@cyanheads/openalex-mcp-server 0.7.13 → 0.7.15

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Files changed (36) hide show
  1. package/AGENTS.md +25 -10
  2. package/CLAUDE.md +25 -10
  3. package/README.md +167 -88
  4. package/changelog/0.7.x/0.7.14.md +28 -0
  5. package/changelog/0.7.x/0.7.15.md +33 -0
  6. package/changelog/template.md +7 -7
  7. package/dist/index.js +2 -0
  8. package/dist/index.js.map +1 -1
  9. package/dist/mcp-server/prompts/definitions/literature-review.prompt.js +1 -1
  10. package/dist/mcp-server/prompts/definitions/literature-review.prompt.js.map +1 -1
  11. package/dist/mcp-server/tools/definitions/analyze-trends.tool.d.ts +19 -0
  12. package/dist/mcp-server/tools/definitions/analyze-trends.tool.d.ts.map +1 -1
  13. package/dist/mcp-server/tools/definitions/analyze-trends.tool.js +32 -3
  14. package/dist/mcp-server/tools/definitions/analyze-trends.tool.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/citation-graph.tool.d.ts +12 -1
  16. package/dist/mcp-server/tools/definitions/citation-graph.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/citation-graph.tool.js +55 -33
  18. package/dist/mcp-server/tools/definitions/citation-graph.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/resolve-name.tool.d.ts +11 -0
  20. package/dist/mcp-server/tools/definitions/resolve-name.tool.d.ts.map +1 -1
  21. package/dist/mcp-server/tools/definitions/resolve-name.tool.js +13 -1
  22. package/dist/mcp-server/tools/definitions/resolve-name.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/search-entities.tool.d.ts +40 -0
  24. package/dist/mcp-server/tools/definitions/search-entities.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/search-entities.tool.js +132 -20
  26. package/dist/mcp-server/tools/definitions/search-entities.tool.js.map +1 -1
  27. package/dist/services/openalex/openalex-service.d.ts +16 -0
  28. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  29. package/dist/services/openalex/openalex-service.js +105 -29
  30. package/dist/services/openalex/openalex-service.js.map +1 -1
  31. package/dist/services/openalex/types.d.ts +11 -0
  32. package/dist/services/openalex/types.d.ts.map +1 -1
  33. package/dist/services/openalex/types.js +7 -0
  34. package/dist/services/openalex/types.js.map +1 -1
  35. package/package.json +7 -7
  36. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,11 +1,11 @@
1
1
  # Developer Protocol
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  **Server:** openalex-mcp-server
4
- **Version:** 0.7.13
5
- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.0`
4
+ **Version:** 0.7.15
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
6
6
  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
7
7
  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
8
- **Zod:** ^4.6.1
8
+ **Zod:** ^4.6.5
9
9
 
10
10
  > **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.
11
11
 
@@ -43,6 +43,8 @@ No resources — entity lookups need `select` for payload control, which fits to
43
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  | `OPENALEX_MAILTO` | No | Email sent as `mailto=` to identify yourself to OpenAlex (the "polite pool"); a courtesy identifier, separate from the API key |
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  | `OPENALEX_BASE_URL` | No | Default: `https://api.openalex.org` |
45
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+ **Session mode:** `createApp({ sessionMode: 'stateless' })` in `src/index.ts` — no tool gates on `ctx.requestInput`, so every call completes in one round trip. An explicit `MCP_SESSION_MODE` still overrides it; `.env.example` and the `Dockerfile` set the same value. No service holds a watcher, socket, or ref'd timer, so there is no `teardown` hook.
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+
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  ---
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  ## What's Next?
@@ -71,6 +73,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
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  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
72
74
  - **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.
73
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  - **Secrets in env vars only** — never hardcoded.
76
+ - **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.
74
77
  - **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.
