pr-review` | Review pass on an open release PR — simplifier + correctness review, fixes as ordinary commits on top of the stack, PR body kept in sync. Release PR mode only |
+| `release-and-publish` | Fast-forward merge (release PR mode) + tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
+| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
+| `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
+| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
+| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
+| `techniques` | Catalog of response/data-shaping techniques — overflow handling, payload shaping, retrieval patterns |
+| `api-auth` | Auth modes, scopes, JWT/OAuth |
+| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
+| `api-config` | AppConfig, parseConfig, env vars |
+| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
+| `api-errors` | McpError, JsonRpcErrorCode, error patterns |
+| `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
+| `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
+| `api-services` | LLM, Speech, Graph services |
+| `api-testing` | createMockContext, test patterns |
+| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
+| `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
+| `api-workers` | Cloudflare Workers runtime |
+
+**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
+
+When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
+
+---
+
+## Commands
+
+**Runtime:** Scripts use Bun's native TypeScript execution — `bun run <cmd>` is the standard invocation. `npm run <cmd>` also works (npm delegates to bun).
+
+| Command | Purpose |
+|:--------|:--------|
+| `bun run build` | Compile TypeScript |
+| `bun run rebuild` | Clean + build |
+| `bun run clean` | Remove build artifacts |
+| `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
+| `bun run audit:fix` | `bun audit fix` — upgrade vulnerable packages to the lowest safe version within existing ranges (`--dry-run` previews, `--latest` rewrites ranges). First response when `devcheck` flags a transitive advisory; then `bun update <name>`, then `bun dedupe` |
+| `bun run audit:refresh` | Delete `bun.lock` and reinstall. Last resort after `audit:fix`, `bun update <name>`, and `bun dedupe` — re-resolves every ranged dep (the framework pin included) and rewrites the lockfile as `lockfileVersion: 2` |
+| `bun run lint:mcp` | Run the MCP definition linter standalone (rule catalog: `api-linter` skill) |
+| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity (run by devcheck) |
+| `bun run list-skills` | Print the skill registry |
+| `bun run tree` | Generate directory structure doc |
+| `bun run format` | Auto-fix formatting (safe fixes only) |
+| `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
+| `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
+| `bun run test:coverage` | Run tests with Istanbul coverage |
+| `bun run start` | Run the built server with the configured transport |
+| `bun run start:stdio` | Production mode (stdio) |
+| `bun run start:http` | Production mode (HTTP) |
+| `bun run release:github` | Create the GitHub Release from the annotated tag |
+| `bun run publish-mcp` | Publish `server.json` to the MCP Registry |
+| `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
+| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
+| `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
+
+**Waived `devcheck` warnings.** `bun run devcheck` emits six `format-parity-depth-limit` warnings, for the `…fragments[].start`, `…fragments[].end`, and `…fragments[].dc-status` output fields of `interpro_find_proteins_by_domain` and `interpro_get_protein_domains`. The schema is finite but deeper than the framework's depth-8 parity walker, and tests prove both surfaces render those fields. The owner waived exactly these six, pending [cyanheads/mcp-ts-core#531](https://github.com/cyanheads/mcp-ts-core/issues/531). Don't flatten or weaken the schema, and don't add suppressions to clear them. Any other warning, or a seventh of this kind, still blocks shipping.
+
+**CI is one file.** `.github/workflows/codeql.yml` (scaffolded) is the only GitHub Actions workflow: CodeQL is GitHub-owned end to end, and the file runs only while the repo's CodeQL *default setup* is turned off. Verification — `devcheck`, tests, the release gates — runs locally; don't add a workflow that re-runs it.
+
+---
+
+## Bundling
+
+`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`framework-skills/`, `skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. A server using DataCanvas therefore ships a portable bundle without the DuckDB native — `@duckdb/node-api` is an optional peer loaded lazily, so canvas tools report an actionable install hint and every other tool works normally. MCPB is stdio-only — HTTP and Cloudflare Workers deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
+
+**Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match, that every `user_config` option is wired into `mcp_config.env` as `"X": "${user_config.X}"` (the host substitutes nothing else — `"${X}"` reaches the server as that literal string), and that an optional string option carries `"default": ""`.
