@cyanheads/pubmed-mcp-server 2.9.0 → 2.9.2

package/AGENTS.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.9.0
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
+**Version:** 2.9.2
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.5`
 **Engines:** Bun ≥1.3.2, 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.
@@ -33,7 +33,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
 - **Use `ctx.log`** for request-scoped logging. No `console` calls.
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
-- **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
+- **Check `ctx.elicit`** for presence before calling (`if (ctx.elicit) { ... }` — defined only when the client advertised elicitation capability).
 - **Secrets in env vars only** — never hardcoded.
 - **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.
 
@@ -137,6 +137,23 @@ 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`).
 
+### Server identity and instructions
+
+`createApp()` accepts optional identity fields forwarded to the SDK's `initialize` response and the server manifest (`/.well-known/mcp.json`):
+
+```ts
+await createApp({
+  name: 'pubmed-mcp-server',
+  title: 'PubMed MCP Server',
+  websiteUrl: 'https://github.com/cyanheads/pubmed-mcp-server',
+  description: 'One-line description.',
+  icons: [{ src: 'https://example.com/icon.png', sizes: ['48x48'], mimeType: 'image/png' }],
+  instructions: 'Use shortcut alpha for the most common case.',
+});
+```
+
+`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.
+
 ---
 
 ## Context
@@ -147,8 +164,7 @@ Handlers receive a unified `ctx` object. Key properties:
 |:---------|:------------|
 | `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.elicit` | Ask user for structured input. **Check for presence first:** `if (ctx.elicit) { ... }` |
-| `ctx.sample` | Request LLM completion from the client. **Check for presence first:** `if (ctx.sample) { ... }` |
+| `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.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. |
@@ -282,6 +298,7 @@ Available skills:
 | `api-testing` | createMockContext, test patterns |
 | `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
 | `api-workers` | Cloudflare Workers runtime |
+| `techniques` | Catalog of reusable response/data-shaping patterns — overflow handling, payload shaping, retrieval. Use when a payload is too large, awkwardly shaped, or expensive to retrieve |
 | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
 | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
 

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.9.0
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
+**Version:** 2.9.2
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.5`
 **Engines:** Bun ≥1.3.2, 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.
@@ -33,7 +33,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
 - **Use `ctx.log`** for request-scoped logging. No `console` calls.
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
-- **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
+- **Check `ctx.elicit`** for presence before calling (`if (ctx.elicit) { ... }` — defined only when the client advertised elicitation capability).
 - **Secrets in env vars only** — never hardcoded.
 - **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.
 
@@ -137,6 +137,23 @@ 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`).
 
+### Server identity and instructions
+
+`createApp()` accepts optional identity fields forwarded to the SDK's `initialize` response and the server manifest (`/.well-known/mcp.json`):
+
+```ts
+await createApp({
+  name: 'pubmed-mcp-server',
+  title: 'PubMed MCP Server',
+  websiteUrl: 'https://github.com/cyanheads/pubmed-mcp-server',
+  description: 'One-line description.',
+  icons: [{ src: 'https://example.com/icon.png', sizes: ['48x48'], mimeType: 'image/png' }],
+  instructions: 'Use shortcut alpha for the most common case.',
+});
+```
+
+`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.
+
 ---
 
 ## Context
@@ -147,8 +164,7 @@ Handlers receive a unified `ctx` object. Key properties:
 |:---------|:------------|
 | `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.elicit` | Ask user for structured input. **Check for presence first:** `if (ctx.elicit) { ... }` |
-| `ctx.sample` | Request LLM completion from the client. **Check for presence first:** `if (ctx.sample) { ... }` |
+| `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.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. |
@@ -282,6 +298,7 @@ Available skills:
 | `api-testing` | createMockContext, test patterns |
 | `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
 | `api-workers` | Cloudflare Workers runtime |
+| `techniques` | Catalog of reusable response/data-shaping patterns — overflow handling, payload shaping, retrieval. Use when a payload is too large, awkwardly shaped, or expensive to retrieve |
 | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
 | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
 

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.9.0-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-2.9.2-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/)
 
