@cyanheads/ensembl-mcp-server 0.4.3 → 0.4.4

package/AGENTS.md

@@ -1,11 +1,11 @@
 # Developer Protocol
 
 **Server:** ensembl-mcp-server
-**Version:** 0.4.3
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
-**Engines:** Bun ≥1.3.0, Node ≥24.0.0
+**Version:** 0.4.4
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
+**Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
-**Zod:** ^4.4.3
+**Zod:** ^4.6.5
 
 > **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.
 
@@ -38,6 +38,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **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.
 
 ---
@@ -141,6 +142,22 @@ The canonical `createApp()` identity for this project is `name: 'ensembl-mcp-ser
 
 `instructions` is optional server-level orientation, sent on every `initialize` as session-level context. Use it for deployment guidance (connection aliases, regional notes, scope hints) instead of repeating the same context across tool descriptions. Client adoption is uneven, but there's no downside when set.
 
+### Session posture and shutdown
+
+Two more `createApp()` options shape how the server runs rather than how it presents itself:
+
+```ts
+await createApp({
+  sessionMode: 'stateless',          // or { default: 'stateful', require: 'stateful' }
+  setup(core) { initEnsemblService(core.config, core.storage); },
+  async teardown() { await releaseResources(); },
+});
+```
+
+`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). This server declares `stateless`: no tool asks the caller for input mid-handler via `ctx.requestInput`, so there is nothing a 2025-era HTTP client would be unable to answer. Add `require: 'stateful'` if that ever changes — startup then fails with a `ConfigurationError` rather than serving a mode in which the prompt can never be answered. Stdio is never refused.
+
+`teardown(core)` is the `setup()` counterpart — release a watcher, socket, or non-`unref()`'d timer there. It runs after the transport stops and before the logger closes, on every shutdown path, and a signal-triggered shutdown then exits the process explicitly (0, or 1 if a step never settles within the framework's 10 s ceiling). `EnsemblService` holds no such handle, so this server declares no `teardown`.
+
 ---
 
 ## Context
@@ -165,7 +182,7 @@ Handlers receive a unified `ctx` object. Key properties:
 
 Handlers throw — the framework catches, classifies, and formats.
 
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` 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. Pass `ctx.recoveryFor('reason')` as the throw's data to put it on the wire (`data.recovery.hint`, mirrored into `content[]` text); override with an explicit `{ recovery: { hint: '...' } }` when dynamic runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
+**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. Pass `ctx.recoveryFor('reason')` as the throw's data to put it on the wire (`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. Forwarding it is lint-enforced per throw site (`error-contract-recovery-unforwarded`). 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';
@@ -248,9 +265,9 @@ src/
 
 ## Skills
 
-Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool. `bun run list-skills` prints the full registry.
+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 `skills/` paths. After framework updates, run the `maintenance` skill — Phase B re-syncs the agent directory.
+**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:
 
@@ -268,10 +285,10 @@ Available skills:
 | `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 |
-| `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
-| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
-| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
+| `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 |
@@ -290,7 +307,7 @@ Available skills:
 | `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*, `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.
+**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`).
 
@@ -306,7 +323,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
-| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
+| `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 |
 | `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 |
@@ -320,15 +338,17 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `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 |
 
+**CI is one file.** `.github/workflows/codeql.yml` 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
 
-`bun 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 (`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.
+`bun 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.
+**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 `skills/polish-docs-meta/references/readme.md`.
+**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`.
 
