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Update Bun workspace dependencies (#1909)

* chore: update Bun workspace dependencies

Refresh safe patch/minor dependency updates for core tooling and daemon/shared packages while recording the Bun package manager version.

* chore: keep daemon dependencies pinned

Leave daemon and shared runtime dependencies on their prior versions because CI exposed flaky provider-service behavior after the zod and Bun type bumps.

* chore: update safe package dependencies

Refresh low-risk CLI and e2e package dependencies, regenerate the Bun lockfile, and sync SDK tool types from the installed Claude Agent SDK package.

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