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fix: patch MCP, Electron, and transitive security dependencies - #12
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Update the MCP client/server to 2.3.1 and the legacy SDK to 1.32.1, Electron to 42.11.3, Zod to 4.6.7, and GraphQL Yoga to 5.24.6. Refresh compatible workspace dependencies and apply security resolutions for Undici, OpenTelemetry, Protobuf, DOMPurify, form-data, shell-quote, and Tinypool. Carry the existing MCP client lazy-loading patch onto 2.3.1 and regenerate the protocol schema and shell bundle.
Validation: The final validation uses the repository-pinned Bun 1.3.11: patched-dependency sentinels, formatting, lint, typecheck, and the complete non-e2e Vitest suite, including browser isolation. Electron 42.11.3 launched for a version check and the desktop production build passed. A Miniflare worker fixture passed with Undici 8.12.3. The separate external-service e2e suite was not run.
Compatibility boundaries: retain the patched agents 0.17.3 dependency, align the Effect prerelease family at beta.59, and keep Kysely 0.28.17 with its SQLite adapter. Oxlint stays on the existing working 1.60 line; newer React Compiler rules require a separate source migration.
Residual audit findings: braces 3.0.3 (high; no published patched release), file-type 16.5.4, request 2.88.2, sprintf-js 1.0.3, and request's uuid 3.4.0 (moderate). These require parent-package migration or upstream fixes. The audit has no remaining critical findings, but is not clean.
Add the patch Changeset required by the release workflow. CLI versions remain owned by the generated Version Packages PR; no manual package version bump or publish is part of this patch. The Changeset parsed successfully and the final formatting check passed.