 ---
 
@@ -353,12 +373,18 @@ security: false                            # optional — true ONLY for a source
 
 `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** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
+**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 gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the changelog entry plus a gates section); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
+
+---
+
 ## Imports
 
 ```ts
@@ -385,7 +411,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] 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` = package name; `interface.shortDescription` from `package.json` description
-- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
-- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
+- [ ] `.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`
 - [ ] `bun run devcheck` passes

package/CLAUDE.md

@@ -1,11 +1,11 @@
 # Developer Protocol
 
 **Server:** ensembl-mcp-server
-**Version:** 0.4.3
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
-**Engines:** Bun ≥1.3.0, Node ≥24.0.0
+**Version:** 0.4.4
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
+**Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
-**Zod:** ^4.4.3
+**Zod:** ^4.6.5
 
 > **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.
 
@@ -38,6 +38,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **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.
 
 ---
@@ -141,6 +142,22 @@ The canonical `createApp()` identity for this project is `name: 'ensembl-mcp-ser
 
 `instructions` is optional server-level orientation, sent on every `initialize` as session-level context. Use it for deployment guidance (connection aliases, regional notes, scope hints) instead of repeating the same context across tool descriptions. Client adoption is uneven, but there's no downside when set.
 
+### Session posture and shutdown
+
+Two more `createApp()` options shape how the server runs rather than how it presents itself:
+
+```ts
+await createApp({
+  sessionMode: 'stateless',          // or { default: 'stateful', require: 'stateful' }
+  setup(core) { initEnsemblService(core.config, core.storage); },
+  async teardown() { await releaseResources(); },
+});
+```
+
+`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). This server declares `stateless`: no tool asks the caller for input mid-handler via `ctx.requestInput`, so there is nothing a 2025-era HTTP client would be unable to answer. Add `require: 'stateful'` if that ever changes — startup then fails with a `ConfigurationError` rather than serving a mode in which the prompt can never be answered. Stdio is never refused.
+
+`teardown(core)` is the `setup()` counterpart — release a watcher, socket, or non-`unref()`'d timer there. It runs after the transport stops and before the logger closes, on every shutdown path, and a signal-triggered shutdown then exits the process explicitly (0, or 1 if a step never settles within the framework's 10 s ceiling). `EnsemblService` holds no such handle, so this server declares no `teardown`.
+
 ---
 
 ## Context
@@ -165,7 +182,7 @@ Handlers receive a unified `ctx` object. Key properties:
 
 Handlers throw — the framework catches, classifies, and formats.
 
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` 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. Pass `ctx.recoveryFor('reason')` as the throw's data to put it on the wire (`data.recovery.hint`, mirrored into `content[]` text); override with an explicit `{ recovery: { hint: '...' } }` when dynamic runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
+**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. Pass `ctx.recoveryFor('reason')` as the throw's data to put it on the wire (`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. Forwarding it is lint-enforced per throw site (`error-contract-recovery-unforwarded`). 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';
@@ -248,9 +265,9 @@ src/
 
 ## Skills
 
-Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool. `bun run list-skills` prints the full registry.
+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 `skills/` paths. After framework updates, run the `maintenance` skill — Phase B re-syncs the agent directory.
+**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:
 
@@ -268,10 +285,10 @@ Available skills:
 | `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 |
-| `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
-| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
-| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
+| `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 |
@@ -290,7 +307,7 @@ Available skills:
 | `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*, `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.
+**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`).
 
@@ -306,7 +323,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
-| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
+| `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 |
 | `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 |
@@ -320,15 +338,17 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `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 |
 
+**CI is one file.** `.github/workflows/codeql.yml` 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
 
-`bun 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 (`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.
+`bun 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.
+**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 `skills/polish-docs-meta/references/readme.md`.
+**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`.
 
 ---
 
@@ -353,12 +373,18 @@ security: false                            # optional — true ONLY for a source
 
 `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** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
+**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 gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the changelog entry plus a gates section); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
+
+---
+
 ## Imports
 
 ```ts
@@ -385,7 +411,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] 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` = package name; `interface.shortDescription` from `package.json` description
-- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
-- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
+- [ ] `.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`
 - [ ] `bun run devcheck` passes

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.4.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.4.4-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 
@@ -27,9 +27,11 @@
 
