Scholar MCP

Paste it into your assistant. It asks for the manifest, the server wiring and the skills, and for an honest account of what this record does not say. Read that second file first.

Draft an Agent Plugin (agent-plugins.org, specification 1.1.0) that wraps the
MCP server described below, so that somebody could install one thing and have
an assistant that knows when and how to use it.

An Agent Plugin is one installable unit: a `plugin.json` manifest, an
`mcp.json` that wires up the servers it needs, and a `skills/` directory
where each skill is a folder holding a `SKILL.md`. Hand back every file in
full, each under its own path, ready to save.

1. Write `plugin.json` with `$schema` exactly `https://agent-plugins.org/schemas/1.1.0/plugin.schema.json`. The name is
   1 to 64 characters of a-z, 0-9, `-` and `.`, alphanumeric at both ends, with
   no `--` and no `..` in it.

2. Write `mcp.json` wiring THIS server exactly as its record declares it. A
   remote keeps the URL and the transport type as written. A package keeps the
   registry, the identifier and the version as written. Do not invent a command,
   a port, a flag or an argument that is not in the record.

3. Every secret stays an input. No key, token, password or connection string
   belongs in either file. Declare what has to be supplied, name it, and say what
   it is for.

4. Do not invent tools. The record lists the tools it lists, and if it lists
   none then the honest plugin says the tool list was not published rather than
   guessing one from the description.

5. Skills are jobs, not tools. Write one skill per thing somebody would actually
   ask for, and inside each one say when to reach for this server, what a good
   result looks like, and what to do when it comes back empty. A skill per tool
   is a manual page with a different filename.

6. Say where it stops. Name what this plugin will not do — what it has no tool
   for, what needs a person, and what it must not be pointed at. A plugin with no
   stated edge reads as one with no edge.

7. Keep the author's own words for the description. If you would rather say it
   differently, say yours somewhere else and leave theirs where it is.

8. Record which version of the server you wrapped, and where the record came
   from, at the top of `plugin.json`'s description or in the readme. A plugin
   nobody can trace back to a version is one nobody can update.

Produce a second file alongside them, `LIMITS.md`, and treat it as the more
important of the two. The plugin is for whoever installs it. This is for
whoever has to decide whether installing it is a good idea, and that is
usually a different person who will never read the manifest.

It has three parts.

**What this is built from.** One paragraph: whose server it is, what the
record says it does, which version, and the fact that the record is all you
had. Say plainly that nobody ran it.

**What the record does not say.** One entry per gap. Whether the tool list was
published. What the server does with what it reads. What it costs. Whether it
writes anything anywhere. What credentials it will ask for and what those
credentials can reach. An unanswered question stays an unanswered question:
do not fill one in from the description or from what similar servers usually do.

**What a person has to check before trusting it.** The specific things
somebody should verify for themselves, in the order that would stop them
soonest if the answer is bad.

Write it in plain English, and do not soften it. A plugin drafted from a
directory record is a starting point to argue with, not something to install
into anything that matters.