 </div>
 

package/dist/config/server-config.d.ts

@@ -16,7 +16,7 @@ declare const ServerConfigSchema: z.ZodObject<{
     totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     unpaywallEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     unpaywallTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    europepmcEnabled: z.ZodDefault<z.ZodPreprocess<z.ZodBoolean>>;
+    europepmcEnabled: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     europepmcEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     europepmcRequestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     europepmcMaxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;

package/dist/config/server-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoB3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;;iBA4DtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA8B9C"}

package/dist/config/server-config.js

@@ -24,22 +24,6 @@ const emptyAsUndefined = (v) => {
         return;
     return v;
 };
-/**
- * Parse a string env var as a boolean. `z.coerce.boolean()` is unusable for
- * env vars because it applies JavaScript truthy semantics — `"false"` coerces
- * to `true`. This mirrors the framework's `envBoolean` so `EUROPEPMC_ENABLED=false`
- * actually disables the service.
- */
-const envBoolean = z.preprocess((v) => {
-    if (typeof v === 'string') {
-        const s = v.trim().toLowerCase();
-        if (s === 'true' || s === '1')
-            return true;
-        if (s === 'false' || s === '0' || s === '')
-            return false;
-    }
-    return v;
-}, z.boolean());
 const ServerConfigSchema = z.object({
     apiKey: z.preprocess(emptyAsUndefined, z.string().optional()).describe('NCBI API key'),
     toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
@@ -73,7 +57,8 @@ const ServerConfigSchema = z.object({
         .max(120000)
         .default(20000)
         .describe('Per-request HTTP timeout for Unpaywall lookups and content fetches, in ms'),
-    europepmcEnabled: envBoolean
+    europepmcEnabled: z
+        .stringbool()
         .default(true)
         .describe('Enable Europe PMC search tool and `pubmed_fetch_fulltext` JATS fallback chain. Set false to fully disable EPMC calls.'),
     europepmcEmail: z

package/dist/config/server-config.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -35,6 +35,10 @@ const tools = [
     ...(config.europepmcEnabled ? [pubmedEuropepmcSearchTool] : []),
 ];
 await createApp({
+    name: 'pubmed-mcp-server',
+    title: 'PubMed MCP Server',
+    websiteUrl: 'https://github.com/cyanheads/pubmed-mcp-server',
+    description: 'Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.',
     tools,
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],

package/dist/index.js.map

@@ -1 +1 @@
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+{"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,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,yBAAyB,EAAE,MAAM,gEAAgE,CAAC;AAC3G,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,oBAAoB,EAAE,MAAM,6CAA6C,CAAC;AACnF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AAEjF,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;AACjC,MAAM,KAAK,GAAG;IACZ,kBAAkB;IAClB,iBAAiB;IACjB,iBAAiB;IACjB,mBAAmB;IACnB,eAAe;IACf,cAAc;IACd,cAAc;IACd,kBAAkB;IAClB,cAAc;IACd,GAAG,CAAC,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;CAChE,CAAC;AAEF,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mBAAmB;IAC1B,UAAU,EAAE,gDAAgD;IAC5D,WAAW,EACT,qGAAqG;IACvG,KAAK;IACL,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,YAAY,EACV,iqBAAiqB;IACnqB,OAAO,EAAE;QACP,WAAW,EAAE,KAAK;QAClB,OAAO,EACL,uGAAuG;QACzG,QAAQ,EAAE,gDAAgD;QAC1D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,kCAAkC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC7E;gBACE,KAAK,EAAE,kBAAkB;gBACzB,IAAI,EAAE,8CAA8C;gBACpD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,qBAAqB;gBAC5B,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD,EAAE,KAAK,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE,QAAQ,EAAE,IAAI,EAAE;SAC9E;QACD,UAAU,EAAE;YACV,YAAY,EAAE,mBAAmB;YACjC,gBAAgB,EAAE,iBAAiB;YACnC,eAAe,EAAE,iBAAiB;SACnC;KACF;IACD,KAAK;QACH,eAAe,EAAE,CAAC;QAClB,oBAAoB,EAAE,CAAC;QACvB,oBAAoB,EAAE,CAAC;QACvB,mBAAmB,EAAE,CAAC;IACxB,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts

@@ -91,7 +91,7 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly recovery: "Retry the request; OpenAlex returned a malformed response that could not be parsed.";
     readonly retryable: true;
 }], {
-    readonly totalFound: z.ZodNumber;
+    readonly totalCount: z.ZodNumber;
     readonly source: z.ZodEnum<{
         europepmc: "europepmc";
         openalex: "openalex";

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6KjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmX1B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js