 ---
 
-## Tools
+## Overview
 
-Seven tools covering the core Ensembl REST API surface — species discovery, gene/transcript lookup, sequence retrieval, genomic region overlap, variant consequence prediction, cross-species homology, and external database cross-references:
+Gene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases from any MCP client. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
+
+### Tools
 
 | Tool | Description |
 |:-----|:------------|
@@ -41,103 +43,125 @@ Seven tools covering the core Ensembl REST API surface — species discovery, ge
 | `ensembl_get_homology` | Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level |
 | `ensembl_get_xrefs` | Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others |
 
-### `ensembl_list_species`
+### Resources
 
-Discovery tool for the Ensembl species catalog.
+| Resource | Description |
+|:---|:---|
+| `ensembl://gene/{id}` | Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list |
+| `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |
+| `ensembl://species` | Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint) |
+| `ensembl://species/{division}` | Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) |
 
-- Filter by division: vertebrates, plants, fungi, metazoa, or protists
-- Optional name filter (`nameContains`) for local substring matching
-- Returns display name, common name, assembly, taxon ID, and Ensembl division for each species
-- Required first step — species names like `homo_sapiens` are opaque to non-biologists and are the input format every other tool expects
+All resource data is also reachable via the `ensembl_list_species` tool, which additionally filters by name.
 
----
+### Prompts
+
+| Prompt | Description |
+|:---|:---|
+| `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |
 
-### `ensembl_lookup_gene`
+## Capability reference
 
-Single entry point for resolving gene identity.
+### `ensembl_list_species` <sub>tool</sub>
 
-- Symbol + species lookup (`BRCA2` + `homo_sapiens`) or direct stable ID lookup (`ENSG00000139618`)
-- Batch lookup of up to 20 IDs or symbols in one call via POST endpoints
-- Optional transcript expansion — returns full transcript list with biotype and canonical flag
-- Returns Ensembl stable ID, genomic location (chr:start-end:strand), biotype, description, and transcript list
-- Errors: `not_found` (symbol or ID not in Ensembl), `invalid_species` (call `ensembl_list_species` to discover valid names)
+- Filter by division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) or `nameContains` for a local substring match against name, display name, and common name
+- Omit `division` to return the endpoint default division (vertebrates, ~356 species on the default GRCh38 endpoint)
+- Returns internal name (the value every other tool expects), display name, common name, taxon ID, assembly, and division
+- Required first step — species names like `homo_sapiens` are opaque to non-biologists
 
 ---
 
-### `ensembl_get_sequence`
+### `ensembl_lookup_gene` <sub>tool</sub>
+
+- Exactly one of `symbol` (+ optional `species`, default `homo_sapiens`), `id`, `ids` (batch, up to 20), or `symbols` (batch, up to 20)
+- `expand_transcripts` (default `false`) adds the full transcript list with biotype and canonical flag
+- Batch modes (`ids`/`symbols`) return a `succeeded`/`failed` split with per-item error strings instead of failing the call
+- Errors: `not_found`, `invalid_species`, `no_input`, `conflicting_input`
+
+---
 
-Fetch any sequence type for any Ensembl feature.
+### `ensembl_get_sequence` <sub>tool</sub>
 
-- Molecule types: `genomic` (default, includes introns), `cdna` (spliced), `cds` (coding only), `protein`
-- Accepts stable IDs or `species:chr:start-end` region format for genomic region mode
-- Optional flanking sequence (`expand_5prime`, `expand_3prime`) in base pairs
-- Returns sequence with stable ID, molecule type, and character count — large sequences (e.g. BRCA2 at 85,183 bp genomic) returned in full with explicit length so callers can budget context usage
+- `type`: `genomic` (default, includes introns), `cdna` (spliced), `cds` (coding only), `protein`
+- Accepts a stable ID (`ENSG…`/`ENST…`/`ENSP…`) or a region — `species:chr:start-end`, or bare `chr:start-end` with `species` set
+- `expand_5prime` / `expand_3prime` (default `0`) extend flanking base pairs for genomic and region queries
+- `protein` and `cds` require a transcript or protein ID, not a gene ID
+- Every response states `length` so callers can budget context before consuming large sequences
+- Errors: `not_found`, `type_mismatch`, `missing_species`
 