The server record follows, exactly as the public index holds it. It is
everything I have: nobody has run this server, called a tool on it, or checked
that the address answers.

```json
{
  "server": {
    "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
    "name": "io.github.pvliesdonk/scholar-mcp",
    "description": "FastMCP server for scholarly papers, patents, books and standards with docling PDF conversion",
    "title": "Scholar MCP",
    "repository": {
      "url": "https://github.com/pvliesdonk/scholar-mcp",
      "source": "github"
    },
    "version": "1.9.1",
    "websiteUrl": "https://pvliesdonk.github.io/scholar-mcp/",
    "packages": [
      {
        "registryType": "pypi",
        "identifier": "pvliesdonk-scholar-mcp",
        "version": "1.9.1",
        "runtimeHint": "uvx",
        "transport": {
          "type": "stdio"
        },
        "environmentVariables": [
          {
            "description": "Persistent-state backend URL shared by every pvl-core subsystem that needs state. `memory://` is in-process and lost on restart; `file:///path` persists on one server; `redis://`, `dynamodb://` and `mongodb://` each need their matching extra. When unset, defaults to `file:///data/state` (the volume family Docker images mount), or to `memory://` — with a warning — on a host where that directory is not usable.",
            "default": "file:///data/state",
            "name": "SCHOLAR_MCP_KV_STORE_URL"
          },
          {
            "description": "Comma-separated explicit tool names this instance exposes; every other tool is hidden from listings and cannot be invoked. Names matching no registered tool are inert. Mutually exclusive with `tools_deny`. Takes effect through `apply_tool_visibility`.",
            "name": "SCHOLAR_MCP_TOOLS_ALLOW"
          },
          {
            "description": "Comma-separated explicit tool names hidden from this instance (absent from listings, cannot be invoked). Names matching no registered tool are inert. Mutually exclusive with `tools_allow`. Takes effect through `apply_tool_visibility`.",
            "name": "SCHOLAR_MCP_TOOLS_DENY"
          },
          {
            "description": "Rename this server instance; defaults to the project name.",
            "name": "SCHOLAR_MCP_SERVER_NAME"
          },
          {
            "description": "Replaces the default MCP instructions text sent to clients.",
            "name": "SCHOLAR_MCP_INSTRUCTIONS"
          },
          {
            "description": "Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG.",
            "default": "INFO",
            "choices": [
              "DEBUG",
              "INFO",
              "WARNING",
              "ERROR",
              "CRITICAL"
            ],
            "name": "FASTMCP_LOG_LEVEL"
          },
          {
            "description": "Set false for plain or structured JSON log output.",
            "format": "boolean",
            "default": "true",
            "name": "FASTMCP_ENABLE_RICH_LOGGING"
          },
          {
            "description": "GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.",
            "name": "SCHOLAR_GITHUB_TOKEN"
          },
          {
            "description": "When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them.",
            "format": "boolean",
            "default": "true",
            "name": "SCHOLAR_MCP_READ_ONLY"
          },
          {
            "description": "Semantic Scholar API key. Optional but strongly recommended: unauthenticated requests are limited to ~1 req/s. Request one at https://www.semanticscholar.org/product/api#api-key-form.",
            "name": "SCHOLAR_MCP_S2_API_KEY"
          },
          {
            "description": "Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error.",
            "name": "SCHOLAR_MCP_DOCLING_URL"
          },
          {
            "description": "OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion.",
            "name": "SCHOLAR_MCP_VLM_API_URL"
          },
          {
            "description": "API key for the VLM endpoint.",
            "name": "SCHOLAR_MCP_VLM_API_KEY"
          },
          {
            "description": "Model name to use with the VLM endpoint.",
            "default": "gpt-4o",
            "name": "SCHOLAR_MCP_VLM_MODEL"
          },
          {
            "description": "Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/).",
            "format": "filepath",
            "default": "/data/scholar-mcp",
            "name": "SCHOLAR_MCP_CACHE_DIR"
          },
          {
            "description": "Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source.",
            "name": "SCHOLAR_MCP_CONTACT_EMAIL"
          },
          {
            "description": "EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register.",
            "name": "SCHOLAR_MCP_EPO_CONSUMER_KEY"
          },
          {
            "description": "EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.",
            "name": "SCHOLAR_MCP_EPO_CONSUMER_SECRET"
          },
          {