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79
  ---
@@ -147,13 +150,13 @@ Handlers receive a unified `ctx` object. Key properties:
147
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  | Property | Description |
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  |:---------|:------------|
150
- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino and client-visible `notifications/message`. |
153
+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
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  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
152
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  | `ctx.requestInput` | Suspend and ask the caller for more input with `return ctx.requestInput(...)`; the handler is re-entered with answers. |
153
156
  | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. |
154
157
  | `ctx.enrich` | Success-path agent context for notices, query echoes, totals, and truncation disclosure. Reaches both client response surfaces. |
155
158
  | `ctx.content` | Non-text content blocks appended to `content[]`; never enters `structuredContent`. |
156
- | `ctx.signal` | `AbortSignal` for cancellation. Passed to `fetch()` in the OpenAlex service. |
159
+ | `ctx.signal` | `AbortSignal` for cancellation. Passed to `withRetry` in the OpenAlex service, whose per-attempt signal reaches `fetch()`. |
157
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  | `ctx.fail` | Typed throw keyed by a declared `errors[]` contract — `ctx.fail(reason, msg?, data?)`. Auto-populates `data.reason` and resolves `code` from the contract. |
158
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  | `ctx.recoveryFor` | Opt-in resolver returning `{ recovery: { hint } }` for a declared reason. Spread into `data` at throw site to surface contract recovery on the wire. |
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  | `ctx.requestId` | Unique request ID. |
@@ -165,7 +168,7 @@ Handlers receive a unified `ctx` object. Key properties:
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166
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  Handlers throw — the framework catches, classifies, and formats.
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168
- **Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union — `ctx.fail('typo')` is a TS error, `data.reason` is auto-populated, and the linter enforces conformance against the handler. The `recovery` field is required (≥5 words). Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire.
171
+ **Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, thrownBy? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union — `ctx.fail('typo')` is a TS error, `data.reason` is auto-populated, and the linter enforces conformance against the handler. The `recovery` field is required (≥5 words). Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire; `error-contract-recovery-unforwarded` warns per `ctx.fail` site that forwards neither the resolver nor its own `recovery` key.
169
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170
173
  ```ts
171
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  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
@@ -174,6 +177,10 @@ errors: [
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  { reason: 'semantic_per_page_cap', code: JsonRpcErrorCode.ValidationError,
175
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  when: 'per_page exceeds the semantic-search cap',
176
179
  recovery: 'Reduce per_page to 50 or less, or switch search_mode to keyword.' },
180
+ { reason: 'upstream_timeout', code: JsonRpcErrorCode.Timeout,
181
+ when: 'OpenAlex did not respond within the request deadline',
182
+ recovery: 'Retry after a short delay, or narrow the request with tighter filters.',
183
+ thrownBy: 'service' },
177
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  ],
178
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  async handler(input, ctx) {
179
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  if (overCap) throw ctx.fail('semantic_per_page_cap', message, { ...ctx.recoveryFor('semantic_per_page_cap') });
@@ -182,7 +189,7 @@ async handler(input, ctx) {
182
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  **Declare contracts inline on each tool, even when similar across tools.** The contract is part of the tool's documented public surface — reading one tool definition file should give the full picture. Don't extract a shared `errors[]` constant; per-tool repetition is the intended cost of locality.
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- The OpenAlex service throws factory errors (`notFound`, `rateLimited`, etc.) based on upstream status codes; those bubble through and are auto-classified. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely without needing to be declared on a contract.
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+ The OpenAlex service throws factory errors (`notFound`, `rateLimited`, etc.) based on upstream status codes, carrying the contract `reason` on `data.reason` and the recovery via `ctx.recoveryFor(reason)`; those bubble through and are auto-classified. Every such entry carries `thrownBy: 'service'` — lint-only metadata that tells `error-contract-unthrown`, whose scan reads the handler body alone, to skip a reason produced a layer below it. Handler-local precondition throws stay inline and unmarked so the rule keeps checking them: `semantic_without_query`, `semantic_per_page_cap`, `semantic_with_cursor`, `page_without_semantic`, `sample_with_cursor`, `sample_with_page`, and `seed_without_sample` on `openalex_search_entities`; `reserved_filter_key` and the seed-lookup `entity_not_found` on `openalex_get_citation_graph`. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely without needing to be declared on a contract.