 ---
 
-### `ensembl_query_region`
+### `ensembl_query_region` <sub>tool</sub>
+
+- `region` in `chr:start-end` format; `feature` array defaults to `["gene"]`, also accepts `transcript`, `variation`, `regulatory`, `exon`; optional `biotype` filter
+- Defaults to genes only — requesting `variation` on a large locus can return 44,000+ features
+- Exon rows carry a `parentId` and `rank`, since one exon is reported once per parent transcript
+- Errors: `invalid_region`, `invalid_species`
 
-Find all genomic features overlapping a chromosomal window.
+---
 
-- Region format: `chr:start-end` (e.g. `13:32315086-32400268`) — no `chr` prefix for vertebrates
-- Feature types: `gene` (default), `transcript`, `variation`, `regulatory`, `exon`
-- Optional biotype filter
-- Defaults to gene only to prevent context overload — a large locus can contain 44,000+ variants when all feature types are selected
+### `ensembl_predict_variant` <sub>tool</sub>
+
+- `variant` accepts HGVS (transcript-relative or genomic), region+allele (`chr:start:end:strand/allele`), or a dbSNP rsID
+- `max_transcript_consequences` (default `10`) and `max_pubmed_ids_per_variant` (default `10`) cap large VEP results; set either to `0` for the full set, or `include_all_colocated_pubmed: true` for uncapped PubMed IDs
+- Returns most severe consequence term, per-transcript impact (HIGH/MODERATE/LOW/MODIFIER), and colocated known variants with clinical significance
+- Totals (`transcriptConsequencesTotal`, `pubmedTotal`) are always reported even when capped
+- Errors: `invalid_notation`, `not_found`
 
 ---
 
-### `ensembl_predict_variant`
+### `ensembl_get_homology` <sub>tool</sub>
+
+- Exactly one of `symbol` (+ `species`, default `homo_sapiens`) or `id`; optional `target_species` filter
+- `type`: `orthologues` (default), `paralogues`, or `all`
+- `max_results` caps the homolog list (default `25`, `0` uncapped); `totalCount` always reports the true count available
+- Errors: `not_found`, `no_input`, `conflicting_input`
 
-Predict variant consequences via the Ensembl VEP.
+---
+
+### `ensembl_get_xrefs` <sub>tool</sub>
 
-- Accepts HGVS notation (transcript-relative: `ENST00000380152.8:c.2T>A`) or genomic region+allele format (`13:32316462:32316462:1/A`)
-- Returns most severe consequence term, affected transcripts and genes, impact level (HIGH/MODERATE/LOW/MODIFIER)
-- Includes colocated known variants with clinical significance (ClinVar, dbSNP)
-- Errors: `invalid_notation` (check format), `not_found` (location outside any known transcript)
+- `id` (`ENSG…`/`ENST…`) required; optional `dbname` filter (e.g. `HGNC`, `Uniprot_gn`, `EntrezGene`, `MIM_GENE`, `RefSeq_mRNA`, `Reactome`, `GO`)
+- Uses the `xrefs/id` endpoint, returning the full cross-reference set (56+ entries for well-annotated genes like BRCA2)
+- Errors: `not_found`
 
 ---
 
-### `ensembl_get_homology`
+### `ensembl://gene/{id}` <sub>resource</sub>
+
+- Returns location, biotype, description, and transcript list for a gene stable ID (`ENSG…`); version suffix optional
+- Errors: `not_found`
+
+---
 
-Cross-species homolog lookup.
+### `ensembl://transcript/{id}` <sub>resource</sub>
 