+
+**README install badges** (Claude Desktop `.mcpb`, Cursor, VS Code) and the `base64` / `encodeURIComponent` config-generation commands are ship-time concerns — run the `polish-docs-meta` skill, which carries the badge format, layout, and generation snippets in `framework-skills/polish-docs-meta/references/readme.md`.
+
+---
+
+## Changelog
+
+Directory-based, grouped by minor series via the `.x` semver-wildcard convention. Source of truth: `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.1.x/0.1.0.md`) — one file per release, shipped in the npm package. At release, author the per-version file with a concrete version and date, then run `npm run changelog:build` to regenerate the rollup. `changelog/template.md` is a **pristine format reference** — never edited or moved; read it for the frontmatter + section layout when scaffolding. `CHANGELOG.md` is a **navigation index** (header + link + summary per version), regenerated by `npm run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
+
+Each per-version file opens with YAML frontmatter:
+
+```markdown
+---
+summary: "One-line headline, ≤350 chars"  # required — powers the rollup index
+breaking: false                            # optional — true flags breaking changes
+security: false                            # optional — true ONLY for a source-code security fix, never a dependency CVE bump
+---
+
+# 0.1.0 — YYYY-MM-DD
+...
+```
+
+`breaking: true` renders a `· ⚠️ Breaking` badge — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames). `security: true` renders a `· 🛡️ Security` badge and pairs with a `## Security` body section — set it only for a security fix in this server's *own source code*, never for a routine dependency or transitive CVE bump (record those under `## Dependencies`). When both are set, badges render `· ⚠️ Breaking · 🛡️ Security`.
+
+`agent-notes` is an optional free-form field for maintenance agents processing the release downstream. Content here won't appear in the rendered CHANGELOG — it's consumed by agents running the `maintenance` skill. Use it for adoption instructions that don't fit the human-facing sections: new files to create, fields to populate, one-time migration steps. Omit entirely when there's nothing to say.
+
+**Section order:** the Keep a Changelog sequence — Added, Changed, Deprecated, Removed, Fixed, Security — then `Dependencies` last. Include only sections with entries — don't ship empty headers.
+
+**Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.
+
+---
+
+## Publishing
+
+Every release goes through a release PR — `git-wrapup`'s "Release PR mode", mode `straight-through`. Run `git-wrapup` and `release-and-publish` sequentially. Open `release/<version>` as a PR and fast-forward it to `main` locally with `git merge --ff-only`; never use the GitHub merge button or `gh pr merge`. There is no independent review gate. CodeQL, required checks, and security alerts must still pass before release.
+
+---
+
+## Imports
+
+```ts
+// Framework — z is re-exported, no separate zod import needed
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { McpError, JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+
+// Server's own code — via path alias
+import { getMyService } from '@/services/my-domain/my-service.js';
+```
+
+---
+
+## Checklist
+
+- [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, `z.bigint()`, `z.symbol()`, `z.void()`, `z.map()`, `z.set()`, `z.function()`, `z.nan()`)
+- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`). When regex/length constraints matter, use `z.union([z.literal(''), z.string().regex(...).describe(...)])` — literal variants are exempt from `describe-on-fields`.
+- [ ] JSDoc `@fileoverview` + `@module` on every file
+- [ ] `ctx.log` for logging, `ctx.state` for storage
+- [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
+- [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Claude Code → `structuredContent`, Claude Desktop → `content[]`); both must carry the same data
+- [ ] If wrapping external API: raw/domain/output schemas reviewed against real upstream sparsity/nullability before finalizing required vs optional fields
+- [ ] If wrapping external API: normalization and `format()` preserve uncertainty; do not fabricate facts from missing upstream data
+- [ ] If wrapping external API: tests include at least one sparse payload case with omitted upstream fields
+- [ ] Registered in `createApp()` arrays (directly or via barrel exports)
+- [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name (never the npm scope — `lint:packaging` enforces this); `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; every user-supplied variable (API key, contact email, instance URL) is listed in `env_vars` so Codex forwards it from the user's environment. Never write `"KEY": ""` into `env` — an empty value replaces the user's exported key and is read as unset
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `author`, `repository`, `license`, `keywords` from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name. Every user-supplied variable is declared under `userConfig` (`type`, `title`, `description`; `sensitive: true` for keys and tokens; `required: true` or `default: ""`) and referenced from `env` as `"KEY": "${user_config.<option>}"` — mirror the `user_config` block in `manifest.json`. Never write `"KEY": ""` into `env`
+- [ ] `npm run devcheck` passes

package/Dockerfile

@@ -0,0 +1,186 @@
+# ==============================================================================
+# Build Stage
+#
+# This stage installs all dependencies (including dev), builds the TypeScript
+# source code into JavaScript, and prepares the production assets.
