refactor(proto)!: use well-known time types

[derekwaynecarr]

Summary

Replace public protobuf timestamp and duration scalars with the standard google.protobuf.Timestamp and google.protobuf.Duration types. This gives API consumers consistent time semantics, preserves sub-second precision, and distinguishes absent optional values from zero-valued times and durations.

Related Issue

Closes #3052

Changes

• Replaced epoch-millisecond, epoch-string, duration-string, and duration-second protobuf fields with well-known time types while reserving the retired field names and numbers.
• Added shared Rust helpers for validating and converting protobuf timestamps and durations without losing nanosecond precision.
• Added transactional startup migration for legacy protobuf payloads stored in SQLite and PostgreSQL, including nested messages and timestamp-valued maps.
• Updated gateway, CLI, sandbox, compute drivers, middleware, TUI, and provider flows to consume and produce the new fields.
• Updated the Go, TypeScript, and Python SDK implementations and tests for the new wire representation while preserving their curated public APIs where applicable.
• Documented the protobuf time conventions, compatibility behavior, and persistence boundary.

Testing

• mise run pre-commit passes
• Unit tests added/updated

Checklist

• Follows Conventional Commits
• Commits are signed off (DCO)
• Architecture and user-facing documentation are updated

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[derekwaynecarr]

/ok to test 62e0845