-- Returns orthologs (default) or paralogs, or both
-- Optional `target_species` filter to narrow to specific organisms
-- Each homolog carries stable ID, species, relationship type (ortholog_one2one, ortholog_one2many, etc.), `perc_id`, `perc_pos`, and taxonomy level
+- Returns parent gene, location, biotype, canonical flag, and length for a transcript stable ID (`ENST…`); version suffix optional
+- Errors: `not_found`
 
 ---
 
-### `ensembl_get_xrefs`
+### `ensembl://species` <sub>resource</sub>
 
-Full cross-database reference set for any Ensembl feature.
+- No parameters — returns the endpoint default division (vertebrates, ~356 species on the default GRCh38 endpoint)
+- For a named division, read `ensembl://species/{division}` instead
 
-- Returns all external IDs by default: HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and more (56 xrefs for BRCA2)
-- Optional `dbname` filter (e.g. `HGNC`, `Uniprot_gn`, `EntrezGene`, `MIM_GENE`) to narrow output
-- Uses the `xrefs/id` endpoint (not `xrefs/symbol`) — returns the full cross-reference set
-- IDs returned here chain directly to protein, literature, disease, and pathway resources in other MCP servers
+---
 
-## Resources and prompts
+### `ensembl://species/{division}` <sub>resource</sub>
 
-| Type | Name | Description |
-|:-----|:-----|:------------|
-| Resource | `ensembl://gene/{id}` | Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list |
-| Resource | `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |
-| Resource | `ensembl://species` | Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint) with name, display name, assembly, taxon ID, and division |
-| Resource | `ensembl://species/{division}` | Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) |
-| Prompt | `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |
+- `division` required: `EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, or `EnsemblProtists`
 
-All resource data is also reachable via tools. `ensembl://species` returns the endpoint default division (vertebrates) and `ensembl://species/{division}` returns a named division; `ensembl_list_species` is the tool equivalent, filtering by division and name.
+---
 
-## Features
+### `ensembl_gene_dossier` <sub>prompt</sub>
 
-Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):
+- Arguments: `gene_symbol` required; `species` optional (default `homo_sapiens`)
+- Sequences a 7-step workflow: resolve the gene → fetch the protein sequence → find variants in the locus → predict variant consequences → find cross-species orthologs → get external database IDs → synthesize the dossier
+
+## Features
 
-- Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
-- Unified error handling — handlers throw, framework catches, classifies, and formats
-- Pluggable auth: `none`, `jwt`, `oauth`
-- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
-- Structured logging with optional OpenTelemetry tracing
-- STDIO and Streamable HTTP transports
+Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.
 
 Ensembl-specific:
 
@@ -151,7 +175,7 @@ Agent-friendly output:
 
 - Sequence character count stated on every `ensembl_get_sequence` response so callers can budget context before consuming large genomic sequences
 - `ensembl_list_species` is explicitly the discovery step — tool descriptions call out the opaque internal-name format and direct agents to it before using species-dependent tools
-- Cross-tool chaining made explicit: xref IDs from `ensembl_get_xrefs` are described as inputs for protein and literature servers; the `ensembl_gene_dossier` prompt sequences the full 7-tool research workflow
+- Cross-tool chaining made explicit: xref IDs from `ensembl_get_xrefs` are described as inputs for protein and literature servers; the `ensembl_gene_dossier` prompt sequences all 6 tools into one research workflow
 