+#
+# Pinned to $BUILDPLATFORM rather than the target platform: `bun run build` emits
+# JavaScript, and only `dist/` crosses into the production stage. Built for the
+# target instead, the non-native leg of a `--platform linux/amd64,linux/arm64`
+# build runs under QEMU, where bun >= 1.4 aborts with a JavaScriptCore allocator
+# assertion and fails the multi-arch push.
+#
+# The constraint this assumes: the build stage produces platform-independent
+# output. A stage that compiles a native addon needs the target-arch toolchain
+# and cannot cross-compile this way — drop the flag there.
+# ==============================================================================
+FROM --platform=$BUILDPLATFORM oven/bun:1.4.4 AS build
+
+WORKDIR /usr/src/app
+
+# Copy dependency manifests for optimized layer caching
+COPY package.json bun.lock ./
+
+# Install all dependencies (including dev dependencies for building).
+# The BuildKit cache mount persists Bun's global package cache across builds.
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --frozen-lockfile --ignore-scripts
+
+# Copy the rest of the source code
+COPY . .
+
+# Build the application
+RUN bun run build
+
+
+# ==============================================================================
+# Production Dependencies Stage
+#
+# Installs the production dependency tree for the target platform. Every step
+# here can run JavaScript — bunfig.toml's security scanner runs as a Bun
+# program, and so do the OTel and musl-prune scripts — so the stage runs on
+# $BUILDPLATFORM and cross-installs with `--os`/`--cpu`, which pick each
+# platform-specific optional dependency (native bindings such as DuckDB's) for
+# the target. Only `node_modules` leaves this stage.
+#
+# A clean image rather than `FROM build`: the build stage's node_modules holds
+# devDependencies.
+# ==============================================================================
+FROM --platform=$BUILDPLATFORM oven/bun:1.4.4 AS deps
+
+WORKDIR /usr/src/app
+
+# Copy dependency manifests. `bunfig.toml` rides along so every install below
+# passes its release-age gate and security scanner, as a local install does.
+COPY package.json bun.lock bunfig.toml ./
+
+# The scanner bunfig.toml names is a devDependency, and Bun installs a missing
+# scanner through the same production-filtered install, which omits it and
+# aborts. Seed it from the build stage's full install instead. Remove this line,
+# and the `rm` at the end of this stage, if bunfig.toml stops naming a scanner.
+COPY --from=build /usr/src/app/node_modules/@socketsecurity/bun-security-scanner ./node_modules/@socketsecurity/bun-security-scanner
+
+# Docker names the target architecture `amd64`/`arm64`; Bun's `--cpu` takes
+# `x64`/`arm64`. Mapped once here, read by both installs below. `oven/bun`
+# publishes only these two architectures, so any other target fails here.
+ARG TARGETOS
+ARG TARGETARCH
+RUN case "$TARGETARCH" in \
+      amd64) echo x64 ;; \
+      arm64) echo arm64 ;; \
+      *) echo "Unsupported TARGETARCH '$TARGETARCH': expected amd64 or arm64" >&2; exit 1 ;; \
+    esac > .bun-cpu
+
+# Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
+# that are not needed in the final production image.
+# `--omit=peer` drops the framework's optional peer tiers (test runner, service
+# SDKs, parsers) that Bun would otherwise auto-install. Anything this server
+# actually imports belongs in its own `dependencies`, so nothing needed at
+# runtime is lost.
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --production --omit=peer --frozen-lockfile --ignore-scripts \
+      --os="$TARGETOS" --cpu="$(cat .bun-cpu)"
+
+# Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
+# Installed by default. Omit them for a leaner image at build time
+# with: docker build --build-arg OTEL_ENABLED=false
+# The script reads the list and each range from the installed framework's
+# `peerDependencies` and passes the target flags on to its `bun install`.
