Fix non-interactive and wizard onboarding reruns so existing agent lists and bindings are preserved unless the user explicitly resets config.
Isolate legacy `plugins.installs` migration into its own write so the config size-drop allowance cannot mask unrelated config loss, while preserving new or repaired install records for the final plugin-index commit. Also keep shrinkwrap generation pinned to pnpm-locked transitive patch versions only when the dependency edge still allows that version, and isolate the tooling Vitest shard that mutates process state.
Fixes#84692.
Replaces #84748.
Co-authored-by: yetval <yetvald@gmail.com>