 ## Getting started
 
@@ -339,7 +363,7 @@ See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rule
 
 ## Contributing
 
-Issues and pull requests are welcome. Run checks and tests before submitting:
+Issues are welcome. Run checks and tests before submitting:
 
 ```sh
 bun run devcheck

package/changelog/0.4.x/0.4.4.md

@@ -0,0 +1,27 @@
+---
+summary: "mcp-ts-core 0.13.6 adoption: an unrecognized or misspelled argument key now succeeds instead of failing, argument rejections carry a reason and recovery hint under Invalid params, and every declared tool error closes with a (reason ...) suffix"
+breaking: false
+security: false
+---
+
+# 0.4.4 — 2026-09-19
+
+## Changed
+
+- **Tool calls tolerate minor argument mismatches instead of rejecting them** — an unrecognized top-level key is dropped, a differently-cased spelling of a declared parameter (`dbName` for `dbname`, `maxTranscriptConsequences` for `max_transcript_consequences`) is rewritten onto the real key, and a JSON-stringified array is parsed and retried once. Advertised `inputSchema` is unchanged; only calls that previously failed now succeed.
+- **Argument rejections report `Invalid params` (`-32602`)** instead of the previous validation-error code, with `data.reason: "invalid_arguments"` and a synthesized `Recovery: …` hint derived from the offending field and the root schema.
+- **Every declared tool error closes with `(reason <reason>)`** — e.g. `not_found`, `invalid_notation` — on the `content[]` text. `structuredContent.error.data.reason` already carried the reason and is unchanged; resource errors are unaffected.
+- **A caller that disconnects mid-call is reported as a cancellation**, not an internal server error.
+- **`sessionMode: 'stateless'`** is declared directly in `src/index.ts`, matching the deployment default it was previously left to.
+- **Bun engines floor raised to `>=1.4.0`**, matching the framework requirement.
+- **Framework scripts, skills, agent protocol, and issue templates** sync to `@cyanheads/mcp-ts-core` 0.13.6 — the development skill tree moves from `skills/` to `framework-skills/` so a plugin install no longer surfaces it to the installing agent, `devcheck` gains a Worker typecheck step and a README version-badge check, and a CodeQL workflow is added.
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` `^0.12.3` → `^0.13.6`
+- `zod` `^4.4.3` → `^4.6.5`
+- `@biomejs/biome` `^2.5.9` → `^2.5.14`
+- `@types/node` `^26.2.0` → `^26.6.1`
+- `ignore` `^7.0.6` → `^7.0.9`
+- `tsc-alias` `^1.9.2` → `^1.9.5`
+- `vitest` `^4.1.11` → `^5.0.1`

package/changelog/template.md

@@ -6,8 +6,8 @@
 
 # Required. One-line GitHub Release-style headline. 350 character cap — a
 # ceiling, not a target. Default short and scannable. Don't pad, don't stitch
-# unrelated changes with commas/semicolons into an inventory — pick the
-# headline, like a tag's theme line. Quotes required: unquoted YAML treats
+# unrelated changes with commas/semicolons into an inventory — pick the one
+# headline the release is about. Quotes required: unquoted YAML treats
 # `: ` inside the value as a key separator and fails GitHub's strict parser.
 summary: ""
 
@@ -117,30 +117,13 @@ security: false
   in that unrelated item's metadata.
 
   TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
-  via `gh release create --notes-from-tag`. The tag is a derivative of this
-  changelog entry — a condensed, scannable version, not a copy. Format:
-
-    <theme — omit version number, GitHub prepends it>
-                                                          ← blank line
-    <1-2 sentence context: what this release does>
-                                                          ← blank line
-    Dependency bumps:                                     ← section header
-                                                          ← blank line
-    - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6          ← bullet
-                                                          ← blank line
-    Changed:                                              ← only sections with entries
-                                                          ← blank line
-    - `format()` output includes `query` in text mode
-                                                          ← blank line
-    Added:
-                                                          ← blank line