            "description": "Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.",
            "name": "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY"
          }
        ]
      },
      {
        "registryType": "oci",
        "identifier": "ghcr.io/pvliesdonk/scholar-mcp:v1.9.1",
        "transport": {
          "type": "streamable-http",
          "url": "http://localhost:{--port}/mcp"
        },
        "packageArguments": [
          {
            "description": "Port for the HTTP transport",
            "default": "8000",
            "type": "named",
            "name": "--port"
          }
        ],
        "environmentVariables": [
          {
            "description": "Public base URL of the deployed server, e.g. `https://mcp.example.com`. Required for OIDC. Also the fallback source of the MCP Apps domain when `app_domain` is unset.",
            "placeholder": "https://mcp.example.com",
            "name": "SCHOLAR_MCP_BASE_URL"
          },
          {
            "description": "Single shared bearer token; enables bearer auth unless `bearer_tokens_file` is set, which takes precedence.",
            "isSecret": true,
            "placeholder": "<secret>",
            "name": "SCHOLAR_MCP_BEARER_TOKEN"
          },
          {
            "description": "OIDC discovery document URL, e.g. `https://auth.example.com/.well-known/openid-configuration`.",
            "placeholder": "https://auth.example.com/.well-known/openid-configuration",
            "name": "SCHOLAR_MCP_OIDC_CONFIG_URL"
          },
          {
            "description": "OIDC client identifier registered with the provider.",
            "placeholder": "mcp-client",
            "name": "SCHOLAR_MCP_OIDC_CLIENT_ID"
          },
          {
            "description": "OIDC client secret registered with the provider.",
            "isSecret": true,
            "placeholder": "your-client-secret",
            "name": "SCHOLAR_MCP_OIDC_CLIENT_SECRET"
          },
          {
            "description": "Expected `aud` claim; tokens issued for another audience are rejected.",
            "placeholder": "mcp-api",
            "name": "SCHOLAR_MCP_OIDC_AUDIENCE"
          },
          {
            "description": "Scopes a caller must present, space- or comma-separated. Defaults to `openid` in oidc-proxy mode.",
            "default": "openid",
            "name": "SCHOLAR_MCP_OIDC_REQUIRED_SCOPES"
          },
          {
            "description": "Scopes advertised to MCP clients in protected-resource metadata, space- or comma-separated. Overrides the default `openid offline_access`; `oidc_required_scopes` is always added on top. Set this when the registered client is not permitted `offline_access`, or to have clients request extra claim scopes (e.g. `groups`) without also requiring them in every token.",
            "default": "openid offline_access",
            "name": "SCHOLAR_MCP_OIDC_ADVERTISED_SCOPES"
          },
          {
            "description": "Signing key for issued JWTs; used in oidc-proxy mode only. When unset, the key is derived deterministically from `oidc_client_secret`, so tokens survive a restart — but rotating that secret invalidates every issued token. Set this explicitly to decouple token validity from secret rotation. Generate with `openssl rand -hex 32`.",
            "isSecret": true,
            "default": "derived",
            "name": "SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY"
          },
          {
            "description": "Validate the access token instead of the id token.",
            "format": "boolean",
            "default": "false",
            "name": "SCHOLAR_MCP_OIDC_VERIFY_ACCESS_TOKEN"
          },
          {
            "description": "Persistent-state backend URL shared by every pvl-core subsystem that needs state. `memory://` is in-process and lost on restart; `file:///path` persists on one server; `redis://`, `dynamodb://` and `mongodb://` each need their matching extra. When unset, defaults to `file:///data/state` (the volume family Docker images mount), or to `memory://` — with a warning — on a host where that directory is not usable.",
            "default": "file:///data/state",
            "name": "SCHOLAR_MCP_KV_STORE_URL"
          },
          {
            "description": "MCP Apps iframe domain, used for CSP sandboxing. Overrides the host derived from `base_url`.",
            "name": "SCHOLAR_MCP_APP_DOMAIN"
          },
          {
            "description": "Comma-separated explicit tool names this instance exposes; every other tool is hidden from listings and cannot be invoked. Names matching no registered tool are inert. Mutually exclusive with `tools_deny`. Takes effect through `apply_tool_visibility`.",
            "name": "SCHOLAR_MCP_TOOLS_ALLOW"
          },
          {
            "description": "Comma-separated explicit tool names hidden from this instance (absent from listings, cannot be invoked). Names matching no registered tool are inert. Mutually exclusive with `tools_allow`. Takes effect through `apply_tool_visibility`.",
            "name": "SCHOLAR_MCP_TOOLS_DENY"
