chore: wrap crate / JS dep bump plus a rustup + cargo-upgrade pass on up.

[acoBOYZ]

Changes

wrap crate / JS dep bump plus a rustup + cargo-upgrade pass on up.

📦 Build & Dependencies

• new scripts/upgrade/rust.ts: rustup update, cargo-edit, cargo upgrade --incompatible --pinned + cargo update on wrap Cargo.toml (skip gitmodules / CI)
• up-dev runs that before upstream pins
• agent: drop rust-version, bump tokio / fs-err / libc / futures-util + lockfile
• oxfmt 0.72 / oxlint 1.87 / react-doctor 0.9.17 / intent 0.5.4
• react-db 0.5.4, pacer/hotkeys, vite 8.3.3, oxc-transform-react 0.153

Checklist

• I followed Contributing
• I ran relevant gates (typecheck / lint / fmtcheck, and doctor for React UI)
• I did not hand edited **/*.gen.ts / generated files (ran bun run codegen if needed)
• I understand the code in this PR (including any AI assisted parts)

Release impact

• User-facing change uses a conventional commit / PR title (fix:, perf:, feat:, feat!: / BREAKING CHANGE)
• Docs / CI / chore only. No release notes needed