Remove graph database access rather than gating it

[adamjohnwright]

Adam, on hosting this publicly: "we don't want the mcp to be providing access to neo4j through cypher or any other direct query." So the capability is gone rather than switched off.

Removed: the three reactome_cypher_* tools, the reactome://graph/schema resource, the Cypher section of the server instructions, the startup schema prefetch, src/clients/neo4j.ts, src/graph/, and the neo4j-driver dependency. NEO4J_URI and MCP_ALLOW_CYPHER are inert — nothing reads them.

Why removed rather than gated, in one fact

Constitution Principle IV already said no deployment holds a Neo4j connection, and enforced it with a gate. That makes the property true of a configuration rather than of the code — and a configuration has as many copies as it has call sites.

#36 found three copies and corrected them. There were four. src/http-server.ts — the entrypoint that actually runs in the hosted deployment — still opened a connection on NEO4J_URI alone:

startHttpServer(port, MCP_HTTP_HOST).then(() => {
  if (NEO4J_URI) { fetchGraphSchema()... }   // still here after #36
})

I missed it while writing a commit message claiming all three surfaces now shared one predicate.

Neither consumer needed graph access anyway. The chatbot queries Neo4j directly, with its own driver in data_generation, when it builds embeddings — the serving path never imports it. The website needs the REST-backed tools only.

The public surface is unchanged at 59 tools. The Cypher tools were only ever the 60th–62nd, and only with both switches on.

The test

tests/no-graph-access.test.ts asserts the absence with the old switches turned on. Asserting it with them off would confirm the gate still works, not that the tools are gone. Five checks: no Cypher tool, no schema resource, no mention in the instructions, no driver dependency, no source file importing a driver.

Verified by sabotage:

• re-registering reactome_cypher_query fails three tests across three files
• the source-walk was checked by pointing it at a package that is imported — an import of a removed dependency cannot compile, and a sabotage that reports "no tests" proves nothing. It named seven real files, so the walker reads what it claims to.

Docs corrected, not deleted

SECURITY.md said the server was designed for a trusted local curator and not hardened for internet-facing use. That is now half wrong and half load-bearing: it still has no auth, TLS or rate limiting of its own, and that belongs at the proxy. What removing graph access changes is the blast radius if the proxy is misconfigured. The constitution and spec 002 record why the gate was replaced, not just that it was.

While in the README: it claimed to list every tool and did not

"Over 40 tools", no GSA section at all, and Pathways undercounted by one — six registered tools documented nowhere, on the file that is about to be the public description of a public server. Now 59, with the missing section, and tests/readme-tools.test.ts fails if a tool goes undocumented or the count drifts. A prose count goes stale the first time someone adds a tool.

Breaking

A curator running this locally over stdio against reactome_neo4j_env loses those three tools, with no replacement in this server. That audience is who they were built for; the decision is deliberate.

104 tests, lint/format/typecheck/build clean under node:22.

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