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  **Fallback for ad-hoc throws:** error factories or plain `Error`.
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@@ -234,7 +241,7 @@ src/
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  ## Skills
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- 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.
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+ 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.
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  **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `framework-skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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@@ -293,8 +300,10 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run audit:fix` | Run `bun audit fix` to upgrade vulnerable packages within existing ranges. |
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  | `bun run audit:refresh` | Delete `bun.lock` and reinstall; last resort after `audit:fix`, targeted updates, and `bun dedupe`. |
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  | `bun run tree` | Generate directory structure doc |
296
- | `bun run format` | Auto-fix formatting |
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- | `bun run lint:mcp` | Validate MCP tool/prompt definitions |
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+ | `bun run format` | Auto-fix formatting (safe fixes only) |
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+ | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
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+ | `bun run lint:mcp` | Validate MCP tool/prompt definitions (rule catalog: `api-linter` skill) |
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+ | `bun run lint:packaging` | Packaging surface checks — env-var parity, plugin metadata, README version badge (run by devcheck) |
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  | `bun run list-skills` | List available skills |
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  | `bun run test` | Run tests |
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  | `bun run start:stdio` | Production mode (stdio, after `rebuild`) |
@@ -304,6 +313,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run release:github` | Create GitHub Release from the latest annotated tag (title `v<VERSION>: <subject>`, optional `.mcpb` attach) |
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  | `bun run bundle` | Build and pack as `.mcpb` for one-click Claude Desktop install |
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315
 
316
+ **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.
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+
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  ---
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309
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  ## Bundling
@@ -319,12 +330,16 @@ Every bundle option must be wired as `${user_config.<option>}`; optional strings
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  Directory-based, grouped by minor series via the `.x` semver-wildcard convention. Source of truth: `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.6.x/0.6.12.md`) — one file per release, shipped in the npm package. At release, author the per-version file with a concrete version and date, then run `bun run changelog:build` to regenerate the rollup. `changelog/template.md` is a **pristine format reference** — never edited or moved. `CHANGELOG.md` is a **navigation index** regenerated by `bun run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
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333
+ Each per-version file opens with YAML frontmatter: `summary` (required, ≤350 chars — powers the rollup index), `breaking` (true when consumers must change code on upgrade), `security` (true only for a security fix in this server's own source, never a dependency CVE bump — those go under `## Dependencies`), and optional `agent-notes` for downstream maintenance agents. See `changelog/template.md` for the full layout.
334
+
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  **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.
323
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324
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  ---
325
338
 
326
339
  ## Publishing
327
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341
+ **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.
342
+
328
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  Run the `release-and-publish` skill — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, then publishes to every applicable destination. The full reference:
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330
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  ```bash
package/CLAUDE.md CHANGED
@@ -1,11 +1,11 @@
1
1
  # Developer Protocol
2
2
 
3
3
  **Server:** openalex-mcp-server
4
- **Version:** 0.7.13
5
- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.0`
4
+ **Version:** 0.7.15
5
+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
6
6
  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
7
7
  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
8
- **Zod:** ^4.6.1
8
+ **Zod:** ^4.6.5
9
9
 
10
10
  > **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.
11
11
 
@@ -43,6 +43,8 @@ No resources — entity lookups need `select` for payload control, which fits to
43
43
  | `OPENALEX_MAILTO` | No | Email sent as `mailto=` to identify yourself to OpenAlex (the "polite pool"); a courtesy identifier, separate from the API key |
44
44
  | `OPENALEX_BASE_URL` | No | Default: `https://api.openalex.org` |
45
45
 
46
+ **Session mode:** `createApp({ sessionMode: 'stateless' })` in `src/index.ts` — no tool gates on `ctx.requestInput`, so every call completes in one round trip. An explicit `MCP_SESSION_MODE` still overrides it; `.env.example` and the `Dockerfile` set the same value. No service holds a watcher, socket, or ref'd timer, so there is no `teardown` hook.