@@ -149,7 +149,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
     // the answering provider, and recovery guidance. Surfaced via ctx.enrich(...)
     // to structuredContent and content[]; kept out of the domain return.
     enrichment: {
-        totalFound: z.number().describe('Total related articles found before windowing'),
+        totalCount: z.number().describe('Total related articles found before windowing'),
         source: z
             .enum(['ncbi', 'europepmc', 'openalex'])
             .describe('Provider that answered this request'),
@@ -159,7 +159,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
             .describe('Guidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page.'),
     },
     enrichmentTrailer: {
-        totalFound: { label: 'Total Found' },
+        totalCount: { label: 'Total Found' },
         source: { label: 'Source' },
     },
     async handler(input, ctx) {
@@ -228,7 +228,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
         }
         // ── Every provider failed ─────────────────────────────────────────────────
         if (providerResult === null) {
-            ctx.enrich({ totalFound: 0, source: 'ncbi' });
+            ctx.enrich({ source: 'ncbi' });
+            ctx.enrich.total(0);
             ctx.enrich.notice(`All providers failed to retrieve related articles (NCBI, Europe PMC, OpenAlex). Last error: ${describeError(providerError ?? 'unknown')}. Retry after a brief delay.`);
             return {
                 sourcePmid: input.pmid,
@@ -261,7 +262,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     sourceConfirmedMissing = true;
             }
             if (sourceConfirmedMissing) {
-                ctx.enrich({ totalFound: 0, source: 'ncbi' });
+                ctx.enrich({ source: 'ncbi' });
+                ctx.enrich.total(0);
                 ctx.enrich.notice(`Source PMID ${input.pmid} not found in PubMed. Verify the ID with \`pubmed_fetch_articles\` or \`pubmed_search_articles\`.`);
                 return {
                     sourcePmid: input.pmid,
@@ -298,7 +300,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     fallbackKind = 'references_coverage';
                 }
                 else {
-                    ctx.enrich({ totalFound: 0, source: 'ncbi' });
+                    ctx.enrich({ source: 'ncbi' });
+                    ctx.enrich.total(0);
                     const sourcePmcId = sourceSummary.pmcId;
                     ctx.enrich.notice(sourcePmcId
                         ? `No reference list found for PMID ${input.pmid} (PMCID ${sourcePmcId}) via NCBI, Europe PMC, or OpenAlex.`
@@ -314,7 +317,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
             else {
                 // similar / cited_by empty for a valid source, or references with an
                 // unconfirmed source — return the honest empty without a notice.
-                ctx.enrich({ totalFound: 0, source: 'ncbi' });
+                ctx.enrich({ source: 'ncbi' });
+                ctx.enrich.total(0);
                 return {
                     sourcePmid: input.pmid,
                     relationship: input.relationship,
@@ -325,7 +329,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
         }
         // ── Window the result set + enrich ──────────────────────────────────────────
         const { allPmids, totalCount, source } = providerResult;
-        ctx.enrich({ totalFound: totalCount, source });
+        ctx.enrich({ source });
+        ctx.enrich.total(totalCount);
         // For NCBI the full neighbor set is in memory; for EPMC/OpenAlex the provider
         // pre-fetched enough to cover the window. Slice the requested page either way.
         const window = allPmids.slice(input.offset, input.offset + input.maxResults);
@@ -333,7 +338,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
         // fragments (overshoot, provenance, enrichment-degraded) and emit them once.
         const notices = [];
         if (input.offset > 0 && input.offset >= totalCount) {
-            notices.push(`Offset ${input.offset} exceeds totalFound (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
+            notices.push(`Offset ${input.offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
         }
         if (source !== 'ncbi') {
             const providerName = source === 'europepmc' ? 'Europe PMC' : 'OpenAlex';

package/dist/mcp-server/tools/definitions/find-related.tool.js.map

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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts

@@ -48,6 +48,7 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
 }], {
+    readonly totalCount: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;
 //# sourceMappingURL=lookup-mesh.tool.d.ts.map

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6GzB,CAAC"}
+{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiHzB,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js

