@cyanheads/pubmed-mcp-server 2.9.8 → 2.9.9

package/AGENTS.md

@@ -1,9 +1,9 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.9.8
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
-**Engines:** Bun ≥1.3.2, Node ≥24.0.0
+**Version:** 2.9.9
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
+**Engines:** Bun ≥1.3.0, Node ≥24.0.0
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
 
@@ -137,6 +137,8 @@ export function getServerConfig(): z.infer<typeof ServerConfigSchema> {
 
 `parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`NCBI_REQUEST_DELAY_MS` must be a number) rather than the internal path (`requestDelayMs: expected number`).
 
+For env booleans use `z.stringbool()`, never `z.coerce.boolean()` — `Boolean("false")` is `true`, so a coerced flag can't be disabled through the environment. `z.stringbool()` parses `true/false/1/0/yes/no/on/off` and rejects anything else, so `=false` actually disables.
+
 ### Server identity and instructions
 
 `createApp()` accepts optional identity fields forwarded to the SDK's `initialize` response and the server manifest (`/.well-known/mcp.json`):
@@ -163,9 +165,11 @@ 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. |
-| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
+| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
 | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
 | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
+| `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.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
 | `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
 | `ctx.signal` | `AbortSignal` for cancellation. |
 | `ctx.requestId` | Unique request ID. |
@@ -197,6 +201,8 @@ async handler(input, ctx) {
 }
 ```
 
+**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):** error factories or plain `Error`.
 
 ```ts
@@ -280,7 +286,6 @@ Available skills:
 | `tool-defs-analysis` | Read-only audit of definition language: voice, leaks, defaults, recovery hints, examples |
 | `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 |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
 | `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
@@ -318,8 +323,11 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run devcheck` | Lint + format + typecheck + security + packaging alignment |
 | `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — `bun 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 tree` | Generate directory structure doc |
-| `bun run format` | Auto-fix formatting |
-| `bun run test` | Run tests |
+| `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 changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
+| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 | `bun run lint:mcp` | Validate MCP definitions against spec |
 | `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
 | `bun run list-skills` | List skills in `skills/` with name + description |
@@ -332,12 +340,26 @@ When you complete a skill's checklist, check the boxes and add a completion time
 
 ## Bundling
 
-`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` 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 dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
+`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` 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. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
 
 **Adding an env var requires both files**: `server.json` stdio `environmentVariables[]` (registry discovery) and `manifest.json` `mcp_config.env` (bundle install UX, plus `user_config` if user-prompted). `bun run lint:packaging` (run by `devcheck`) verifies the env var names align.
 
 ---
 
+## 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/2.9.x/2.9.8.md`) — one file per release. At release, author the per-version file with a concrete version and date, then run `bun 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 `bun run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
+
+`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`).
+
+`agent-notes` is an optional free-form field consumed by agents running the `maintenance` skill downstream — adoption instructions that don't fit the human-facing sections. Omit entirely when there's nothing to say.
+
+**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries.
+
+**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
 
 Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, GHCR, and attaches the `.mcpb` bundle to the GitHub Release, halting on the first failure. For reference, the underlying commands are:

package/CLAUDE.md

@@ -1,9 +1,9 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.9.8
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
-**Engines:** Bun ≥1.3.2, Node ≥24.0.0
+**Version:** 2.9.9
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
+**Engines:** Bun ≥1.3.0, Node ≥24.0.0
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
 
@@ -137,6 +137,8 @@ export function getServerConfig(): z.infer<typeof ServerConfigSchema> {
 
 `parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`NCBI_REQUEST_DELAY_MS` must be a number) rather than the internal path (`requestDelayMs: expected number`).
 
+For env booleans use `z.stringbool()`, never `z.coerce.boolean()` — `Boolean("false")` is `true`, so a coerced flag can't be disabled through the environment. `z.stringbool()` parses `true/false/1/0/yes/no/on/off` and rejects anything else, so `=false` actually disables.
+
 ### Server identity and instructions
 
 `createApp()` accepts optional identity fields forwarded to the SDK's `initialize` response and the server manifest (`/.well-known/mcp.json`):
@@ -163,9 +165,11 @@ 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. |
-| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
+| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
 | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
 | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
+| `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.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
 | `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
 | `ctx.signal` | `AbortSignal` for cancellation. |
 | `ctx.requestId` | Unique request ID. |
@@ -197,6 +201,8 @@ async handler(input, ctx) {
 }
 ```
 
+**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):** error factories or plain `Error`.
 