47
+
46
48
  ---
47
49
 
48
50
  ## What's Next?
@@ -71,6 +73,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
71
73
  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
72
74
  - **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.
73
75
  - **Secrets in env vars only** — never hardcoded.
76
+ - **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.
74
77
  - **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.
75
78
 
76
79
  ---
@@ -147,13 +150,13 @@ Handlers receive a unified `ctx` object. Key properties:
147
150
 
148
151
  | Property | Description |
149
152
  |:---------|:------------|
150
- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino and client-visible `notifications/message`. |
153
+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
151
154
  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
152
155
  | `ctx.requestInput` | Suspend and ask the caller for more input with `return ctx.requestInput(...)`; the handler is re-entered with answers. |
153
156
  | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. |
154
157
  | `ctx.enrich` | Success-path agent context for notices, query echoes, totals, and truncation disclosure. Reaches both client response surfaces. |
155
158
  | `ctx.content` | Non-text content blocks appended to `content[]`; never enters `structuredContent`. |
156
- | `ctx.signal` | `AbortSignal` for cancellation. Passed to `fetch()` in the OpenAlex service. |
159
+ | `ctx.signal` | `AbortSignal` for cancellation. Passed to `withRetry` in the OpenAlex service, whose per-attempt signal reaches `fetch()`. |
157
160
  | `ctx.fail` | Typed throw keyed by a declared `errors[]` contract — `ctx.fail(reason, msg?, data?)`. Auto-populates `data.reason` and resolves `code` from the contract. |
158
161
  | `ctx.recoveryFor` | Opt-in resolver returning `{ recovery: { hint } }` for a declared reason. Spread into `data` at throw site to surface contract recovery on the wire. |
159
162
  | `ctx.requestId` | Unique request ID. |
@@ -165,7 +168,7 @@ Handlers receive a unified `ctx` object. Key properties:
165
168
 
166
169
  Handlers throw — the framework catches, classifies, and formats.
167
170
 
168
- **Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union — `ctx.fail('typo')` is a TS error, `data.reason` is auto-populated, and the linter enforces conformance against the handler. The `recovery` field is required (≥5 words). Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire.
171
+ **Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, thrownBy? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union — `ctx.fail('typo')` is a TS error, `data.reason` is auto-populated, and the linter enforces conformance against the handler. The `recovery` field is required (≥5 words). Spread `ctx.recoveryFor('reason')` into `data` to opt the contract recovery onto the wire; `error-contract-recovery-unforwarded` warns per `ctx.fail` site that forwards neither the resolver nor its own `recovery` key.
169
172
 
170
173
  ```ts
171
174
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
@@ -174,6 +177,10 @@ errors: [
174
177
  { reason: 'semantic_per_page_cap', code: JsonRpcErrorCode.ValidationError,
175
178
  when: 'per_page exceeds the semantic-search cap',
176
179
  recovery: 'Reduce per_page to 50 or less, or switch search_mode to keyword.' },
180
+ { reason: 'upstream_timeout', code: JsonRpcErrorCode.Timeout,
181
+ when: 'OpenAlex did not respond within the request deadline',
182
+ recovery: 'Retry after a short delay, or narrow the request with tighter filters.',
183
+ thrownBy: 'service' },
177
184
  ],
178
185
  async handler(input, ctx) {
179
186
  if (overCap) throw ctx.fail('semantic_per_page_cap', message, { ...ctx.recoveryFor('semantic_per_page_cap') });
@@ -182,7 +189,7 @@ async handler(input, ctx) {
182
189
 
183
190
  **Declare contracts inline on each tool, even when similar across tools.** The contract is part of the tool's documented public surface — reading one tool definition file should give the full picture. Don't extract a shared `errors[]` constant; per-tool repetition is the intended cost of locality.
