Fix pnpm format command failing with some files (#622)

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* Fix `pnpm format` command failure
 - Update prettier and plugins dependencies
 - Add auto-install-peers to .npmrc
 - Fix formating of previously failing files
 - Some basic security mitigations (`pnpm audit --fix`)

* setup-system.sh: Don't do a full system update on ArchLinux

* Revert "Some basic security mitigations (`pnpm audit --fix`)"

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