@@ -102,9 +102,11 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             .describe('Matching MeSH descriptor record'))
             .describe('Matching MeSH records'),
     }),
-    // Recovery guidance when no descriptor matched — agent-facing context, surfaced via
-    // ctx.enrich.notice() to both structuredContent and content[]; absent on success.
+    // Result-set context — total match count for disclosure against the maxResults cap,
+    // and recovery guidance when no descriptor matched. Surfaced via ctx.enrich(...)
+    // to structuredContent and content[]; absent on success.
     enrichment: {
+        totalCount: z.number().describe('Total matching MeSH descriptors'),
         notice: z
             .string()
             .optional()
@@ -131,6 +133,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         }
         ids.length = Math.min(ids.length, maxResults);
         if (ids.length === 0) {
+            ctx.enrich.total(0);
             ctx.enrich.notice(`No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`);
             return { query, results: [] };
         }
@@ -142,6 +145,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             const bExact = b.name.toLowerCase() === queryLower ? 0 : 1;
             return aExact - bExact;
         });
+        ctx.enrich.total(results.length);
         return { query, results };
     },
     format: (result) => {

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map

@@ -1 +1 @@
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+{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAC9E,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,yBAAyB,EACzB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,gBAAgB,CAAC;AAYxB,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,IAAI,GAAG;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IAC9B,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,mBAAmB,CAAC,IAAa,EAAE,GAAa,EAAE,cAAuB;IAChF,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1F,MAAM,IAAI,GAAG,IAA+B,CAAC;IAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,cAAqD,CAAC;IACjF,MAAM,OAAO,GAAG,WAAW,CACzB,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,MAAiC,CAC1D,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE7E,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAC/B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,IAAI,CAA8B,CAAC;QACjE,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,IAAI,MAAM,CAAC;QACpE,MAAM,MAAM,GAAe,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QAC5C,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YAC/D,IAAI,SAAS;gBAAE,MAAM,CAAC,SAAS,GAAG,SAAS,CAAC;YAC5C,MAAM,UAAU,GAAG,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YACjE,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC1D,MAAM,WAAW,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,WAAW,GAAG,WAAW,CAAC;QAC/D,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC,CAAC;AACL,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,2JAA2J;IAC7J,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC;QACjB,mBAAmB;QACnB,uBAAuB;QACvB,yBAAyB;QACzB,mBAAmB;KACpB,CAAC;IACF,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACtF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACnF,cAAc,EAAE,CAAC;aACd,OAAO,EAAE;aACT,OAAO,CAAC,IAAI,CAAC;aACb,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;YAChE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;YACvD,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SAC9E,CAAC;aACD,QAAQ,CAAC,iCAAiC,CAAC,CAC/C;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,oFAAoF;IACpF,iFAAiF;IACjF,yDAAyD;IACzD,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAClE,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yHAAyH,CAC1H;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QACpD,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE5E,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACzC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;QACxC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE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package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts

@@ -81,7 +81,7 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
     readonly recovery: "Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.";
 }], {
     readonly query: z.ZodString;
-    readonly hitCount: z.ZodNumber;
+    readonly totalCount: z.ZodNumber;
     readonly appliedSources: z.ZodArray<z.ZodEnum<{
         MED: "MED";
         PMC: "PMC";

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js

@@ -111,7 +111,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
     // Surfaced via ctx.enrich(...) to structuredContent and content[]; out of the return.
     enrichment: {
         query: z.string().describe('Effective query string echoed by Europe PMC'),
-        hitCount: z.number().describe('Total matching records across all pages'),
+        totalCount: z.number().describe('Total matching records across all pages'),
         appliedSources: z
             .array(SourceEnum)
             .describe('Sources the query was filtered against (defaults applied)'),
@@ -124,7 +124,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
     // carries the full structured value; this only shapes the human-facing trailer line.
     enrichmentTrailer: {
         query: { label: 'Effective Query' },
-        hitCount: { label: 'Total Hits' },
+        totalCount: { label: 'Total Hits' },
         appliedSources: {
             render: (sources) => `**Sources:** ${sources.join(', ')}`,
         },
@@ -187,9 +187,9 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         });
         ctx.enrich({
             query: result.query,
-            hitCount: result.hitCount,
             appliedSources: [...sources],
         });
+        ctx.enrich.total(result.hitCount);
         if (notice)
             ctx.enrich.notice(notice);
         return {

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts

@@ -83,7 +83,7 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     readonly retryable: false;
 }], {
     readonly effectiveQuery: z.ZodString;
-    readonly totalFound: z.ZodNumber;
+    readonly totalCount: z.ZodNumber;
     readonly appliedFilters: z.ZodObject<{
         dateRange: z.ZodOptional<z.ZodObject<{
             minDate: z.ZodString;

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

@@ -1 +1 @@
-{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6T7B,CAAC"}
+{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8T7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js