          },
          {
            "description": "Explicit auth-mode override, accepting `remote` or `oidc-proxy` (case- and whitespace-insensitive). When unset the mode is auto-detected from which auth variables are set; the override exists because having all four OIDC variables set is ambiguous between those two modes. Other values are ignored with a warning.",
            "name": "SCHOLAR_MCP_AUTH_MODE"
          },
          {
            "description": "Path to a TOML file mapping bearer tokens to subjects; overrides the single-token `bearer_token` mode.",
            "format": "filepath",
            "placeholder": "/etc/scholar-mcp/tokens.toml",
            "name": "SCHOLAR_MCP_BEARER_TOKENS_FILE"
          },
          {
            "description": "Subject assigned to the single-token bearer mode; ignored when `bearer_tokens_file` is set, since mapped mode carries per-token subjects.",
            "default": "bearer-anon",
            "name": "SCHOLAR_MCP_BEARER_DEFAULT_SUBJECT"
          },
          {
            "description": "Rename this server instance; defaults to the project name.",
            "name": "SCHOLAR_MCP_SERVER_NAME"
          },
          {
            "description": "Replaces the default MCP instructions text sent to clients.",
            "name": "SCHOLAR_MCP_INSTRUCTIONS"
          },
          {
            "description": "Mount path for the MCP endpoint.",
            "default": "/mcp",
            "name": "SCHOLAR_MCP_HTTP_PATH"
          },
          {
            "description": "Run the server process as this UID; the container entrypoint chowns writable paths to match.",
            "format": "number",
            "default": "1000",
            "name": "PUID"
          },
          {
            "description": "Run the server process as this GID; pair with PUID to match the owner of a mounted volume.",
            "format": "number",
            "default": "1000",
            "name": "PGID"
          },
          {
            "description": "Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG.",
            "default": "INFO",
            "choices": [
              "DEBUG",
              "INFO",
              "WARNING",
              "ERROR",
              "CRITICAL"
            ],
            "name": "FASTMCP_LOG_LEVEL"
          },
          {
            "description": "Set false for plain or structured JSON log output.",
            "format": "boolean",
            "default": "true",
            "name": "FASTMCP_ENABLE_RICH_LOGGING"
          },
          {
            "description": "GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.",
            "name": "SCHOLAR_GITHUB_TOKEN"
          },
          {
            "description": "When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them.",
            "format": "boolean",
            "default": "true",
            "name": "SCHOLAR_MCP_READ_ONLY"
          },
          {
            "description": "Semantic Scholar API key. Optional but strongly recommended: unauthenticated requests are limited to ~1 req/s. Request one at https://www.semanticscholar.org/product/api#api-key-form.",
            "name": "SCHOLAR_MCP_S2_API_KEY"
          },
          {
            "description": "Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error.",
            "name": "SCHOLAR_MCP_DOCLING_URL"
          },
          {
            "description": "OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion.",
            "name": "SCHOLAR_MCP_VLM_API_URL"
          },
          {
            "description": "API key for the VLM endpoint.",
            "name": "SCHOLAR_MCP_VLM_API_KEY"
          },
          {
            "description": "Model name to use with the VLM endpoint.",
            "default": "gpt-4o",
            "name": "SCHOLAR_MCP_VLM_MODEL"
          },
          {
            "description": "Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/).",
            "format": "filepath",
            "default": "/data/scholar-mcp",
            "name": "SCHOLAR_MCP_CACHE_DIR"
          },
          {
            "description": "Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source.",
            "name": "SCHOLAR_MCP_CONTACT_EMAIL"
          },
          {
            "description": "EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register.",
            "name": "SCHOLAR_MCP_EPO_CONSUMER_KEY"
          },
          {
            "description": "EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.",
            "name": "SCHOLAR_MCP_EPO_CONSUMER_SECRET"
          },
          {
            "description": "Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.",
            "name": "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY"
          }
        ]
      }
    ]
  },
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "active",
      "statusChangedAt": "2026-08-22T08:56:19.258569Z",
      "publishedAt": "2026-08-22T08:56:19.258569Z",
      "updatedAt": "2026-08-22T08:56:19.258569Z",
      "isLatest": true
    }
  }
}
```

The server is listed as "Scholar MCP".