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rust-manifest: encode flags as `Option<NonZeroU8>`

This makes the compiler use the niche optimization for all flags: since 0 is
not a valid representation of any flags, we can use 0 as a replacement for
`None`, which reduces memory footprint and could yield a little performance
improvement over many iterations.

# So GitLab doesn't think we're using tons of Perl
*.t -linguist-detectable