+COPY scripts/install-otel.ts ./scripts/
+ARG OTEL_ENABLED=true
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    if [ "$OTEL_ENABLED" = "true" ]; then \
+      bun scripts/install-otel.ts --os="$TARGETOS" --cpu="$(cat .bun-cpu)"; \
+    fi
+
+# `--os`/`--cpu` have no libc counterpart, so a native dependency published in
+# glibc and musl variants (DuckDB's bindings, for one) installs both. The
+# runtime image is Debian (glibc) and never loads the musl copy; the script
+# deletes every package whose own `libc` admits only musl. It follows every
+# install, since a later `bun install` restores what it removes. A server on a
+# musl (Alpine) runtime image drops these two lines.
+COPY scripts/prune-musl-packages.ts ./scripts/
+RUN bun scripts/prune-musl-packages.ts
+
+# The seeded scanner served only the installs above; keep it out of the image.
+RUN rm -rf node_modules/@socketsecurity/bun-security-scanner
+
+
+# ==============================================================================
+# Production Stage
+#
+# This stage creates a minimal, optimized, and secure image for running the
+# application. It uses a slim base image and only includes production
+# dependencies and build artifacts. Its only Bun invocations are HEALTHCHECK
+# and CMD, which run on the real target at container start.
+# ==============================================================================
+FROM oven/bun:1.4.4-slim AS production
+
+WORKDIR /usr/src/app
+
+# Set the environment to production for performance.
+ENV NODE_ENV=production
+
+# OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
+ARG APP_VERSION
+LABEL org.opencontainers.image.title="interpro-mcp-server"
+LABEL org.opencontainers.image.description="Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP."
+LABEL org.opencontainers.image.licenses="Apache-2.0"
+LABEL org.opencontainers.image.version="${APP_VERSION}"
+LABEL org.opencontainers.image.source="https://github.com/cyanheads/interpro-mcp-server"
+
+# The manifest comes from the build context: the deps stage's copy was rewritten
+# by the OTel install, and the runtime reads only its name, version, and type.
+COPY package.json ./
+COPY --from=deps /usr/src/app/node_modules ./node_modules
+
+# Copy the compiled application code from the build stage
+COPY --from=build /usr/src/app/dist ./dist
+
+# Mirror CLI (MirrorService adopters only — Tier 3, opt-in):
+# Copy your mirror lifecycle scripts and emit a runtime tsconfig so Bun resolves
+# the @/ path alias against ./dist/ rather than ./src/.
+# See the api-mirror skill for the full recipe.
+#
+# COPY --from=build /usr/src/app/scripts/<your>-mirror-init.ts \
+#                   /usr/src/app/scripts/<your>-mirror-refresh.ts \
+#                   /usr/src/app/scripts/<your>-mirror-verify.ts \
+#                   /usr/src/app/scripts/_mirror-context.ts \
+#                   ./scripts/
+# RUN echo '{"compilerOptions":{"baseUrl":".","paths":{"@/*":["./dist/*"]}}}' > tsconfig.json
+
+# The 'oven/bun' image already provides a non-root user named 'bun'.
+# We will use this existing user for enhanced security.
+
+# Create and set permissions for the log directory, assigning ownership to the 'bun' user.
+RUN mkdir -p /var/log/interpro-mcp-server && chown -R bun:bun /var/log/interpro-mcp-server
+
+# Writable data dirs for on-disk SQLite stores (catalog index / observations
+# mirror), owned by the runtime user. Mount a volume over either in production.
+RUN mkdir -p /usr/src/app/.cache /usr/src/app/.mirror \
+  && chown -R bun:bun /usr/src/app/.cache /usr/src/app/.mirror
+
+# Switch to the non-root user
+USER bun
+
+# Define an argument for the port, allowing it to be overridden at build time.
+# The `PORT` variable is often injected by cloud environments at runtime.
+ARG PORT
+
+# Set runtime environment variables
+# Note: PORT is an automatic variable in many cloud environments (e.g., Cloud Run)
+ENV MCP_HTTP_PORT=${PORT:-3010}
+ENV MCP_HTTP_HOST="0.0.0.0"
+ENV MCP_TRANSPORT_TYPE="http"
+ENV MCP_SESSION_MODE="stateless"
+ENV MCP_LOG_LEVEL="info"
+ENV LOGS_DIR="/var/log/interpro-mcp-server"
+
+# Expose the port the server listens on
+EXPOSE ${MCP_HTTP_PORT}
+
+# Health check using a bun-native fetch (slim image ships no curl/wget)
+HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
+
+# The command to start the server
+CMD ["bun", "run", "dist/index.js"]