184
191
 
185
- The OpenAlex service throws factory errors (`notFound`, `rateLimited`, etc.) based on upstream status codes; those bubble through and are auto-classified. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely without needing to be declared on a contract.
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+ The OpenAlex service throws factory errors (`notFound`, `rateLimited`, etc.) based on upstream status codes, carrying the contract `reason` on `data.reason` and the recovery via `ctx.recoveryFor(reason)`; those bubble through and are auto-classified. Every such entry carries `thrownBy: 'service'` — lint-only metadata that tells `error-contract-unthrown`, whose scan reads the handler body alone, to skip a reason produced a layer below it. Handler-local precondition throws stay inline and unmarked so the rule keeps checking them: `semantic_without_query`, `semantic_per_page_cap`, `semantic_with_cursor`, `page_without_semantic`, `sample_with_cursor`, `sample_with_page`, and `seed_without_sample` on `openalex_search_entities`; `reserved_filter_key` and the seed-lookup `entity_not_found` on `openalex_get_citation_graph`. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely without needing to be declared on a contract.
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  **Fallback for ad-hoc throws:** error factories or plain `Error`.
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@@ -234,7 +241,7 @@ src/
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  ## Skills
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- 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.
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+ 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.
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  **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `framework-skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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@@ -293,8 +300,10 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run audit:fix` | Run `bun audit fix` to upgrade vulnerable packages within existing ranges. |
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  | `bun run audit:refresh` | Delete `bun.lock` and reinstall; last resort after `audit:fix`, targeted updates, and `bun dedupe`. |
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  | `bun run tree` | Generate directory structure doc |
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- | `bun run format` | Auto-fix formatting |
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- | `bun run lint:mcp` | Validate MCP tool/prompt definitions |
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+ | `bun run format` | Auto-fix formatting (safe fixes only) |
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+ | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
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+ | `bun run lint:mcp` | Validate MCP tool/prompt definitions (rule catalog: `api-linter` skill) |
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+ | `bun run lint:packaging` | Packaging surface checks — env-var parity, plugin metadata, README version badge (run by devcheck) |
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  | `bun run list-skills` | List available skills |
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  | `bun run test` | Run tests |
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  | `bun run start:stdio` | Production mode (stdio, after `rebuild`) |
@@ -304,6 +313,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run release:github` | Create GitHub Release from the latest annotated tag (title `v<VERSION>: <subject>`, optional `.mcpb` attach) |
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  | `bun run bundle` | Build and pack as `.mcpb` for one-click Claude Desktop install |
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+ **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.
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+
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  ---
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  ## Bundling
@@ -319,12 +330,16 @@ Every bundle option must be wired as `${user_config.<option>}`; optional strings
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  Directory-based, grouped by minor series via the `.x` semver-wildcard convention. Source of truth: `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.6.x/0.6.12.md`) — one file per release, shipped in the npm package. At release, author the per-version file with a concrete version and date, then run `bun run changelog:build` to regenerate the rollup. `changelog/template.md` is a **pristine format reference** — never edited or moved. `CHANGELOG.md` is a **navigation index** regenerated by `bun run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
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+ Each per-version file opens with YAML frontmatter: `summary` (required, ≤350 chars — powers the rollup index), `breaking` (true when consumers must change code on upgrade), `security` (true only for a security fix in this server's own source, never a dependency CVE bump — those go under `## Dependencies`), and optional `agent-notes` for downstream maintenance agents. See `changelog/template.md` for the full layout.
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+
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  **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.
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  ---
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  ## Publishing
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+ **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.
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+
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  Run the `release-and-publish` skill — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, then publishes to every applicable destination. The full reference:
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  ```bash