-    - `manifest.json` scaffolded for MCPB bundle support
-    - Install badges (Claude Desktop, Cursor, VS Code)
-                                                          ← blank line
-    <N> tests pass; `bun run devcheck` clean.             ← footer
-
-  Never a flat comma-separated string. Always structured markdown with
-  sections. The tag must scan well as a rendered GitHub Release page.
+  via `gh release create --notes-from-tag`. It is a condensed digest of this
+  entry, never a copy, and its format is owned by the `release-and-publish`
+  skill (step 4, "Create the annotated tag"): a short subject line without the
+  version, flat headline bullets — no Keep-a-Changelog section headers, no
+  gates line — at most one deps line, issue backlinks, and the changelog link
+  last. In release-PR mode the `git-wrapup` skill authors those bullets as the
+  PR body's `## Changes` and the tag copies them.
 -->
 
 ## Added

package/dist/index.js

@@ -19,6 +19,13 @@ import { initEnsemblService } from './services/ensembl/ensembl-service.js';
 await createApp({
     name: 'ensembl-mcp-server',
     title: 'ensembl-mcp-server',
+    /**
+     * Every tool here is a read-only Ensembl REST lookup — no handler calls
+     * `ctx.requestInput`, so nothing needs a session to come back to. `stateless`
+     * is declared in source rather than left to the deployment's
+     * `MCP_SESSION_MODE`, which still wins when it carries a meaningful value.
+     */
+    sessionMode: 'stateless',
     cacheHints: {
         'prompts/list': { ttlMs: 3_600_000, cacheScope: 'public' },
         'resources/list': { ttlMs: 3_600_000, cacheScope: 'public' },

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EACL,gCAAgC,EAChC,sBAAsB,GACvB,MAAM,wDAAwD,CAAC;AAChE,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,UAAU,EAAE;QACV,cAAc,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,gBAAgB,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KACzD;IACD,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE;QACT,mBAAmB;QACnB,yBAAyB;QACzB,sBAAsB;QACtB,gCAAgC;KACjC;IACD,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EACL,gCAAgC,EAChC,sBAAsB,GACvB,MAAM,wDAAwD,CAAC;AAChE,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B;;;;;OAKG;IACH,WAAW,EAAE,WAAW;IACxB,UAAU,EAAE;QACV,cAAc,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,gBAAgB,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KACzD;IACD,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE;QACT,mBAAmB;QACnB,yBAAyB;QACzB,sBAAsB;QACtB,gCAAgC;KACjC;IACD,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/ensembl-mcp-server",
-  "version": "0.4.3",
+  "version": "0.4.4",
   "mcpName": "io.github.cyanheads/ensembl-mcp-server",
   "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -24,6 +24,7 @@
     "rebuild": "bun run scripts/clean.ts && bun run scripts/build.ts",
     "clean": "bun run scripts/clean.ts",
     "devcheck": "bun run scripts/devcheck.ts",
+    "audit:fix": "bun audit fix",
     "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "tree": "bun run scripts/tree.ts",
     "list-skills": "bun run scripts/list-skills.ts",
@@ -83,26 +84,26 @@
   "license": "Apache-2.0",
   "packageManager": "bun@1.4.0",
   "engines": {
-    "bun": ">=1.3.0",
+    "bun": ">=1.4.0",
     "node": ">=24.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.3",
+    "@cyanheads/mcp-ts-core": "^0.13.6",
     "pino-pretty": "^13.1.3",
-    "zod": "^4.4.3"
+    "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.9",
+    "@biomejs/biome": "^2.5.14",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.2.0",
+    "@types/node": "^26.6.1",
     "depcheck": "^1.4.7",
-    "ignore": "^7.0.6",
-    "tsc-alias": "^1.9.2",
+    "ignore": "^7.0.9",
+    "tsc-alias": "^1.9.5",
     "typescript": "^7.0.2",
-    "vitest": "^4.1.11"
+    "vitest": "^5.0.1"
   },
   "trustedDependencies": ["@socketsecurity/bun-security-scanner"]
 }

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/ensembl-mcp-server",
     "source": "github"
   },
-  "version": "0.4.3",
+  "version": "0.4.4",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.3",
+      "version": "0.4.4",
       "packageArguments": [
         {
           "type": "positional",
@@ -55,7 +55,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.3",
+      "version": "0.4.4",
       "packageArguments": [
         {
           "type": "positional",