@@ -20,17 +20,17 @@ const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
  * bare empty arrays leave the caller without enough signal to recover:
  * - No matches at all (suggest spell-check / removing filters)
  * - Filters applied but nothing matched (suggest relaxing filters)
- * - Pagination overshoot (offset ≥ totalFound)
+ * - Pagination overshoot (offset ≥ totalCount)
  */
 function buildNotice(args) {
-    const { totalFound, pmidCount, offset, hasFilters } = args;
-    if (totalFound === 0) {
+    const { totalCount, pmidCount, offset, hasFilters } = args;
+    if (totalCount === 0) {
         return hasFilters
             ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
             : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.';
     }
-    if (pmidCount === 0 && offset > 0 && offset >= totalFound) {
-        return `Offset ${offset} exceeds totalFound (${totalFound}). Reset offset to 0 or reduce it below ${totalFound} to page through results.`;
+    if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
+        return `Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`;
     }
     return;
 }
@@ -148,7 +148,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         effectiveQuery: z
             .string()
             .describe('Sanitized query sent to PubMed after applying all active filters'),
-        totalFound: z.number().describe('Total matching articles'),
+        totalCount: z.number().describe('Total matching articles'),
         appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
         notice: z
             .string()
@@ -159,7 +159,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     // carries the full structured value; this only shapes the human-facing trailer line.
     enrichmentTrailer: {
         effectiveQuery: { label: 'Effective Query' },
-        totalFound: { label: 'Total Found' },
+        totalCount: { label: 'Total Found' },
         appliedFilters: {
             render: (filters) => {
                 const lines = [];
@@ -289,16 +289,17 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             ...(input.species && { species: input.species }),
         };
         ctx.log.info('pubmed_search completed', {
-            totalFound: esResult.count,
+            totalCount: esResult.count,
             pmidCount: pmids.length,
         });
         const notice = buildNotice({
-            totalFound: esResult.count,
+            totalCount: esResult.count,
             pmidCount: pmids.length,
             offset: input.offset,
             hasFilters: Object.keys(appliedFilters).length > 0,
         });
-        ctx.enrich({ effectiveQuery, totalFound: esResult.count, appliedFilters });
+        ctx.enrich({ effectiveQuery, appliedFilters });
+        ctx.enrich.total(esResult.count);
         if (notice)
             ctx.enrich.notice(notice);
         return {

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts

@@ -19,9 +19,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
- * Extract references from a `<back>` node. Prefers mixed-citation over
- * element-citation, descending into `<citation-alternatives>` when a ref carries
- * both forms there rather than as direct children of `<ref>`.
+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
+ * carries both forms there rather than as direct children of `<ref>`. Mixed
+ * citations are read verbatim; structured element citations are rendered
+ * field-by-field with separators (see `renderElementCitation`).
  */
 export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
 /**

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CA4BlF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
+{"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AAgFD;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAoClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}