 ```ts
@@ -280,7 +286,6 @@ Available skills:
 | `tool-defs-analysis` | Read-only audit of definition language: voice, leaks, defaults, recovery hints, examples |
 | `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 |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
 | `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
@@ -318,8 +323,11 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run devcheck` | Lint + format + typecheck + security + packaging alignment |
 | `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — `bun 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 tree` | Generate directory structure doc |
-| `bun run format` | Auto-fix formatting |
-| `bun run test` | Run tests |
+| `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 changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
+| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 | `bun run lint:mcp` | Validate MCP definitions against spec |
 | `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
 | `bun run list-skills` | List skills in `skills/` with name + description |
@@ -332,12 +340,26 @@ When you complete a skill's checklist, check the boxes and add a completion time
 
 ## Bundling
 
-`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` 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 dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
+`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` 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. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
 
 **Adding an env var requires both files**: `server.json` stdio `environmentVariables[]` (registry discovery) and `manifest.json` `mcp_config.env` (bundle install UX, plus `user_config` if user-prompted). `bun run lint:packaging` (run by `devcheck`) verifies the env var names align.
 
 ---
 
+## 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/2.9.x/2.9.8.md`) — one file per release. At release, author the per-version file with a concrete version and date, then run `bun 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 `bun run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
+
+`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`).
+
+`agent-notes` is an optional free-form field consumed by agents running the `maintenance` skill downstream — adoption instructions that don't fit the human-facing sections. Omit entirely when there's nothing to say.
+
+**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries.
+
+**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
 
 Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, GHCR, and attaches the `.mcpb` bundle to the GitHub Release, halting on the first failure. For reference, the underlying commands are:

package/Dockerfile

@@ -4,15 +4,19 @@
 # This stage installs all dependencies (including dev), builds the TypeScript
 # source code into JavaScript, and prepares the production assets.
 # ==============================================================================
-FROM oven/bun:1.3 AS build
+FROM oven/bun:1.3.14 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)
-RUN bun install --frozen-lockfile
+# Install all dependencies (including dev dependencies for building). Lifecycle
+# scripts are skipped — the build only runs `tsc`, which needs type declarations,
+# not compiled native bindings.
+# 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 . .
@@ -28,7 +32,7 @@ RUN bun run build
 # application. It uses a slim base image and only includes production
 # dependencies and build artifacts.
 # ==============================================================================
-FROM oven/bun:1.3-slim AS production
+FROM oven/bun:1.3.14-slim AS production
 
 WORKDIR /usr/src/app
 
@@ -47,14 +51,16 @@ COPY package.json bun.lock ./
 
 # Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
 # that are not needed in the final production image.
-RUN bun install --production --frozen-lockfile --ignore-scripts
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --production --frozen-lockfile --ignore-scripts
 
 # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
 # These are not bundled by default to keep the base image lean. Enable at build time
 # with: docker build --build-arg OTEL_ENABLED=true
 ARG OTEL_ENABLED=true
-RUN if [ "$OTEL_ENABLED" = "true" ]; then \
-      bun add @hono/otel \
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    if [ "$OTEL_ENABLED" = "true" ]; then \
+      bun add --omit=dev --ignore-scripts @hono/otel \
         @opentelemetry/instrumentation-http \
         @opentelemetry/exporter-metrics-otlp-http \
         @opentelemetry/exporter-trace-otlp-http \

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.9.8-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/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.9.9-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/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 

package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts

@@ -11,8 +11,8 @@ export declare const researchPlanPrompt: import("@cyanheads/mcp-ts-core").Prompt
     keywords: z.ZodString;
     organism: z.ZodOptional<z.ZodString>;
     includeAgentPrompts: z.ZodDefault<z.ZodEnum<{
-        true: "true";
         false: "false";
+        true: "true";
     }>>;
 }, z.core.$strip>>;
 //# sourceMappingURL=research-plan.prompt.d.ts.map

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts

@@ -7,9 +7,9 @@ import { z } from '@cyanheads/mcp-ts-core';
 export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     ids: z.ZodArray<z.ZodString>;
     idType: z.ZodEnum<{
-        pmid: "pmid";
-        pmcid: "pmcid";
         doi: "doi";
+        pmcid: "pmcid";
+        pmid: "pmid";
     }>;
 }, z.core.$strip>, z.ZodObject<{
     records: z.ZodArray<z.ZodObject<{
@@ -22,34 +22,34 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
     totalConverted: z.ZodNumber;
     totalSubmitted: z.ZodNumber;
 }, z.core.$strip>, readonly [{
-    readonly reason: "queue_full";
+    readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: "Local NCBI request queue is at capacity.";
-    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
+    readonly when: 'Local NCBI request queue is at capacity.';
+    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_unreachable";
+    readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
+    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_deadline_exceeded";
+    readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
-    readonly when: "Total request deadline expired before NCBI returned a response.";
-    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
+    readonly when: 'Total request deadline expired before NCBI returned a response.';
+    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }], undefined>;
 //# sourceMappingURL=convert-ids.tool.d.ts.map

