Bug: workers-bindings MCP emits {"not":{}} in tool schemas, breaking strict LLM function-calling (Kimi, Gemini, OpenAI strict)

Describe the bug

The hosted workers-bindings MCP server (https://bindings.mcp.cloudflare.com/mcp, serverInfo.version: "0.4.7") returns tool input schemas in which every optional parameter is encoded as a {"not":{}} ("match nothing") branch inside an anyOf:

"primary_location_hint": {
  "anyOf": [
    { "not": {} },
    { "type": "string", "enum": ["wnam","enam","weur","eeur","apac","oc"] }
  ]
}

Several LLM providers' function-calling validators reject the JSON Schema not keyword outright and fail the entire request (not just the one tool) the moment any such tool is in the tool list. Observed errors:

• Kimi / Moonshot: Error from provider: JSON Schema not supported: could not understand the instance {'not': {}}
• Google Gemini: rejects anyOf/not tool schemas (see v4: toJSONSchema anyOf incompatibility with Gemini API Function Calling colinhacks/zod#5807)
• OpenAI strict mode / Fireworks: same class of rejection

Because the failure aborts the whole request, enabling this MCP server makes the agent unusable with these models — every message fails, regardless of whether the user ever calls a binding tool.

To Reproduce

1. Connect any MCP client backed by a strict-schema model (e.g. Kimi K2.x, Gemini) to https://bindings.mcp.cloudflare.com/mcp.
2. Send any message that includes the server's tools in the request.
3. The provider rejects the request with JSON Schema not supported: could not understand the instance {'not': {}}.

Affected tools include d1_database_create (primary_location_hint), d1_database_query (params), hyperdrive_configs_list (page, per_page, order, direction), and hyperdrive_config_edit (name, database, host, port, scheme, user, caching_*). A tools/list against the live server shows 18 distinct {"not":{}} instances.

Expected behavior

Optional parameters should be expressed by omitting them from required (and/or a representable union), without a {"not":{}} branch, so the schemas are accepted by mainstream function-calling validators.

Root cause

The tool params are defined with Zod .optional() / .optional().nullable(), e.g. in packages/mcp-common/src/types/d1.types.ts:

export const D1DatabasePrimaryLocationHintParam: z.ZodType<...> =
  z.enum(['wnam','enam','weur','eeur','apac','oc']).optional()

mcp-common pins zod@3.24.2 and @modelcontextprotocol/sdk@1.20.2. The SDK converts schemas with zod-to-json-schema (zodToJsonSchema(tool.inputSchema, { strictUnions: true }) in src/server/mcp.ts). zod-to-json-schema's parseOptionalDef (src/parsers/optional.ts) renders an optional field as:

return { anyOf: [ { not: parseAnyDef(refs) }, innerSchema ] }
// parseAnyDef(refs) === {}  ->  { not: {} }

strictUnions: true does not remove this — it only filters catch-all union members, not the not: {} "not-undefined" arm. So .optional() → { anyOf: [{ not: {} }, T] } for every optional field.

Proposed fix

Option A — schema sanitizer in mcp-common (low-risk, immediate). Post-process each tool's generated JSON Schema before registration: recursively, for any anyOf containing a {"not":{}} member, drop that member; if only one branch remains, inline it. The field is already absent from required, so semantics are preserved. Sketch:

function stripNotEmpty(node: unknown): unknown {
  if (Array.isArray(node)) return node.map(stripNotEmpty)
  if (node && typeof node === 'object') {
    const obj = node as Record<string, unknown>
    if (Array.isArray(obj.anyOf)) {
      const kept = obj.anyOf.filter(
        (m) => !(m && typeof m === 'object'
          && 'not' in m
          && Object.keys((m as any).not ?? {}).length === 0
          && Object.keys(m).length === 1),
      )
      if (kept.length === 1) return { ...stripNotEmpty(kept[0]),
        ...(obj.description ? { description: obj.description } : {}) }
      obj.anyOf = kept.map(stripNotEmpty)
    }
    for (const k of Object.keys(obj)) if (k !== 'anyOf') obj[k] = stripNotEmpty(obj[k])
  }
  return node
}

Option B — migrate to Zod v4 native z.toJSONSchema() (long-term). Zod v4 omits optionals from required without emitting {"not":{}}. Requires bumping zod to ^4, agents to >=0.8.0, and the MCP SDK to a version that calls z.toJSONSchema().

Option C — upstream in @modelcontextprotocol/sdk. The same sanitizer applied after zodToJsonSchema in src/server/mcp.ts would fix this for all MCP servers built on the SDK; cross-referencing modelcontextprotocol/typescript-sdk#745.

Option A is the smallest change that unblocks affected users immediately.

Environment

• Server: workers-bindings 0.4.7 (hosted, https://bindings.mcp.cloudflare.com/mcp)
• mcp-common 0.20.5 — zod@3.24.2, agents@0.2.19, @modelcontextprotocol/sdk@1.20.2
• Clients reproduced with: opencode (Kimi K2.x); also reported with Gemini

References

• zod-to-json-schema optional parser: https://github.com/StefanTerdell/zod-to-json-schema/blob/master/src/parsers/optional.ts
• MCP SDK conversion call: MCP TypeScript SDK generates JSON Schema draft-07, breaking compatibility with modern MCP clients requiring draft-2020-12 modelcontextprotocol/typescript-sdk#745
• Zod v4 / Gemini anyOf incompatibility: v4: toJSONSchema anyOf incompatibility with Gemini API Function Calling colinhacks/zod#5807

Happy to open a PR implementing Option A (sanitizer + test) if a maintainer would like — just give the nod.