fix(rate-limit): make unstable resource fields optional and allow passthrough

[qyo123oyq]

Problem

get_rate_limit fails with:

MCP error -32603: Invalid input: [{"code":"invalid_type","expected":"object","received":"undefined","path":["resources","code_scanning_upload"],"message":"Required"}]

Root cause

RateLimitSchema in src/operations/rate_limit.ts marks every resource field as required (z.object defaults to required). GitHub's /rate_limit response no longer includes code_scanning_upload, and the set of resource fields varies by account type and over time, so RateLimitSchema.parse(response) throws on real responses.

Changes

In src/operations/rate_limit.ts:

• Keep core, search, graphql required (always present in practice).
• Mark integration_manifest, code_scanning_upload, actions_runner_registration, scim, dependency_snapshots as .optional().
• Add .passthrough() on the resources object so newly introduced resource fields don't break parsing.

Verification

Against the live GitHub API, get_rate_limit now returns the full payload instead of throwing. The real response contains 14 resource entries — code_scanning_upload is absent (confirming the root cause), and 7 fields not present in the schema (source_import, code_scanning_autofix, dependency_sbom, audit_log, audit_log_streaming, code_search, copilot_usage_records) are now tolerated by .passthrough().

Sample (excerpt):

{
  "resources": {
    "core": { "limit": 5000, "used": 2, "remaining": 4998, "reset": 1782318768 },
    "search": { "limit": 30, "used": 0, "remaining": 30, "reset": 1782315333 },
    "graphql": { "limit": 5000, "used": 0, "remaining": 5000, "reset": 1782318873 },
    "integration_manifest": { "limit": 5000, "used": 0, "remaining": 5000, "reset": 1782318873 },
    "actions_runner_registration": { "limit": 10000, "used": 0, "remaining": 10000, "reset": 1782318873 },
    "scim": { "limit": 15000, "used": 0, "remaining": 15000, "reset": 1782318873 },
    "dependency_snapshots": { "limit": 100, "used": 0, "remaining": 100, "reset": 1782315333 },
    "source_import": { "limit": 100, "used": 0, "remaining": 100, "reset": 1782315333 },
    "audit_log": { "limit": 1750, "used": 0, "remaining": 1750, "reset": 1782318873 },
    "code_search": { "limit": 10, "used": 0, "remaining": 10, "reset": 1782315333 }
  },
  "rate": { "limit": 5000, "used": 2, "remaining": 4998, "reset": 1782318768 }
}

Build passes (yarn build → tsc && shx chmod +x dist/*.js) with no errors.

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🤖 AI usage disclosure: The bug analysis, patch, build verification, and the live get_rate_limit API test for this PR were produced with assistance from an AI coding agent (ZCode). The change was validated end-to-end against the live GitHub API. Submitted at the human contributor's request and under their review; human author confirms the patch and description are accurate.