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts

@@ -70,40 +70,40 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
     totalReturned: z.ZodNumber;
     unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "queue_full";
+    readonly reason: 'queue_full';
     readonly code: JsonRpcErrorCode.RateLimited;
-    readonly when: "Local NCBI request queue is at capacity.";
-    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
+    readonly when: 'Local NCBI request queue is at capacity.';
+    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_unreachable";
+    readonly reason: 'ncbi_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
+    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_deadline_exceeded";
+    readonly reason: 'ncbi_deadline_exceeded';
     readonly code: JsonRpcErrorCode.Timeout;
-    readonly when: "Total request deadline expired before NCBI returned a response.";
-    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
+    readonly when: 'Total request deadline expired before NCBI returned a response.';
+    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }, {
-    readonly reason: "invalid_efetch_response";
+    readonly reason: 'invalid_efetch_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
-    readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
+    readonly when: 'NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.';
+    readonly recovery: 'Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.';
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqL5B,CAAC"}
+{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAsK3F,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts

@@ -40,8 +40,8 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     articles: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
         source: z.ZodLiteral<"pmc">;
         viaSource: z.ZodEnum<{
-            pmc: "pmc";
             europepmc: "europepmc";
+            pmc: "pmc";
         }>;
         pmcId: z.ZodOptional<z.ZodString>;
         pmcUrl: z.ZodOptional<z.ZodString>;
@@ -110,92 +110,92 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     unavailable: z.ZodOptional<z.ZodArray<z.ZodObject<{
         id: z.ZodString;
         idType: z.ZodEnum<{
-            pmid: "pmid";
-            pmcid: "pmcid";
             doi: "doi";
+            pmcid: "pmcid";
+            pmid: "pmid";
         }>;
         reason: z.ZodEnum<{
+            "fetch-failed": "fetch-failed";
+            "no-doi": "no-doi";
+            "no-epmc-fulltext": "no-epmc-fulltext";
             "no-oa": "no-oa";
-            "not-found": "not-found";
             "no-pmc-fallback-disabled": "no-pmc-fallback-disabled";
-            "no-epmc-fulltext": "no-epmc-fulltext";
-            "no-doi": "no-doi";
-            "fetch-failed": "fetch-failed";
+            "not-found": "not-found";
             "parse-failed": "parse-failed";
             "service-error": "service-error";
         }>;
         triedTiers: z.ZodArray<z.ZodObject<{
             tier: z.ZodEnum<{
-                pmc: "pmc";
                 europepmc: "europepmc";
+                pmc: "pmc";
                 unpaywall: "unpaywall";
             }>;
             outcome: z.ZodEnum<{
-                "no-oa": "no-oa";
-                "no-doi": "no-doi";
                 "fetch-failed": "fetch-failed";
-                "parse-failed": "parse-failed";
-                "service-error": "service-error";
-                "not-attempted": "not-attempted";
                 miss: "miss";
+                "no-doi": "no-doi";
                 "no-fulltext": "no-fulltext";
+                "no-oa": "no-oa";
+                "not-attempted": "not-attempted";
+                "parse-failed": "parse-failed";
+                "service-error": "service-error";
             }>;
             detail: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>>;
     }, z.core.$strip>>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "queue_full";
+    readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: "Local NCBI request queue is at capacity.";
-    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
+    readonly when: 'Local NCBI request queue is at capacity.';
+    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_unreachable";
+    readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
+    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_deadline_exceeded";
+    readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
-    readonly when: "Total request deadline expired before NCBI returned a response.";
-    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
+    readonly when: 'Total request deadline expired before NCBI returned a response.';
+    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }, {
-    readonly reason: "unpaywall_unreachable";
+    readonly reason: 'unpaywall_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Unpaywall was unreachable when resolving a DOI or fetching content.";
-    readonly recovery: "Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.";
+    readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
+    readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_unreachable";
+    readonly reason: 'europepmc_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Europe PMC was unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly when: 'Europe PMC was unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_response";
+    readonly reason: 'europepmc_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
-    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
+    readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_input";
+    readonly reason: 'europepmc_invalid_input';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
-    readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
-    readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
+    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
+    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
     readonly retryable: false;
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;