package/dist/services/ncbi/parsing/pmc-article-parser.js

@@ -207,9 +207,68 @@ function extractSection(sec) {
 }
 // ─── References ─────────────────────────────────────────────────────────────
 /**
- * Extract references from a `<back>` node. Prefers mixed-citation over
- * element-citation, descending into `<citation-alternatives>` when a ref carries
- * both forms there rather than as direct children of `<ref>`.
+ * `pub-id-type` → human label, so the trailing identifiers in a rendered
+ * `<element-citation>` read as `PMID 37657419` rather than a bare number run.
+ */
+const PUB_ID_LABELS = {
+    pmid: 'PMID',
+    doi: 'DOI',
+    pmcid: 'PMCID',
+};
+/** Render one `<person-group>` child — a `<name>`, `<collab>`, or `<etal>`. */
+function renderCitationName(node) {
+    const tag = tagNameOf(node);
+    if (tag === 'name' || tag === 'string-name') {
+        const surname = textContent(findOne(node, 'surname'));
+        const given = textContent(findOne(node, 'given-names'));
+        return [surname, given].filter(Boolean).join(' ') || textContent(node);
+    }
+    if (tag === 'collab')
+        return textContent(node);
+    if (tag === 'etal')
+        return 'et al.';
+    return '';
+}
+/**
+ * Render a structured `<element-citation>` as a readable, delimited string.
+ * Its child elements carry no punctuation between them, so a flat
+ * `textContent()` runs every field together (`DomanJ.L.…Cell18618…`). Walk the
+ * direct children in document order, joining author names with `, ` and
+ * labeling typed `<pub-id>`s, so the output reads as a citation rather than a
+ * token run. (#69)
+ */
+function renderElementCitation(node) {
+    const parts = [];
+    for (const child of childrenOf(node)) {
+        const tag = tagNameOf(child);
+        if (tag === 'person-group') {
+            const names = childrenOf(child).map(renderCitationName).filter(Boolean);
+            if (names.length > 0)
+                parts.push(names.join(', '));
+        }
+        else if (tag === 'pub-id') {
+            const value = textContent(child);
+            if (value) {
+                const label = PUB_ID_LABELS[attrOf(child, 'pub-id-type') ?? ''];
+                parts.push(label ? `${label} ${value}` : value);
+            }
+        }
+        else {
+            // Element field (source, volume, year, fpage, …) or a bare text node;
+            // textContent renders both, and empty results drop out of the join.
+            const text = textContent(child);
+            if (text)
+                parts.push(text);
+        }
+    }
+    return parts.join(' ');
+}
+/**
+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
+ * carries both forms there rather than as direct children of `<ref>`. Mixed
+ * citations are read verbatim; structured element citations are rendered
+ * field-by-field with separators (see `renderElementCitation`).
  */
 export function extractReferences(back) {
     if (!back)
@@ -224,10 +283,18 @@ export function extractReferences(back) {
         // <mixed-citation>). findOne matches direct children only, so resolve that
         // container first; refs with a direct citation node fall through to `ref`.
         const container = findOne(ref, 'citation-alternatives') ?? ref;
-        const citationNode = findOne(container, 'mixed-citation') ?? findOne(container, 'element-citation');
-        if (!citationNode)
-            continue;
-        const citation = textContent(citationNode);
+        const mixedCitation = findOne(container, 'mixed-citation');
+        const elementCitation = findOne(container, 'element-citation');
+        // <mixed-citation> carries punctuation in the text nodes between its
+        // elements, so textContent() reads correctly. <element-citation> children
+        // have no separators — render the structured fields explicitly. (#69)
+        let citation = '';
+        if (mixedCitation) {
+            citation = textContent(mixedCitation);
+        }
+        else if (elementCitation) {
+            citation = renderElementCitation(elementCitation);
+        }
         if (!citation)
             continue;
         const id = attrOf(ref, 'id');

package/dist/services/ncbi/parsing/pmc-article-parser.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts

@@ -33,7 +33,12 @@ export declare class NcbiResponseHandler {
      * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
      * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
      * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children.
+     * between text nodes and adjacent inline children. `parseTagValue: false`
+     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
+     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
+     * every value on this path is `String()`-ed downstream, so coercion is pure
+     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
+     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     private readonly orderedXmlParser;
     constructor();

package/dist/services/ncbi/response-handler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}

package/dist/services/ncbi/response-handler.js

@@ -230,7 +230,12 @@ export class NcbiResponseHandler {
      * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
      * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
      * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children.
+     * between text nodes and adjacent inline children. `parseTagValue: false`
+     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
+     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
+     * every value on this path is `String()`-ed downstream, so coercion is pure
+     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
+     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     orderedXmlParser;
     constructor() {
@@ -246,7 +251,7 @@ export class NcbiResponseHandler {
             preserveOrder: true,
             ignoreAttributes: false,
             attributeNamePrefix: '@_',
-            parseTagValue: true,
+            parseTagValue: false,
             trimValues: false,
             processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,

package/dist/services/ncbi/response-handler.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.9.0",
+  "version": "2.9.2",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -81,18 +81,18 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.21",
+    "@cyanheads/mcp-ts-core": "^0.10.5",
     "defuddle": "^0.18.1",
     "fast-xml-parser": "^5.8.0",
     "linkedom": "^0.18.12",
     "pino-pretty": "^13.1.3",
-    "sanitize-html": "^2.17.4",
+    "sanitize-html": "^2.17.5",
     "unpdf": "^1.6.2",
     "zod": "^4.4.3"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.16",
-    "@types/node": "^25.9.2",
+    "@types/node": "^25.9.3",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.8",
     "depcheck": "^1.4.7",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.9.0",
+  "version": "2.9.2",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.9.0",
+      "version": "2.9.2",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.9.0",
+      "version": "2.9.2",
       "packageArguments": [
         {
           "type": "positional",